1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 33b1 August 15, 2006 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.6.18-274.12.1.el5(x86_64)@plommebarl Created on 12/21/11 at 15:39:46 by user: cgr061 Maximum number of ATOMS: 360720, and RESidues: 120240 Current HEAP size: 10240000, and STACK size: 10000000 RDTITL> * ========================================= RDTITL> * JOB: RDTITL> * CHARMM> CHARMM> bomb -2 CHARMM> CHARMM> ! { parameters passed } CHARMM> set i 0 ! Counter Parameter: I <- "0" CHARMM> SET skip 1 ! skip size for the energy calculation Parameter: SKIP <- "1" CHARMM> SET conf_n 8002 ! number of conformations Parameter: CONF_N <- "8002" CHARMM> SET path . ! absolute path of the working directory Parameter: PATH <- "." CHARMM> SET count 1 ! COR files processed Parameter: COUNT <- "1" CHARMM> SET pdb wt_lz ! file name Parameter: PDB <- "WT_LZ" CHARMM> SET etat desolv ! solv or desolv Parameter: ETAT <- "DESOLV" CHARMM> SET fc L ! first chain Parameter: FC <- "L" CHARMM> SET sc Z ! second chain Parameter: SC <- "Z" CHARMM> SET fp (segid l) ! first part Parameter: FP <- "(SEGID L)" CHARMM> SET sp (segid z) ! second part Parameter: SP <- "(SEGID Z)" CHARMM> CHARMM> ! get parameters CHARMM> !par and top files CHARMM> open unit 1 card read name lib/top_all27_prot_na.rtf VOPEN> Attempting to open::lib/top_all27_prot_na.rtf:: OPNLGU> Unit 1 opened for READONLY access to /net/lutefisk/cgr061/hnaa10p/trajectories/50p_mut_pept_ser_leu_gly_ct3_-_1z4r-aco/merge/lib/top_all27_prot_na.rtf CHARMM> read RTF card unit 1 MAINIO> Residue topology file being read from unit 1. TITLE> *>>>>>>>>CHARMM22 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>> AND NUCLEIC ACIDS <<<<<<<<<<<<<<<<<<<<<<<<< TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>>> JULY, 2004 <<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: WWW.CHARMM.ORG TITLE> * PARAMETER SET DISCUSSION FORUM TITLE> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> open unit 1 card read name lib/par_all27_prot_na.prm VOPEN> Attempting to open::lib/par_all27_prot_na.prm:: OPNLGU> Unit 1 opened for READONLY access to /net/lutefisk/cgr061/hnaa10p/trajectories/50p_mut_pept_ser_leu_gly_ct3_-_1z4r-aco/merge/lib/par_all27_prot_na.prm CHARMM> read PARA card unit 1 PARAMETER FILE BEING READ FROM UNIT 1 TITLE> *>>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>> AND NUCLEIC ACIDS <<<<<<<<<<<<<<<<<<<<<<<<< TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>>> DECEMBER, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: WWW.CHARMM.ORG TITLE> * PARAMETER SET DISCUSSION FORUM TITLE> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> stream lib/aco.rtf VOPEN> Attempting to open::lib/aco.rtf:: OPNLGU> Unit 99 opened for READONLY access to /net/lutefisk/cgr061/hnaa10p/trajectories/50p_mut_pept_ser_leu_gly_ct3_-_1z4r-aco/merge/lib/aco.rtf INPUT STREAM SWITCHING TO UNIT 99 RDTITL> * TOPOLOGY FILE FOR ACETYL COENZYME A RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 99. RDTITL> * TOPOLOGY FOR MODIFIED HISTONE RESIDUES RDTITL> * CHARMM> CHARMM> read param card append PARAMETER FILE BEING READ FROM UNIT 99 RDTITL> * PARAMETERS FOR ACETYL COENZYME A RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> !!! CYS CHARMM> !ATOM CB CT2 -0.11 ! | | \ CHARMM> !ATOM HB1 HA 0.09 ! | HB2 HG1 CHARMM> !ATOM HB2 HA 0.09 ! O=C CHARMM> !ATOM SG S -0.23 ! | CHARMM> !ATOM HG1 HS 0.16 CHARMM> VCLOSE: Closing unit 99 with status "KEEP" RETURNING TO INPUT STREAM 5 CHARMM> CHARMM> calc stopdyna = @{conf_n} * @skip Parameter: CONF_N -> "8002" Parameter: SKIP -> "1" Evaluating: 8002*1 Parameter: STOPDYNA <- "8002" CHARMM> CHARMM> ! { psf } CHARMM> open unit 1 read formatted name @path/scr/@pdb.dyna_@etat.psf Parameter: PATH -> "." Parameter: PDB -> "WT_LZ" Parameter: ETAT -> "DESOLV" VOPEN> Attempting to open::./scr/wt_lz.dyna_desolv.psf:: OPNLGU> Unit 1 opened for READONLY access to /net/lutefisk/cgr061/hnaa10p/trajectories/50p_mut_pept_ser_leu_gly_ct3_-_1z4r-aco/merge/./scr/wt_lz.dyna_desolv.psf CHARMM> read psf card unit 1 MAINIO> Protein structure file being read from unit 1. TITLE> * TEST TITLE> * DATE: 11/11/11 8:41:47 CREATED BY USER: cgr061 TITLE> * PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 2 Number of residues = 162 Number of atoms = 2683 Number of groups = 812 Number of bonds = 2708 Number of angles = 4880 Number of dihedrals = 7109 Number of impropers = 445 Number of cross-terms = 155 Number of HB acceptors = 255 Number of HB donors = 314 Number of NB exclusions = 0 Total charge = 3.00000 CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> ! { coordinates } CHARMM> OPEN UNIT 1 READ FORMatted NAME @path/scr/@pdb.dyna_@etat.crd Parameter: PATH -> "." Parameter: PDB -> "WT_LZ" Parameter: ETAT -> "DESOLV" VOPEN> Attempting to open::./scr/wt_lz.dyna_desolv.crd:: OPNLGU> Unit 1 opened for READONLY access to /net/lutefisk/cgr061/hnaa10p/trajectories/50p_mut_pept_ser_leu_gly_ct3_-_1z4r-aco/merge/./scr/wt_lz.dyna_desolv.crd CHARMM> READ COORdinate CARD UNIT 1 SPATIAL COORDINATES BEING READ FROM UNIT 1 TITLE> * TEST TITLE> * DATE: 11/11/11 8:41:48 CREATED BY USER: CGR061 TITLE> * CHARMM> CLOSE UNIT 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> stream @path/inp/all-traj.dat Parameter: PATH -> "." VOPEN> Attempting to open::./inp/all-traj.dat:: OPNLGU> Unit 99 opened for READONLY access to /net/lutefisk/cgr061/hnaa10p/trajectories/50p_mut_pept_ser_leu_gly_ct3_-_1z4r-aco/merge/./inp/all-traj.dat INPUT STREAM SWITCHING TO UNIT 99 RDTITL> OPEN READ UNFORMATTED UNIT 21 NAME ./SCR/WT_LZ.DYNA_PROD1.COR RDTITL> No title read. Parameter: IN1 <- "" CHARMM> open read unformatted unit 21 name @path/scr/@pdb.dyna_prod1.cor Parameter: PATH -> "." Parameter: PDB -> "WT_LZ" VOPEN> Attempting to open::./scr/wt_lz.dyna_prod1.cor:: OPNLGU> Unit 21 opened for READONLY access to /net/lutefisk/cgr061/hnaa10p/trajectories/50p_mut_pept_ser_leu_gly_ct3_-_1z4r-aco/merge/./scr/wt_lz.dyna_prod1.cor CHARMM> return VCLOSE: Closing unit 99 with status "KEEP" RETURNING TO INPUT STREAM 5 CHARMM> CHARMM> open unit 12 write formatted name @path/scr/@pdb.ener.inte Parameter: PATH -> "." Parameter: PDB -> "WT_LZ" VOPEN> Attempting to open::./scr/wt_lz.ener.inte:: OPNLGU> Unit 12 opened for WRITE access to /net/lutefisk/cgr061/hnaa10p/trajectories/50p_mut_pept_ser_leu_gly_ct3_-_1z4r-aco/merge/./scr/wt_lz.ener.inte CHARMM> write title unit 12 RDTITL> *# JOBNAME: WT_LZ RDTITL> *# INTERACTION ENERGY CALCULATION RDTITL> *# CONFORMATION TOT. VDW. ELEC. RDTITL> * CHARMM> CHARMM> trajectory iread 21 nread 1 skip 1 begin 0 stop 20005 TRAJ: INITIATING READ OF A TRAJECTORY, OPTIONS; FIRSTU = 21 NUNIT = 1 SKIP = 1 CHARMM> CHARMM> CHARMM> LABEL loop1 CHARMM> incr i by 1 Parameter: I <- "1" CHARMM> CHARMM> traj read READING TRAJECTORY FROM UNIT 21 NUMBER OF COORDINATE SETS IN FILE: 8002 NUMBER OF PREVIOUS DYNAMICS STEPS: 0 FREQUENCY FOR SAVING COORDINATES: 1 NUMBER OF STEPS FOR CREATION RUN: 8002 TITLE> Created by DCD plugin TITLE> REMARKS Created 21 December, 2011 at 15:02ÿÌ·ø@è÷„³€ÿ TITLE> * ***** WARNING ***** BEGIN= 0 Was not specified. It has been set to: 0 CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions. with mode 5 found 7585 exclusions and 7003 interactions(1-4) found 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 691276 ATOM PAIRS AND 0 GROUP PAIRS == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754506 ATOM PAIRS WERE FOUND FOR ATOM LIST 41370 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29613 from a total of 754506 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1 -68.35575 0.00000 0.67628 INTE EXTERN> -24.21834 -44.13741 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3557" Parameter: A <- "-68.3557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2183" Parameter: B <- "-24.2183" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1374" Parameter: C <- "-44.1374" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1 TOTAL ENERGY = -68.3557 RDTITL> * VAN DER WAALS = -24.2183 ELECTROSTATIC = -44.1374 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1" Parameter: CONF_N -> "8002" Comparing "1" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754506 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745055 ATOM PAIRS WERE FOUND FOR ATOM LIST 40988 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29428 from a total of 745055 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2 -66.93865 -1.41709 0.51981 INTE EXTERN> -28.64526 -38.29339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9387" Parameter: A <- "-66.9387" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6453" Parameter: B <- "-28.6453" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2934" Parameter: C <- "-38.2934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2 TOTAL ENERGY = -66.9387 RDTITL> * VAN DER WAALS = -28.6453 ELECTROSTATIC = -38.2934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2" Parameter: CONF_N -> "8002" Comparing "2" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745055 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748931 ATOM PAIRS WERE FOUND FOR ATOM LIST 41223 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29242 from a total of 748931 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3 -66.79620 -0.14245 0.58051 INTE EXTERN> -29.98640 -36.80981 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7962" Parameter: A <- "-66.7962" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9864" Parameter: B <- "-29.9864" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8098" Parameter: C <- "-36.8098" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3 TOTAL ENERGY = -66.7962 RDTITL> * VAN DER WAALS = -29.9864 ELECTROSTATIC = -36.8098 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3" Parameter: CONF_N -> "8002" Comparing "3" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748931 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747455 ATOM PAIRS WERE FOUND FOR ATOM LIST 41163 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29106 from a total of 747455 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4 -70.48113 3.68492 0.60116 INTE EXTERN> -27.50421 -42.97692 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4811" Parameter: A <- "-70.4811" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5042" Parameter: B <- "-27.5042" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9769" Parameter: C <- "-42.9769" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4 TOTAL ENERGY = -70.4811 RDTITL> * VAN DER WAALS = -27.5042 ELECTROSTATIC = -42.9769 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4" Parameter: CONF_N -> "8002" Comparing "4" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747455 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750798 ATOM PAIRS WERE FOUND FOR ATOM LIST 41267 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29675 from a total of 750798 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5 -71.68704 1.20591 0.63276 INTE EXTERN> -27.02463 -44.66241 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.687" Parameter: A <- "-71.687" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0246" Parameter: B <- "-27.0246" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6624" Parameter: C <- "-44.6624" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5 TOTAL ENERGY = -71.687 RDTITL> * VAN DER WAALS = -27.0246 ELECTROSTATIC = -44.6624 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5" Parameter: CONF_N -> "8002" Comparing "5" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750798 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755100 ATOM PAIRS WERE FOUND FOR ATOM LIST 41584 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29390 from a total of 755100 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6 -65.11524 -6.57180 0.79864 INTE EXTERN> -20.72551 -44.38973 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1152" Parameter: A <- "-65.1152" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.7255" Parameter: B <- "-20.7255" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3897" Parameter: C <- "-44.3897" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6 TOTAL ENERGY = -65.1152 RDTITL> * VAN DER WAALS = -20.7255 ELECTROSTATIC = -44.3897 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6" Parameter: CONF_N -> "8002" Comparing "6" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755100 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751363 ATOM PAIRS WERE FOUND FOR ATOM LIST 41281 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29608 from a total of 751363 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7 -65.50142 0.38618 0.62838 INTE EXTERN> -26.98134 -38.52008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5014" Parameter: A <- "-65.5014" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9813" Parameter: B <- "-26.9813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5201" Parameter: C <- "-38.5201" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7 TOTAL ENERGY = -65.5014 RDTITL> * VAN DER WAALS = -26.9813 ELECTROSTATIC = -38.5201 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7" Parameter: CONF_N -> "8002" Comparing "7" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "8" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751363 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754728 ATOM PAIRS WERE FOUND FOR ATOM LIST 41408 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29636 from a total of 754728 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 8 -75.42023 9.91881 0.58582 INTE EXTERN> -30.10697 -45.31326 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4202" Parameter: A <- "-75.4202" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.107" Parameter: B <- "-30.107" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3133" Parameter: C <- "-45.3133" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 8 TOTAL ENERGY = -75.4202 RDTITL> * VAN DER WAALS = -30.107 ELECTROSTATIC = -45.3133 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "8" Parameter: CONF_N -> "8002" Comparing "8" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "9" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754728 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757131 ATOM PAIRS WERE FOUND FOR ATOM LIST 41423 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29782 from a total of 757131 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 9 -65.26010 -10.16013 0.48062 INTE EXTERN> -33.42410 -31.83600 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2601" Parameter: A <- "-65.2601" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4241" Parameter: B <- "-33.4241" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.836" Parameter: C <- "-31.836" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 9 TOTAL ENERGY = -65.2601 RDTITL> * VAN DER WAALS = -33.4241 ELECTROSTATIC = -31.836 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "9" Parameter: CONF_N -> "8002" Comparing "9" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "10" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757131 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757224 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29246 from a total of 757224 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 10 -60.74592 -4.51418 0.45988 INTE EXTERN> -31.23607 -29.50985 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.7459" Parameter: A <- "-60.7459" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2361" Parameter: B <- "-31.2361" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.5099" Parameter: C <- "-29.5099" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 10 TOTAL ENERGY = -60.7459 RDTITL> * VAN DER WAALS = -31.2361 ELECTROSTATIC = -29.5099 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "10" Parameter: CONF_N -> "8002" Comparing "10" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "11" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757224 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754447 ATOM PAIRS WERE FOUND FOR ATOM LIST 41335 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29816 from a total of 754447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 11 -64.09183 3.34590 0.50972 INTE EXTERN> -29.90155 -34.19028 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0918" Parameter: A <- "-64.0918" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9015" Parameter: B <- "-29.9015" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1903" Parameter: C <- "-34.1903" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 11 TOTAL ENERGY = -64.0918 RDTITL> * VAN DER WAALS = -29.9015 ELECTROSTATIC = -34.1903 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "11" Parameter: CONF_N -> "8002" Comparing "11" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "12" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754890 ATOM PAIRS WERE FOUND FOR ATOM LIST 41416 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29946 from a total of 754890 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 12 -63.66477 -0.42706 0.63846 INTE EXTERN> -27.21199 -36.45278 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6648" Parameter: A <- "-63.6648" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.212" Parameter: B <- "-27.212" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4528" Parameter: C <- "-36.4528" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 12 TOTAL ENERGY = -63.6648 RDTITL> * VAN DER WAALS = -27.212 ELECTROSTATIC = -36.4528 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "12" Parameter: CONF_N -> "8002" Comparing "12" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "13" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754890 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752297 ATOM PAIRS WERE FOUND FOR ATOM LIST 41412 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29888 from a total of 752297 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 13 -63.55612 -0.10864 0.58416 INTE EXTERN> -28.39904 -35.15709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5561" Parameter: A <- "-63.5561" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.399" Parameter: B <- "-28.399" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1571" Parameter: C <- "-35.1571" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 13 TOTAL ENERGY = -63.5561 RDTITL> * VAN DER WAALS = -28.399 ELECTROSTATIC = -35.1571 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "13" Parameter: CONF_N -> "8002" Comparing "13" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "14" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752297 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754534 ATOM PAIRS WERE FOUND FOR ATOM LIST 41482 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29719 from a total of 754534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 14 -69.63173 6.07560 0.65845 INTE EXTERN> -29.23388 -40.39785 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6317" Parameter: A <- "-69.6317" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2339" Parameter: B <- "-29.2339" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3979" Parameter: C <- "-40.3979" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 14 TOTAL ENERGY = -69.6317 RDTITL> * VAN DER WAALS = -29.2339 ELECTROSTATIC = -40.3979 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "14" Parameter: CONF_N -> "8002" Comparing "14" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "15" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754978 ATOM PAIRS WERE FOUND FOR ATOM LIST 41439 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29778 from a total of 754978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 15 -66.83982 -2.79191 0.60492 INTE EXTERN> -29.54611 -37.29371 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8398" Parameter: A <- "-66.8398" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5461" Parameter: B <- "-29.5461" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2937" Parameter: C <- "-37.2937" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 15 TOTAL ENERGY = -66.8398 RDTITL> * VAN DER WAALS = -29.5461 ELECTROSTATIC = -37.2937 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "15" Parameter: CONF_N -> "8002" Comparing "15" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "16" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750803 ATOM PAIRS WERE FOUND FOR ATOM LIST 41231 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29583 from a total of 750803 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 16 -69.25791 2.41808 0.56635 INTE EXTERN> -32.97074 -36.28716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2579" Parameter: A <- "-69.2579" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9707" Parameter: B <- "-32.9707" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2872" Parameter: C <- "-36.2872" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 16 TOTAL ENERGY = -69.2579 RDTITL> * VAN DER WAALS = -32.9707 ELECTROSTATIC = -36.2872 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "16" Parameter: CONF_N -> "8002" Comparing "16" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "17" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750803 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755957 ATOM PAIRS WERE FOUND FOR ATOM LIST 41434 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29788 from a total of 755957 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 17 -60.81555 -8.44236 0.61435 INTE EXTERN> -28.87444 -31.94110 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.8155" Parameter: A <- "-60.8155" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8744" Parameter: B <- "-28.8744" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.9411" Parameter: C <- "-31.9411" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 17 TOTAL ENERGY = -60.8155 RDTITL> * VAN DER WAALS = -28.8744 ELECTROSTATIC = -31.9411 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "17" Parameter: CONF_N -> "8002" Comparing "17" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "18" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755957 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753967 ATOM PAIRS WERE FOUND FOR ATOM LIST 41299 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29698 from a total of 753967 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 18 -63.11076 2.29522 0.72308 INTE EXTERN> -24.72773 -38.38303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1108" Parameter: A <- "-63.1108" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7277" Parameter: B <- "-24.7277" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.383" Parameter: C <- "-38.383" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 18 TOTAL ENERGY = -63.1108 RDTITL> * VAN DER WAALS = -24.7277 ELECTROSTATIC = -38.383 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "18" Parameter: CONF_N -> "8002" Comparing "18" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "19" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753967 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748652 ATOM PAIRS WERE FOUND FOR ATOM LIST 41026 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29626 from a total of 748652 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 19 -70.91584 7.80508 0.65625 INTE EXTERN> -29.79674 -41.11911 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9158" Parameter: A <- "-70.9158" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7967" Parameter: B <- "-29.7967" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1191" Parameter: C <- "-41.1191" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 19 TOTAL ENERGY = -70.9158 RDTITL> * VAN DER WAALS = -29.7967 ELECTROSTATIC = -41.1191 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "19" Parameter: CONF_N -> "8002" Comparing "19" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "20" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748652 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754483 ATOM PAIRS WERE FOUND FOR ATOM LIST 41412 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30153 from a total of 754483 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 20 -68.94115 -1.97470 0.69069 INTE EXTERN> -24.88844 -44.05270 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9411" Parameter: A <- "-68.9411" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8884" Parameter: B <- "-24.8884" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0527" Parameter: C <- "-44.0527" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 20 TOTAL ENERGY = -68.9411 RDTITL> * VAN DER WAALS = -24.8884 ELECTROSTATIC = -44.0527 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "20" Parameter: CONF_N -> "8002" Comparing "20" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "21" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754483 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756146 ATOM PAIRS WERE FOUND FOR ATOM LIST 41425 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29305 from a total of 756146 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 21 -72.83620 3.89506 0.79960 INTE EXTERN> -23.94058 -48.89562 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8362" Parameter: A <- "-72.8362" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9406" Parameter: B <- "-23.9406" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8956" Parameter: C <- "-48.8956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 21 TOTAL ENERGY = -72.8362 RDTITL> * VAN DER WAALS = -23.9406 ELECTROSTATIC = -48.8956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "21" Parameter: CONF_N -> "8002" Comparing "21" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "22" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756146 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755702 ATOM PAIRS WERE FOUND FOR ATOM LIST 41458 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29146 from a total of 755702 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 22 -73.38248 0.54628 0.61425 INTE EXTERN> -29.09449 -44.28799 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3825" Parameter: A <- "-73.3825" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0945" Parameter: B <- "-29.0945" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.288" Parameter: C <- "-44.288" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 22 TOTAL ENERGY = -73.3825 RDTITL> * VAN DER WAALS = -29.0945 ELECTROSTATIC = -44.288 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "22" Parameter: CONF_N -> "8002" Comparing "22" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "23" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755702 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753983 ATOM PAIRS WERE FOUND FOR ATOM LIST 41288 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29628 from a total of 753983 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 23 -71.76022 -1.62226 0.59350 INTE EXTERN> -29.17160 -42.58862 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7602" Parameter: A <- "-71.7602" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1716" Parameter: B <- "-29.1716" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5886" Parameter: C <- "-42.5886" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 23 TOTAL ENERGY = -71.7602 RDTITL> * VAN DER WAALS = -29.1716 ELECTROSTATIC = -42.5886 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "23" Parameter: CONF_N -> "8002" Comparing "23" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "24" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753983 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748442 ATOM PAIRS WERE FOUND FOR ATOM LIST 41105 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28548 from a total of 748442 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 24 -66.23753 -5.52269 0.57897 INTE EXTERN> -27.49319 -38.74435 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2375" Parameter: A <- "-66.2375" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4932" Parameter: B <- "-27.4932" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7443" Parameter: C <- "-38.7443" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 24 TOTAL ENERGY = -66.2375 RDTITL> * VAN DER WAALS = -27.4932 ELECTROSTATIC = -38.7443 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "24" Parameter: CONF_N -> "8002" Comparing "24" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "25" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748442 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753312 ATOM PAIRS WERE FOUND FOR ATOM LIST 41369 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29041 from a total of 753312 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 25 -69.93160 3.69407 0.58771 INTE EXTERN> -31.13409 -38.79751 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9316" Parameter: A <- "-69.9316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1341" Parameter: B <- "-31.1341" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7975" Parameter: C <- "-38.7975" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 25 TOTAL ENERGY = -69.9316 RDTITL> * VAN DER WAALS = -31.1341 ELECTROSTATIC = -38.7975 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "25" Parameter: CONF_N -> "8002" Comparing "25" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "26" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753312 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750271 ATOM PAIRS WERE FOUND FOR ATOM LIST 41053 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29007 from a total of 750271 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 26 -68.86072 -1.07089 0.54262 INTE EXTERN> -28.92845 -39.93227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8607" Parameter: A <- "-68.8607" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9285" Parameter: B <- "-28.9285" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9323" Parameter: C <- "-39.9323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 26 TOTAL ENERGY = -68.8607 RDTITL> * VAN DER WAALS = -28.9285 ELECTROSTATIC = -39.9323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "26" Parameter: CONF_N -> "8002" Comparing "26" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "27" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750271 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758951 ATOM PAIRS WERE FOUND FOR ATOM LIST 41798 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29096 from a total of 758951 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 27 -66.57367 -2.28705 0.49588 INTE EXTERN> -31.47295 -35.10072 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5737" Parameter: A <- "-66.5737" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4729" Parameter: B <- "-31.4729" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1007" Parameter: C <- "-35.1007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 27 TOTAL ENERGY = -66.5737 RDTITL> * VAN DER WAALS = -31.4729 ELECTROSTATIC = -35.1007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "27" Parameter: CONF_N -> "8002" Comparing "27" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "28" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758951 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753709 ATOM PAIRS WERE FOUND FOR ATOM LIST 41347 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29470 from a total of 753709 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 28 -59.23673 -7.33694 0.46476 INTE EXTERN> -32.16461 -27.07212 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.2367" Parameter: A <- "-59.2367" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1646" Parameter: B <- "-32.1646" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.0721" Parameter: C <- "-27.0721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 28 TOTAL ENERGY = -59.2367 RDTITL> * VAN DER WAALS = -32.1646 ELECTROSTATIC = -27.0721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "28" Parameter: CONF_N -> "8002" Comparing "28" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "29" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753709 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756786 ATOM PAIRS WERE FOUND FOR ATOM LIST 41453 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29544 from a total of 756786 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 29 -69.47712 10.24039 0.49870 INTE EXTERN> -32.95451 -36.52261 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4771" Parameter: A <- "-69.4771" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9545" Parameter: B <- "-32.9545" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5226" Parameter: C <- "-36.5226" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 29 TOTAL ENERGY = -69.4771 RDTITL> * VAN DER WAALS = -32.9545 ELECTROSTATIC = -36.5226 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "29" Parameter: CONF_N -> "8002" Comparing "29" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "30" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756786 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41293 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29500 from a total of 755422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 30 -62.15238 -7.32474 0.47752 INTE EXTERN> -32.71931 -29.43307 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.1524" Parameter: A <- "-62.1524" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7193" Parameter: B <- "-32.7193" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.4331" Parameter: C <- "-29.4331" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 30 TOTAL ENERGY = -62.1524 RDTITL> * VAN DER WAALS = -32.7193 ELECTROSTATIC = -29.4331 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "30" Parameter: CONF_N -> "8002" Comparing "30" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "31" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754999 ATOM PAIRS WERE FOUND FOR ATOM LIST 41433 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29805 from a total of 754999 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 31 -68.74635 6.59397 0.51916 INTE EXTERN> -33.12319 -35.62316 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7464" Parameter: A <- "-68.7464" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1232" Parameter: B <- "-33.1232" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6232" Parameter: C <- "-35.6232" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 31 TOTAL ENERGY = -68.7464 RDTITL> * VAN DER WAALS = -33.1232 ELECTROSTATIC = -35.6232 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "31" Parameter: CONF_N -> "8002" Comparing "31" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "32" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754999 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755029 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29377 from a total of 755029 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 32 -59.44446 -9.30189 0.45043 INTE EXTERN> -32.37169 -27.07277 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.4445" Parameter: A <- "-59.4445" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3717" Parameter: B <- "-32.3717" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.0728" Parameter: C <- "-27.0728" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 32 TOTAL ENERGY = -59.4445 RDTITL> * VAN DER WAALS = -32.3717 ELECTROSTATIC = -27.0728 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "32" Parameter: CONF_N -> "8002" Comparing "32" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "33" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755029 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750632 ATOM PAIRS WERE FOUND FOR ATOM LIST 41283 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28909 from a total of 750632 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 33 -64.17279 4.72833 0.59561 INTE EXTERN> -27.88889 -36.28390 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1728" Parameter: A <- "-64.1728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8889" Parameter: B <- "-27.8889" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2839" Parameter: C <- "-36.2839" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 33 TOTAL ENERGY = -64.1728 RDTITL> * VAN DER WAALS = -27.8889 ELECTROSTATIC = -36.2839 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "33" Parameter: CONF_N -> "8002" Comparing "33" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "34" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750632 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752460 ATOM PAIRS WERE FOUND FOR ATOM LIST 41437 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29532 from a total of 752460 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 34 -67.16977 2.99698 0.51660 INTE EXTERN> -32.27837 -34.89140 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1698" Parameter: A <- "-67.1698" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2784" Parameter: B <- "-32.2784" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8914" Parameter: C <- "-34.8914" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 34 TOTAL ENERGY = -67.1698 RDTITL> * VAN DER WAALS = -32.2784 ELECTROSTATIC = -34.8914 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "34" Parameter: CONF_N -> "8002" Comparing "34" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "35" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752460 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758442 ATOM PAIRS WERE FOUND FOR ATOM LIST 41707 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30448 from a total of 758442 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 35 -66.13105 -1.03872 0.58247 INTE EXTERN> -32.18444 -33.94661 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1311" Parameter: A <- "-66.1311" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1844" Parameter: B <- "-32.1844" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9466" Parameter: C <- "-33.9466" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 35 TOTAL ENERGY = -66.1311 RDTITL> * VAN DER WAALS = -32.1844 ELECTROSTATIC = -33.9466 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "35" Parameter: CONF_N -> "8002" Comparing "35" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "36" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758442 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761061 ATOM PAIRS WERE FOUND FOR ATOM LIST 41712 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29958 from a total of 761061 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 36 -67.58178 1.45073 0.54302 INTE EXTERN> -31.44570 -36.13609 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5818" Parameter: A <- "-67.5818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4457" Parameter: B <- "-31.4457" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1361" Parameter: C <- "-36.1361" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 36 TOTAL ENERGY = -67.5818 RDTITL> * VAN DER WAALS = -31.4457 ELECTROSTATIC = -36.1361 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "36" Parameter: CONF_N -> "8002" Comparing "36" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "37" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761061 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755112 ATOM PAIRS WERE FOUND FOR ATOM LIST 41631 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29872 from a total of 755112 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 37 -77.09192 9.51014 0.55858 INTE EXTERN> -33.20130 -43.89062 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0919" Parameter: A <- "-77.0919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2013" Parameter: B <- "-33.2013" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8906" Parameter: C <- "-43.8906" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 37 TOTAL ENERGY = -77.0919 RDTITL> * VAN DER WAALS = -33.2013 ELECTROSTATIC = -43.8906 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "37" Parameter: CONF_N -> "8002" Comparing "37" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "38" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755112 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758576 ATOM PAIRS WERE FOUND FOR ATOM LIST 41830 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29838 from a total of 758576 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 38 -69.06584 -8.02608 0.50335 INTE EXTERN> -33.77093 -35.29491 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0658" Parameter: A <- "-69.0658" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7709" Parameter: B <- "-33.7709" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2949" Parameter: C <- "-35.2949" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 38 TOTAL ENERGY = -69.0658 RDTITL> * VAN DER WAALS = -33.7709 ELECTROSTATIC = -35.2949 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "38" Parameter: CONF_N -> "8002" Comparing "38" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "39" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758576 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765867 ATOM PAIRS WERE FOUND FOR ATOM LIST 42077 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30176 from a total of 765867 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 39 -71.32740 2.26156 0.45756 INTE EXTERN> -35.21166 -36.11574 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3274" Parameter: A <- "-71.3274" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.2117" Parameter: B <- "-35.2117" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1157" Parameter: C <- "-36.1157" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 39 TOTAL ENERGY = -71.3274 RDTITL> * VAN DER WAALS = -35.2117 ELECTROSTATIC = -36.1157 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "39" Parameter: CONF_N -> "8002" Comparing "39" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "40" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765867 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758261 ATOM PAIRS WERE FOUND FOR ATOM LIST 41545 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29688 from a total of 758261 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 40 -71.21757 -0.10983 0.49722 INTE EXTERN> -33.80500 -37.41257 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2176" Parameter: A <- "-71.2176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.805" Parameter: B <- "-33.805" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4126" Parameter: C <- "-37.4126" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 40 TOTAL ENERGY = -71.2176 RDTITL> * VAN DER WAALS = -33.805 ELECTROSTATIC = -37.4126 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "40" Parameter: CONF_N -> "8002" Comparing "40" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "41" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758261 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757041 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30227 from a total of 757041 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 41 -70.95816 -0.25941 0.67949 INTE EXTERN> -29.70176 -41.25640 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9582" Parameter: A <- "-70.9582" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7018" Parameter: B <- "-29.7018" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2564" Parameter: C <- "-41.2564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 41 TOTAL ENERGY = -70.9582 RDTITL> * VAN DER WAALS = -29.7018 ELECTROSTATIC = -41.2564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "41" Parameter: CONF_N -> "8002" Comparing "41" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "42" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757041 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752343 ATOM PAIRS WERE FOUND FOR ATOM LIST 41452 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30312 from a total of 752343 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 42 -74.47206 3.51390 0.55473 INTE EXTERN> -31.64526 -42.82680 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4721" Parameter: A <- "-74.4721" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6453" Parameter: B <- "-31.6453" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8268" Parameter: C <- "-42.8268" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 42 TOTAL ENERGY = -74.4721 RDTITL> * VAN DER WAALS = -31.6453 ELECTROSTATIC = -42.8268 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "42" Parameter: CONF_N -> "8002" Comparing "42" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "43" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752343 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759799 ATOM PAIRS WERE FOUND FOR ATOM LIST 41743 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30323 from a total of 759799 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 43 -70.59953 -3.87254 0.62179 INTE EXTERN> -26.96417 -43.63536 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5995" Parameter: A <- "-70.5995" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9642" Parameter: B <- "-26.9642" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6354" Parameter: C <- "-43.6354" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 43 TOTAL ENERGY = -70.5995 RDTITL> * VAN DER WAALS = -26.9642 ELECTROSTATIC = -43.6354 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "43" Parameter: CONF_N -> "8002" Comparing "43" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "44" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759799 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756872 ATOM PAIRS WERE FOUND FOR ATOM LIST 41569 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30087 from a total of 756872 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 44 -71.49312 0.89359 0.68507 INTE EXTERN> -24.85618 -46.63694 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4931" Parameter: A <- "-71.4931" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8562" Parameter: B <- "-24.8562" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6369" Parameter: C <- "-46.6369" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 44 TOTAL ENERGY = -71.4931 RDTITL> * VAN DER WAALS = -24.8562 ELECTROSTATIC = -46.6369 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "44" Parameter: CONF_N -> "8002" Comparing "44" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "45" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756872 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757831 ATOM PAIRS WERE FOUND FOR ATOM LIST 41646 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29698 from a total of 757831 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 45 -70.65044 -0.84267 0.56559 INTE EXTERN> -29.78958 -40.86086 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6504" Parameter: A <- "-70.6504" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7896" Parameter: B <- "-29.7896" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8609" Parameter: C <- "-40.8609" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 45 TOTAL ENERGY = -70.6504 RDTITL> * VAN DER WAALS = -29.7896 ELECTROSTATIC = -40.8609 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "45" Parameter: CONF_N -> "8002" Comparing "45" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "46" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757831 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752383 ATOM PAIRS WERE FOUND FOR ATOM LIST 41564 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28981 from a total of 752383 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 46 -70.98344 0.33300 0.59997 INTE EXTERN> -31.05539 -39.92806 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9834" Parameter: A <- "-70.9834" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0554" Parameter: B <- "-31.0554" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9281" Parameter: C <- "-39.9281" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 46 TOTAL ENERGY = -70.9834 RDTITL> * VAN DER WAALS = -31.0554 ELECTROSTATIC = -39.9281 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "46" Parameter: CONF_N -> "8002" Comparing "46" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "47" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752383 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752538 ATOM PAIRS WERE FOUND FOR ATOM LIST 41696 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29177 from a total of 752538 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 47 -61.58513 -9.39831 0.60961 INTE EXTERN> -28.30496 -33.28016 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.5851" Parameter: A <- "-61.5851" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.305" Parameter: B <- "-28.305" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2802" Parameter: C <- "-33.2802" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 47 TOTAL ENERGY = -61.5851 RDTITL> * VAN DER WAALS = -28.305 ELECTROSTATIC = -33.2802 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "47" Parameter: CONF_N -> "8002" Comparing "47" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "48" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752538 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756237 ATOM PAIRS WERE FOUND FOR ATOM LIST 41510 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29325 from a total of 756237 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 48 -71.58569 10.00056 0.71282 INTE EXTERN> -28.15201 -43.43368 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5857" Parameter: A <- "-71.5857" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.152" Parameter: B <- "-28.152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4337" Parameter: C <- "-43.4337" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 48 TOTAL ENERGY = -71.5857 RDTITL> * VAN DER WAALS = -28.152 ELECTROSTATIC = -43.4337 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "48" Parameter: CONF_N -> "8002" Comparing "48" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "49" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756237 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752890 ATOM PAIRS WERE FOUND FOR ATOM LIST 41389 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29701 from a total of 752890 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 49 -70.64300 -0.94269 0.47954 INTE EXTERN> -32.40100 -38.24200 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.643" Parameter: A <- "-70.643" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.401" Parameter: B <- "-32.401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.242" Parameter: C <- "-38.242" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 49 TOTAL ENERGY = -70.643 RDTITL> * VAN DER WAALS = -32.401 ELECTROSTATIC = -38.242 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "49" Parameter: CONF_N -> "8002" Comparing "49" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "50" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752890 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745524 ATOM PAIRS WERE FOUND FOR ATOM LIST 41129 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29155 from a total of 745524 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 50 -67.51362 -3.12938 0.60728 INTE EXTERN> -30.28172 -37.23190 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5136" Parameter: A <- "-67.5136" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2817" Parameter: B <- "-30.2817" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2319" Parameter: C <- "-37.2319" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 50 TOTAL ENERGY = -67.5136 RDTITL> * VAN DER WAALS = -30.2817 ELECTROSTATIC = -37.2319 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "50" Parameter: CONF_N -> "8002" Comparing "50" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "51" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745524 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753103 ATOM PAIRS WERE FOUND FOR ATOM LIST 41419 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29559 from a total of 753103 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 51 -69.53816 2.02454 0.61260 INTE EXTERN> -29.15855 -40.37961 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5382" Parameter: A <- "-69.5382" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1586" Parameter: B <- "-29.1586" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3796" Parameter: C <- "-40.3796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 51 TOTAL ENERGY = -69.5382 RDTITL> * VAN DER WAALS = -29.1586 ELECTROSTATIC = -40.3796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "51" Parameter: CONF_N -> "8002" Comparing "51" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "52" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753103 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758983 ATOM PAIRS WERE FOUND FOR ATOM LIST 41616 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29830 from a total of 758983 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 52 -68.66293 -0.87523 0.61197 INTE EXTERN> -28.33183 -40.33111 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6629" Parameter: A <- "-68.6629" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3318" Parameter: B <- "-28.3318" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3311" Parameter: C <- "-40.3311" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 52 TOTAL ENERGY = -68.6629 RDTITL> * VAN DER WAALS = -28.3318 ELECTROSTATIC = -40.3311 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "52" Parameter: CONF_N -> "8002" Comparing "52" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "53" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758983 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754833 ATOM PAIRS WERE FOUND FOR ATOM LIST 41654 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29768 from a total of 754833 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 53 -75.19621 6.53328 0.57524 INTE EXTERN> -32.51177 -42.68445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1962" Parameter: A <- "-75.1962" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5118" Parameter: B <- "-32.5118" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6844" Parameter: C <- "-42.6844" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 53 TOTAL ENERGY = -75.1962 RDTITL> * VAN DER WAALS = -32.5118 ELECTROSTATIC = -42.6844 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "53" Parameter: CONF_N -> "8002" Comparing "53" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "54" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754833 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752057 ATOM PAIRS WERE FOUND FOR ATOM LIST 41253 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29660 from a total of 752057 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 54 -67.27096 -7.92526 0.54023 INTE EXTERN> -32.27314 -34.99781 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.271" Parameter: A <- "-67.271" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2731" Parameter: B <- "-32.2731" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9978" Parameter: C <- "-34.9978" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 54 TOTAL ENERGY = -67.271 RDTITL> * VAN DER WAALS = -32.2731 ELECTROSTATIC = -34.9978 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "54" Parameter: CONF_N -> "8002" Comparing "54" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "55" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752057 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744875 ATOM PAIRS WERE FOUND FOR ATOM LIST 40775 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28988 from a total of 744875 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 55 -67.98825 0.71730 0.54519 INTE EXTERN> -30.31181 -37.67644 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9883" Parameter: A <- "-67.9883" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3118" Parameter: B <- "-30.3118" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6764" Parameter: C <- "-37.6764" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 55 TOTAL ENERGY = -67.9883 RDTITL> * VAN DER WAALS = -30.3118 ELECTROSTATIC = -37.6764 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "55" Parameter: CONF_N -> "8002" Comparing "55" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "56" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744875 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754551 ATOM PAIRS WERE FOUND FOR ATOM LIST 41333 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29859 from a total of 754551 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 56 -72.26301 4.27476 0.58897 INTE EXTERN> -33.47909 -38.78392 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.263" Parameter: A <- "-72.263" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4791" Parameter: B <- "-33.4791" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7839" Parameter: C <- "-38.7839" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 56 TOTAL ENERGY = -72.263 RDTITL> * VAN DER WAALS = -33.4791 ELECTROSTATIC = -38.7839 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "56" Parameter: CONF_N -> "8002" Comparing "56" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "57" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754551 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763657 ATOM PAIRS WERE FOUND FOR ATOM LIST 41948 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30221 from a total of 763657 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 57 -78.96805 6.70504 0.68479 INTE EXTERN> -30.50930 -48.45875 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.968" Parameter: A <- "-78.968" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5093" Parameter: B <- "-30.5093" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4587" Parameter: C <- "-48.4587" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 57 TOTAL ENERGY = -78.968 RDTITL> * VAN DER WAALS = -30.5093 ELECTROSTATIC = -48.4587 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "57" Parameter: CONF_N -> "8002" Comparing "57" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "58" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763657 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759669 ATOM PAIRS WERE FOUND FOR ATOM LIST 41630 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29699 from a total of 759669 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 58 -76.69434 -2.27371 0.66604 INTE EXTERN> -30.53631 -46.15803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6943" Parameter: A <- "-76.6943" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5363" Parameter: B <- "-30.5363" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.158" Parameter: C <- "-46.158" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 58 TOTAL ENERGY = -76.6943 RDTITL> * VAN DER WAALS = -30.5363 ELECTROSTATIC = -46.158 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "58" Parameter: CONF_N -> "8002" Comparing "58" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "59" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759669 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754902 ATOM PAIRS WERE FOUND FOR ATOM LIST 41586 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29649 from a total of 754902 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 59 -72.42248 -4.27186 0.62203 INTE EXTERN> -30.89918 -41.52330 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4225" Parameter: A <- "-72.4225" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8992" Parameter: B <- "-30.8992" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5233" Parameter: C <- "-41.5233" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 59 TOTAL ENERGY = -72.4225 RDTITL> * VAN DER WAALS = -30.8992 ELECTROSTATIC = -41.5233 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "59" Parameter: CONF_N -> "8002" Comparing "59" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "60" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754902 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748000 ATOM PAIRS WERE FOUND FOR ATOM LIST 41184 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29495 from a total of 748000 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 60 -72.79060 0.36812 0.70106 INTE EXTERN> -27.31648 -45.47412 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7906" Parameter: A <- "-72.7906" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3165" Parameter: B <- "-27.3165" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4741" Parameter: C <- "-45.4741" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 60 TOTAL ENERGY = -72.7906 RDTITL> * VAN DER WAALS = -27.3165 ELECTROSTATIC = -45.4741 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "60" Parameter: CONF_N -> "8002" Comparing "60" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "61" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748000 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752597 ATOM PAIRS WERE FOUND FOR ATOM LIST 41315 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29905 from a total of 752597 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 61 -75.29097 2.50036 0.69540 INTE EXTERN> -28.89432 -46.39665 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.291" Parameter: A <- "-75.291" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8943" Parameter: B <- "-28.8943" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3966" Parameter: C <- "-46.3966" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 61 TOTAL ENERGY = -75.291 RDTITL> * VAN DER WAALS = -28.8943 ELECTROSTATIC = -46.3966 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "61" Parameter: CONF_N -> "8002" Comparing "61" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "62" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752597 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754303 ATOM PAIRS WERE FOUND FOR ATOM LIST 41448 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 754303 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 62 -67.16817 -8.12279 0.67274 INTE EXTERN> -28.17866 -38.98951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1682" Parameter: A <- "-67.1682" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1787" Parameter: B <- "-28.1787" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9895" Parameter: C <- "-38.9895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 62 TOTAL ENERGY = -67.1682 RDTITL> * VAN DER WAALS = -28.1787 ELECTROSTATIC = -38.9895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "62" Parameter: CONF_N -> "8002" Comparing "62" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "63" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754303 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751713 ATOM PAIRS WERE FOUND FOR ATOM LIST 41166 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29480 from a total of 751713 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 63 -65.54013 -1.62804 0.69855 INTE EXTERN> -24.76713 -40.77300 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5401" Parameter: A <- "-65.5401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7671" Parameter: B <- "-24.7671" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.773" Parameter: C <- "-40.773" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 63 TOTAL ENERGY = -65.5401 RDTITL> * VAN DER WAALS = -24.7671 ELECTROSTATIC = -40.773 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "63" Parameter: CONF_N -> "8002" Comparing "63" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "64" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751713 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751858 ATOM PAIRS WERE FOUND FOR ATOM LIST 41469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29543 from a total of 751858 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 64 -67.87583 2.33570 0.73289 INTE EXTERN> -26.39890 -41.47693 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8758" Parameter: A <- "-67.8758" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3989" Parameter: B <- "-26.3989" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4769" Parameter: C <- "-41.4769" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 64 TOTAL ENERGY = -67.8758 RDTITL> * VAN DER WAALS = -26.3989 ELECTROSTATIC = -41.4769 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "64" Parameter: CONF_N -> "8002" Comparing "64" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "65" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751858 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750319 ATOM PAIRS WERE FOUND FOR ATOM LIST 41545 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29712 from a total of 750319 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 65 -68.73208 0.85625 0.64410 INTE EXTERN> -30.54671 -38.18537 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7321" Parameter: A <- "-68.7321" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5467" Parameter: B <- "-30.5467" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1854" Parameter: C <- "-38.1854" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 65 TOTAL ENERGY = -68.7321 RDTITL> * VAN DER WAALS = -30.5467 ELECTROSTATIC = -38.1854 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "65" Parameter: CONF_N -> "8002" Comparing "65" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "66" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750319 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758537 ATOM PAIRS WERE FOUND FOR ATOM LIST 41627 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30414 from a total of 758537 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 66 -66.30335 -2.42872 0.73653 INTE EXTERN> -24.48935 -41.81400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3034" Parameter: A <- "-66.3034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4894" Parameter: B <- "-24.4894" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.814" Parameter: C <- "-41.814" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 66 TOTAL ENERGY = -66.3034 RDTITL> * VAN DER WAALS = -24.4894 ELECTROSTATIC = -41.814 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "66" Parameter: CONF_N -> "8002" Comparing "66" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "67" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758537 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754839 ATOM PAIRS WERE FOUND FOR ATOM LIST 41362 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29349 from a total of 754839 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 67 -66.48246 0.17910 0.61393 INTE EXTERN> -29.29002 -37.19244 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4825" Parameter: A <- "-66.4825" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.29" Parameter: B <- "-29.29" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1924" Parameter: C <- "-37.1924" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 67 TOTAL ENERGY = -66.4825 RDTITL> * VAN DER WAALS = -29.29 ELECTROSTATIC = -37.1924 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "67" Parameter: CONF_N -> "8002" Comparing "67" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "68" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754839 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752078 ATOM PAIRS WERE FOUND FOR ATOM LIST 41456 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29594 from a total of 752078 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 68 -65.98560 -0.49686 0.63345 INTE EXTERN> -29.69788 -36.28772 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9856" Parameter: A <- "-65.9856" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6979" Parameter: B <- "-29.6979" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2877" Parameter: C <- "-36.2877" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 68 TOTAL ENERGY = -65.9856 RDTITL> * VAN DER WAALS = -29.6979 ELECTROSTATIC = -36.2877 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "68" Parameter: CONF_N -> "8002" Comparing "68" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "69" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752078 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763183 ATOM PAIRS WERE FOUND FOR ATOM LIST 41996 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30127 from a total of 763183 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 69 -70.11186 4.12626 0.65126 INTE EXTERN> -27.31159 -42.80027 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1119" Parameter: A <- "-70.1119" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3116" Parameter: B <- "-27.3116" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8003" Parameter: C <- "-42.8003" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 69 TOTAL ENERGY = -70.1119 RDTITL> * VAN DER WAALS = -27.3116 ELECTROSTATIC = -42.8003 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "69" Parameter: CONF_N -> "8002" Comparing "69" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "70" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763183 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754747 ATOM PAIRS WERE FOUND FOR ATOM LIST 41450 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29943 from a total of 754747 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 70 -74.61067 4.49881 0.57956 INTE EXTERN> -31.83562 -42.77505 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6107" Parameter: A <- "-74.6107" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8356" Parameter: B <- "-31.8356" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.775" Parameter: C <- "-42.775" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 70 TOTAL ENERGY = -74.6107 RDTITL> * VAN DER WAALS = -31.8356 ELECTROSTATIC = -42.775 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "70" Parameter: CONF_N -> "8002" Comparing "70" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "71" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754747 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751239 ATOM PAIRS WERE FOUND FOR ATOM LIST 41457 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29772 from a total of 751239 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 71 -64.58758 -10.02309 0.66044 INTE EXTERN> -26.58991 -37.99768 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5876" Parameter: A <- "-64.5876" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5899" Parameter: B <- "-26.5899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9977" Parameter: C <- "-37.9977" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 71 TOTAL ENERGY = -64.5876 RDTITL> * VAN DER WAALS = -26.5899 ELECTROSTATIC = -37.9977 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "71" Parameter: CONF_N -> "8002" Comparing "71" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "72" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751239 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754553 ATOM PAIRS WERE FOUND FOR ATOM LIST 41455 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29785 from a total of 754553 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 72 -68.46755 3.87997 0.60169 INTE EXTERN> -32.73665 -35.73089 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4675" Parameter: A <- "-68.4675" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7367" Parameter: B <- "-32.7367" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7309" Parameter: C <- "-35.7309" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 72 TOTAL ENERGY = -68.4675 RDTITL> * VAN DER WAALS = -32.7367 ELECTROSTATIC = -35.7309 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "72" Parameter: CONF_N -> "8002" Comparing "72" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "73" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754553 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752349 ATOM PAIRS WERE FOUND FOR ATOM LIST 41486 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29094 from a total of 752349 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 73 -59.89882 -8.56873 0.51853 INTE EXTERN> -30.96383 -28.93499 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.8988" Parameter: A <- "-59.8988" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9638" Parameter: B <- "-30.9638" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.935" Parameter: C <- "-28.935" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 73 TOTAL ENERGY = -59.8988 RDTITL> * VAN DER WAALS = -30.9638 ELECTROSTATIC = -28.935 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "73" Parameter: CONF_N -> "8002" Comparing "73" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "74" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752349 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745995 ATOM PAIRS WERE FOUND FOR ATOM LIST 41283 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29207 from a total of 745995 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 74 -55.87298 -4.02584 0.51951 INTE EXTERN> -30.15191 -25.72107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.873" Parameter: A <- "-55.873" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1519" Parameter: B <- "-30.1519" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-25.7211" Parameter: C <- "-25.7211" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 74 TOTAL ENERGY = -55.873 RDTITL> * VAN DER WAALS = -30.1519 ELECTROSTATIC = -25.7211 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "74" Parameter: CONF_N -> "8002" Comparing "74" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "75" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745995 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756337 ATOM PAIRS WERE FOUND FOR ATOM LIST 41625 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29961 from a total of 756337 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 75 -75.38176 19.50878 0.59833 INTE EXTERN> -31.13047 -44.25129 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3818" Parameter: A <- "-75.3818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1305" Parameter: B <- "-31.1305" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2513" Parameter: C <- "-44.2513" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 75 TOTAL ENERGY = -75.3818 RDTITL> * VAN DER WAALS = -31.1305 ELECTROSTATIC = -44.2513 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "75" Parameter: CONF_N -> "8002" Comparing "75" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "76" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756337 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753032 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29605 from a total of 753032 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 76 -65.31090 -10.07086 0.52733 INTE EXTERN> -33.27970 -32.03120 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3109" Parameter: A <- "-65.3109" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2797" Parameter: B <- "-33.2797" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.0312" Parameter: C <- "-32.0312" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 76 TOTAL ENERGY = -65.3109 RDTITL> * VAN DER WAALS = -33.2797 ELECTROSTATIC = -32.0312 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "76" Parameter: CONF_N -> "8002" Comparing "76" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "77" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753032 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748097 ATOM PAIRS WERE FOUND FOR ATOM LIST 41070 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29285 from a total of 748097 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 77 -67.81756 2.50666 0.53017 INTE EXTERN> -32.45195 -35.36561 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8176" Parameter: A <- "-67.8176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.452" Parameter: B <- "-32.452" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3656" Parameter: C <- "-35.3656" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 77 TOTAL ENERGY = -67.8176 RDTITL> * VAN DER WAALS = -32.452 ELECTROSTATIC = -35.3656 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "77" Parameter: CONF_N -> "8002" Comparing "77" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "78" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748097 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746453 ATOM PAIRS WERE FOUND FOR ATOM LIST 41023 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29084 from a total of 746453 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 78 -59.42694 -8.39062 0.48297 INTE EXTERN> -33.81677 -25.61017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.4269" Parameter: A <- "-59.4269" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8168" Parameter: B <- "-33.8168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-25.6102" Parameter: C <- "-25.6102" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 78 TOTAL ENERGY = -59.4269 RDTITL> * VAN DER WAALS = -33.8168 ELECTROSTATIC = -25.6102 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "78" Parameter: CONF_N -> "8002" Comparing "78" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "79" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746453 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752902 ATOM PAIRS WERE FOUND FOR ATOM LIST 41476 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29789 from a total of 752902 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 79 -64.37918 4.95223 0.59204 INTE EXTERN> -28.97723 -35.40195 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3792" Parameter: A <- "-64.3792" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9772" Parameter: B <- "-28.9772" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4019" Parameter: C <- "-35.4019" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 79 TOTAL ENERGY = -64.3792 RDTITL> * VAN DER WAALS = -28.9772 ELECTROSTATIC = -35.4019 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "79" Parameter: CONF_N -> "8002" Comparing "79" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "80" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752902 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750086 ATOM PAIRS WERE FOUND FOR ATOM LIST 41350 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28902 from a total of 750086 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 80 -65.54278 1.16360 0.45047 INTE EXTERN> -31.73923 -33.80355 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5428" Parameter: A <- "-65.5428" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7392" Parameter: B <- "-31.7392" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8035" Parameter: C <- "-33.8035" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 80 TOTAL ENERGY = -65.5428 RDTITL> * VAN DER WAALS = -31.7392 ELECTROSTATIC = -33.8035 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "80" Parameter: CONF_N -> "8002" Comparing "80" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "81" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750086 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751004 ATOM PAIRS WERE FOUND FOR ATOM LIST 41495 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29645 from a total of 751004 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 81 -71.86578 6.32300 0.58584 INTE EXTERN> -31.11790 -40.74788 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8658" Parameter: A <- "-71.8658" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1179" Parameter: B <- "-31.1179" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7479" Parameter: C <- "-40.7479" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 81 TOTAL ENERGY = -71.8658 RDTITL> * VAN DER WAALS = -31.1179 ELECTROSTATIC = -40.7479 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "81" Parameter: CONF_N -> "8002" Comparing "81" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "82" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751004 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754790 ATOM PAIRS WERE FOUND FOR ATOM LIST 41905 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29723 from a total of 754790 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 82 -65.74969 -6.11609 0.56239 INTE EXTERN> -29.09016 -36.65953 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7497" Parameter: A <- "-65.7497" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0902" Parameter: B <- "-29.0902" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6595" Parameter: C <- "-36.6595" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 82 TOTAL ENERGY = -65.7497 RDTITL> * VAN DER WAALS = -29.0902 ELECTROSTATIC = -36.6595 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "82" Parameter: CONF_N -> "8002" Comparing "82" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "83" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754790 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754265 ATOM PAIRS WERE FOUND FOR ATOM LIST 41606 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29277 from a total of 754265 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 83 -66.09394 0.34425 0.53128 INTE EXTERN> -28.05216 -38.04179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0939" Parameter: A <- "-66.0939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0522" Parameter: B <- "-28.0522" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0418" Parameter: C <- "-38.0418" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 83 TOTAL ENERGY = -66.0939 RDTITL> * VAN DER WAALS = -28.0522 ELECTROSTATIC = -38.0418 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "83" Parameter: CONF_N -> "8002" Comparing "83" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "84" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754265 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747073 ATOM PAIRS WERE FOUND FOR ATOM LIST 41203 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28602 from a total of 747073 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 84 -59.95942 -6.13453 0.44602 INTE EXTERN> -32.31414 -27.64527 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.9594" Parameter: A <- "-59.9594" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3141" Parameter: B <- "-32.3141" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.6453" Parameter: C <- "-27.6453" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 84 TOTAL ENERGY = -59.9594 RDTITL> * VAN DER WAALS = -32.3141 ELECTROSTATIC = -27.6453 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "84" Parameter: CONF_N -> "8002" Comparing "84" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "85" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747073 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749880 ATOM PAIRS WERE FOUND FOR ATOM LIST 41324 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29636 from a total of 749880 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 85 -72.17901 12.21960 0.58694 INTE EXTERN> -29.73560 -42.44341 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.179" Parameter: A <- "-72.179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7356" Parameter: B <- "-29.7356" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4434" Parameter: C <- "-42.4434" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 85 TOTAL ENERGY = -72.179 RDTITL> * VAN DER WAALS = -29.7356 ELECTROSTATIC = -42.4434 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "85" Parameter: CONF_N -> "8002" Comparing "85" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "86" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749880 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749774 ATOM PAIRS WERE FOUND FOR ATOM LIST 41332 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29265 from a total of 749774 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 86 -68.87627 -3.30274 0.59914 INTE EXTERN> -29.23940 -39.63687 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8763" Parameter: A <- "-68.8763" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2394" Parameter: B <- "-29.2394" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6369" Parameter: C <- "-39.6369" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 86 TOTAL ENERGY = -68.8763 RDTITL> * VAN DER WAALS = -29.2394 ELECTROSTATIC = -39.6369 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "86" Parameter: CONF_N -> "8002" Comparing "86" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "87" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749774 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757050 ATOM PAIRS WERE FOUND FOR ATOM LIST 41458 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29104 from a total of 757050 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 87 -73.48448 4.60821 0.56897 INTE EXTERN> -31.63729 -41.84719 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4845" Parameter: A <- "-73.4845" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6373" Parameter: B <- "-31.6373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8472" Parameter: C <- "-41.8472" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 87 TOTAL ENERGY = -73.4845 RDTITL> * VAN DER WAALS = -31.6373 ELECTROSTATIC = -41.8472 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "87" Parameter: CONF_N -> "8002" Comparing "87" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "88" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757050 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755880 ATOM PAIRS WERE FOUND FOR ATOM LIST 41571 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29344 from a total of 755880 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 88 -65.41668 -8.06780 0.70380 INTE EXTERN> -25.37825 -40.03843 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4167" Parameter: A <- "-65.4167" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3783" Parameter: B <- "-25.3783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0384" Parameter: C <- "-40.0384" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 88 TOTAL ENERGY = -65.4167 RDTITL> * VAN DER WAALS = -25.3783 ELECTROSTATIC = -40.0384 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "88" Parameter: CONF_N -> "8002" Comparing "88" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "89" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755880 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751632 ATOM PAIRS WERE FOUND FOR ATOM LIST 41466 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28916 from a total of 751632 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 89 -65.93755 0.52087 0.51267 INTE EXTERN> -30.30884 -35.62871 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9375" Parameter: A <- "-65.9375" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3088" Parameter: B <- "-30.3088" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6287" Parameter: C <- "-35.6287" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 89 TOTAL ENERGY = -65.9375 RDTITL> * VAN DER WAALS = -30.3088 ELECTROSTATIC = -35.6287 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "89" Parameter: CONF_N -> "8002" Comparing "89" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "90" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751632 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749992 ATOM PAIRS WERE FOUND FOR ATOM LIST 41484 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28874 from a total of 749992 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 90 -71.85884 5.92129 0.58603 INTE EXTERN> -30.72299 -41.13585 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8588" Parameter: A <- "-71.8588" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.723" Parameter: B <- "-30.723" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1359" Parameter: C <- "-41.1359" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 90 TOTAL ENERGY = -71.8588 RDTITL> * VAN DER WAALS = -30.723 ELECTROSTATIC = -41.1359 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "90" Parameter: CONF_N -> "8002" Comparing "90" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "91" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749992 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745622 ATOM PAIRS WERE FOUND FOR ATOM LIST 40943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28620 from a total of 745622 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 91 -60.54588 -11.31297 0.49199 INTE EXTERN> -29.92813 -30.61775 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.5459" Parameter: A <- "-60.5459" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9281" Parameter: B <- "-29.9281" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.6177" Parameter: C <- "-30.6177" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 91 TOTAL ENERGY = -60.5459 RDTITL> * VAN DER WAALS = -29.9281 ELECTROSTATIC = -30.6177 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "91" Parameter: CONF_N -> "8002" Comparing "91" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "92" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745622 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747517 ATOM PAIRS WERE FOUND FOR ATOM LIST 41286 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29613 from a total of 747517 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 92 -62.77251 2.22664 0.60155 INTE EXTERN> -29.35091 -33.42160 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7725" Parameter: A <- "-62.7725" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3509" Parameter: B <- "-29.3509" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.4216" Parameter: C <- "-33.4216" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 92 TOTAL ENERGY = -62.7725 RDTITL> * VAN DER WAALS = -29.3509 ELECTROSTATIC = -33.4216 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "92" Parameter: CONF_N -> "8002" Comparing "92" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "93" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747517 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754432 ATOM PAIRS WERE FOUND FOR ATOM LIST 41501 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28821 from a total of 754432 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 93 -67.84345 5.07094 0.51098 INTE EXTERN> -32.40811 -35.43535 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8435" Parameter: A <- "-67.8435" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4081" Parameter: B <- "-32.4081" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4353" Parameter: C <- "-35.4353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 93 TOTAL ENERGY = -67.8435 RDTITL> * VAN DER WAALS = -32.4081 ELECTROSTATIC = -35.4353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "93" Parameter: CONF_N -> "8002" Comparing "93" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "94" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754432 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752982 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29418 from a total of 752982 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 94 -71.94869 4.10524 0.59672 INTE EXTERN> -28.65700 -43.29169 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9487" Parameter: A <- "-71.9487" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.657" Parameter: B <- "-28.657" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2917" Parameter: C <- "-43.2917" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 94 TOTAL ENERGY = -71.9487 RDTITL> * VAN DER WAALS = -28.657 ELECTROSTATIC = -43.2917 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "94" Parameter: CONF_N -> "8002" Comparing "94" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "95" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752982 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753358 ATOM PAIRS WERE FOUND FOR ATOM LIST 41514 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29353 from a total of 753358 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 95 -72.21917 0.27048 0.52826 INTE EXTERN> -30.52498 -41.69419 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2192" Parameter: A <- "-72.2192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.525" Parameter: B <- "-30.525" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6942" Parameter: C <- "-41.6942" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 95 TOTAL ENERGY = -72.2192 RDTITL> * VAN DER WAALS = -30.525 ELECTROSTATIC = -41.6942 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "95" Parameter: CONF_N -> "8002" Comparing "95" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "96" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753358 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757204 ATOM PAIRS WERE FOUND FOR ATOM LIST 41641 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28791 from a total of 757204 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 96 -66.78751 -5.43166 0.49950 INTE EXTERN> -32.37948 -34.40803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7875" Parameter: A <- "-66.7875" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3795" Parameter: B <- "-32.3795" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.408" Parameter: C <- "-34.408" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 96 TOTAL ENERGY = -66.7875 RDTITL> * VAN DER WAALS = -32.3795 ELECTROSTATIC = -34.408 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "96" Parameter: CONF_N -> "8002" Comparing "96" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "97" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757204 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756538 ATOM PAIRS WERE FOUND FOR ATOM LIST 41705 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29696 from a total of 756538 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 97 -70.09274 3.30523 0.47784 INTE EXTERN> -33.39577 -36.69697 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0927" Parameter: A <- "-70.0927" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3958" Parameter: B <- "-33.3958" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.697" Parameter: C <- "-36.697" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 97 TOTAL ENERGY = -70.0927 RDTITL> * VAN DER WAALS = -33.3958 ELECTROSTATIC = -36.697 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "97" Parameter: CONF_N -> "8002" Comparing "97" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "98" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756538 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756645 ATOM PAIRS WERE FOUND FOR ATOM LIST 41609 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29669 from a total of 756645 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 98 -75.84346 5.75071 0.52450 INTE EXTERN> -32.77956 -43.06389 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8435" Parameter: A <- "-75.8435" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7796" Parameter: B <- "-32.7796" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0639" Parameter: C <- "-43.0639" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 98 TOTAL ENERGY = -75.8435 RDTITL> * VAN DER WAALS = -32.7796 ELECTROSTATIC = -43.0639 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "98" Parameter: CONF_N -> "8002" Comparing "98" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "99" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756645 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753013 ATOM PAIRS WERE FOUND FOR ATOM LIST 41657 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29260 from a total of 753013 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 99 -70.12553 -5.71792 0.54260 INTE EXTERN> -32.28912 -37.83641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1255" Parameter: A <- "-70.1255" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2891" Parameter: B <- "-32.2891" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8364" Parameter: C <- "-37.8364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 99 TOTAL ENERGY = -70.1255 RDTITL> * VAN DER WAALS = -32.2891 ELECTROSTATIC = -37.8364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "99" Parameter: CONF_N -> "8002" Comparing "99" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "100" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753013 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757214 ATOM PAIRS WERE FOUND FOR ATOM LIST 41756 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29254 from a total of 757214 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 100 -70.22249 0.09696 0.72145 INTE EXTERN> -25.78431 -44.43818 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2225" Parameter: A <- "-70.2225" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7843" Parameter: B <- "-25.7843" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4382" Parameter: C <- "-44.4382" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 100 TOTAL ENERGY = -70.2225 RDTITL> * VAN DER WAALS = -25.7843 ELECTROSTATIC = -44.4382 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "100" Parameter: CONF_N -> "8002" Comparing "100" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "101" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757214 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760331 ATOM PAIRS WERE FOUND FOR ATOM LIST 41888 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29727 from a total of 760331 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 101 -73.26264 3.04015 0.51685 INTE EXTERN> -31.89265 -41.37000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2626" Parameter: A <- "-73.2626" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8926" Parameter: B <- "-31.8926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.37" Parameter: C <- "-41.37" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 101 TOTAL ENERGY = -73.2626 RDTITL> * VAN DER WAALS = -31.8926 ELECTROSTATIC = -41.37 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "101" Parameter: CONF_N -> "8002" Comparing "101" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "102" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760331 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754273 ATOM PAIRS WERE FOUND FOR ATOM LIST 41507 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30019 from a total of 754273 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 102 -71.63969 -1.62295 0.59633 INTE EXTERN> -31.65236 -39.98733 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6397" Parameter: A <- "-71.6397" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6524" Parameter: B <- "-31.6524" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9873" Parameter: C <- "-39.9873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 102 TOTAL ENERGY = -71.6397 RDTITL> * VAN DER WAALS = -31.6524 ELECTROSTATIC = -39.9873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "102" Parameter: CONF_N -> "8002" Comparing "102" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "103" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754273 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753296 ATOM PAIRS WERE FOUND FOR ATOM LIST 41472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29429 from a total of 753296 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 103 -64.62502 -7.01468 0.54130 INTE EXTERN> -30.67488 -33.95013 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.625" Parameter: A <- "-64.625" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6749" Parameter: B <- "-30.6749" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9501" Parameter: C <- "-33.9501" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 103 TOTAL ENERGY = -64.625 RDTITL> * VAN DER WAALS = -30.6749 ELECTROSTATIC = -33.9501 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "103" Parameter: CONF_N -> "8002" Comparing "103" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "104" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753296 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751494 ATOM PAIRS WERE FOUND FOR ATOM LIST 41524 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29331 from a total of 751494 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 104 -59.07590 -5.54912 0.46445 INTE EXTERN> -30.00876 -29.06714 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.0759" Parameter: A <- "-59.0759" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0088" Parameter: B <- "-30.0088" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.0671" Parameter: C <- "-29.0671" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 104 TOTAL ENERGY = -59.0759 RDTITL> * VAN DER WAALS = -30.0088 ELECTROSTATIC = -29.0671 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "104" Parameter: CONF_N -> "8002" Comparing "104" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "105" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751494 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751941 ATOM PAIRS WERE FOUND FOR ATOM LIST 41427 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29307 from a total of 751941 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 105 -67.83464 8.75874 0.54400 INTE EXTERN> -29.84429 -37.99035 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8346" Parameter: A <- "-67.8346" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8443" Parameter: B <- "-29.8443" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9903" Parameter: C <- "-37.9903" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 105 TOTAL ENERGY = -67.8346 RDTITL> * VAN DER WAALS = -29.8443 ELECTROSTATIC = -37.9903 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "105" Parameter: CONF_N -> "8002" Comparing "105" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "106" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751941 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756660 ATOM PAIRS WERE FOUND FOR ATOM LIST 41543 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29815 from a total of 756660 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 106 -66.74844 -1.08620 0.56159 INTE EXTERN> -28.31674 -38.43170 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7484" Parameter: A <- "-66.7484" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3167" Parameter: B <- "-28.3167" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4317" Parameter: C <- "-38.4317" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 106 TOTAL ENERGY = -66.7484 RDTITL> * VAN DER WAALS = -28.3167 ELECTROSTATIC = -38.4317 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "106" Parameter: CONF_N -> "8002" Comparing "106" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "107" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756660 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41629 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29458 from a total of 755601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 107 -69.91425 3.16581 0.53317 INTE EXTERN> -29.24641 -40.66784 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9142" Parameter: A <- "-69.9142" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2464" Parameter: B <- "-29.2464" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6678" Parameter: C <- "-40.6678" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 107 TOTAL ENERGY = -69.9142 RDTITL> * VAN DER WAALS = -29.2464 ELECTROSTATIC = -40.6678 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "107" Parameter: CONF_N -> "8002" Comparing "107" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "108" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755768 ATOM PAIRS WERE FOUND FOR ATOM LIST 41515 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29439 from a total of 755768 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 108 -72.03294 2.11869 0.54810 INTE EXTERN> -31.49538 -40.53756 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0329" Parameter: A <- "-72.0329" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4954" Parameter: B <- "-31.4954" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5376" Parameter: C <- "-40.5376" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 108 TOTAL ENERGY = -72.0329 RDTITL> * VAN DER WAALS = -31.4954 ELECTROSTATIC = -40.5376 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "108" Parameter: CONF_N -> "8002" Comparing "108" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "109" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755768 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757710 ATOM PAIRS WERE FOUND FOR ATOM LIST 41677 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29855 from a total of 757710 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 109 -65.42865 -6.60428 0.58956 INTE EXTERN> -28.92215 -36.50651 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4287" Parameter: A <- "-65.4287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9221" Parameter: B <- "-28.9221" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5065" Parameter: C <- "-36.5065" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 109 TOTAL ENERGY = -65.4287 RDTITL> * VAN DER WAALS = -28.9221 ELECTROSTATIC = -36.5065 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "109" Parameter: CONF_N -> "8002" Comparing "109" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "110" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757710 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753747 ATOM PAIRS WERE FOUND FOR ATOM LIST 41588 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29345 from a total of 753747 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 110 -60.76580 -4.66285 0.45892 INTE EXTERN> -30.39488 -30.37092 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.7658" Parameter: A <- "-60.7658" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3949" Parameter: B <- "-30.3949" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.3709" Parameter: C <- "-30.3709" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 110 TOTAL ENERGY = -60.7658 RDTITL> * VAN DER WAALS = -30.3949 ELECTROSTATIC = -30.3709 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "110" Parameter: CONF_N -> "8002" Comparing "110" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "111" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753747 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757666 ATOM PAIRS WERE FOUND FOR ATOM LIST 41602 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29483 from a total of 757666 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 111 -63.51640 2.75060 0.56188 INTE EXTERN> -29.41034 -34.10605 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5164" Parameter: A <- "-63.5164" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4103" Parameter: B <- "-29.4103" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1061" Parameter: C <- "-34.1061" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 111 TOTAL ENERGY = -63.5164 RDTITL> * VAN DER WAALS = -29.4103 ELECTROSTATIC = -34.1061 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "111" Parameter: CONF_N -> "8002" Comparing "111" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "112" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757666 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756658 ATOM PAIRS WERE FOUND FOR ATOM LIST 41553 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29224 from a total of 756658 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 112 -71.87599 8.35959 0.55162 INTE EXTERN> -33.41605 -38.45994 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.876" Parameter: A <- "-71.876" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4161" Parameter: B <- "-33.4161" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4599" Parameter: C <- "-38.4599" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 112 TOTAL ENERGY = -71.876 RDTITL> * VAN DER WAALS = -33.4161 ELECTROSTATIC = -38.4599 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "112" Parameter: CONF_N -> "8002" Comparing "112" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "113" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756658 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757836 ATOM PAIRS WERE FOUND FOR ATOM LIST 41674 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29980 from a total of 757836 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 113 -62.00888 -9.86711 0.50759 INTE EXTERN> -29.57204 -32.43684 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.0089" Parameter: A <- "-62.0089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.572" Parameter: B <- "-29.572" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.4368" Parameter: C <- "-32.4368" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 113 TOTAL ENERGY = -62.0089 RDTITL> * VAN DER WAALS = -29.572 ELECTROSTATIC = -32.4368 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "113" Parameter: CONF_N -> "8002" Comparing "113" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "114" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757836 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754977 ATOM PAIRS WERE FOUND FOR ATOM LIST 41422 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29704 from a total of 754977 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 114 -73.92364 11.91477 0.68325 INTE EXTERN> -27.99120 -45.93244 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9236" Parameter: A <- "-73.9236" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9912" Parameter: B <- "-27.9912" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9324" Parameter: C <- "-45.9324" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 114 TOTAL ENERGY = -73.9236 RDTITL> * VAN DER WAALS = -27.9912 ELECTROSTATIC = -45.9324 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "114" Parameter: CONF_N -> "8002" Comparing "114" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "115" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754977 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759873 ATOM PAIRS WERE FOUND FOR ATOM LIST 41792 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30041 from a total of 759873 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 115 -69.50728 -4.41636 0.63246 INTE EXTERN> -29.57057 -39.93671 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5073" Parameter: A <- "-69.5073" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5706" Parameter: B <- "-29.5706" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9367" Parameter: C <- "-39.9367" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 115 TOTAL ENERGY = -69.5073 RDTITL> * VAN DER WAALS = -29.5706 ELECTROSTATIC = -39.9367 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "115" Parameter: CONF_N -> "8002" Comparing "115" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "116" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759873 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760924 ATOM PAIRS WERE FOUND FOR ATOM LIST 41991 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29795 from a total of 760924 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 116 -72.72962 3.22234 0.62833 INTE EXTERN> -29.72568 -43.00395 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7296" Parameter: A <- "-72.7296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7257" Parameter: B <- "-29.7257" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0039" Parameter: C <- "-43.0039" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 116 TOTAL ENERGY = -72.7296 RDTITL> * VAN DER WAALS = -29.7257 ELECTROSTATIC = -43.0039 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "116" Parameter: CONF_N -> "8002" Comparing "116" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "117" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760924 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760217 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29555 from a total of 760217 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 117 -65.59960 -7.13002 0.53823 INTE EXTERN> -31.57058 -34.02901 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5996" Parameter: A <- "-65.5996" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5706" Parameter: B <- "-31.5706" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.029" Parameter: C <- "-34.029" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 117 TOTAL ENERGY = -65.5996 RDTITL> * VAN DER WAALS = -31.5706 ELECTROSTATIC = -34.029 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "117" Parameter: CONF_N -> "8002" Comparing "117" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "118" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760217 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760871 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29727 from a total of 760871 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 118 -72.72216 7.12257 0.53126 INTE EXTERN> -32.24732 -40.47485 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7222" Parameter: A <- "-72.7222" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2473" Parameter: B <- "-32.2473" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4748" Parameter: C <- "-40.4748" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 118 TOTAL ENERGY = -72.7222 RDTITL> * VAN DER WAALS = -32.2473 ELECTROSTATIC = -40.4748 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "118" Parameter: CONF_N -> "8002" Comparing "118" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "119" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760871 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759718 ATOM PAIRS WERE FOUND FOR ATOM LIST 41643 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30110 from a total of 759718 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 119 -63.92769 -8.79447 0.55442 INTE EXTERN> -29.14697 -34.78072 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.9277" Parameter: A <- "-63.9277" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.147" Parameter: B <- "-29.147" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7807" Parameter: C <- "-34.7807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 119 TOTAL ENERGY = -63.9277 RDTITL> * VAN DER WAALS = -29.147 ELECTROSTATIC = -34.7807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "119" Parameter: CONF_N -> "8002" Comparing "119" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "120" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759718 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763628 ATOM PAIRS WERE FOUND FOR ATOM LIST 41944 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30117 from a total of 763628 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 120 -65.99394 2.06625 0.63302 INTE EXTERN> -26.86687 -39.12707 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9939" Parameter: A <- "-65.9939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8669" Parameter: B <- "-26.8669" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1271" Parameter: C <- "-39.1271" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 120 TOTAL ENERGY = -65.9939 RDTITL> * VAN DER WAALS = -26.8669 ELECTROSTATIC = -39.1271 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "120" Parameter: CONF_N -> "8002" Comparing "120" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "121" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763628 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763591 ATOM PAIRS WERE FOUND FOR ATOM LIST 42102 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29612 from a total of 763591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 121 -80.98763 14.99369 0.62214 INTE EXTERN> -31.78094 -49.20669 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9876" Parameter: A <- "-80.9876" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7809" Parameter: B <- "-31.7809" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2067" Parameter: C <- "-49.2067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 121 TOTAL ENERGY = -80.9876 RDTITL> * VAN DER WAALS = -31.7809 ELECTROSTATIC = -49.2067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "121" Parameter: CONF_N -> "8002" Comparing "121" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "122" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759149 ATOM PAIRS WERE FOUND FOR ATOM LIST 41676 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30049 from a total of 759149 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 122 -72.73690 -8.25074 0.61306 INTE EXTERN> -28.37293 -44.36397 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7369" Parameter: A <- "-72.7369" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3729" Parameter: B <- "-28.3729" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.364" Parameter: C <- "-44.364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 122 TOTAL ENERGY = -72.7369 RDTITL> * VAN DER WAALS = -28.3729 ELECTROSTATIC = -44.364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "122" Parameter: CONF_N -> "8002" Comparing "122" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "123" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759149 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755724 ATOM PAIRS WERE FOUND FOR ATOM LIST 41435 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29460 from a total of 755724 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 123 -73.08857 0.35167 0.54425 INTE EXTERN> -32.18052 -40.90805 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0886" Parameter: A <- "-73.0886" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1805" Parameter: B <- "-32.1805" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.908" Parameter: C <- "-40.908" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 123 TOTAL ENERGY = -73.0886 RDTITL> * VAN DER WAALS = -32.1805 ELECTROSTATIC = -40.908 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "123" Parameter: CONF_N -> "8002" Comparing "123" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "124" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755724 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759591 ATOM PAIRS WERE FOUND FOR ATOM LIST 41692 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30054 from a total of 759591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 124 -77.38370 4.29514 0.66113 INTE EXTERN> -29.34534 -48.03837 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3837" Parameter: A <- "-77.3837" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3453" Parameter: B <- "-29.3453" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0384" Parameter: C <- "-48.0384" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 124 TOTAL ENERGY = -77.3837 RDTITL> * VAN DER WAALS = -29.3453 ELECTROSTATIC = -48.0384 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "124" Parameter: CONF_N -> "8002" Comparing "124" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "125" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766356 ATOM PAIRS WERE FOUND FOR ATOM LIST 41712 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30056 from a total of 766356 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 125 -74.37464 -3.00906 0.64691 INTE EXTERN> -28.87947 -45.49517 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3746" Parameter: A <- "-74.3746" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8795" Parameter: B <- "-28.8795" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4952" Parameter: C <- "-45.4952" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 125 TOTAL ENERGY = -74.3746 RDTITL> * VAN DER WAALS = -28.8795 ELECTROSTATIC = -45.4952 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "125" Parameter: CONF_N -> "8002" Comparing "125" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "126" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766356 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753790 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29112 from a total of 753790 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 126 -68.61503 -5.75961 0.56479 INTE EXTERN> -30.28695 -38.32808 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.615" Parameter: A <- "-68.615" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.287" Parameter: B <- "-30.287" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3281" Parameter: C <- "-38.3281" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 126 TOTAL ENERGY = -68.615 RDTITL> * VAN DER WAALS = -30.287 ELECTROSTATIC = -38.3281 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "126" Parameter: CONF_N -> "8002" Comparing "126" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "127" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753790 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750142 ATOM PAIRS WERE FOUND FOR ATOM LIST 41225 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29128 from a total of 750142 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 127 -71.39999 2.78495 0.59412 INTE EXTERN> -28.96675 -42.43324 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4" Parameter: A <- "-71.4" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9667" Parameter: B <- "-28.9667" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4332" Parameter: C <- "-42.4332" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 127 TOTAL ENERGY = -71.4 RDTITL> * VAN DER WAALS = -28.9667 ELECTROSTATIC = -42.4332 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "127" Parameter: CONF_N -> "8002" Comparing "127" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "128" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750142 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755402 ATOM PAIRS WERE FOUND FOR ATOM LIST 41406 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29485 from a total of 755402 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 128 -74.99614 3.59616 0.64525 INTE EXTERN> -30.09389 -44.90225 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9961" Parameter: A <- "-74.9961" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0939" Parameter: B <- "-30.0939" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9022" Parameter: C <- "-44.9022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 128 TOTAL ENERGY = -74.9961 RDTITL> * VAN DER WAALS = -30.0939 ELECTROSTATIC = -44.9022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "128" Parameter: CONF_N -> "8002" Comparing "128" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "129" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755402 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756187 ATOM PAIRS WERE FOUND FOR ATOM LIST 41371 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29323 from a total of 756187 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 129 -70.86013 -4.13601 0.63258 INTE EXTERN> -29.39037 -41.46976 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8601" Parameter: A <- "-70.8601" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3904" Parameter: B <- "-29.3904" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4698" Parameter: C <- "-41.4698" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 129 TOTAL ENERGY = -70.8601 RDTITL> * VAN DER WAALS = -29.3904 ELECTROSTATIC = -41.4698 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "129" Parameter: CONF_N -> "8002" Comparing "129" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "130" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756187 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758294 ATOM PAIRS WERE FOUND FOR ATOM LIST 41546 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29253 from a total of 758294 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 130 -71.46483 0.60471 0.69428 INTE EXTERN> -27.06759 -44.39724 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4648" Parameter: A <- "-71.4648" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0676" Parameter: B <- "-27.0676" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3972" Parameter: C <- "-44.3972" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 130 TOTAL ENERGY = -71.4648 RDTITL> * VAN DER WAALS = -27.0676 ELECTROSTATIC = -44.3972 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "130" Parameter: CONF_N -> "8002" Comparing "130" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "131" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758294 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750313 ATOM PAIRS WERE FOUND FOR ATOM LIST 41310 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29249 from a total of 750313 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 131 -72.98642 1.52159 0.67698 INTE EXTERN> -29.28415 -43.70227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9864" Parameter: A <- "-72.9864" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2841" Parameter: B <- "-29.2841" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7023" Parameter: C <- "-43.7023" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 131 TOTAL ENERGY = -72.9864 RDTITL> * VAN DER WAALS = -29.2841 ELECTROSTATIC = -43.7023 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "131" Parameter: CONF_N -> "8002" Comparing "131" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "132" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750313 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754451 ATOM PAIRS WERE FOUND FOR ATOM LIST 41515 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29751 from a total of 754451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 132 -67.97244 -5.01398 0.53286 INTE EXTERN> -33.23342 -34.73903 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9724" Parameter: A <- "-67.9724" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2334" Parameter: B <- "-33.2334" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.739" Parameter: C <- "-34.739" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 132 TOTAL ENERGY = -67.9724 RDTITL> * VAN DER WAALS = -33.2334 ELECTROSTATIC = -34.739 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "132" Parameter: CONF_N -> "8002" Comparing "132" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "133" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760027 ATOM PAIRS WERE FOUND FOR ATOM LIST 41734 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29964 from a total of 760027 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 133 -71.73610 3.76366 0.52247 INTE EXTERN> -34.15583 -37.58028 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7361" Parameter: A <- "-71.7361" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1558" Parameter: B <- "-34.1558" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5803" Parameter: C <- "-37.5803" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 133 TOTAL ENERGY = -71.7361 RDTITL> * VAN DER WAALS = -34.1558 ELECTROSTATIC = -37.5803 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "133" Parameter: CONF_N -> "8002" Comparing "133" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "134" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760027 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760749 ATOM PAIRS WERE FOUND FOR ATOM LIST 41876 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29325 from a total of 760749 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 134 -71.51333 -0.22277 0.60465 INTE EXTERN> -28.42731 -43.08602 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5133" Parameter: A <- "-71.5133" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4273" Parameter: B <- "-28.4273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.086" Parameter: C <- "-43.086" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 134 TOTAL ENERGY = -71.5133 RDTITL> * VAN DER WAALS = -28.4273 ELECTROSTATIC = -43.086 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "134" Parameter: CONF_N -> "8002" Comparing "134" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "135" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760749 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754807 ATOM PAIRS WERE FOUND FOR ATOM LIST 41587 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29428 from a total of 754807 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 135 -72.26785 0.75452 0.58625 INTE EXTERN> -31.03930 -41.22855 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2679" Parameter: A <- "-72.2679" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0393" Parameter: B <- "-31.0393" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2285" Parameter: C <- "-41.2285" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 135 TOTAL ENERGY = -72.2679 RDTITL> * VAN DER WAALS = -31.0393 ELECTROSTATIC = -41.2285 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "135" Parameter: CONF_N -> "8002" Comparing "135" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "136" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754807 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756929 ATOM PAIRS WERE FOUND FOR ATOM LIST 41378 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29474 from a total of 756929 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 136 -71.70957 -0.55829 0.61076 INTE EXTERN> -31.69112 -40.01845 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7096" Parameter: A <- "-71.7096" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6911" Parameter: B <- "-31.6911" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0184" Parameter: C <- "-40.0184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 136 TOTAL ENERGY = -71.7096 RDTITL> * VAN DER WAALS = -31.6911 ELECTROSTATIC = -40.0184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "136" Parameter: CONF_N -> "8002" Comparing "136" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "137" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756929 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757555 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29701 from a total of 757555 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 137 -71.99496 0.28539 0.60294 INTE EXTERN> -30.75609 -41.23887 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.995" Parameter: A <- "-71.995" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7561" Parameter: B <- "-30.7561" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2389" Parameter: C <- "-41.2389" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 137 TOTAL ENERGY = -71.995 RDTITL> * VAN DER WAALS = -30.7561 ELECTROSTATIC = -41.2389 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "137" Parameter: CONF_N -> "8002" Comparing "137" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "138" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757555 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751149 ATOM PAIRS WERE FOUND FOR ATOM LIST 41362 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29458 from a total of 751149 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 138 -69.01991 -2.97505 0.54735 INTE EXTERN> -30.69201 -38.32790 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0199" Parameter: A <- "-69.0199" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.692" Parameter: B <- "-30.692" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3279" Parameter: C <- "-38.3279" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 138 TOTAL ENERGY = -69.0199 RDTITL> * VAN DER WAALS = -30.692 ELECTROSTATIC = -38.3279 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "138" Parameter: CONF_N -> "8002" Comparing "138" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "139" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751149 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753623 ATOM PAIRS WERE FOUND FOR ATOM LIST 41516 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29388 from a total of 753623 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 139 -70.74555 1.72564 0.61057 INTE EXTERN> -29.61224 -41.13331 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7455" Parameter: A <- "-70.7455" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6122" Parameter: B <- "-29.6122" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1333" Parameter: C <- "-41.1333" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 139 TOTAL ENERGY = -70.7455 RDTITL> * VAN DER WAALS = -29.6122 ELECTROSTATIC = -41.1333 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "139" Parameter: CONF_N -> "8002" Comparing "139" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "140" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753623 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758279 ATOM PAIRS WERE FOUND FOR ATOM LIST 41587 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29689 from a total of 758279 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 140 -68.96205 -1.78350 0.61474 INTE EXTERN> -28.24250 -40.71955 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.962" Parameter: A <- "-68.962" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2425" Parameter: B <- "-28.2425" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7196" Parameter: C <- "-40.7196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 140 TOTAL ENERGY = -68.962 RDTITL> * VAN DER WAALS = -28.2425 ELECTROSTATIC = -40.7196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "140" Parameter: CONF_N -> "8002" Comparing "140" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "141" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758279 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757898 ATOM PAIRS WERE FOUND FOR ATOM LIST 41758 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28971 from a total of 757898 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 141 -67.70724 -1.25481 0.80386 INTE EXTERN> -26.03557 -41.67168 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7072" Parameter: A <- "-67.7072" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0356" Parameter: B <- "-26.0356" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6717" Parameter: C <- "-41.6717" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 141 TOTAL ENERGY = -67.7072 RDTITL> * VAN DER WAALS = -26.0356 ELECTROSTATIC = -41.6717 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "141" Parameter: CONF_N -> "8002" Comparing "141" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "142" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757898 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761593 ATOM PAIRS WERE FOUND FOR ATOM LIST 41831 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29851 from a total of 761593 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 142 -72.91682 5.20957 0.64237 INTE EXTERN> -29.79550 -43.12131 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9168" Parameter: A <- "-72.9168" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7955" Parameter: B <- "-29.7955" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1213" Parameter: C <- "-43.1213" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 142 TOTAL ENERGY = -72.9168 RDTITL> * VAN DER WAALS = -29.7955 ELECTROSTATIC = -43.1213 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "142" Parameter: CONF_N -> "8002" Comparing "142" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "143" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761593 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762457 ATOM PAIRS WERE FOUND FOR ATOM LIST 41937 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29129 from a total of 762457 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 143 -67.69886 -5.21796 0.68434 INTE EXTERN> -26.41660 -41.28226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6989" Parameter: A <- "-67.6989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4166" Parameter: B <- "-26.4166" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2823" Parameter: C <- "-41.2823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 143 TOTAL ENERGY = -67.6989 RDTITL> * VAN DER WAALS = -26.4166 ELECTROSTATIC = -41.2823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "143" Parameter: CONF_N -> "8002" Comparing "143" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "144" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762457 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757994 ATOM PAIRS WERE FOUND FOR ATOM LIST 41589 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29339 from a total of 757994 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 144 -68.86267 1.16381 0.68617 INTE EXTERN> -26.70519 -42.15748 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8627" Parameter: A <- "-68.8627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7052" Parameter: B <- "-26.7052" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1575" Parameter: C <- "-42.1575" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 144 TOTAL ENERGY = -68.8627 RDTITL> * VAN DER WAALS = -26.7052 ELECTROSTATIC = -42.1575 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "144" Parameter: CONF_N -> "8002" Comparing "144" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "145" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757994 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753966 ATOM PAIRS WERE FOUND FOR ATOM LIST 41670 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28875 from a total of 753966 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 145 -61.93012 -6.93255 0.60988 INTE EXTERN> -27.98575 -33.94436 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.9301" Parameter: A <- "-61.9301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9858" Parameter: B <- "-27.9858" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9444" Parameter: C <- "-33.9444" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 145 TOTAL ENERGY = -61.9301 RDTITL> * VAN DER WAALS = -27.9858 ELECTROSTATIC = -33.9444 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "145" Parameter: CONF_N -> "8002" Comparing "145" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "146" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753966 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754897 ATOM PAIRS WERE FOUND FOR ATOM LIST 41779 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29173 from a total of 754897 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 146 -71.25043 9.32031 0.71034 INTE EXTERN> -24.42229 -46.82814 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2504" Parameter: A <- "-71.2504" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4223" Parameter: B <- "-24.4223" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8281" Parameter: C <- "-46.8281" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 146 TOTAL ENERGY = -71.2504 RDTITL> * VAN DER WAALS = -24.4223 ELECTROSTATIC = -46.8281 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "146" Parameter: CONF_N -> "8002" Comparing "146" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "147" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754897 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761658 ATOM PAIRS WERE FOUND FOR ATOM LIST 41783 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29024 from a total of 761658 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 147 -60.08284 -11.16758 0.59932 INTE EXTERN> -27.27537 -32.80747 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.0828" Parameter: A <- "-60.0828" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2754" Parameter: B <- "-27.2754" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.8075" Parameter: C <- "-32.8075" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 147 TOTAL ENERGY = -60.0828 RDTITL> * VAN DER WAALS = -27.2754 ELECTROSTATIC = -32.8075 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "147" Parameter: CONF_N -> "8002" Comparing "147" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "148" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761658 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751848 ATOM PAIRS WERE FOUND FOR ATOM LIST 41308 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29342 from a total of 751848 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 148 -73.71345 13.63061 0.63801 INTE EXTERN> -31.24132 -42.47213 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7135" Parameter: A <- "-73.7135" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2413" Parameter: B <- "-31.2413" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4721" Parameter: C <- "-42.4721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 148 TOTAL ENERGY = -73.7135 RDTITL> * VAN DER WAALS = -31.2413 ELECTROSTATIC = -42.4721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "148" Parameter: CONF_N -> "8002" Comparing "148" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "149" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751848 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753487 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28565 from a total of 753487 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 149 -70.75358 -2.95988 0.51892 INTE EXTERN> -33.73452 -37.01905 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7536" Parameter: A <- "-70.7536" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7345" Parameter: B <- "-33.7345" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0191" Parameter: C <- "-37.0191" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 149 TOTAL ENERGY = -70.7536 RDTITL> * VAN DER WAALS = -33.7345 ELECTROSTATIC = -37.0191 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "149" Parameter: CONF_N -> "8002" Comparing "149" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "150" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753487 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749956 ATOM PAIRS WERE FOUND FOR ATOM LIST 41185 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29303 from a total of 749956 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 150 -69.50360 -1.24998 0.64694 INTE EXTERN> -29.61332 -39.89028 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5036" Parameter: A <- "-69.5036" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6133" Parameter: B <- "-29.6133" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8903" Parameter: C <- "-39.8903" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 150 TOTAL ENERGY = -69.5036 RDTITL> * VAN DER WAALS = -29.6133 ELECTROSTATIC = -39.8903 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "150" Parameter: CONF_N -> "8002" Comparing "150" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "151" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749956 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756912 ATOM PAIRS WERE FOUND FOR ATOM LIST 41380 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29007 from a total of 756912 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 151 -72.81336 3.30976 0.66602 INTE EXTERN> -30.18283 -42.63053 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8134" Parameter: A <- "-72.8134" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1828" Parameter: B <- "-30.1828" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6305" Parameter: C <- "-42.6305" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 151 TOTAL ENERGY = -72.8134 RDTITL> * VAN DER WAALS = -30.1828 ELECTROSTATIC = -42.6305 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "151" Parameter: CONF_N -> "8002" Comparing "151" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "152" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756912 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758369 ATOM PAIRS WERE FOUND FOR ATOM LIST 41486 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29455 from a total of 758369 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 152 -70.37956 -2.43380 0.59645 INTE EXTERN> -29.88317 -40.49639 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3796" Parameter: A <- "-70.3796" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8832" Parameter: B <- "-29.8832" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4964" Parameter: C <- "-40.4964" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 152 TOTAL ENERGY = -70.3796 RDTITL> * VAN DER WAALS = -29.8832 ELECTROSTATIC = -40.4964 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "152" Parameter: CONF_N -> "8002" Comparing "152" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "153" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758369 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758727 ATOM PAIRS WERE FOUND FOR ATOM LIST 41467 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30002 from a total of 758727 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 153 -72.34946 1.96990 0.59600 INTE EXTERN> -31.77931 -40.57015 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3495" Parameter: A <- "-72.3495" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7793" Parameter: B <- "-31.7793" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5702" Parameter: C <- "-40.5702" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 153 TOTAL ENERGY = -72.3495 RDTITL> * VAN DER WAALS = -31.7793 ELECTROSTATIC = -40.5702 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "153" Parameter: CONF_N -> "8002" Comparing "153" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "154" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758727 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751626 ATOM PAIRS WERE FOUND FOR ATOM LIST 41159 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28892 from a total of 751626 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 154 -69.09821 -3.25125 0.60906 INTE EXTERN> -28.27301 -40.82519 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0982" Parameter: A <- "-69.0982" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.273" Parameter: B <- "-28.273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8252" Parameter: C <- "-40.8252" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 154 TOTAL ENERGY = -69.0982 RDTITL> * VAN DER WAALS = -28.273 ELECTROSTATIC = -40.8252 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "154" Parameter: CONF_N -> "8002" Comparing "154" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "155" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751626 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759016 ATOM PAIRS WERE FOUND FOR ATOM LIST 41658 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30193 from a total of 759016 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 155 -72.40340 3.30519 0.60682 INTE EXTERN> -30.61945 -41.78395 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4034" Parameter: A <- "-72.4034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6195" Parameter: B <- "-30.6195" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.784" Parameter: C <- "-41.784" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 155 TOTAL ENERGY = -72.4034 RDTITL> * VAN DER WAALS = -30.6195 ELECTROSTATIC = -41.784 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "155" Parameter: CONF_N -> "8002" Comparing "155" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "156" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759016 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755562 ATOM PAIRS WERE FOUND FOR ATOM LIST 41380 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29507 from a total of 755562 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 156 -72.90700 0.50360 0.56734 INTE EXTERN> -31.75248 -41.15452 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.907" Parameter: A <- "-72.907" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7525" Parameter: B <- "-31.7525" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1545" Parameter: C <- "-41.1545" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 156 TOTAL ENERGY = -72.907 RDTITL> * VAN DER WAALS = -31.7525 ELECTROSTATIC = -41.1545 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "156" Parameter: CONF_N -> "8002" Comparing "156" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "157" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755562 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757856 ATOM PAIRS WERE FOUND FOR ATOM LIST 41517 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29450 from a total of 757856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 157 -70.37988 -2.52712 0.55239 INTE EXTERN> -29.33645 -41.04343 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3799" Parameter: A <- "-70.3799" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3365" Parameter: B <- "-29.3365" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0434" Parameter: C <- "-41.0434" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 157 TOTAL ENERGY = -70.3799 RDTITL> * VAN DER WAALS = -29.3365 ELECTROSTATIC = -41.0434 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "157" Parameter: CONF_N -> "8002" Comparing "157" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "158" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758467 ATOM PAIRS WERE FOUND FOR ATOM LIST 41516 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29528 from a total of 758467 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 158 -66.21918 -4.16070 0.51001 INTE EXTERN> -30.28354 -35.93564 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2192" Parameter: A <- "-66.2192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2835" Parameter: B <- "-30.2835" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9356" Parameter: C <- "-35.9356" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 158 TOTAL ENERGY = -66.2192 RDTITL> * VAN DER WAALS = -30.2835 ELECTROSTATIC = -35.9356 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "158" Parameter: CONF_N -> "8002" Comparing "158" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "159" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758467 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753397 ATOM PAIRS WERE FOUND FOR ATOM LIST 41392 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29381 from a total of 753397 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 159 -63.18491 -3.03427 0.44320 INTE EXTERN> -34.19782 -28.98710 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1849" Parameter: A <- "-63.1849" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1978" Parameter: B <- "-34.1978" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.9871" Parameter: C <- "-28.9871" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 159 TOTAL ENERGY = -63.1849 RDTITL> * VAN DER WAALS = -34.1978 ELECTROSTATIC = -28.9871 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "159" Parameter: CONF_N -> "8002" Comparing "159" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "160" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753397 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753213 ATOM PAIRS WERE FOUND FOR ATOM LIST 41561 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28747 from a total of 753213 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 160 -68.52167 5.33676 0.54608 INTE EXTERN> -30.54261 -37.97906 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5217" Parameter: A <- "-68.5217" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5426" Parameter: B <- "-30.5426" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9791" Parameter: C <- "-37.9791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 160 TOTAL ENERGY = -68.5217 RDTITL> * VAN DER WAALS = -30.5426 ELECTROSTATIC = -37.9791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "160" Parameter: CONF_N -> "8002" Comparing "160" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "161" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753213 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753302 ATOM PAIRS WERE FOUND FOR ATOM LIST 41358 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29097 from a total of 753302 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 161 -67.84735 -0.67433 0.53447 INTE EXTERN> -29.54204 -38.30530 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8473" Parameter: A <- "-67.8473" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.542" Parameter: B <- "-29.542" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3053" Parameter: C <- "-38.3053" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 161 TOTAL ENERGY = -67.8473 RDTITL> * VAN DER WAALS = -29.542 ELECTROSTATIC = -38.3053 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "161" Parameter: CONF_N -> "8002" Comparing "161" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "162" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753302 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756295 ATOM PAIRS WERE FOUND FOR ATOM LIST 41442 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29573 from a total of 756295 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 162 -67.51944 -0.32791 0.69947 INTE EXTERN> -24.17955 -43.33988 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5194" Parameter: A <- "-67.5194" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1796" Parameter: B <- "-24.1796" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3399" Parameter: C <- "-43.3399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 162 TOTAL ENERGY = -67.5194 RDTITL> * VAN DER WAALS = -24.1796 ELECTROSTATIC = -43.3399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "162" Parameter: CONF_N -> "8002" Comparing "162" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "163" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756295 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755147 ATOM PAIRS WERE FOUND FOR ATOM LIST 41591 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29384 from a total of 755147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 163 -67.57062 0.05119 0.70668 INTE EXTERN> -25.77283 -41.79779 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5706" Parameter: A <- "-67.5706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7728" Parameter: B <- "-25.7728" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7978" Parameter: C <- "-41.7978" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 163 TOTAL ENERGY = -67.5706 RDTITL> * VAN DER WAALS = -25.7728 ELECTROSTATIC = -41.7978 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "163" Parameter: CONF_N -> "8002" Comparing "163" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "164" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753345 ATOM PAIRS WERE FOUND FOR ATOM LIST 41495 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29707 from a total of 753345 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 164 -71.51060 3.93998 0.68812 INTE EXTERN> -26.84197 -44.66863 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5106" Parameter: A <- "-71.5106" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.842" Parameter: B <- "-26.842" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6686" Parameter: C <- "-44.6686" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 164 TOTAL ENERGY = -71.5106 RDTITL> * VAN DER WAALS = -26.842 ELECTROSTATIC = -44.6686 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "164" Parameter: CONF_N -> "8002" Comparing "164" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "165" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753345 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756059 ATOM PAIRS WERE FOUND FOR ATOM LIST 41543 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29458 from a total of 756059 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 165 -68.86003 -2.65058 0.62894 INTE EXTERN> -25.79786 -43.06217 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.86" Parameter: A <- "-68.86" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7979" Parameter: B <- "-25.7979" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0622" Parameter: C <- "-43.0622" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 165 TOTAL ENERGY = -68.86 RDTITL> * VAN DER WAALS = -25.7979 ELECTROSTATIC = -43.0622 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "165" Parameter: CONF_N -> "8002" Comparing "165" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "166" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756059 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752307 ATOM PAIRS WERE FOUND FOR ATOM LIST 41496 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29111 from a total of 752307 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 166 -71.82114 2.96111 0.62387 INTE EXTERN> -27.08708 -44.73406 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8211" Parameter: A <- "-71.8211" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0871" Parameter: B <- "-27.0871" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7341" Parameter: C <- "-44.7341" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 166 TOTAL ENERGY = -71.8211 RDTITL> * VAN DER WAALS = -27.0871 ELECTROSTATIC = -44.7341 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "166" Parameter: CONF_N -> "8002" Comparing "166" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "167" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752307 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757515 ATOM PAIRS WERE FOUND FOR ATOM LIST 41780 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29002 from a total of 757515 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 167 -70.71139 -1.10974 0.59214 INTE EXTERN> -29.32974 -41.38165 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7114" Parameter: A <- "-70.7114" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3297" Parameter: B <- "-29.3297" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3817" Parameter: C <- "-41.3817" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 167 TOTAL ENERGY = -70.7114 RDTITL> * VAN DER WAALS = -29.3297 ELECTROSTATIC = -41.3817 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "167" Parameter: CONF_N -> "8002" Comparing "167" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "168" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757515 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751200 ATOM PAIRS WERE FOUND FOR ATOM LIST 41434 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29234 from a total of 751200 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 168 -66.84646 -3.86494 0.60683 INTE EXTERN> -26.18273 -40.66373 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8465" Parameter: A <- "-66.8465" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1827" Parameter: B <- "-26.1827" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6637" Parameter: C <- "-40.6637" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 168 TOTAL ENERGY = -66.8465 RDTITL> * VAN DER WAALS = -26.1827 ELECTROSTATIC = -40.6637 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "168" Parameter: CONF_N -> "8002" Comparing "168" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "169" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751200 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755049 ATOM PAIRS WERE FOUND FOR ATOM LIST 41524 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29873 from a total of 755049 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 169 -71.52854 4.68209 0.58790 INTE EXTERN> -31.47716 -40.05138 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5285" Parameter: A <- "-71.5285" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4772" Parameter: B <- "-31.4772" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0514" Parameter: C <- "-40.0514" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 169 TOTAL ENERGY = -71.5285 RDTITL> * VAN DER WAALS = -31.4772 ELECTROSTATIC = -40.0514 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "169" Parameter: CONF_N -> "8002" Comparing "169" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "170" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755049 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749469 ATOM PAIRS WERE FOUND FOR ATOM LIST 41404 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30092 from a total of 749469 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 170 -72.99078 1.46224 0.68324 INTE EXTERN> -27.17286 -45.81793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9908" Parameter: A <- "-72.9908" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1729" Parameter: B <- "-27.1729" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8179" Parameter: C <- "-45.8179" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 170 TOTAL ENERGY = -72.9908 RDTITL> * VAN DER WAALS = -27.1729 ELECTROSTATIC = -45.8179 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "170" Parameter: CONF_N -> "8002" Comparing "170" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "171" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749469 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756842 ATOM PAIRS WERE FOUND FOR ATOM LIST 41684 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29475 from a total of 756842 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 171 -63.20749 -9.78329 0.65746 INTE EXTERN> -26.29588 -36.91161 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.2075" Parameter: A <- "-63.2075" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2959" Parameter: B <- "-26.2959" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9116" Parameter: C <- "-36.9116" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 171 TOTAL ENERGY = -63.2075 RDTITL> * VAN DER WAALS = -26.2959 ELECTROSTATIC = -36.9116 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "171" Parameter: CONF_N -> "8002" Comparing "171" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "172" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756842 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761576 ATOM PAIRS WERE FOUND FOR ATOM LIST 41935 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29939 from a total of 761576 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 172 -76.92133 13.71384 0.65248 INTE EXTERN> -30.30673 -46.61460 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9213" Parameter: A <- "-76.9213" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3067" Parameter: B <- "-30.3067" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6146" Parameter: C <- "-46.6146" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 172 TOTAL ENERGY = -76.9213 RDTITL> * VAN DER WAALS = -30.3067 ELECTROSTATIC = -46.6146 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "172" Parameter: CONF_N -> "8002" Comparing "172" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "173" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761576 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749012 ATOM PAIRS WERE FOUND FOR ATOM LIST 41221 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29043 from a total of 749012 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 173 -75.85398 -1.06734 0.54450 INTE EXTERN> -32.17562 -43.67836 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.854" Parameter: A <- "-75.854" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1756" Parameter: B <- "-32.1756" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6784" Parameter: C <- "-43.6784" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 173 TOTAL ENERGY = -75.854 RDTITL> * VAN DER WAALS = -32.1756 ELECTROSTATIC = -43.6784 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "173" Parameter: CONF_N -> "8002" Comparing "173" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "174" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749012 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751747 ATOM PAIRS WERE FOUND FOR ATOM LIST 41550 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29286 from a total of 751747 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 174 -71.12736 -4.72663 0.65868 INTE EXTERN> -27.90944 -43.21792 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1274" Parameter: A <- "-71.1274" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9094" Parameter: B <- "-27.9094" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2179" Parameter: C <- "-43.2179" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 174 TOTAL ENERGY = -71.1274 RDTITL> * VAN DER WAALS = -27.9094 ELECTROSTATIC = -43.2179 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "174" Parameter: CONF_N -> "8002" Comparing "174" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "175" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751747 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757417 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29338 from a total of 757417 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 175 -68.58878 -2.53858 0.57216 INTE EXTERN> -30.48380 -38.10498 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5888" Parameter: A <- "-68.5888" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4838" Parameter: B <- "-30.4838" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.105" Parameter: C <- "-38.105" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 175 TOTAL ENERGY = -68.5888 RDTITL> * VAN DER WAALS = -30.4838 ELECTROSTATIC = -38.105 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "175" Parameter: CONF_N -> "8002" Comparing "175" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "176" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757417 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760599 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29483 from a total of 760599 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 176 -72.12348 3.53470 0.58869 INTE EXTERN> -30.66341 -41.46007 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1235" Parameter: A <- "-72.1235" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6634" Parameter: B <- "-30.6634" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4601" Parameter: C <- "-41.4601" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 176 TOTAL ENERGY = -72.1235 RDTITL> * VAN DER WAALS = -30.6634 ELECTROSTATIC = -41.4601 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "176" Parameter: CONF_N -> "8002" Comparing "176" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "177" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760599 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760992 ATOM PAIRS WERE FOUND FOR ATOM LIST 42002 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29173 from a total of 760992 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 177 -67.73003 -4.39345 0.70844 INTE EXTERN> -26.34097 -41.38905 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.73" Parameter: A <- "-67.73" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.341" Parameter: B <- "-26.341" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3891" Parameter: C <- "-41.3891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 177 TOTAL ENERGY = -67.73 RDTITL> * VAN DER WAALS = -26.341 ELECTROSTATIC = -41.3891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "177" Parameter: CONF_N -> "8002" Comparing "177" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "178" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760992 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763053 ATOM PAIRS WERE FOUND FOR ATOM LIST 42040 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29371 from a total of 763053 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 178 -68.76259 1.03256 0.71910 INTE EXTERN> -24.57612 -44.18647 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7626" Parameter: A <- "-68.7626" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5761" Parameter: B <- "-24.5761" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1865" Parameter: C <- "-44.1865" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 178 TOTAL ENERGY = -68.7626 RDTITL> * VAN DER WAALS = -24.5761 ELECTROSTATIC = -44.1865 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "178" Parameter: CONF_N -> "8002" Comparing "178" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "179" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763053 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758149 ATOM PAIRS WERE FOUND FOR ATOM LIST 41618 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28916 from a total of 758149 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 179 -63.32704 -5.43555 0.44991 INTE EXTERN> -33.59465 -29.73238 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.327" Parameter: A <- "-63.327" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5947" Parameter: B <- "-33.5947" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.7324" Parameter: C <- "-29.7324" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 179 TOTAL ENERGY = -63.327 RDTITL> * VAN DER WAALS = -33.5947 ELECTROSTATIC = -29.7324 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "179" Parameter: CONF_N -> "8002" Comparing "179" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "180" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758149 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755178 ATOM PAIRS WERE FOUND FOR ATOM LIST 41677 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28742 from a total of 755178 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 180 -71.08302 7.75598 0.60846 INTE EXTERN> -32.31491 -38.76811 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.083" Parameter: A <- "-71.083" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3149" Parameter: B <- "-32.3149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7681" Parameter: C <- "-38.7681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 180 TOTAL ENERGY = -71.083 RDTITL> * VAN DER WAALS = -32.3149 ELECTROSTATIC = -38.7681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "180" Parameter: CONF_N -> "8002" Comparing "180" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "181" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755178 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760318 ATOM PAIRS WERE FOUND FOR ATOM LIST 41972 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29245 from a total of 760318 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 181 -67.70708 -3.37594 0.72036 INTE EXTERN> -24.72522 -42.98186 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7071" Parameter: A <- "-67.7071" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7252" Parameter: B <- "-24.7252" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9819" Parameter: C <- "-42.9819" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 181 TOTAL ENERGY = -67.7071 RDTITL> * VAN DER WAALS = -24.7252 ELECTROSTATIC = -42.9819 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "181" Parameter: CONF_N -> "8002" Comparing "181" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "182" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760318 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761193 ATOM PAIRS WERE FOUND FOR ATOM LIST 41907 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29231 from a total of 761193 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 182 -71.08410 3.37702 0.52608 INTE EXTERN> -31.75239 -39.33171 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0841" Parameter: A <- "-71.0841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7524" Parameter: B <- "-31.7524" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3317" Parameter: C <- "-39.3317" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 182 TOTAL ENERGY = -71.0841 RDTITL> * VAN DER WAALS = -31.7524 ELECTROSTATIC = -39.3317 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "182" Parameter: CONF_N -> "8002" Comparing "182" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "183" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761193 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759053 ATOM PAIRS WERE FOUND FOR ATOM LIST 41873 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29549 from a total of 759053 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 183 -68.10278 -2.98133 0.60259 INTE EXTERN> -29.48026 -38.62252 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1028" Parameter: A <- "-68.1028" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4803" Parameter: B <- "-29.4803" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6225" Parameter: C <- "-38.6225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 183 TOTAL ENERGY = -68.1028 RDTITL> * VAN DER WAALS = -29.4803 ELECTROSTATIC = -38.6225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "183" Parameter: CONF_N -> "8002" Comparing "183" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "184" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759053 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759617 ATOM PAIRS WERE FOUND FOR ATOM LIST 41781 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29479 from a total of 759617 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 184 -67.37229 -0.73049 0.59834 INTE EXTERN> -30.49662 -36.87567 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3723" Parameter: A <- "-67.3723" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4966" Parameter: B <- "-30.4966" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8757" Parameter: C <- "-36.8757" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 184 TOTAL ENERGY = -67.3723 RDTITL> * VAN DER WAALS = -30.4966 ELECTROSTATIC = -36.8757 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "184" Parameter: CONF_N -> "8002" Comparing "184" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "185" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759617 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757918 ATOM PAIRS WERE FOUND FOR ATOM LIST 41844 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29490 from a total of 757918 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 185 -69.30497 1.93268 0.66171 INTE EXTERN> -28.60205 -40.70292 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.305" Parameter: A <- "-69.305" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.602" Parameter: B <- "-28.602" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7029" Parameter: C <- "-40.7029" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 185 TOTAL ENERGY = -69.305 RDTITL> * VAN DER WAALS = -28.602 ELECTROSTATIC = -40.7029 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "185" Parameter: CONF_N -> "8002" Comparing "185" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "186" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757918 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758434 ATOM PAIRS WERE FOUND FOR ATOM LIST 41946 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29266 from a total of 758434 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 186 -66.36022 -2.94475 0.52223 INTE EXTERN> -33.72665 -32.63357 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3602" Parameter: A <- "-66.3602" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7267" Parameter: B <- "-33.7267" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.6336" Parameter: C <- "-32.6336" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 186 TOTAL ENERGY = -66.3602 RDTITL> * VAN DER WAALS = -33.7267 ELECTROSTATIC = -32.6336 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "186" Parameter: CONF_N -> "8002" Comparing "186" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "187" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758434 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761517 ATOM PAIRS WERE FOUND FOR ATOM LIST 41959 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29706 from a total of 761517 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 187 -64.09988 -2.26034 0.49882 INTE EXTERN> -31.86766 -32.23222 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0999" Parameter: A <- "-64.0999" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8677" Parameter: B <- "-31.8677" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2322" Parameter: C <- "-32.2322" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 187 TOTAL ENERGY = -64.0999 RDTITL> * VAN DER WAALS = -31.8677 ELECTROSTATIC = -32.2322 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "187" Parameter: CONF_N -> "8002" Comparing "187" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "188" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761517 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764705 ATOM PAIRS WERE FOUND FOR ATOM LIST 42180 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29433 from a total of 764705 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 188 -75.25709 11.15721 0.68081 INTE EXTERN> -29.90245 -45.35464 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2571" Parameter: A <- "-75.2571" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9024" Parameter: B <- "-29.9024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3546" Parameter: C <- "-45.3546" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 188 TOTAL ENERGY = -75.2571 RDTITL> * VAN DER WAALS = -29.9024 ELECTROSTATIC = -45.3546 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "188" Parameter: CONF_N -> "8002" Comparing "188" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "189" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764705 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759827 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29383 from a total of 759827 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 189 -70.77455 -4.48254 0.61126 INTE EXTERN> -29.64148 -41.13307 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7746" Parameter: A <- "-70.7746" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6415" Parameter: B <- "-29.6415" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1331" Parameter: C <- "-41.1331" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 189 TOTAL ENERGY = -70.7746 RDTITL> * VAN DER WAALS = -29.6415 ELECTROSTATIC = -41.1331 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "189" Parameter: CONF_N -> "8002" Comparing "189" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "190" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759827 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765223 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29169 from a total of 765223 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 190 -71.46457 0.69002 0.59880 INTE EXTERN> -30.56066 -40.90391 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4646" Parameter: A <- "-71.4646" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5607" Parameter: B <- "-30.5607" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9039" Parameter: C <- "-40.9039" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 190 TOTAL ENERGY = -71.4646 RDTITL> * VAN DER WAALS = -30.5607 ELECTROSTATIC = -40.9039 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "190" Parameter: CONF_N -> "8002" Comparing "190" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "191" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765223 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761236 ATOM PAIRS WERE FOUND FOR ATOM LIST 41709 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28577 from a total of 761236 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 191 -66.22993 -5.23464 0.61967 INTE EXTERN> -24.61940 -41.61053 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2299" Parameter: A <- "-66.2299" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6194" Parameter: B <- "-24.6194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6105" Parameter: C <- "-41.6105" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 191 TOTAL ENERGY = -66.2299 RDTITL> * VAN DER WAALS = -24.6194 ELECTROSTATIC = -41.6105 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "191" Parameter: CONF_N -> "8002" Comparing "191" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "192" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761236 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757257 ATOM PAIRS WERE FOUND FOR ATOM LIST 41542 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29115 from a total of 757257 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 192 -65.49496 -0.73497 0.54319 INTE EXTERN> -31.51027 -33.98469 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.495" Parameter: A <- "-65.495" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5103" Parameter: B <- "-31.5103" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9847" Parameter: C <- "-33.9847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 192 TOTAL ENERGY = -65.495 RDTITL> * VAN DER WAALS = -31.5103 ELECTROSTATIC = -33.9847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "192" Parameter: CONF_N -> "8002" Comparing "192" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "193" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757257 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753195 ATOM PAIRS WERE FOUND FOR ATOM LIST 41391 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29136 from a total of 753195 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 193 -65.46675 -0.02821 0.80683 INTE EXTERN> -25.67299 -39.79376 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4668" Parameter: A <- "-65.4668" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.673" Parameter: B <- "-25.673" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7938" Parameter: C <- "-39.7938" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 193 TOTAL ENERGY = -65.4668 RDTITL> * VAN DER WAALS = -25.673 ELECTROSTATIC = -39.7938 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "193" Parameter: CONF_N -> "8002" Comparing "193" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "194" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753195 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756210 ATOM PAIRS WERE FOUND FOR ATOM LIST 41599 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29506 from a total of 756210 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 194 -74.60457 9.13782 0.59533 INTE EXTERN> -32.97278 -41.63179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6046" Parameter: A <- "-74.6046" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9728" Parameter: B <- "-32.9728" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6318" Parameter: C <- "-41.6318" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 194 TOTAL ENERGY = -74.6046 RDTITL> * VAN DER WAALS = -32.9728 ELECTROSTATIC = -41.6318 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "194" Parameter: CONF_N -> "8002" Comparing "194" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "195" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756210 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752074 ATOM PAIRS WERE FOUND FOR ATOM LIST 41392 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29387 from a total of 752074 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 195 -77.97246 3.36790 0.61582 INTE EXTERN> -31.91678 -46.05568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9725" Parameter: A <- "-77.9725" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9168" Parameter: B <- "-31.9168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0557" Parameter: C <- "-46.0557" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 195 TOTAL ENERGY = -77.9725 RDTITL> * VAN DER WAALS = -31.9168 ELECTROSTATIC = -46.0557 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "195" Parameter: CONF_N -> "8002" Comparing "195" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "196" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752074 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759943 ATOM PAIRS WERE FOUND FOR ATOM LIST 41692 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29965 from a total of 759943 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 196 -73.65838 -4.31408 0.61009 INTE EXTERN> -30.34377 -43.31462 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6584" Parameter: A <- "-73.6584" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3438" Parameter: B <- "-30.3438" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3146" Parameter: C <- "-43.3146" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 196 TOTAL ENERGY = -73.6584 RDTITL> * VAN DER WAALS = -30.3438 ELECTROSTATIC = -43.3146 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "196" Parameter: CONF_N -> "8002" Comparing "196" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "197" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759943 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755200 ATOM PAIRS WERE FOUND FOR ATOM LIST 41422 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29526 from a total of 755200 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 197 -73.28752 -0.37086 0.79023 INTE EXTERN> -23.43494 -49.85258 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2875" Parameter: A <- "-73.2875" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4349" Parameter: B <- "-23.4349" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8526" Parameter: C <- "-49.8526" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 197 TOTAL ENERGY = -73.2875 RDTITL> * VAN DER WAALS = -23.4349 ELECTROSTATIC = -49.8526 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "197" Parameter: CONF_N -> "8002" Comparing "197" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "198" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755200 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762594 ATOM PAIRS WERE FOUND FOR ATOM LIST 42077 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28791 from a total of 762594 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 198 -74.91330 1.62578 0.65560 INTE EXTERN> -28.95889 -45.95441 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9133" Parameter: A <- "-74.9133" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9589" Parameter: B <- "-28.9589" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9544" Parameter: C <- "-45.9544" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 198 TOTAL ENERGY = -74.9133 RDTITL> * VAN DER WAALS = -28.9589 ELECTROSTATIC = -45.9544 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "198" Parameter: CONF_N -> "8002" Comparing "198" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "199" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762594 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766142 ATOM PAIRS WERE FOUND FOR ATOM LIST 42237 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30072 from a total of 766142 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 199 -67.51331 -7.39999 0.53508 INTE EXTERN> -33.21776 -34.29555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5133" Parameter: A <- "-67.5133" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2178" Parameter: B <- "-33.2178" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2956" Parameter: C <- "-34.2956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 199 TOTAL ENERGY = -67.5133 RDTITL> * VAN DER WAALS = -33.2178 ELECTROSTATIC = -34.2956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "199" Parameter: CONF_N -> "8002" Comparing "199" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "200" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766142 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764218 ATOM PAIRS WERE FOUND FOR ATOM LIST 42043 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29412 from a total of 764218 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 200 -66.40719 -1.10612 0.52618 INTE EXTERN> -32.17039 -34.23681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4072" Parameter: A <- "-66.4072" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1704" Parameter: B <- "-32.1704" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2368" Parameter: C <- "-34.2368" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 200 TOTAL ENERGY = -66.4072 RDTITL> * VAN DER WAALS = -32.1704 ELECTROSTATIC = -34.2368 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "200" Parameter: CONF_N -> "8002" Comparing "200" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "201" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764218 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761677 ATOM PAIRS WERE FOUND FOR ATOM LIST 41864 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29838 from a total of 761677 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 201 -72.50403 6.09684 0.61770 INTE EXTERN> -30.93025 -41.57379 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.504" Parameter: A <- "-72.504" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9302" Parameter: B <- "-30.9302" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5738" Parameter: C <- "-41.5738" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 201 TOTAL ENERGY = -72.504 RDTITL> * VAN DER WAALS = -30.9302 ELECTROSTATIC = -41.5738 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "201" Parameter: CONF_N -> "8002" Comparing "201" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "202" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761677 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760117 ATOM PAIRS WERE FOUND FOR ATOM LIST 41991 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29365 from a total of 760117 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 202 -67.55546 -4.94857 0.54293 INTE EXTERN> -32.98665 -34.56881 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5555" Parameter: A <- "-67.5555" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9866" Parameter: B <- "-32.9866" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5688" Parameter: C <- "-34.5688" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 202 TOTAL ENERGY = -67.5555 RDTITL> * VAN DER WAALS = -32.9866 ELECTROSTATIC = -34.5688 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "202" Parameter: CONF_N -> "8002" Comparing "202" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "203" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760117 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765133 ATOM PAIRS WERE FOUND FOR ATOM LIST 42013 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29503 from a total of 765133 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 203 -74.93411 7.37865 0.72847 INTE EXTERN> -28.22343 -46.71067 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9341" Parameter: A <- "-74.9341" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2234" Parameter: B <- "-28.2234" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7107" Parameter: C <- "-46.7107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 203 TOTAL ENERGY = -74.9341 RDTITL> * VAN DER WAALS = -28.2234 ELECTROSTATIC = -46.7107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "203" Parameter: CONF_N -> "8002" Comparing "203" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "204" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765133 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764178 ATOM PAIRS WERE FOUND FOR ATOM LIST 42110 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29795 from a total of 764178 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 204 -70.03888 -4.89523 0.64851 INTE EXTERN> -27.64048 -42.39840 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0389" Parameter: A <- "-70.0389" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6405" Parameter: B <- "-27.6405" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3984" Parameter: C <- "-42.3984" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 204 TOTAL ENERGY = -70.0389 RDTITL> * VAN DER WAALS = -27.6405 ELECTROSTATIC = -42.3984 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "204" Parameter: CONF_N -> "8002" Comparing "204" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "205" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764178 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763364 ATOM PAIRS WERE FOUND FOR ATOM LIST 42017 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29673 from a total of 763364 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 205 -72.69444 2.65556 0.62454 INTE EXTERN> -29.49376 -43.20068 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6944" Parameter: A <- "-72.6944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4938" Parameter: B <- "-29.4938" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2007" Parameter: C <- "-43.2007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 205 TOTAL ENERGY = -72.6944 RDTITL> * VAN DER WAALS = -29.4938 ELECTROSTATIC = -43.2007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "205" Parameter: CONF_N -> "8002" Comparing "205" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "206" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763364 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758025 ATOM PAIRS WERE FOUND FOR ATOM LIST 41727 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30233 from a total of 758025 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 206 -73.02701 0.33257 0.62814 INTE EXTERN> -29.20424 -43.82277 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.027" Parameter: A <- "-73.027" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2042" Parameter: B <- "-29.2042" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8228" Parameter: C <- "-43.8228" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 206 TOTAL ENERGY = -73.027 RDTITL> * VAN DER WAALS = -29.2042 ELECTROSTATIC = -43.8228 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "206" Parameter: CONF_N -> "8002" Comparing "206" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "207" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758025 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761806 ATOM PAIRS WERE FOUND FOR ATOM LIST 41917 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29929 from a total of 761806 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 207 -72.03367 -0.99334 0.61907 INTE EXTERN> -30.00629 -42.02738 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0337" Parameter: A <- "-72.0337" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0063" Parameter: B <- "-30.0063" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0274" Parameter: C <- "-42.0274" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 207 TOTAL ENERGY = -72.0337 RDTITL> * VAN DER WAALS = -30.0063 ELECTROSTATIC = -42.0274 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "207" Parameter: CONF_N -> "8002" Comparing "207" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "208" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761806 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764200 ATOM PAIRS WERE FOUND FOR ATOM LIST 42043 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30175 from a total of 764200 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 208 -69.08548 -2.94819 0.66083 INTE EXTERN> -27.86003 -41.22545 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0855" Parameter: A <- "-69.0855" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.86" Parameter: B <- "-27.86" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2254" Parameter: C <- "-41.2254" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 208 TOTAL ENERGY = -69.0855 RDTITL> * VAN DER WAALS = -27.86 ELECTROSTATIC = -41.2254 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "208" Parameter: CONF_N -> "8002" Comparing "208" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "209" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764200 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764721 ATOM PAIRS WERE FOUND FOR ATOM LIST 42116 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30003 from a total of 764721 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 209 -69.67593 0.59045 0.54091 INTE EXTERN> -34.64541 -35.03052 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6759" Parameter: A <- "-69.6759" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6454" Parameter: B <- "-34.6454" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0305" Parameter: C <- "-35.0305" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 209 TOTAL ENERGY = -69.6759 RDTITL> * VAN DER WAALS = -34.6454 ELECTROSTATIC = -35.0305 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "209" Parameter: CONF_N -> "8002" Comparing "209" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "210" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764721 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765603 ATOM PAIRS WERE FOUND FOR ATOM LIST 41907 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29448 from a total of 765603 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 210 -68.28573 -1.39020 0.55128 INTE EXTERN> -30.88992 -37.39581 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2857" Parameter: A <- "-68.2857" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8899" Parameter: B <- "-30.8899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3958" Parameter: C <- "-37.3958" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 210 TOTAL ENERGY = -68.2857 RDTITL> * VAN DER WAALS = -30.8899 ELECTROSTATIC = -37.3958 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "210" Parameter: CONF_N -> "8002" Comparing "210" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "211" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765603 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763995 ATOM PAIRS WERE FOUND FOR ATOM LIST 41995 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30081 from a total of 763995 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 211 -69.47060 1.18487 0.67521 INTE EXTERN> -24.78030 -44.69030 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4706" Parameter: A <- "-69.4706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7803" Parameter: B <- "-24.7803" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6903" Parameter: C <- "-44.6903" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 211 TOTAL ENERGY = -69.4706 RDTITL> * VAN DER WAALS = -24.7803 ELECTROSTATIC = -44.6903 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "211" Parameter: CONF_N -> "8002" Comparing "211" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "212" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763995 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763689 ATOM PAIRS WERE FOUND FOR ATOM LIST 42026 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29423 from a total of 763689 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 212 -74.45322 4.98262 0.55789 INTE EXTERN> -33.51111 -40.94211 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4532" Parameter: A <- "-74.4532" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5111" Parameter: B <- "-33.5111" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9421" Parameter: C <- "-40.9421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 212 TOTAL ENERGY = -74.4532 RDTITL> * VAN DER WAALS = -33.5111 ELECTROSTATIC = -40.9421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "212" Parameter: CONF_N -> "8002" Comparing "212" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "213" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763689 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762849 ATOM PAIRS WERE FOUND FOR ATOM LIST 42222 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30337 from a total of 762849 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 213 -72.49997 -1.95326 0.60149 INTE EXTERN> -30.96469 -41.53527 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5" Parameter: A <- "-72.5" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9647" Parameter: B <- "-30.9647" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5353" Parameter: C <- "-41.5353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 213 TOTAL ENERGY = -72.5 RDTITL> * VAN DER WAALS = -30.9647 ELECTROSTATIC = -41.5353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "213" Parameter: CONF_N -> "8002" Comparing "213" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "214" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762849 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761625 ATOM PAIRS WERE FOUND FOR ATOM LIST 41995 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29888 from a total of 761625 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 214 -65.77775 -6.72221 0.61099 INTE EXTERN> -31.91950 -33.85825 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7778" Parameter: A <- "-65.7778" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9195" Parameter: B <- "-31.9195" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8583" Parameter: C <- "-33.8583" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 214 TOTAL ENERGY = -65.7778 RDTITL> * VAN DER WAALS = -31.9195 ELECTROSTATIC = -33.8583 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "214" Parameter: CONF_N -> "8002" Comparing "214" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "215" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761625 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760459 ATOM PAIRS WERE FOUND FOR ATOM LIST 42091 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29916 from a total of 760459 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 215 -70.04492 4.26717 0.61299 INTE EXTERN> -32.85610 -37.18882 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0449" Parameter: A <- "-70.0449" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8561" Parameter: B <- "-32.8561" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1888" Parameter: C <- "-37.1888" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 215 TOTAL ENERGY = -70.0449 RDTITL> * VAN DER WAALS = -32.8561 ELECTROSTATIC = -37.1888 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "215" Parameter: CONF_N -> "8002" Comparing "215" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "216" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760459 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758971 ATOM PAIRS WERE FOUND FOR ATOM LIST 41803 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29870 from a total of 758971 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 216 -64.18058 -5.86434 0.63925 INTE EXTERN> -28.01648 -36.16410 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1806" Parameter: A <- "-64.1806" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0165" Parameter: B <- "-28.0165" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1641" Parameter: C <- "-36.1641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 216 TOTAL ENERGY = -64.1806 RDTITL> * VAN DER WAALS = -28.0165 ELECTROSTATIC = -36.1641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "216" Parameter: CONF_N -> "8002" Comparing "216" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "217" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758971 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767239 ATOM PAIRS WERE FOUND FOR ATOM LIST 42372 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30044 from a total of 767239 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 217 -74.77863 10.59805 0.51696 INTE EXTERN> -37.66190 -37.11672 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7786" Parameter: A <- "-74.7786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-37.6619" Parameter: B <- "-37.6619" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1167" Parameter: C <- "-37.1167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 217 TOTAL ENERGY = -74.7786 RDTITL> * VAN DER WAALS = -37.6619 ELECTROSTATIC = -37.1167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "217" Parameter: CONF_N -> "8002" Comparing "217" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "218" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767239 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768309 ATOM PAIRS WERE FOUND FOR ATOM LIST 42235 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30024 from a total of 768309 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 218 -75.34310 0.56447 0.58601 INTE EXTERN> -35.39560 -39.94750 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3431" Parameter: A <- "-75.3431" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.3956" Parameter: B <- "-35.3956" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9475" Parameter: C <- "-39.9475" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 218 TOTAL ENERGY = -75.3431 RDTITL> * VAN DER WAALS = -35.3956 ELECTROSTATIC = -39.9475 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "218" Parameter: CONF_N -> "8002" Comparing "218" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "219" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768309 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769561 ATOM PAIRS WERE FOUND FOR ATOM LIST 42349 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30476 from a total of 769561 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 219 -73.45789 -1.88521 0.55292 INTE EXTERN> -33.11740 -40.34050 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4579" Parameter: A <- "-73.4579" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1174" Parameter: B <- "-33.1174" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3405" Parameter: C <- "-40.3405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 219 TOTAL ENERGY = -73.4579 RDTITL> * VAN DER WAALS = -33.1174 ELECTROSTATIC = -40.3405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "219" Parameter: CONF_N -> "8002" Comparing "219" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "220" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769561 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764868 ATOM PAIRS WERE FOUND FOR ATOM LIST 41927 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30487 from a total of 764868 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 220 -74.88495 1.42706 0.68660 INTE EXTERN> -28.95478 -45.93017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8849" Parameter: A <- "-74.8849" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9548" Parameter: B <- "-28.9548" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9302" Parameter: C <- "-45.9302" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 220 TOTAL ENERGY = -74.8849 RDTITL> * VAN DER WAALS = -28.9548 ELECTROSTATIC = -45.9302 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "220" Parameter: CONF_N -> "8002" Comparing "220" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "221" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764868 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769363 ATOM PAIRS WERE FOUND FOR ATOM LIST 42437 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30387 from a total of 769363 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 221 -72.76217 -2.12278 0.57605 INTE EXTERN> -33.65391 -39.10826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7622" Parameter: A <- "-72.7622" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6539" Parameter: B <- "-33.6539" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1083" Parameter: C <- "-39.1083" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 221 TOTAL ENERGY = -72.7622 RDTITL> * VAN DER WAALS = -33.6539 ELECTROSTATIC = -39.1083 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "221" Parameter: CONF_N -> "8002" Comparing "221" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "222" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769363 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760681 ATOM PAIRS WERE FOUND FOR ATOM LIST 42079 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29330 from a total of 760681 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 222 -72.15355 -0.60862 0.60854 INTE EXTERN> -35.13790 -37.01564 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1535" Parameter: A <- "-72.1535" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.1379" Parameter: B <- "-35.1379" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0156" Parameter: C <- "-37.0156" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 222 TOTAL ENERGY = -72.1535 RDTITL> * VAN DER WAALS = -35.1379 ELECTROSTATIC = -37.0156 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "222" Parameter: CONF_N -> "8002" Comparing "222" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "223" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760681 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757427 ATOM PAIRS WERE FOUND FOR ATOM LIST 41674 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29576 from a total of 757427 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 223 -71.63090 -0.52265 0.74593 INTE EXTERN> -25.21268 -46.41822 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6309" Parameter: A <- "-71.6309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2127" Parameter: B <- "-25.2127" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4182" Parameter: C <- "-46.4182" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 223 TOTAL ENERGY = -71.6309 RDTITL> * VAN DER WAALS = -25.2127 ELECTROSTATIC = -46.4182 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "223" Parameter: CONF_N -> "8002" Comparing "223" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "224" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757427 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760800 ATOM PAIRS WERE FOUND FOR ATOM LIST 41988 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29730 from a total of 760800 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 224 -69.96913 -1.66177 0.60051 INTE EXTERN> -34.53813 -35.43100 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9691" Parameter: A <- "-69.9691" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.5381" Parameter: B <- "-34.5381" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.431" Parameter: C <- "-35.431" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 224 TOTAL ENERGY = -69.9691 RDTITL> * VAN DER WAALS = -34.5381 ELECTROSTATIC = -35.431 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "224" Parameter: CONF_N -> "8002" Comparing "224" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "225" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760800 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760859 ATOM PAIRS WERE FOUND FOR ATOM LIST 41996 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29307 from a total of 760859 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 225 -63.71459 -6.25454 0.55594 INTE EXTERN> -33.28931 -30.42528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7146" Parameter: A <- "-63.7146" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2893" Parameter: B <- "-33.2893" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.4253" Parameter: C <- "-30.4253" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 225 TOTAL ENERGY = -63.7146 RDTITL> * VAN DER WAALS = -33.2893 ELECTROSTATIC = -30.4253 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "225" Parameter: CONF_N -> "8002" Comparing "225" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "226" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760859 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762241 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29740 from a total of 762241 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 226 -67.18932 3.47473 0.52976 INTE EXTERN> -34.95463 -32.23469 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1893" Parameter: A <- "-67.1893" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9546" Parameter: B <- "-34.9546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2347" Parameter: C <- "-32.2347" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 226 TOTAL ENERGY = -67.1893 RDTITL> * VAN DER WAALS = -34.9546 ELECTROSTATIC = -32.2347 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "226" Parameter: CONF_N -> "8002" Comparing "226" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "227" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762241 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766224 ATOM PAIRS WERE FOUND FOR ATOM LIST 42261 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29974 from a total of 766224 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 227 -65.13473 -2.05459 0.55172 INTE EXTERN> -31.94013 -33.19460 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1347" Parameter: A <- "-65.1347" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9401" Parameter: B <- "-31.9401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1946" Parameter: C <- "-33.1946" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 227 TOTAL ENERGY = -65.1347 RDTITL> * VAN DER WAALS = -31.9401 ELECTROSTATIC = -33.1946 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "227" Parameter: CONF_N -> "8002" Comparing "227" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "228" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766224 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765344 ATOM PAIRS WERE FOUND FOR ATOM LIST 42208 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 765344 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 228 -65.70681 0.57209 0.67536 INTE EXTERN> -26.32581 -39.38101 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7068" Parameter: A <- "-65.7068" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3258" Parameter: B <- "-26.3258" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.381" Parameter: C <- "-39.381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 228 TOTAL ENERGY = -65.7068 RDTITL> * VAN DER WAALS = -26.3258 ELECTROSTATIC = -39.381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "228" Parameter: CONF_N -> "8002" Comparing "228" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "229" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765344 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763978 ATOM PAIRS WERE FOUND FOR ATOM LIST 42102 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29615 from a total of 763978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 229 -67.60621 1.89940 0.58201 INTE EXTERN> -34.12041 -33.48580 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6062" Parameter: A <- "-67.6062" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1204" Parameter: B <- "-34.1204" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.4858" Parameter: C <- "-33.4858" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 229 TOTAL ENERGY = -67.6062 RDTITL> * VAN DER WAALS = -34.1204 ELECTROSTATIC = -33.4858 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "229" Parameter: CONF_N -> "8002" Comparing "229" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "230" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761657 ATOM PAIRS WERE FOUND FOR ATOM LIST 41902 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29287 from a total of 761657 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 230 -60.95470 -6.65151 0.64155 INTE EXTERN> -28.60913 -32.34557 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.9547" Parameter: A <- "-60.9547" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6091" Parameter: B <- "-28.6091" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.3456" Parameter: C <- "-32.3456" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 230 TOTAL ENERGY = -60.9547 RDTITL> * VAN DER WAALS = -28.6091 ELECTROSTATIC = -32.3456 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "230" Parameter: CONF_N -> "8002" Comparing "230" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "231" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761657 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759450 ATOM PAIRS WERE FOUND FOR ATOM LIST 41662 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30219 from a total of 759450 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 231 -64.75926 3.80456 0.62767 INTE EXTERN> -30.80806 -33.95121 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7593" Parameter: A <- "-64.7593" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8081" Parameter: B <- "-30.8081" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9512" Parameter: C <- "-33.9512" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 231 TOTAL ENERGY = -64.7593 RDTITL> * VAN DER WAALS = -30.8081 ELECTROSTATIC = -33.9512 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "231" Parameter: CONF_N -> "8002" Comparing "231" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "232" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759450 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764985 ATOM PAIRS WERE FOUND FOR ATOM LIST 42215 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29665 from a total of 764985 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 232 -69.36638 4.60712 0.59873 INTE EXTERN> -30.79986 -38.56652 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3664" Parameter: A <- "-69.3664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7999" Parameter: B <- "-30.7999" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5665" Parameter: C <- "-38.5665" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 232 TOTAL ENERGY = -69.3664 RDTITL> * VAN DER WAALS = -30.7999 ELECTROSTATIC = -38.5665 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "232" Parameter: CONF_N -> "8002" Comparing "232" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "233" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764985 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763689 ATOM PAIRS WERE FOUND FOR ATOM LIST 42066 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30169 from a total of 763689 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 233 -72.34158 2.97520 0.54121 INTE EXTERN> -36.66291 -35.67866 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3416" Parameter: A <- "-72.3416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.6629" Parameter: B <- "-36.6629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6787" Parameter: C <- "-35.6787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 233 TOTAL ENERGY = -72.3416 RDTITL> * VAN DER WAALS = -36.6629 ELECTROSTATIC = -35.6787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "233" Parameter: CONF_N -> "8002" Comparing "233" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "234" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763689 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765249 ATOM PAIRS WERE FOUND FOR ATOM LIST 42204 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30159 from a total of 765249 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 234 -62.03182 -10.30976 0.59279 INTE EXTERN> -32.39443 -29.63739 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.0318" Parameter: A <- "-62.0318" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3944" Parameter: B <- "-32.3944" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.6374" Parameter: C <- "-29.6374" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 234 TOTAL ENERGY = -62.0318 RDTITL> * VAN DER WAALS = -32.3944 ELECTROSTATIC = -29.6374 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "234" Parameter: CONF_N -> "8002" Comparing "234" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "235" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765249 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768112 ATOM PAIRS WERE FOUND FOR ATOM LIST 42180 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30387 from a total of 768112 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 235 -64.33548 2.30366 0.48468 INTE EXTERN> -33.55836 -30.77712 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3355" Parameter: A <- "-64.3355" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5584" Parameter: B <- "-33.5584" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.7771" Parameter: C <- "-30.7771" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 235 TOTAL ENERGY = -64.3355 RDTITL> * VAN DER WAALS = -33.5584 ELECTROSTATIC = -30.7771 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "235" Parameter: CONF_N -> "8002" Comparing "235" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "236" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768112 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765141 ATOM PAIRS WERE FOUND FOR ATOM LIST 42227 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29850 from a total of 765141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 236 -72.69121 8.35573 0.54937 INTE EXTERN> -33.77990 -38.91131 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6912" Parameter: A <- "-72.6912" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7799" Parameter: B <- "-33.7799" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9113" Parameter: C <- "-38.9113" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 236 TOTAL ENERGY = -72.6912 RDTITL> * VAN DER WAALS = -33.7799 ELECTROSTATIC = -38.9113 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "236" Parameter: CONF_N -> "8002" Comparing "236" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "237" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765893 ATOM PAIRS WERE FOUND FOR ATOM LIST 42011 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30290 from a total of 765893 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 237 -72.05489 -0.63632 0.70710 INTE EXTERN> -26.08230 -45.97259 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0549" Parameter: A <- "-72.0549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0823" Parameter: B <- "-26.0823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9726" Parameter: C <- "-45.9726" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 237 TOTAL ENERGY = -72.0549 RDTITL> * VAN DER WAALS = -26.0823 ELECTROSTATIC = -45.9726 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "237" Parameter: CONF_N -> "8002" Comparing "237" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "238" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765893 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760233 ATOM PAIRS WERE FOUND FOR ATOM LIST 41977 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30295 from a total of 760233 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 238 -76.35185 4.29696 0.57731 INTE EXTERN> -35.00767 -41.34418 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3519" Parameter: A <- "-76.3519" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.0077" Parameter: B <- "-35.0077" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3442" Parameter: C <- "-41.3442" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 238 TOTAL ENERGY = -76.3519 RDTITL> * VAN DER WAALS = -35.0077 ELECTROSTATIC = -41.3442 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "238" Parameter: CONF_N -> "8002" Comparing "238" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "239" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760233 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765149 ATOM PAIRS WERE FOUND FOR ATOM LIST 42083 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29906 from a total of 765149 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 239 -70.42393 -5.92793 0.56323 INTE EXTERN> -33.92995 -36.49397 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4239" Parameter: A <- "-70.4239" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.93" Parameter: B <- "-33.93" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.494" Parameter: C <- "-36.494" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 239 TOTAL ENERGY = -70.4239 RDTITL> * VAN DER WAALS = -33.93 ELECTROSTATIC = -36.494 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "239" Parameter: CONF_N -> "8002" Comparing "239" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "240" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765149 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768587 ATOM PAIRS WERE FOUND FOR ATOM LIST 42131 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30212 from a total of 768587 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 240 -67.18755 -3.23638 0.53743 INTE EXTERN> -35.42399 -31.76356 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1875" Parameter: A <- "-67.1875" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.424" Parameter: B <- "-35.424" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.7636" Parameter: C <- "-31.7636" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 240 TOTAL ENERGY = -67.1875 RDTITL> * VAN DER WAALS = -35.424 ELECTROSTATIC = -31.7636 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "240" Parameter: CONF_N -> "8002" Comparing "240" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "241" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768587 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760534 ATOM PAIRS WERE FOUND FOR ATOM LIST 41965 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30252 from a total of 760534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 241 -70.77394 3.58640 0.65368 INTE EXTERN> -29.91571 -40.85823 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7739" Parameter: A <- "-70.7739" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9157" Parameter: B <- "-29.9157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8582" Parameter: C <- "-40.8582" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 241 TOTAL ENERGY = -70.7739 RDTITL> * VAN DER WAALS = -29.9157 ELECTROSTATIC = -40.8582 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "241" Parameter: CONF_N -> "8002" Comparing "241" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "242" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763481 ATOM PAIRS WERE FOUND FOR ATOM LIST 42119 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30433 from a total of 763481 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 242 -73.74079 2.96685 0.70322 INTE EXTERN> -29.12689 -44.61391 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7408" Parameter: A <- "-73.7408" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1269" Parameter: B <- "-29.1269" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6139" Parameter: C <- "-44.6139" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 242 TOTAL ENERGY = -73.7408 RDTITL> * VAN DER WAALS = -29.1269 ELECTROSTATIC = -44.6139 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "242" Parameter: CONF_N -> "8002" Comparing "242" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "243" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763481 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765174 ATOM PAIRS WERE FOUND FOR ATOM LIST 42137 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29678 from a total of 765174 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 243 -78.25882 4.51802 0.61210 INTE EXTERN> -31.50236 -46.75646 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2588" Parameter: A <- "-78.2588" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5024" Parameter: B <- "-31.5024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7565" Parameter: C <- "-46.7565" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 243 TOTAL ENERGY = -78.2588 RDTITL> * VAN DER WAALS = -31.5024 ELECTROSTATIC = -46.7565 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "243" Parameter: CONF_N -> "8002" Comparing "243" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "244" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765174 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761330 ATOM PAIRS WERE FOUND FOR ATOM LIST 41920 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30187 from a total of 761330 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 244 -77.40605 -0.85277 0.63647 INTE EXTERN> -33.05699 -44.34906 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.406" Parameter: A <- "-77.406" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.057" Parameter: B <- "-33.057" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3491" Parameter: C <- "-44.3491" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 244 TOTAL ENERGY = -77.406 RDTITL> * VAN DER WAALS = -33.057 ELECTROSTATIC = -44.3491 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "244" Parameter: CONF_N -> "8002" Comparing "244" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "245" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761330 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764206 ATOM PAIRS WERE FOUND FOR ATOM LIST 42029 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30081 from a total of 764206 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 245 -75.70897 -1.69708 0.58230 INTE EXTERN> -33.07393 -42.63504 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.709" Parameter: A <- "-75.709" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0739" Parameter: B <- "-33.0739" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.635" Parameter: C <- "-42.635" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 245 TOTAL ENERGY = -75.709 RDTITL> * VAN DER WAALS = -33.0739 ELECTROSTATIC = -42.635 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "245" Parameter: CONF_N -> "8002" Comparing "245" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "246" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764206 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763793 ATOM PAIRS WERE FOUND FOR ATOM LIST 42212 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30022 from a total of 763793 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 246 -70.80093 -4.90804 0.60332 INTE EXTERN> -32.90745 -37.89347 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8009" Parameter: A <- "-70.8009" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9075" Parameter: B <- "-32.9075" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8935" Parameter: C <- "-37.8935" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 246 TOTAL ENERGY = -70.8009 RDTITL> * VAN DER WAALS = -32.9075 ELECTROSTATIC = -37.8935 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "246" Parameter: CONF_N -> "8002" Comparing "246" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "247" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763793 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765030 ATOM PAIRS WERE FOUND FOR ATOM LIST 42171 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30153 from a total of 765030 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 247 -76.12435 5.32343 0.66642 INTE EXTERN> -30.42312 -45.70124 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1244" Parameter: A <- "-76.1244" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4231" Parameter: B <- "-30.4231" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7012" Parameter: C <- "-45.7012" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 247 TOTAL ENERGY = -76.1244 RDTITL> * VAN DER WAALS = -30.4231 ELECTROSTATIC = -45.7012 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "247" Parameter: CONF_N -> "8002" Comparing "247" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "248" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765030 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772048 ATOM PAIRS WERE FOUND FOR ATOM LIST 42230 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30026 from a total of 772048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 248 -80.45929 4.33494 0.68287 INTE EXTERN> -32.06258 -48.39671 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4593" Parameter: A <- "-80.4593" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0626" Parameter: B <- "-32.0626" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3967" Parameter: C <- "-48.3967" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 248 TOTAL ENERGY = -80.4593 RDTITL> * VAN DER WAALS = -32.0626 ELECTROSTATIC = -48.3967 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "248" Parameter: CONF_N -> "8002" Comparing "248" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "249" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 774025 ATOM PAIRS WERE FOUND FOR ATOM LIST 42499 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30535 from a total of 774025 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 249 -68.80287 -11.65642 0.61165 INTE EXTERN> -33.46421 -35.33866 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8029" Parameter: A <- "-68.8029" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4642" Parameter: B <- "-33.4642" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3387" Parameter: C <- "-35.3387" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 249 TOTAL ENERGY = -68.8029 RDTITL> * VAN DER WAALS = -33.4642 ELECTROSTATIC = -35.3387 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "249" Parameter: CONF_N -> "8002" Comparing "249" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "250" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 774025 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 775353 ATOM PAIRS WERE FOUND FOR ATOM LIST 42608 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30343 from a total of 775353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 250 -71.06579 2.26292 0.51144 INTE EXTERN> -36.82284 -34.24294 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0658" Parameter: A <- "-71.0658" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.8228" Parameter: B <- "-36.8228" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2429" Parameter: C <- "-34.2429" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 250 TOTAL ENERGY = -71.0658 RDTITL> * VAN DER WAALS = -36.8228 ELECTROSTATIC = -34.2429 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "250" Parameter: CONF_N -> "8002" Comparing "250" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "251" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 775353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763387 ATOM PAIRS WERE FOUND FOR ATOM LIST 42092 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29236 from a total of 763387 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 251 -69.61149 -1.45430 0.58314 INTE EXTERN> -31.16201 -38.44948 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6115" Parameter: A <- "-69.6115" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.162" Parameter: B <- "-31.162" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4495" Parameter: C <- "-38.4495" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 251 TOTAL ENERGY = -69.6115 RDTITL> * VAN DER WAALS = -31.162 ELECTROSTATIC = -38.4495 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "251" Parameter: CONF_N -> "8002" Comparing "251" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "252" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763387 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763837 ATOM PAIRS WERE FOUND FOR ATOM LIST 42122 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29827 from a total of 763837 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 252 -68.67855 -0.93294 0.63982 INTE EXTERN> -29.49284 -39.18571 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6785" Parameter: A <- "-68.6785" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4928" Parameter: B <- "-29.4928" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1857" Parameter: C <- "-39.1857" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 252 TOTAL ENERGY = -68.6785 RDTITL> * VAN DER WAALS = -29.4928 ELECTROSTATIC = -39.1857 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "252" Parameter: CONF_N -> "8002" Comparing "252" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "253" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763837 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765557 ATOM PAIRS WERE FOUND FOR ATOM LIST 42232 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30276 from a total of 765557 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 253 -64.92895 -3.74960 0.62241 INTE EXTERN> -29.82054 -35.10841 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.929" Parameter: A <- "-64.929" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8205" Parameter: B <- "-29.8205" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1084" Parameter: C <- "-35.1084" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 253 TOTAL ENERGY = -64.929 RDTITL> * VAN DER WAALS = -29.8205 ELECTROSTATIC = -35.1084 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "253" Parameter: CONF_N -> "8002" Comparing "253" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "254" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765557 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769413 ATOM PAIRS WERE FOUND FOR ATOM LIST 42344 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30597 from a total of 769413 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 254 -68.98578 4.05682 0.61694 INTE EXTERN> -30.38819 -38.59758 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9858" Parameter: A <- "-68.9858" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3882" Parameter: B <- "-30.3882" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5976" Parameter: C <- "-38.5976" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 254 TOTAL ENERGY = -68.9858 RDTITL> * VAN DER WAALS = -30.3882 ELECTROSTATIC = -38.5976 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "254" Parameter: CONF_N -> "8002" Comparing "254" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "255" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769413 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763227 ATOM PAIRS WERE FOUND FOR ATOM LIST 42104 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30480 from a total of 763227 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 255 -78.02497 9.03919 0.68452 INTE EXTERN> -30.82130 -47.20367 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.025" Parameter: A <- "-78.025" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8213" Parameter: B <- "-30.8213" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2037" Parameter: C <- "-47.2037" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 255 TOTAL ENERGY = -78.025 RDTITL> * VAN DER WAALS = -30.8213 ELECTROSTATIC = -47.2037 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "255" Parameter: CONF_N -> "8002" Comparing "255" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "256" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763227 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756583 ATOM PAIRS WERE FOUND FOR ATOM LIST 41749 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29756 from a total of 756583 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 256 -71.00358 -7.02139 0.66826 INTE EXTERN> -31.20167 -39.80191 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0036" Parameter: A <- "-71.0036" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2017" Parameter: B <- "-31.2017" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8019" Parameter: C <- "-39.8019" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 256 TOTAL ENERGY = -71.0036 RDTITL> * VAN DER WAALS = -31.2017 ELECTROSTATIC = -39.8019 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "256" Parameter: CONF_N -> "8002" Comparing "256" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "257" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756583 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763574 ATOM PAIRS WERE FOUND FOR ATOM LIST 42270 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29900 from a total of 763574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 257 -67.36532 -3.63825 0.50200 INTE EXTERN> -32.89003 -34.47529 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3653" Parameter: A <- "-67.3653" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.89" Parameter: B <- "-32.89" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4753" Parameter: C <- "-34.4753" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 257 TOTAL ENERGY = -67.3653 RDTITL> * VAN DER WAALS = -32.89 ELECTROSTATIC = -34.4753 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "257" Parameter: CONF_N -> "8002" Comparing "257" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "258" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764046 ATOM PAIRS WERE FOUND FOR ATOM LIST 42195 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29878 from a total of 764046 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 258 -66.48843 -0.87689 0.63731 INTE EXTERN> -28.67858 -37.80986 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4884" Parameter: A <- "-66.4884" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6786" Parameter: B <- "-28.6786" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8099" Parameter: C <- "-37.8099" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 258 TOTAL ENERGY = -66.4884 RDTITL> * VAN DER WAALS = -28.6786 ELECTROSTATIC = -37.8099 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "258" Parameter: CONF_N -> "8002" Comparing "258" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "259" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764046 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759321 ATOM PAIRS WERE FOUND FOR ATOM LIST 41880 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29158 from a total of 759321 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 259 -69.75857 3.27014 0.61340 INTE EXTERN> -31.28832 -38.47025 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7586" Parameter: A <- "-69.7586" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2883" Parameter: B <- "-31.2883" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4703" Parameter: C <- "-38.4703" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 259 TOTAL ENERGY = -69.7586 RDTITL> * VAN DER WAALS = -31.2883 ELECTROSTATIC = -38.4703 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "259" Parameter: CONF_N -> "8002" Comparing "259" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "260" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759321 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765249 ATOM PAIRS WERE FOUND FOR ATOM LIST 42058 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30050 from a total of 765249 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 260 -68.72008 -1.03849 0.61201 INTE EXTERN> -29.40676 -39.31332 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7201" Parameter: A <- "-68.7201" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4068" Parameter: B <- "-29.4068" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3133" Parameter: C <- "-39.3133" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 260 TOTAL ENERGY = -68.7201 RDTITL> * VAN DER WAALS = -29.4068 ELECTROSTATIC = -39.3133 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "260" Parameter: CONF_N -> "8002" Comparing "260" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "261" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765249 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768513 ATOM PAIRS WERE FOUND FOR ATOM LIST 42270 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30126 from a total of 768513 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 261 -68.92672 0.20664 0.67102 INTE EXTERN> -28.94981 -39.97691 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9267" Parameter: A <- "-68.9267" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9498" Parameter: B <- "-28.9498" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9769" Parameter: C <- "-39.9769" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 261 TOTAL ENERGY = -68.9267 RDTITL> * VAN DER WAALS = -28.9498 ELECTROSTATIC = -39.9769 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "261" Parameter: CONF_N -> "8002" Comparing "261" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "262" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768513 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769562 ATOM PAIRS WERE FOUND FOR ATOM LIST 42232 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30061 from a total of 769562 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 262 -76.10915 7.18242 0.70799 INTE EXTERN> -28.28719 -47.82195 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1091" Parameter: A <- "-76.1091" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2872" Parameter: B <- "-28.2872" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.822" Parameter: C <- "-47.822" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 262 TOTAL ENERGY = -76.1091 RDTITL> * VAN DER WAALS = -28.2872 ELECTROSTATIC = -47.822 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "262" Parameter: CONF_N -> "8002" Comparing "262" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "263" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769562 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765803 ATOM PAIRS WERE FOUND FOR ATOM LIST 42011 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30057 from a total of 765803 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 263 -75.15190 -0.95724 0.61664 INTE EXTERN> -31.89367 -43.25823 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1519" Parameter: A <- "-75.1519" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8937" Parameter: B <- "-31.8937" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2582" Parameter: C <- "-43.2582" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 263 TOTAL ENERGY = -75.1519 RDTITL> * VAN DER WAALS = -31.8937 ELECTROSTATIC = -43.2582 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "263" Parameter: CONF_N -> "8002" Comparing "263" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "264" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765803 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770801 ATOM PAIRS WERE FOUND FOR ATOM LIST 42568 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29718 from a total of 770801 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 264 -74.23047 -0.92143 0.63446 INTE EXTERN> -29.02064 -45.20983 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2305" Parameter: A <- "-74.2305" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0206" Parameter: B <- "-29.0206" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2098" Parameter: C <- "-45.2098" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 264 TOTAL ENERGY = -74.2305 RDTITL> * VAN DER WAALS = -29.0206 ELECTROSTATIC = -45.2098 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "264" Parameter: CONF_N -> "8002" Comparing "264" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "265" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770801 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765684 ATOM PAIRS WERE FOUND FOR ATOM LIST 42180 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29940 from a total of 765684 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 265 -71.28977 -2.94070 0.74822 INTE EXTERN> -25.58908 -45.70069 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2898" Parameter: A <- "-71.2898" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5891" Parameter: B <- "-25.5891" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7007" Parameter: C <- "-45.7007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 265 TOTAL ENERGY = -71.2898 RDTITL> * VAN DER WAALS = -25.5891 ELECTROSTATIC = -45.7007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "265" Parameter: CONF_N -> "8002" Comparing "265" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "266" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765684 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768826 ATOM PAIRS WERE FOUND FOR ATOM LIST 42297 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30197 from a total of 768826 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 266 -74.44717 3.15740 0.60922 INTE EXTERN> -31.11825 -43.32892 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4472" Parameter: A <- "-74.4472" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1182" Parameter: B <- "-31.1182" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3289" Parameter: C <- "-43.3289" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 266 TOTAL ENERGY = -74.4472 RDTITL> * VAN DER WAALS = -31.1182 ELECTROSTATIC = -43.3289 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "266" Parameter: CONF_N -> "8002" Comparing "266" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "267" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768826 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761890 ATOM PAIRS WERE FOUND FOR ATOM LIST 42008 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29653 from a total of 761890 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 267 -70.51757 -3.92960 0.59395 INTE EXTERN> -31.91008 -38.60749 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5176" Parameter: A <- "-70.5176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9101" Parameter: B <- "-31.9101" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6075" Parameter: C <- "-38.6075" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 267 TOTAL ENERGY = -70.5176 RDTITL> * VAN DER WAALS = -31.9101 ELECTROSTATIC = -38.6075 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "267" Parameter: CONF_N -> "8002" Comparing "267" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "268" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761890 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765411 ATOM PAIRS WERE FOUND FOR ATOM LIST 42083 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30049 from a total of 765411 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 268 -77.66664 7.14907 0.63943 INTE EXTERN> -31.94686 -45.71978 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6666" Parameter: A <- "-77.6666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9469" Parameter: B <- "-31.9469" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7198" Parameter: C <- "-45.7198" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 268 TOTAL ENERGY = -77.6666 RDTITL> * VAN DER WAALS = -31.9469 ELECTROSTATIC = -45.7198 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "268" Parameter: CONF_N -> "8002" Comparing "268" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "269" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765411 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770601 ATOM PAIRS WERE FOUND FOR ATOM LIST 42179 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30481 from a total of 770601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 269 -73.72403 -3.94261 0.64755 INTE EXTERN> -28.80085 -44.92318 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.724" Parameter: A <- "-73.724" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8009" Parameter: B <- "-28.8009" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9232" Parameter: C <- "-44.9232" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 269 TOTAL ENERGY = -73.724 RDTITL> * VAN DER WAALS = -28.8009 ELECTROSTATIC = -44.9232 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "269" Parameter: CONF_N -> "8002" Comparing "269" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "270" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768622 ATOM PAIRS WERE FOUND FOR ATOM LIST 42423 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29743 from a total of 768622 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 270 -67.92361 -5.80043 0.58766 INTE EXTERN> -31.41249 -36.51112 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9236" Parameter: A <- "-67.9236" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4125" Parameter: B <- "-31.4125" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5111" Parameter: C <- "-36.5111" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 270 TOTAL ENERGY = -67.9236 RDTITL> * VAN DER WAALS = -31.4125 ELECTROSTATIC = -36.5111 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "270" Parameter: CONF_N -> "8002" Comparing "270" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "271" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768622 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766341 ATOM PAIRS WERE FOUND FOR ATOM LIST 42208 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29981 from a total of 766341 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 271 -68.68258 0.75897 0.70749 INTE EXTERN> -25.41891 -43.26368 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6826" Parameter: A <- "-68.6826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4189" Parameter: B <- "-25.4189" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2637" Parameter: C <- "-43.2637" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 271 TOTAL ENERGY = -68.6826 RDTITL> * VAN DER WAALS = -25.4189 ELECTROSTATIC = -43.2637 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "271" Parameter: CONF_N -> "8002" Comparing "271" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "272" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766341 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29970 from a total of 757526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 272 -69.40690 0.72431 0.50885 INTE EXTERN> -31.59611 -37.81079 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4069" Parameter: A <- "-69.4069" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5961" Parameter: B <- "-31.5961" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8108" Parameter: C <- "-37.8108" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 272 TOTAL ENERGY = -69.4069 RDTITL> * VAN DER WAALS = -31.5961 ELECTROSTATIC = -37.8108 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "272" Parameter: CONF_N -> "8002" Comparing "272" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "273" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764422 ATOM PAIRS WERE FOUND FOR ATOM LIST 42036 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29722 from a total of 764422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 273 -65.04691 -4.35999 0.57836 INTE EXTERN> -32.90987 -32.13704 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0469" Parameter: A <- "-65.0469" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9099" Parameter: B <- "-32.9099" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.137" Parameter: C <- "-32.137" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 273 TOTAL ENERGY = -65.0469 RDTITL> * VAN DER WAALS = -32.9099 ELECTROSTATIC = -32.137 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "273" Parameter: CONF_N -> "8002" Comparing "273" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "274" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764367 ATOM PAIRS WERE FOUND FOR ATOM LIST 42247 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30047 from a total of 764367 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 274 -72.95137 7.90446 0.64831 INTE EXTERN> -31.25360 -41.69777 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9514" Parameter: A <- "-72.9514" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2536" Parameter: B <- "-31.2536" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6978" Parameter: C <- "-41.6978" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 274 TOTAL ENERGY = -72.9514 RDTITL> * VAN DER WAALS = -31.2536 ELECTROSTATIC = -41.6978 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "274" Parameter: CONF_N -> "8002" Comparing "274" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "275" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764367 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767834 ATOM PAIRS WERE FOUND FOR ATOM LIST 42396 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30021 from a total of 767834 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 275 -71.26232 -1.68905 0.57241 INTE EXTERN> -32.70734 -38.55498 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2623" Parameter: A <- "-71.2623" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7073" Parameter: B <- "-32.7073" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.555" Parameter: C <- "-38.555" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 275 TOTAL ENERGY = -71.2623 RDTITL> * VAN DER WAALS = -32.7073 ELECTROSTATIC = -38.555 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "275" Parameter: CONF_N -> "8002" Comparing "275" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "276" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767834 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765451 ATOM PAIRS WERE FOUND FOR ATOM LIST 42043 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29521 from a total of 765451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 276 -73.10435 1.84203 0.60067 INTE EXTERN> -32.50464 -40.59971 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1043" Parameter: A <- "-73.1043" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5046" Parameter: B <- "-32.5046" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5997" Parameter: C <- "-40.5997" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 276 TOTAL ENERGY = -73.1043 RDTITL> * VAN DER WAALS = -32.5046 ELECTROSTATIC = -40.5997 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "276" Parameter: CONF_N -> "8002" Comparing "276" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "277" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763022 ATOM PAIRS WERE FOUND FOR ATOM LIST 41947 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29890 from a total of 763022 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 277 -72.11078 -0.99357 0.67005 INTE EXTERN> -27.57505 -44.53572 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1108" Parameter: A <- "-72.1108" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5751" Parameter: B <- "-27.5751" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5357" Parameter: C <- "-44.5357" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 277 TOTAL ENERGY = -72.1108 RDTITL> * VAN DER WAALS = -27.5751 ELECTROSTATIC = -44.5357 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "277" Parameter: CONF_N -> "8002" Comparing "277" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "278" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763022 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763701 ATOM PAIRS WERE FOUND FOR ATOM LIST 42003 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29495 from a total of 763701 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 278 -64.58051 -7.53027 0.58662 INTE EXTERN> -30.27460 -34.30591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5805" Parameter: A <- "-64.5805" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2746" Parameter: B <- "-30.2746" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3059" Parameter: C <- "-34.3059" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 278 TOTAL ENERGY = -64.5805 RDTITL> * VAN DER WAALS = -30.2746 ELECTROSTATIC = -34.3059 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "278" Parameter: CONF_N -> "8002" Comparing "278" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "279" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763701 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769608 ATOM PAIRS WERE FOUND FOR ATOM LIST 42424 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29423 from a total of 769608 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 279 -73.66338 9.08288 0.62471 INTE EXTERN> -30.64548 -43.01790 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6634" Parameter: A <- "-73.6634" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6455" Parameter: B <- "-30.6455" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0179" Parameter: C <- "-43.0179" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 279 TOTAL ENERGY = -73.6634 RDTITL> * VAN DER WAALS = -30.6455 ELECTROSTATIC = -43.0179 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "279" Parameter: CONF_N -> "8002" Comparing "279" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "280" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769608 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770661 ATOM PAIRS WERE FOUND FOR ATOM LIST 42336 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29578 from a total of 770661 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 280 -74.28874 0.62536 0.72295 INTE EXTERN> -27.88272 -46.40602 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2887" Parameter: A <- "-74.2887" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8827" Parameter: B <- "-27.8827" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.406" Parameter: C <- "-46.406" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 280 TOTAL ENERGY = -74.2887 RDTITL> * VAN DER WAALS = -27.8827 ELECTROSTATIC = -46.406 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "280" Parameter: CONF_N -> "8002" Comparing "280" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "281" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770661 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764439 ATOM PAIRS WERE FOUND FOR ATOM LIST 42107 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29713 from a total of 764439 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 281 -69.38631 -4.90244 0.59619 INTE EXTERN> -28.37263 -41.01367 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3863" Parameter: A <- "-69.3863" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3726" Parameter: B <- "-28.3726" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0137" Parameter: C <- "-41.0137" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 281 TOTAL ENERGY = -69.3863 RDTITL> * VAN DER WAALS = -28.3726 ELECTROSTATIC = -41.0137 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "281" Parameter: CONF_N -> "8002" Comparing "281" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "282" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764439 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756141 ATOM PAIRS WERE FOUND FOR ATOM LIST 41612 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28790 from a total of 756141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 282 -70.10866 0.72236 0.59147 INTE EXTERN> -32.18230 -37.92636 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1087" Parameter: A <- "-70.1087" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1823" Parameter: B <- "-32.1823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9264" Parameter: C <- "-37.9264" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 282 TOTAL ENERGY = -70.1087 RDTITL> * VAN DER WAALS = -32.1823 ELECTROSTATIC = -37.9264 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "282" Parameter: CONF_N -> "8002" Comparing "282" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "283" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762549 ATOM PAIRS WERE FOUND FOR ATOM LIST 41905 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29652 from a total of 762549 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 283 -71.75086 1.64219 0.52455 INTE EXTERN> -32.59284 -39.15802 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7509" Parameter: A <- "-71.7509" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5928" Parameter: B <- "-32.5928" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.158" Parameter: C <- "-39.158" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 283 TOTAL ENERGY = -71.7509 RDTITL> * VAN DER WAALS = -32.5928 ELECTROSTATIC = -39.158 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "283" Parameter: CONF_N -> "8002" Comparing "283" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "284" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762549 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29639 from a total of 759526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 284 -70.60249 -1.14837 0.60056 INTE EXTERN> -31.49578 -39.10670 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6025" Parameter: A <- "-70.6025" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4958" Parameter: B <- "-31.4958" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1067" Parameter: C <- "-39.1067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 284 TOTAL ENERGY = -70.6025 RDTITL> * VAN DER WAALS = -31.4958 ELECTROSTATIC = -39.1067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "284" Parameter: CONF_N -> "8002" Comparing "284" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "285" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757155 ATOM PAIRS WERE FOUND FOR ATOM LIST 41842 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29086 from a total of 757155 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 285 -67.86246 -2.74003 0.60701 INTE EXTERN> -28.10829 -39.75416 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8625" Parameter: A <- "-67.8625" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1083" Parameter: B <- "-28.1083" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7542" Parameter: C <- "-39.7542" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 285 TOTAL ENERGY = -67.8625 RDTITL> * VAN DER WAALS = -28.1083 ELECTROSTATIC = -39.7542 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "285" Parameter: CONF_N -> "8002" Comparing "285" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "286" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757155 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769813 ATOM PAIRS WERE FOUND FOR ATOM LIST 42180 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29956 from a total of 769813 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 286 -72.69779 4.83534 0.60281 INTE EXTERN> -31.37208 -41.32571 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6978" Parameter: A <- "-72.6978" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3721" Parameter: B <- "-31.3721" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3257" Parameter: C <- "-41.3257" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 286 TOTAL ENERGY = -72.6978 RDTITL> * VAN DER WAALS = -31.3721 ELECTROSTATIC = -41.3257 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "286" Parameter: CONF_N -> "8002" Comparing "286" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "287" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769813 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766634 ATOM PAIRS WERE FOUND FOR ATOM LIST 42170 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29363 from a total of 766634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 287 -67.36812 -5.32967 0.59561 INTE EXTERN> -29.89387 -37.47426 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3681" Parameter: A <- "-67.3681" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8939" Parameter: B <- "-29.8939" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4743" Parameter: C <- "-37.4743" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 287 TOTAL ENERGY = -67.3681 RDTITL> * VAN DER WAALS = -29.8939 ELECTROSTATIC = -37.4743 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "287" Parameter: CONF_N -> "8002" Comparing "287" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "288" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769955 ATOM PAIRS WERE FOUND FOR ATOM LIST 42282 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29969 from a total of 769955 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 288 -67.03898 -0.32915 0.57704 INTE EXTERN> -31.76866 -35.27031 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.039" Parameter: A <- "-67.039" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7687" Parameter: B <- "-31.7687" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2703" Parameter: C <- "-35.2703" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 288 TOTAL ENERGY = -67.039 RDTITL> * VAN DER WAALS = -31.7687 ELECTROSTATIC = -35.2703 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "288" Parameter: CONF_N -> "8002" Comparing "288" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "289" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769955 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765712 ATOM PAIRS WERE FOUND FOR ATOM LIST 42136 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30186 from a total of 765712 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 289 -64.13071 -2.90827 0.55714 INTE EXTERN> -30.94718 -33.18352 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1307" Parameter: A <- "-64.1307" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9472" Parameter: B <- "-30.9472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1835" Parameter: C <- "-33.1835" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 289 TOTAL ENERGY = -64.1307 RDTITL> * VAN DER WAALS = -30.9472 ELECTROSTATIC = -33.1835 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "289" Parameter: CONF_N -> "8002" Comparing "289" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "290" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765712 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764946 ATOM PAIRS WERE FOUND FOR ATOM LIST 42018 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30029 from a total of 764946 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 290 -69.40359 5.27288 0.57216 INTE EXTERN> -31.84110 -37.56249 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4036" Parameter: A <- "-69.4036" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8411" Parameter: B <- "-31.8411" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5625" Parameter: C <- "-37.5625" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 290 TOTAL ENERGY = -69.4036 RDTITL> * VAN DER WAALS = -31.8411 ELECTROSTATIC = -37.5625 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "290" Parameter: CONF_N -> "8002" Comparing "290" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "291" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764946 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758683 ATOM PAIRS WERE FOUND FOR ATOM LIST 41832 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28896 from a total of 758683 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 291 -71.58222 2.17863 0.51778 INTE EXTERN> -33.29219 -38.29003 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5822" Parameter: A <- "-71.5822" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2922" Parameter: B <- "-33.2922" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.29" Parameter: C <- "-38.29" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 291 TOTAL ENERGY = -71.5822 RDTITL> * VAN DER WAALS = -33.2922 ELECTROSTATIC = -38.29 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "291" Parameter: CONF_N -> "8002" Comparing "291" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "292" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758683 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766128 ATOM PAIRS WERE FOUND FOR ATOM LIST 42004 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29536 from a total of 766128 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 292 -72.95919 1.37697 0.60816 INTE EXTERN> -31.58659 -41.37260 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9592" Parameter: A <- "-72.9592" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5866" Parameter: B <- "-31.5866" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3726" Parameter: C <- "-41.3726" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 292 TOTAL ENERGY = -72.9592 RDTITL> * VAN DER WAALS = -31.5866 ELECTROSTATIC = -41.3726 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "292" Parameter: CONF_N -> "8002" Comparing "292" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "293" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766128 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768137 ATOM PAIRS WERE FOUND FOR ATOM LIST 42299 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29567 from a total of 768137 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 293 -73.16626 0.20707 0.58787 INTE EXTERN> -33.43329 -39.73297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1663" Parameter: A <- "-73.1663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4333" Parameter: B <- "-33.4333" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.733" Parameter: C <- "-39.733" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 293 TOTAL ENERGY = -73.1663 RDTITL> * VAN DER WAALS = -33.4333 ELECTROSTATIC = -39.733 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "293" Parameter: CONF_N -> "8002" Comparing "293" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "294" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768137 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765521 ATOM PAIRS WERE FOUND FOR ATOM LIST 42238 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29150 from a total of 765521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 294 -72.09528 -1.07098 0.60748 INTE EXTERN> -32.41819 -39.67709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0953" Parameter: A <- "-72.0953" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4182" Parameter: B <- "-32.4182" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6771" Parameter: C <- "-39.6771" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 294 TOTAL ENERGY = -72.0953 RDTITL> * VAN DER WAALS = -32.4182 ELECTROSTATIC = -39.6771 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "294" Parameter: CONF_N -> "8002" Comparing "294" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "295" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764225 ATOM PAIRS WERE FOUND FOR ATOM LIST 41936 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29284 from a total of 764225 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 295 -72.56398 0.46871 0.63238 INTE EXTERN> -30.76863 -41.79535 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.564" Parameter: A <- "-72.564" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7686" Parameter: B <- "-30.7686" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7954" Parameter: C <- "-41.7954" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 295 TOTAL ENERGY = -72.564 RDTITL> * VAN DER WAALS = -30.7686 ELECTROSTATIC = -41.7954 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "295" Parameter: CONF_N -> "8002" Comparing "295" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "296" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764225 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768173 ATOM PAIRS WERE FOUND FOR ATOM LIST 42306 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29144 from a total of 768173 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 296 -66.84014 -5.72385 0.60103 INTE EXTERN> -29.99392 -36.84622 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8401" Parameter: A <- "-66.8401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9939" Parameter: B <- "-29.9939" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8462" Parameter: C <- "-36.8462" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 296 TOTAL ENERGY = -66.8401 RDTITL> * VAN DER WAALS = -29.9939 ELECTROSTATIC = -36.8462 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "296" Parameter: CONF_N -> "8002" Comparing "296" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "297" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768173 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766111 ATOM PAIRS WERE FOUND FOR ATOM LIST 42079 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29613 from a total of 766111 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 297 -66.66233 -0.17781 0.67742 INTE EXTERN> -28.43396 -38.22837 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6623" Parameter: A <- "-66.6623" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.434" Parameter: B <- "-28.434" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2284" Parameter: C <- "-38.2284" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 297 TOTAL ENERGY = -66.6623 RDTITL> * VAN DER WAALS = -28.434 ELECTROSTATIC = -38.2284 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "297" Parameter: CONF_N -> "8002" Comparing "297" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "298" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766111 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763605 ATOM PAIRS WERE FOUND FOR ATOM LIST 41984 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29042 from a total of 763605 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 298 -65.72537 -0.93696 0.51292 INTE EXTERN> -32.01298 -33.71239 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7254" Parameter: A <- "-65.7254" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.013" Parameter: B <- "-32.013" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7124" Parameter: C <- "-33.7124" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 298 TOTAL ENERGY = -65.7254 RDTITL> * VAN DER WAALS = -32.013 ELECTROSTATIC = -33.7124 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "298" Parameter: CONF_N -> "8002" Comparing "298" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "299" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763605 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764774 ATOM PAIRS WERE FOUND FOR ATOM LIST 41860 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28988 from a total of 764774 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 299 -63.66197 -2.06340 0.59356 INTE EXTERN> -29.83069 -33.83128 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.662" Parameter: A <- "-63.662" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8307" Parameter: B <- "-29.8307" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8313" Parameter: C <- "-33.8313" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 299 TOTAL ENERGY = -63.662 RDTITL> * VAN DER WAALS = -29.8307 ELECTROSTATIC = -33.8313 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "299" Parameter: CONF_N -> "8002" Comparing "299" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "300" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764774 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41955 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29149 from a total of 761794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 300 -62.72062 -0.94135 0.55850 INTE EXTERN> -31.96282 -30.75780 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7206" Parameter: A <- "-62.7206" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9628" Parameter: B <- "-31.9628" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.7578" Parameter: C <- "-30.7578" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 300 TOTAL ENERGY = -62.7206 RDTITL> * VAN DER WAALS = -31.9628 ELECTROSTATIC = -30.7578 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "300" Parameter: CONF_N -> "8002" Comparing "300" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "301" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766210 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29348 from a total of 766210 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 301 -71.01439 8.29377 0.62587 INTE EXTERN> -32.06322 -38.95117 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0144" Parameter: A <- "-71.0144" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0632" Parameter: B <- "-32.0632" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9512" Parameter: C <- "-38.9512" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 301 TOTAL ENERGY = -71.0144 RDTITL> * VAN DER WAALS = -32.0632 ELECTROSTATIC = -38.9512 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "301" Parameter: CONF_N -> "8002" Comparing "301" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "302" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766210 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763924 ATOM PAIRS WERE FOUND FOR ATOM LIST 41988 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29191 from a total of 763924 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 302 -73.34946 2.33506 0.68005 INTE EXTERN> -29.68164 -43.66782 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3495" Parameter: A <- "-73.3495" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6816" Parameter: B <- "-29.6816" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6678" Parameter: C <- "-43.6678" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 302 TOTAL ENERGY = -73.3495 RDTITL> * VAN DER WAALS = -29.6816 ELECTROSTATIC = -43.6678 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "302" Parameter: CONF_N -> "8002" Comparing "302" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "303" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763924 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769636 ATOM PAIRS WERE FOUND FOR ATOM LIST 42247 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29869 from a total of 769636 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 303 -73.80240 0.45295 0.55579 INTE EXTERN> -32.03308 -41.76932 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8024" Parameter: A <- "-73.8024" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0331" Parameter: B <- "-32.0331" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7693" Parameter: C <- "-41.7693" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 303 TOTAL ENERGY = -73.8024 RDTITL> * VAN DER WAALS = -32.0331 ELECTROSTATIC = -41.7693 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "303" Parameter: CONF_N -> "8002" Comparing "303" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "304" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769636 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769564 ATOM PAIRS WERE FOUND FOR ATOM LIST 42148 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30087 from a total of 769564 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 304 -66.55580 -7.24660 0.61437 INTE EXTERN> -28.61608 -37.93972 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5558" Parameter: A <- "-66.5558" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6161" Parameter: B <- "-28.6161" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9397" Parameter: C <- "-37.9397" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 304 TOTAL ENERGY = -66.5558 RDTITL> * VAN DER WAALS = -28.6161 ELECTROSTATIC = -37.9397 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "304" Parameter: CONF_N -> "8002" Comparing "304" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "305" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769564 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763425 ATOM PAIRS WERE FOUND FOR ATOM LIST 42052 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29202 from a total of 763425 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 305 -66.83080 0.27499 0.52674 INTE EXTERN> -30.70376 -36.12704 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8308" Parameter: A <- "-66.8308" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7038" Parameter: B <- "-30.7038" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.127" Parameter: C <- "-36.127" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 305 TOTAL ENERGY = -66.8308 RDTITL> * VAN DER WAALS = -30.7038 ELECTROSTATIC = -36.127 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "305" Parameter: CONF_N -> "8002" Comparing "305" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "306" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763425 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765918 ATOM PAIRS WERE FOUND FOR ATOM LIST 42058 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29657 from a total of 765918 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 306 -70.35012 3.51933 0.57256 INTE EXTERN> -32.89417 -37.45596 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3501" Parameter: A <- "-70.3501" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8942" Parameter: B <- "-32.8942" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.456" Parameter: C <- "-37.456" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 306 TOTAL ENERGY = -70.3501 RDTITL> * VAN DER WAALS = -32.8942 ELECTROSTATIC = -37.456 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "306" Parameter: CONF_N -> "8002" Comparing "306" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "307" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765918 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762546 ATOM PAIRS WERE FOUND FOR ATOM LIST 41905 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29917 from a total of 762546 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 307 -72.97916 2.62904 0.57191 INTE EXTERN> -31.75958 -41.21958 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9792" Parameter: A <- "-72.9792" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7596" Parameter: B <- "-31.7596" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2196" Parameter: C <- "-41.2196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 307 TOTAL ENERGY = -72.9792 RDTITL> * VAN DER WAALS = -31.7596 ELECTROSTATIC = -41.2196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "307" Parameter: CONF_N -> "8002" Comparing "307" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "308" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762546 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768183 ATOM PAIRS WERE FOUND FOR ATOM LIST 42002 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29800 from a total of 768183 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 308 -74.47243 1.49327 0.75343 INTE EXTERN> -27.05861 -47.41382 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4724" Parameter: A <- "-74.4724" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0586" Parameter: B <- "-27.0586" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4138" Parameter: C <- "-47.4138" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 308 TOTAL ENERGY = -74.4724 RDTITL> * VAN DER WAALS = -27.0586 ELECTROSTATIC = -47.4138 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "308" Parameter: CONF_N -> "8002" Comparing "308" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "309" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768183 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763320 ATOM PAIRS WERE FOUND FOR ATOM LIST 41947 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30145 from a total of 763320 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 309 -69.50823 -4.96420 0.63963 INTE EXTERN> -29.51566 -39.99257 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5082" Parameter: A <- "-69.5082" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5157" Parameter: B <- "-29.5157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9926" Parameter: C <- "-39.9926" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 309 TOTAL ENERGY = -69.5082 RDTITL> * VAN DER WAALS = -29.5157 ELECTROSTATIC = -39.9926 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "309" Parameter: CONF_N -> "8002" Comparing "309" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "310" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763320 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763873 ATOM PAIRS WERE FOUND FOR ATOM LIST 42096 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30218 from a total of 763873 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 310 -65.45991 -4.04832 0.55337 INTE EXTERN> -31.37885 -34.08106 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4599" Parameter: A <- "-65.4599" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3789" Parameter: B <- "-31.3789" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.0811" Parameter: C <- "-34.0811" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 310 TOTAL ENERGY = -65.4599 RDTITL> * VAN DER WAALS = -31.3789 ELECTROSTATIC = -34.0811 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "310" Parameter: CONF_N -> "8002" Comparing "310" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "311" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763873 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765202 ATOM PAIRS WERE FOUND FOR ATOM LIST 42150 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30316 from a total of 765202 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 311 -73.41745 7.95754 0.71153 INTE EXTERN> -29.12007 -44.29738 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4174" Parameter: A <- "-73.4174" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1201" Parameter: B <- "-29.1201" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2974" Parameter: C <- "-44.2974" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 311 TOTAL ENERGY = -73.4174 RDTITL> * VAN DER WAALS = -29.1201 ELECTROSTATIC = -44.2974 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "311" Parameter: CONF_N -> "8002" Comparing "311" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "312" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765202 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769549 ATOM PAIRS WERE FOUND FOR ATOM LIST 42322 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30043 from a total of 769549 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 312 -67.55422 -5.86323 0.60352 INTE EXTERN> -32.04472 -35.50950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5542" Parameter: A <- "-67.5542" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0447" Parameter: B <- "-32.0447" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5095" Parameter: C <- "-35.5095" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 312 TOTAL ENERGY = -67.5542 RDTITL> * VAN DER WAALS = -32.0447 ELECTROSTATIC = -35.5095 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "312" Parameter: CONF_N -> "8002" Comparing "312" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "313" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769549 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768699 ATOM PAIRS WERE FOUND FOR ATOM LIST 42397 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30361 from a total of 768699 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 313 -74.54441 6.99019 0.68508 INTE EXTERN> -29.55555 -44.98886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5444" Parameter: A <- "-74.5444" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5555" Parameter: B <- "-29.5555" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9889" Parameter: C <- "-44.9889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 313 TOTAL ENERGY = -74.5444 RDTITL> * VAN DER WAALS = -29.5555 ELECTROSTATIC = -44.9889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "313" Parameter: CONF_N -> "8002" Comparing "313" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "314" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768699 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761017 ATOM PAIRS WERE FOUND FOR ATOM LIST 42024 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29702 from a total of 761017 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 314 -70.47107 -4.07334 0.52916 INTE EXTERN> -34.79957 -35.67150 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4711" Parameter: A <- "-70.4711" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.7996" Parameter: B <- "-34.7996" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6715" Parameter: C <- "-35.6715" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 314 TOTAL ENERGY = -70.4711 RDTITL> * VAN DER WAALS = -34.7996 ELECTROSTATIC = -35.6715 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "314" Parameter: CONF_N -> "8002" Comparing "314" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "315" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761017 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764151 ATOM PAIRS WERE FOUND FOR ATOM LIST 42142 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29526 from a total of 764151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 315 -68.31089 -2.16018 0.62205 INTE EXTERN> -30.13206 -38.17883 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3109" Parameter: A <- "-68.3109" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1321" Parameter: B <- "-30.1321" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1788" Parameter: C <- "-38.1788" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 315 TOTAL ENERGY = -68.3109 RDTITL> * VAN DER WAALS = -30.1321 ELECTROSTATIC = -38.1788 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "315" Parameter: CONF_N -> "8002" Comparing "315" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "316" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766336 ATOM PAIRS WERE FOUND FOR ATOM LIST 42249 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30102 from a total of 766336 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 316 -70.22772 1.91684 0.58690 INTE EXTERN> -33.27683 -36.95089 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2277" Parameter: A <- "-70.2277" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2768" Parameter: B <- "-33.2768" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9509" Parameter: C <- "-36.9509" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 316 TOTAL ENERGY = -70.2277 RDTITL> * VAN DER WAALS = -33.2768 ELECTROSTATIC = -36.9509 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "316" Parameter: CONF_N -> "8002" Comparing "316" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "317" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766336 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766752 ATOM PAIRS WERE FOUND FOR ATOM LIST 42367 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29987 from a total of 766752 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 317 -71.54585 1.31813 0.62233 INTE EXTERN> -30.31529 -41.23056 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5459" Parameter: A <- "-71.5459" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3153" Parameter: B <- "-30.3153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2306" Parameter: C <- "-41.2306" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 317 TOTAL ENERGY = -71.5459 RDTITL> * VAN DER WAALS = -30.3153 ELECTROSTATIC = -41.2306 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "317" Parameter: CONF_N -> "8002" Comparing "317" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "318" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766752 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764000 ATOM PAIRS WERE FOUND FOR ATOM LIST 42226 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29729 from a total of 764000 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 318 -72.03024 0.48438 0.62056 INTE EXTERN> -28.86649 -43.16374 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0302" Parameter: A <- "-72.0302" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8665" Parameter: B <- "-28.8665" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1637" Parameter: C <- "-43.1637" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 318 TOTAL ENERGY = -72.0302 RDTITL> * VAN DER WAALS = -28.8665 ELECTROSTATIC = -43.1637 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "318" Parameter: CONF_N -> "8002" Comparing "318" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "319" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764000 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767702 ATOM PAIRS WERE FOUND FOR ATOM LIST 42256 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28944 from a total of 767702 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 319 -73.47281 1.44257 0.61362 INTE EXTERN> -30.45348 -43.01933 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4728" Parameter: A <- "-73.4728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4535" Parameter: B <- "-30.4535" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0193" Parameter: C <- "-43.0193" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 319 TOTAL ENERGY = -73.4728 RDTITL> * VAN DER WAALS = -30.4535 ELECTROSTATIC = -43.0193 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "319" Parameter: CONF_N -> "8002" Comparing "319" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "320" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767702 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762652 ATOM PAIRS WERE FOUND FOR ATOM LIST 42114 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29116 from a total of 762652 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 320 -70.41525 -3.05756 0.60976 INTE EXTERN> -31.44612 -38.96913 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4153" Parameter: A <- "-70.4153" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4461" Parameter: B <- "-31.4461" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9691" Parameter: C <- "-38.9691" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 320 TOTAL ENERGY = -70.4153 RDTITL> * VAN DER WAALS = -31.4461 ELECTROSTATIC = -38.9691 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "320" Parameter: CONF_N -> "8002" Comparing "320" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "321" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762652 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767028 ATOM PAIRS WERE FOUND FOR ATOM LIST 42060 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29783 from a total of 767028 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 321 -70.89525 0.48000 0.66918 INTE EXTERN> -29.23225 -41.66299 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8952" Parameter: A <- "-70.8952" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2323" Parameter: B <- "-29.2323" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.663" Parameter: C <- "-41.663" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 321 TOTAL ENERGY = -70.8952 RDTITL> * VAN DER WAALS = -29.2323 ELECTROSTATIC = -41.663 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "321" Parameter: CONF_N -> "8002" Comparing "321" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "322" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767028 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764749 ATOM PAIRS WERE FOUND FOR ATOM LIST 41950 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29863 from a total of 764749 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 322 -64.71234 -6.18290 0.60691 INTE EXTERN> -28.93209 -35.78026 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7123" Parameter: A <- "-64.7123" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9321" Parameter: B <- "-28.9321" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7803" Parameter: C <- "-35.7803" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 322 TOTAL ENERGY = -64.7123 RDTITL> * VAN DER WAALS = -28.9321 ELECTROSTATIC = -35.7803 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "322" Parameter: CONF_N -> "8002" Comparing "322" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "323" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764749 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765950 ATOM PAIRS WERE FOUND FOR ATOM LIST 42181 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29078 from a total of 765950 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 323 -66.50422 1.79187 0.63162 INTE EXTERN> -28.54402 -37.96020 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5042" Parameter: A <- "-66.5042" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.544" Parameter: B <- "-28.544" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9602" Parameter: C <- "-37.9602" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 323 TOTAL ENERGY = -66.5042 RDTITL> * VAN DER WAALS = -28.544 ELECTROSTATIC = -37.9602 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "323" Parameter: CONF_N -> "8002" Comparing "323" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "324" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765950 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757575 ATOM PAIRS WERE FOUND FOR ATOM LIST 41799 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29836 from a total of 757575 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 324 -69.50187 2.99766 0.65901 INTE EXTERN> -28.02816 -41.47372 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5019" Parameter: A <- "-69.5019" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0282" Parameter: B <- "-28.0282" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4737" Parameter: C <- "-41.4737" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 324 TOTAL ENERGY = -69.5019 RDTITL> * VAN DER WAALS = -28.0282 ELECTROSTATIC = -41.4737 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "324" Parameter: CONF_N -> "8002" Comparing "324" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "325" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757575 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762882 ATOM PAIRS WERE FOUND FOR ATOM LIST 41902 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29265 from a total of 762882 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 325 -68.08415 -1.41772 0.54670 INTE EXTERN> -32.04787 -36.03628 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0842" Parameter: A <- "-68.0842" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0479" Parameter: B <- "-32.0479" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0363" Parameter: C <- "-36.0363" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 325 TOTAL ENERGY = -68.0842 RDTITL> * VAN DER WAALS = -32.0479 ELECTROSTATIC = -36.0363 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "325" Parameter: CONF_N -> "8002" Comparing "325" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "326" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762882 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767656 ATOM PAIRS WERE FOUND FOR ATOM LIST 42231 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29724 from a total of 767656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 326 -72.73595 4.65180 0.57618 INTE EXTERN> -30.85274 -41.88321 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7359" Parameter: A <- "-72.7359" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8527" Parameter: B <- "-30.8527" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8832" Parameter: C <- "-41.8832" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 326 TOTAL ENERGY = -72.7359 RDTITL> * VAN DER WAALS = -30.8527 ELECTROSTATIC = -41.8832 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "326" Parameter: CONF_N -> "8002" Comparing "326" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "327" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764877 ATOM PAIRS WERE FOUND FOR ATOM LIST 42228 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30293 from a total of 764877 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 327 -77.27997 4.54403 0.59272 INTE EXTERN> -32.62599 -44.65399 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.28" Parameter: A <- "-77.28" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.626" Parameter: B <- "-32.626" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.654" Parameter: C <- "-44.654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 327 TOTAL ENERGY = -77.28 RDTITL> * VAN DER WAALS = -32.626 ELECTROSTATIC = -44.654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "327" Parameter: CONF_N -> "8002" Comparing "327" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "328" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764877 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765352 ATOM PAIRS WERE FOUND FOR ATOM LIST 42196 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30004 from a total of 765352 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 328 -66.01574 -11.26424 0.56660 INTE EXTERN> -32.42107 -33.59467 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0157" Parameter: A <- "-66.0157" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4211" Parameter: B <- "-32.4211" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.5947" Parameter: C <- "-33.5947" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 328 TOTAL ENERGY = -66.0157 RDTITL> * VAN DER WAALS = -32.4211 ELECTROSTATIC = -33.5947 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "328" Parameter: CONF_N -> "8002" Comparing "328" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "329" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765352 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766948 ATOM PAIRS WERE FOUND FOR ATOM LIST 42359 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29831 from a total of 766948 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 329 -72.14077 6.12503 0.65828 INTE EXTERN> -30.24464 -41.89613 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1408" Parameter: A <- "-72.1408" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2446" Parameter: B <- "-30.2446" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8961" Parameter: C <- "-41.8961" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 329 TOTAL ENERGY = -72.1408 RDTITL> * VAN DER WAALS = -30.2446 ELECTROSTATIC = -41.8961 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "329" Parameter: CONF_N -> "8002" Comparing "329" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "330" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766948 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766780 ATOM PAIRS WERE FOUND FOR ATOM LIST 42193 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29395 from a total of 766780 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 330 -76.19315 4.05237 0.56046 INTE EXTERN> -33.36384 -42.82930 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1931" Parameter: A <- "-76.1931" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3638" Parameter: B <- "-33.3638" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8293" Parameter: C <- "-42.8293" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 330 TOTAL ENERGY = -76.1931 RDTITL> * VAN DER WAALS = -33.3638 ELECTROSTATIC = -42.8293 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "330" Parameter: CONF_N -> "8002" Comparing "330" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "331" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766780 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766555 ATOM PAIRS WERE FOUND FOR ATOM LIST 42139 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29136 from a total of 766555 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 331 -72.51571 -3.67743 0.71944 INTE EXTERN> -26.80819 -45.70752 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5157" Parameter: A <- "-72.5157" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8082" Parameter: B <- "-26.8082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7075" Parameter: C <- "-45.7075" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 331 TOTAL ENERGY = -72.5157 RDTITL> * VAN DER WAALS = -26.8082 ELECTROSTATIC = -45.7075 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "331" Parameter: CONF_N -> "8002" Comparing "331" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "332" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766555 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765139 ATOM PAIRS WERE FOUND FOR ATOM LIST 42163 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29517 from a total of 765139 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 332 -69.89688 -2.61884 0.63507 INTE EXTERN> -28.85335 -41.04353 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8969" Parameter: A <- "-69.8969" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8534" Parameter: B <- "-28.8534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0435" Parameter: C <- "-41.0435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 332 TOTAL ENERGY = -69.8969 RDTITL> * VAN DER WAALS = -28.8534 ELECTROSTATIC = -41.0435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "332" Parameter: CONF_N -> "8002" Comparing "332" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "333" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765139 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769238 ATOM PAIRS WERE FOUND FOR ATOM LIST 42286 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29814 from a total of 769238 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 333 -73.69767 3.80079 0.63678 INTE EXTERN> -30.79554 -42.90213 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6977" Parameter: A <- "-73.6977" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7955" Parameter: B <- "-30.7955" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9021" Parameter: C <- "-42.9021" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 333 TOTAL ENERGY = -73.6977 RDTITL> * VAN DER WAALS = -30.7955 ELECTROSTATIC = -42.9021 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "333" Parameter: CONF_N -> "8002" Comparing "333" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "334" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769238 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768725 ATOM PAIRS WERE FOUND FOR ATOM LIST 42140 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29452 from a total of 768725 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 334 -68.93671 -4.76096 0.57128 INTE EXTERN> -32.81615 -36.12057 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9367" Parameter: A <- "-68.9367" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8161" Parameter: B <- "-32.8161" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1206" Parameter: C <- "-36.1206" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 334 TOTAL ENERGY = -68.9367 RDTITL> * VAN DER WAALS = -32.8161 ELECTROSTATIC = -36.1206 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "334" Parameter: CONF_N -> "8002" Comparing "334" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "335" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768725 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765627 ATOM PAIRS WERE FOUND FOR ATOM LIST 42284 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29974 from a total of 765627 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 335 -70.89583 1.95911 0.67990 INTE EXTERN> -30.21108 -40.68475 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8958" Parameter: A <- "-70.8958" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2111" Parameter: B <- "-30.2111" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6847" Parameter: C <- "-40.6847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 335 TOTAL ENERGY = -70.8958 RDTITL> * VAN DER WAALS = -30.2111 ELECTROSTATIC = -40.6847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "335" Parameter: CONF_N -> "8002" Comparing "335" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "336" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765627 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765991 ATOM PAIRS WERE FOUND FOR ATOM LIST 42181 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28910 from a total of 765991 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 336 -71.93377 1.03794 0.62701 INTE EXTERN> -28.89749 -43.03628 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9338" Parameter: A <- "-71.9338" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8975" Parameter: B <- "-28.8975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0363" Parameter: C <- "-43.0363" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 336 TOTAL ENERGY = -71.9338 RDTITL> * VAN DER WAALS = -28.8975 ELECTROSTATIC = -43.0363 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "336" Parameter: CONF_N -> "8002" Comparing "336" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "337" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765991 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 774881 ATOM PAIRS WERE FOUND FOR ATOM LIST 42435 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29615 from a total of 774881 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 337 -72.44194 0.50817 0.63118 INTE EXTERN> -29.77160 -42.67033 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4419" Parameter: A <- "-72.4419" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7716" Parameter: B <- "-29.7716" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6703" Parameter: C <- "-42.6703" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 337 TOTAL ENERGY = -72.4419 RDTITL> * VAN DER WAALS = -29.7716 ELECTROSTATIC = -42.6703 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "337" Parameter: CONF_N -> "8002" Comparing "337" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "338" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 774881 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767318 ATOM PAIRS WERE FOUND FOR ATOM LIST 42259 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29556 from a total of 767318 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 338 -70.86842 -1.57352 0.57213 INTE EXTERN> -34.27387 -36.59455 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8684" Parameter: A <- "-70.8684" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.2739" Parameter: B <- "-34.2739" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5945" Parameter: C <- "-36.5945" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 338 TOTAL ENERGY = -70.8684 RDTITL> * VAN DER WAALS = -34.2739 ELECTROSTATIC = -36.5945 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "338" Parameter: CONF_N -> "8002" Comparing "338" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "339" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767318 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772587 ATOM PAIRS WERE FOUND FOR ATOM LIST 42229 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29967 from a total of 772587 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 339 -70.05187 -0.81654 0.71538 INTE EXTERN> -26.64219 -43.40968 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0519" Parameter: A <- "-70.0519" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6422" Parameter: B <- "-26.6422" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4097" Parameter: C <- "-43.4097" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 339 TOTAL ENERGY = -70.0519 RDTITL> * VAN DER WAALS = -26.6422 ELECTROSTATIC = -43.4097 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "339" Parameter: CONF_N -> "8002" Comparing "339" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "340" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772587 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 774377 ATOM PAIRS WERE FOUND FOR ATOM LIST 42750 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29948 from a total of 774377 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 340 -74.44010 4.38823 0.74613 INTE EXTERN> -23.74772 -50.69238 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4401" Parameter: A <- "-74.4401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7477" Parameter: B <- "-23.7477" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6924" Parameter: C <- "-50.6924" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 340 TOTAL ENERGY = -74.4401 RDTITL> * VAN DER WAALS = -23.7477 ELECTROSTATIC = -50.6924 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "340" Parameter: CONF_N -> "8002" Comparing "340" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "341" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 774377 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768442 ATOM PAIRS WERE FOUND FOR ATOM LIST 42269 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29075 from a total of 768442 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 341 -79.91831 5.47821 0.75481 INTE EXTERN> -27.53097 -52.38734 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9183" Parameter: A <- "-79.9183" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.531" Parameter: B <- "-27.531" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3873" Parameter: C <- "-52.3873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 341 TOTAL ENERGY = -79.9183 RDTITL> * VAN DER WAALS = -27.531 ELECTROSTATIC = -52.3873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "341" Parameter: CONF_N -> "8002" Comparing "341" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "342" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768442 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770884 ATOM PAIRS WERE FOUND FOR ATOM LIST 42696 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29737 from a total of 770884 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 342 -81.99184 2.07353 0.71772 INTE EXTERN> -28.30996 -53.68188 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9918" Parameter: A <- "-81.9918" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.31" Parameter: B <- "-28.31" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6819" Parameter: C <- "-53.6819" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 342 TOTAL ENERGY = -81.9918 RDTITL> * VAN DER WAALS = -28.31 ELECTROSTATIC = -53.6819 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "342" Parameter: CONF_N -> "8002" Comparing "342" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "343" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770884 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769552 ATOM PAIRS WERE FOUND FOR ATOM LIST 42476 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29020 from a total of 769552 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 343 -77.13117 -4.86067 0.66666 INTE EXTERN> -27.40438 -49.72679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1312" Parameter: A <- "-77.1312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4044" Parameter: B <- "-27.4044" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7268" Parameter: C <- "-49.7268" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 343 TOTAL ENERGY = -77.1312 RDTITL> * VAN DER WAALS = -27.4044 ELECTROSTATIC = -49.7268 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "343" Parameter: CONF_N -> "8002" Comparing "343" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "344" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769552 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772376 ATOM PAIRS WERE FOUND FOR ATOM LIST 42524 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29444 from a total of 772376 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 344 -75.63660 -1.49458 0.51733 INTE EXTERN> -32.33943 -43.29717 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6366" Parameter: A <- "-75.6366" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3394" Parameter: B <- "-32.3394" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2972" Parameter: C <- "-43.2972" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 344 TOTAL ENERGY = -75.6366 RDTITL> * VAN DER WAALS = -32.3394 ELECTROSTATIC = -43.2972 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "344" Parameter: CONF_N -> "8002" Comparing "344" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "345" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772376 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 774107 ATOM PAIRS WERE FOUND FOR ATOM LIST 42611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30738 from a total of 774107 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 345 -69.72065 -5.91595 0.60454 INTE EXTERN> -27.84821 -41.87244 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7206" Parameter: A <- "-69.7206" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8482" Parameter: B <- "-27.8482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8724" Parameter: C <- "-41.8724" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 345 TOTAL ENERGY = -69.7206 RDTITL> * VAN DER WAALS = -27.8482 ELECTROSTATIC = -41.8724 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "345" Parameter: CONF_N -> "8002" Comparing "345" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "346" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 774107 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767676 ATOM PAIRS WERE FOUND FOR ATOM LIST 42311 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29803 from a total of 767676 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 346 -76.78036 7.05972 0.54895 INTE EXTERN> -34.92539 -41.85497 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7804" Parameter: A <- "-76.7804" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9254" Parameter: B <- "-34.9254" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.855" Parameter: C <- "-41.855" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 346 TOTAL ENERGY = -76.7804 RDTITL> * VAN DER WAALS = -34.9254 ELECTROSTATIC = -41.855 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "346" Parameter: CONF_N -> "8002" Comparing "346" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "347" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767676 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769234 ATOM PAIRS WERE FOUND FOR ATOM LIST 42347 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29874 from a total of 769234 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 347 -72.47446 -4.30590 0.70265 INTE EXTERN> -27.34260 -45.13186 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4745" Parameter: A <- "-72.4745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3426" Parameter: B <- "-27.3426" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1319" Parameter: C <- "-45.1319" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 347 TOTAL ENERGY = -72.4745 RDTITL> * VAN DER WAALS = -27.3426 ELECTROSTATIC = -45.1319 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "347" Parameter: CONF_N -> "8002" Comparing "347" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "348" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769234 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767067 ATOM PAIRS WERE FOUND FOR ATOM LIST 42209 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29789 from a total of 767067 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 348 -74.61290 2.13844 0.72712 INTE EXTERN> -28.19481 -46.41809 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6129" Parameter: A <- "-74.6129" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1948" Parameter: B <- "-28.1948" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4181" Parameter: C <- "-46.4181" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 348 TOTAL ENERGY = -74.6129 RDTITL> * VAN DER WAALS = -28.1948 ELECTROSTATIC = -46.4181 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "348" Parameter: CONF_N -> "8002" Comparing "348" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "349" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767067 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772083 ATOM PAIRS WERE FOUND FOR ATOM LIST 42540 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30014 from a total of 772083 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 349 -70.26573 -4.34717 0.54997 INTE EXTERN> -33.73592 -36.52980 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2657" Parameter: A <- "-70.2657" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7359" Parameter: B <- "-33.7359" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5298" Parameter: C <- "-36.5298" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 349 TOTAL ENERGY = -70.2657 RDTITL> * VAN DER WAALS = -33.7359 ELECTROSTATIC = -36.5298 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "349" Parameter: CONF_N -> "8002" Comparing "349" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "350" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772083 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768975 ATOM PAIRS WERE FOUND FOR ATOM LIST 42369 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29685 from a total of 768975 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 350 -76.10573 5.84000 0.62757 INTE EXTERN> -30.14199 -45.96374 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1057" Parameter: A <- "-76.1057" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.142" Parameter: B <- "-30.142" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9637" Parameter: C <- "-45.9637" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 350 TOTAL ENERGY = -76.1057 RDTITL> * VAN DER WAALS = -30.142 ELECTROSTATIC = -45.9637 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "350" Parameter: CONF_N -> "8002" Comparing "350" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "351" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768975 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766585 ATOM PAIRS WERE FOUND FOR ATOM LIST 42358 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29257 from a total of 766585 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 351 -74.14227 -1.96346 0.64853 INTE EXTERN> -30.25438 -43.88789 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1423" Parameter: A <- "-74.1423" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2544" Parameter: B <- "-30.2544" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8879" Parameter: C <- "-43.8879" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 351 TOTAL ENERGY = -74.1423 RDTITL> * VAN DER WAALS = -30.2544 ELECTROSTATIC = -43.8879 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "351" Parameter: CONF_N -> "8002" Comparing "351" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "352" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766585 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770642 ATOM PAIRS WERE FOUND FOR ATOM LIST 42320 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30128 from a total of 770642 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 352 -73.23689 -0.90538 0.66930 INTE EXTERN> -29.84190 -43.39498 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2369" Parameter: A <- "-73.2369" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8419" Parameter: B <- "-29.8419" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.395" Parameter: C <- "-43.395" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 352 TOTAL ENERGY = -73.2369 RDTITL> * VAN DER WAALS = -29.8419 ELECTROSTATIC = -43.395 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "352" Parameter: CONF_N -> "8002" Comparing "352" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "353" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770642 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765326 ATOM PAIRS WERE FOUND FOR ATOM LIST 42139 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29763 from a total of 765326 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 353 -76.86540 3.62852 0.71915 INTE EXTERN> -27.45290 -49.41250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8654" Parameter: A <- "-76.8654" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4529" Parameter: B <- "-27.4529" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4125" Parameter: C <- "-49.4125" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 353 TOTAL ENERGY = -76.8654 RDTITL> * VAN DER WAALS = -27.4529 ELECTROSTATIC = -49.4125 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "353" Parameter: CONF_N -> "8002" Comparing "353" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "354" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765326 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766912 ATOM PAIRS WERE FOUND FOR ATOM LIST 41987 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29544 from a total of 766912 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 354 -74.76394 -2.10146 0.61643 INTE EXTERN> -29.91564 -44.84830 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7639" Parameter: A <- "-74.7639" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9156" Parameter: B <- "-29.9156" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8483" Parameter: C <- "-44.8483" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 354 TOTAL ENERGY = -74.7639 RDTITL> * VAN DER WAALS = -29.9156 ELECTROSTATIC = -44.8483 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "354" Parameter: CONF_N -> "8002" Comparing "354" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "355" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766912 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771362 ATOM PAIRS WERE FOUND FOR ATOM LIST 42277 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30375 from a total of 771362 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 355 -68.25944 -6.50451 0.67423 INTE EXTERN> -27.61980 -40.63964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2594" Parameter: A <- "-68.2594" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6198" Parameter: B <- "-27.6198" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6396" Parameter: C <- "-40.6396" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 355 TOTAL ENERGY = -68.2594 RDTITL> * VAN DER WAALS = -27.6198 ELECTROSTATIC = -40.6396 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "355" Parameter: CONF_N -> "8002" Comparing "355" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "356" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771362 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772253 ATOM PAIRS WERE FOUND FOR ATOM LIST 42788 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29628 from a total of 772253 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 356 -72.35591 4.09648 0.60363 INTE EXTERN> -30.77712 -41.57880 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3559" Parameter: A <- "-72.3559" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7771" Parameter: B <- "-30.7771" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5788" Parameter: C <- "-41.5788" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 356 TOTAL ENERGY = -72.3559 RDTITL> * VAN DER WAALS = -30.7771 ELECTROSTATIC = -41.5788 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "356" Parameter: CONF_N -> "8002" Comparing "356" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "357" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772253 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760072 ATOM PAIRS WERE FOUND FOR ATOM LIST 42076 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29569 from a total of 760072 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 357 -74.66748 2.31156 0.71321 INTE EXTERN> -29.13952 -45.52796 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6675" Parameter: A <- "-74.6675" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1395" Parameter: B <- "-29.1395" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.528" Parameter: C <- "-45.528" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 357 TOTAL ENERGY = -74.6675 RDTITL> * VAN DER WAALS = -29.1395 ELECTROSTATIC = -45.528 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "357" Parameter: CONF_N -> "8002" Comparing "357" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "358" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760072 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765557 ATOM PAIRS WERE FOUND FOR ATOM LIST 42011 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29501 from a total of 765557 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 358 -76.79908 2.13161 0.69599 INTE EXTERN> -28.38928 -48.40981 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7991" Parameter: A <- "-76.7991" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3893" Parameter: B <- "-28.3893" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4098" Parameter: C <- "-48.4098" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 358 TOTAL ENERGY = -76.7991 RDTITL> * VAN DER WAALS = -28.3893 ELECTROSTATIC = -48.4098 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "358" Parameter: CONF_N -> "8002" Comparing "358" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "359" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765557 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767990 ATOM PAIRS WERE FOUND FOR ATOM LIST 42362 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29433 from a total of 767990 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 359 -73.64404 -3.15505 0.54708 INTE EXTERN> -33.68208 -39.96196 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.644" Parameter: A <- "-73.644" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6821" Parameter: B <- "-33.6821" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.962" Parameter: C <- "-39.962" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 359 TOTAL ENERGY = -73.644 RDTITL> * VAN DER WAALS = -33.6821 ELECTROSTATIC = -39.962 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "359" Parameter: CONF_N -> "8002" Comparing "359" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "360" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767990 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765307 ATOM PAIRS WERE FOUND FOR ATOM LIST 42250 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28557 from a total of 765307 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 360 -75.97719 2.33316 0.60847 INTE EXTERN> -31.71146 -44.26573 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9772" Parameter: A <- "-75.9772" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7115" Parameter: B <- "-31.7115" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2657" Parameter: C <- "-44.2657" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 360 TOTAL ENERGY = -75.9772 RDTITL> * VAN DER WAALS = -31.7115 ELECTROSTATIC = -44.2657 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "360" Parameter: CONF_N -> "8002" Comparing "360" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "361" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765307 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764668 ATOM PAIRS WERE FOUND FOR ATOM LIST 42093 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29629 from a total of 764668 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 361 -65.40984 -10.56736 0.58504 INTE EXTERN> -31.50225 -33.90759 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4098" Parameter: A <- "-65.4098" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5022" Parameter: B <- "-31.5022" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9076" Parameter: C <- "-33.9076" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 361 TOTAL ENERGY = -65.4098 RDTITL> * VAN DER WAALS = -31.5022 ELECTROSTATIC = -33.9076 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "361" Parameter: CONF_N -> "8002" Comparing "361" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "362" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764668 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772117 ATOM PAIRS WERE FOUND FOR ATOM LIST 42358 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29768 from a total of 772117 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 362 -70.32034 4.91050 0.53858 INTE EXTERN> -33.73929 -36.58104 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3203" Parameter: A <- "-70.3203" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7393" Parameter: B <- "-33.7393" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.581" Parameter: C <- "-36.581" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 362 TOTAL ENERGY = -70.3203 RDTITL> * VAN DER WAALS = -33.7393 ELECTROSTATIC = -36.581 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "362" Parameter: CONF_N -> "8002" Comparing "362" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "363" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772117 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 773444 ATOM PAIRS WERE FOUND FOR ATOM LIST 42532 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30281 from a total of 773444 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 363 -75.35619 5.03585 0.59205 INTE EXTERN> -33.48129 -41.87490 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3562" Parameter: A <- "-75.3562" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4813" Parameter: B <- "-33.4813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8749" Parameter: C <- "-41.8749" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 363 TOTAL ENERGY = -75.3562 RDTITL> * VAN DER WAALS = -33.4813 ELECTROSTATIC = -41.8749 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "363" Parameter: CONF_N -> "8002" Comparing "363" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "364" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 773444 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765788 ATOM PAIRS WERE FOUND FOR ATOM LIST 42243 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29714 from a total of 765788 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 364 -81.49451 6.13832 0.63063 INTE EXTERN> -33.46312 -48.03139 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4945" Parameter: A <- "-81.4945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4631" Parameter: B <- "-33.4631" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0314" Parameter: C <- "-48.0314" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 364 TOTAL ENERGY = -81.4945 RDTITL> * VAN DER WAALS = -33.4631 ELECTROSTATIC = -48.0314 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "364" Parameter: CONF_N -> "8002" Comparing "364" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "365" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765788 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764816 ATOM PAIRS WERE FOUND FOR ATOM LIST 42361 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29669 from a total of 764816 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 365 -74.97903 -6.51548 0.56110 INTE EXTERN> -33.57546 -41.40358 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.979" Parameter: A <- "-74.979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5755" Parameter: B <- "-33.5755" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4036" Parameter: C <- "-41.4036" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 365 TOTAL ENERGY = -74.979 RDTITL> * VAN DER WAALS = -33.5755 ELECTROSTATIC = -41.4036 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "365" Parameter: CONF_N -> "8002" Comparing "365" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "366" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764816 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760070 ATOM PAIRS WERE FOUND FOR ATOM LIST 41964 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29183 from a total of 760070 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 366 -69.65870 -5.32034 0.65191 INTE EXTERN> -25.80952 -43.84917 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6587" Parameter: A <- "-69.6587" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8095" Parameter: B <- "-25.8095" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8492" Parameter: C <- "-43.8492" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 366 TOTAL ENERGY = -69.6587 RDTITL> * VAN DER WAALS = -25.8095 ELECTROSTATIC = -43.8492 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "366" Parameter: CONF_N -> "8002" Comparing "366" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "367" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760070 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765203 ATOM PAIRS WERE FOUND FOR ATOM LIST 42151 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29763 from a total of 765203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 367 -73.72802 4.06933 0.72188 INTE EXTERN> -27.76394 -45.96408 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.728" Parameter: A <- "-73.728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7639" Parameter: B <- "-27.7639" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9641" Parameter: C <- "-45.9641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 367 TOTAL ENERGY = -73.728 RDTITL> * VAN DER WAALS = -27.7639 ELECTROSTATIC = -45.9641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "367" Parameter: CONF_N -> "8002" Comparing "367" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "368" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760185 ATOM PAIRS WERE FOUND FOR ATOM LIST 41617 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29603 from a total of 760185 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 368 -75.72463 1.99660 0.74699 INTE EXTERN> -26.41902 -49.30561 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7246" Parameter: A <- "-75.7246" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.419" Parameter: B <- "-26.419" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3056" Parameter: C <- "-49.3056" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 368 TOTAL ENERGY = -75.7246 RDTITL> * VAN DER WAALS = -26.419 ELECTROSTATIC = -49.3056 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "368" Parameter: CONF_N -> "8002" Comparing "368" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "369" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760185 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761832 ATOM PAIRS WERE FOUND FOR ATOM LIST 41876 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29583 from a total of 761832 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 369 -70.81628 -4.90835 0.57578 INTE EXTERN> -32.28835 -38.52793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8163" Parameter: A <- "-70.8163" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2884" Parameter: B <- "-32.2884" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5279" Parameter: C <- "-38.5279" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 369 TOTAL ENERGY = -70.8163 RDTITL> * VAN DER WAALS = -32.2884 ELECTROSTATIC = -38.5279 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "369" Parameter: CONF_N -> "8002" Comparing "369" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "370" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761832 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759030 ATOM PAIRS WERE FOUND FOR ATOM LIST 41892 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29423 from a total of 759030 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 370 -77.83778 7.02149 0.68407 INTE EXTERN> -29.72538 -48.11240 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8378" Parameter: A <- "-77.8378" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7254" Parameter: B <- "-29.7254" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1124" Parameter: C <- "-48.1124" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 370 TOTAL ENERGY = -77.8378 RDTITL> * VAN DER WAALS = -29.7254 ELECTROSTATIC = -48.1124 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "370" Parameter: CONF_N -> "8002" Comparing "370" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "371" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759030 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763196 ATOM PAIRS WERE FOUND FOR ATOM LIST 41867 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29659 from a total of 763196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 371 -66.49270 -11.34508 0.54262 INTE EXTERN> -31.93223 -34.56047 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4927" Parameter: A <- "-66.4927" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9322" Parameter: B <- "-31.9322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5605" Parameter: C <- "-34.5605" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 371 TOTAL ENERGY = -66.4927 RDTITL> * VAN DER WAALS = -31.9322 ELECTROSTATIC = -34.5605 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "371" Parameter: CONF_N -> "8002" Comparing "371" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "372" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763786 ATOM PAIRS WERE FOUND FOR ATOM LIST 42046 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29670 from a total of 763786 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 372 -74.92626 8.43356 0.61564 INTE EXTERN> -30.37577 -44.55049 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9263" Parameter: A <- "-74.9263" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3758" Parameter: B <- "-30.3758" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5505" Parameter: C <- "-44.5505" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 372 TOTAL ENERGY = -74.9263 RDTITL> * VAN DER WAALS = -30.3758 ELECTROSTATIC = -44.5505 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "372" Parameter: CONF_N -> "8002" Comparing "372" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "373" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763786 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763944 ATOM PAIRS WERE FOUND FOR ATOM LIST 42003 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29267 from a total of 763944 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 373 -71.87055 -3.05570 0.60243 INTE EXTERN> -30.76102 -41.10953 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8706" Parameter: A <- "-71.8706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.761" Parameter: B <- "-30.761" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1095" Parameter: C <- "-41.1095" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 373 TOTAL ENERGY = -71.8706 RDTITL> * VAN DER WAALS = -30.761 ELECTROSTATIC = -41.1095 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "373" Parameter: CONF_N -> "8002" Comparing "373" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "374" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763944 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762249 ATOM PAIRS WERE FOUND FOR ATOM LIST 41915 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29415 from a total of 762249 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 374 -72.69070 0.82015 0.61633 INTE EXTERN> -30.38496 -42.30574 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6907" Parameter: A <- "-72.6907" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.385" Parameter: B <- "-30.385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3057" Parameter: C <- "-42.3057" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 374 TOTAL ENERGY = -72.6907 RDTITL> * VAN DER WAALS = -30.385 ELECTROSTATIC = -42.3057 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "374" Parameter: CONF_N -> "8002" Comparing "374" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "375" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762249 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767793 ATOM PAIRS WERE FOUND FOR ATOM LIST 42286 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30392 from a total of 767793 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 375 -79.36961 6.67891 0.62764 INTE EXTERN> -31.02212 -48.34749 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.3696" Parameter: A <- "-79.3696" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0221" Parameter: B <- "-31.0221" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3475" Parameter: C <- "-48.3475" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 375 TOTAL ENERGY = -79.3696 RDTITL> * VAN DER WAALS = -31.0221 ELECTROSTATIC = -48.3475 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "375" Parameter: CONF_N -> "8002" Comparing "375" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "376" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767793 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769102 ATOM PAIRS WERE FOUND FOR ATOM LIST 42031 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30092 from a total of 769102 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 376 -78.74824 -0.62137 0.67083 INTE EXTERN> -31.20294 -47.54530 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7482" Parameter: A <- "-78.7482" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2029" Parameter: B <- "-31.2029" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5453" Parameter: C <- "-47.5453" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 376 TOTAL ENERGY = -78.7482 RDTITL> * VAN DER WAALS = -31.2029 ELECTROSTATIC = -47.5453 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "376" Parameter: CONF_N -> "8002" Comparing "376" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "377" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769102 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763995 ATOM PAIRS WERE FOUND FOR ATOM LIST 41882 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29087 from a total of 763995 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 377 -78.34139 -0.40685 0.59196 INTE EXTERN> -31.48776 -46.85363 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3414" Parameter: A <- "-78.3414" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4878" Parameter: B <- "-31.4878" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8536" Parameter: C <- "-46.8536" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 377 TOTAL ENERGY = -78.3414 RDTITL> * VAN DER WAALS = -31.4878 ELECTROSTATIC = -46.8536 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "377" Parameter: CONF_N -> "8002" Comparing "377" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "378" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763995 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761157 ATOM PAIRS WERE FOUND FOR ATOM LIST 41634 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29348 from a total of 761157 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 378 -66.22740 -12.11399 0.58209 INTE EXTERN> -27.62951 -38.59789 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2274" Parameter: A <- "-66.2274" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6295" Parameter: B <- "-27.6295" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5979" Parameter: C <- "-38.5979" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 378 TOTAL ENERGY = -66.2274 RDTITL> * VAN DER WAALS = -27.6295 ELECTROSTATIC = -38.5979 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "378" Parameter: CONF_N -> "8002" Comparing "378" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "379" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761157 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766109 ATOM PAIRS WERE FOUND FOR ATOM LIST 42071 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29201 from a total of 766109 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 379 -66.53526 0.30786 0.58589 INTE EXTERN> -31.15150 -35.38376 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5353" Parameter: A <- "-66.5353" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1515" Parameter: B <- "-31.1515" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3838" Parameter: C <- "-35.3838" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 379 TOTAL ENERGY = -66.5353 RDTITL> * VAN DER WAALS = -31.1515 ELECTROSTATIC = -35.3838 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "379" Parameter: CONF_N -> "8002" Comparing "379" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "380" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766109 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768562 ATOM PAIRS WERE FOUND FOR ATOM LIST 42111 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29462 from a total of 768562 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 380 -75.61885 9.08359 0.54962 INTE EXTERN> -32.19243 -43.42642 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6189" Parameter: A <- "-75.6189" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1924" Parameter: B <- "-32.1924" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4264" Parameter: C <- "-43.4264" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 380 TOTAL ENERGY = -75.6189 RDTITL> * VAN DER WAALS = -32.1924 ELECTROSTATIC = -43.4264 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "380" Parameter: CONF_N -> "8002" Comparing "380" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "381" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768562 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766978 ATOM PAIRS WERE FOUND FOR ATOM LIST 41972 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29343 from a total of 766978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 381 -68.79051 -6.82835 0.57054 INTE EXTERN> -32.43416 -36.35635 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7905" Parameter: A <- "-68.7905" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4342" Parameter: B <- "-32.4342" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3564" Parameter: C <- "-36.3564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 381 TOTAL ENERGY = -68.7905 RDTITL> * VAN DER WAALS = -32.4342 ELECTROSTATIC = -36.3564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "381" Parameter: CONF_N -> "8002" Comparing "381" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "382" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767302 ATOM PAIRS WERE FOUND FOR ATOM LIST 42259 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29314 from a total of 767302 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 382 -78.26954 9.47903 0.73309 INTE EXTERN> -27.45697 -50.81257 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2695" Parameter: A <- "-78.2695" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.457" Parameter: B <- "-27.457" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8126" Parameter: C <- "-50.8126" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 382 TOTAL ENERGY = -78.2695 RDTITL> * VAN DER WAALS = -27.457 ELECTROSTATIC = -50.8126 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "382" Parameter: CONF_N -> "8002" Comparing "382" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "383" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767302 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766647 ATOM PAIRS WERE FOUND FOR ATOM LIST 42130 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29660 from a total of 766647 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 383 -71.88691 -6.38263 0.73602 INTE EXTERN> -26.48199 -45.40492 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8869" Parameter: A <- "-71.8869" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.482" Parameter: B <- "-26.482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4049" Parameter: C <- "-45.4049" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 383 TOTAL ENERGY = -71.8869 RDTITL> * VAN DER WAALS = -26.482 ELECTROSTATIC = -45.4049 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "383" Parameter: CONF_N -> "8002" Comparing "383" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "384" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766647 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770431 ATOM PAIRS WERE FOUND FOR ATOM LIST 42152 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29885 from a total of 770431 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 384 -66.90044 -4.98647 0.59330 INTE EXTERN> -29.74977 -37.15068 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9004" Parameter: A <- "-66.9004" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7498" Parameter: B <- "-29.7498" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1507" Parameter: C <- "-37.1507" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 384 TOTAL ENERGY = -66.9004 RDTITL> * VAN DER WAALS = -29.7498 ELECTROSTATIC = -37.1507 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "384" Parameter: CONF_N -> "8002" Comparing "384" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "385" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770431 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 776389 ATOM PAIRS WERE FOUND FOR ATOM LIST 42403 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30203 from a total of 776389 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 385 -77.73809 10.83765 0.71865 INTE EXTERN> -25.61189 -52.12620 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7381" Parameter: A <- "-77.7381" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6119" Parameter: B <- "-25.6119" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1262" Parameter: C <- "-52.1262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 385 TOTAL ENERGY = -77.7381 RDTITL> * VAN DER WAALS = -25.6119 ELECTROSTATIC = -52.1262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "385" Parameter: CONF_N -> "8002" Comparing "385" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "386" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 776389 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768324 ATOM PAIRS WERE FOUND FOR ATOM LIST 42098 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29035 from a total of 768324 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 386 -76.15893 -1.57917 0.54258 INTE EXTERN> -34.19161 -41.96732 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1589" Parameter: A <- "-76.1589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1916" Parameter: B <- "-34.1916" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9673" Parameter: C <- "-41.9673" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 386 TOTAL ENERGY = -76.1589 RDTITL> * VAN DER WAALS = -34.1916 ELECTROSTATIC = -41.9673 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "386" Parameter: CONF_N -> "8002" Comparing "386" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "387" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768324 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766004 ATOM PAIRS WERE FOUND FOR ATOM LIST 41908 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28936 from a total of 766004 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 387 -77.64849 1.48956 0.65479 INTE EXTERN> -29.21047 -48.43801 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6485" Parameter: A <- "-77.6485" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2105" Parameter: B <- "-29.2105" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.438" Parameter: C <- "-48.438" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 387 TOTAL ENERGY = -77.6485 RDTITL> * VAN DER WAALS = -29.2105 ELECTROSTATIC = -48.438 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "387" Parameter: CONF_N -> "8002" Comparing "387" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "388" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766004 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768271 ATOM PAIRS WERE FOUND FOR ATOM LIST 42111 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29702 from a total of 768271 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 388 -79.96403 2.31554 0.59225 INTE EXTERN> -32.80189 -47.16214 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.964" Parameter: A <- "-79.964" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8019" Parameter: B <- "-32.8019" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1621" Parameter: C <- "-47.1621" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 388 TOTAL ENERGY = -79.964 RDTITL> * VAN DER WAALS = -32.8019 ELECTROSTATIC = -47.1621 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "388" Parameter: CONF_N -> "8002" Comparing "388" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "389" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768271 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766342 ATOM PAIRS WERE FOUND FOR ATOM LIST 41971 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29446 from a total of 766342 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 389 -68.26080 -11.70322 0.70482 INTE EXTERN> -26.36012 -41.90068 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2608" Parameter: A <- "-68.2608" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3601" Parameter: B <- "-26.3601" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9007" Parameter: C <- "-41.9007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 389 TOTAL ENERGY = -68.2608 RDTITL> * VAN DER WAALS = -26.3601 ELECTROSTATIC = -41.9007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "389" Parameter: CONF_N -> "8002" Comparing "389" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "390" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766342 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766552 ATOM PAIRS WERE FOUND FOR ATOM LIST 42142 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29512 from a total of 766552 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 390 -71.41791 3.15711 0.59043 INTE EXTERN> -34.16159 -37.25633 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4179" Parameter: A <- "-71.4179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1616" Parameter: B <- "-34.1616" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2563" Parameter: C <- "-37.2563" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 390 TOTAL ENERGY = -71.4179 RDTITL> * VAN DER WAALS = -34.1616 ELECTROSTATIC = -37.2563 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "390" Parameter: CONF_N -> "8002" Comparing "390" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "391" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766552 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761105 ATOM PAIRS WERE FOUND FOR ATOM LIST 41706 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28967 from a total of 761105 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 391 -77.72770 6.30979 0.62699 INTE EXTERN> -30.58868 -47.13902 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7277" Parameter: A <- "-77.7277" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5887" Parameter: B <- "-30.5887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.139" Parameter: C <- "-47.139" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 391 TOTAL ENERGY = -77.7277 RDTITL> * VAN DER WAALS = -30.5887 ELECTROSTATIC = -47.139 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "391" Parameter: CONF_N -> "8002" Comparing "391" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "392" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761105 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764968 ATOM PAIRS WERE FOUND FOR ATOM LIST 41926 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29341 from a total of 764968 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 392 -73.30410 -4.42360 0.64245 INTE EXTERN> -28.31854 -44.98556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3041" Parameter: A <- "-73.3041" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3185" Parameter: B <- "-28.3185" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9856" Parameter: C <- "-44.9856" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 392 TOTAL ENERGY = -73.3041 RDTITL> * VAN DER WAALS = -28.3185 ELECTROSTATIC = -44.9856 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "392" Parameter: CONF_N -> "8002" Comparing "392" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "393" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764968 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764339 ATOM PAIRS WERE FOUND FOR ATOM LIST 41955 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29521 from a total of 764339 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 393 -88.73563 15.43153 0.74221 INTE EXTERN> -29.05987 -59.67577 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.7356" Parameter: A <- "-88.7356" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0599" Parameter: B <- "-29.0599" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.6758" Parameter: C <- "-59.6758" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 393 TOTAL ENERGY = -88.7356 RDTITL> * VAN DER WAALS = -29.0599 ELECTROSTATIC = -59.6758 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "393" Parameter: CONF_N -> "8002" Comparing "393" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "394" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764339 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763275 ATOM PAIRS WERE FOUND FOR ATOM LIST 41925 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29207 from a total of 763275 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 394 -79.64264 -9.09299 0.60381 INTE EXTERN> -32.33279 -47.30985 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6426" Parameter: A <- "-79.6426" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3328" Parameter: B <- "-32.3328" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3099" Parameter: C <- "-47.3099" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 394 TOTAL ENERGY = -79.6426 RDTITL> * VAN DER WAALS = -32.3328 ELECTROSTATIC = -47.3099 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "394" Parameter: CONF_N -> "8002" Comparing "394" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "395" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763275 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769087 ATOM PAIRS WERE FOUND FOR ATOM LIST 42171 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29819 from a total of 769087 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 395 -75.63526 -4.00738 0.63078 INTE EXTERN> -31.38085 -44.25442 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6353" Parameter: A <- "-75.6353" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3808" Parameter: B <- "-31.3808" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2544" Parameter: C <- "-44.2544" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 395 TOTAL ENERGY = -75.6353 RDTITL> * VAN DER WAALS = -31.3808 ELECTROSTATIC = -44.2544 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "395" Parameter: CONF_N -> "8002" Comparing "395" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "396" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769087 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769719 ATOM PAIRS WERE FOUND FOR ATOM LIST 42249 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29757 from a total of 769719 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 396 -77.68206 2.04679 0.63403 INTE EXTERN> -31.77636 -45.90569 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6821" Parameter: A <- "-77.6821" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7764" Parameter: B <- "-31.7764" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9057" Parameter: C <- "-45.9057" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 396 TOTAL ENERGY = -77.6821 RDTITL> * VAN DER WAALS = -31.7764 ELECTROSTATIC = -45.9057 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "396" Parameter: CONF_N -> "8002" Comparing "396" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "397" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769719 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768170 ATOM PAIRS WERE FOUND FOR ATOM LIST 42284 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29489 from a total of 768170 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 397 -82.44037 4.75831 0.70403 INTE EXTERN> -27.54830 -54.89207 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.4404" Parameter: A <- "-82.4404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5483" Parameter: B <- "-27.5483" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8921" Parameter: C <- "-54.8921" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 397 TOTAL ENERGY = -82.4404 RDTITL> * VAN DER WAALS = -27.5483 ELECTROSTATIC = -54.8921 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "397" Parameter: CONF_N -> "8002" Comparing "397" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "398" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768170 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759792 ATOM PAIRS WERE FOUND FOR ATOM LIST 41771 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29081 from a total of 759792 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 398 -74.69249 -7.74788 0.67289 INTE EXTERN> -29.87550 -44.81700 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6925" Parameter: A <- "-74.6925" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8755" Parameter: B <- "-29.8755" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.817" Parameter: C <- "-44.817" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 398 TOTAL ENERGY = -74.6925 RDTITL> * VAN DER WAALS = -29.8755 ELECTROSTATIC = -44.817 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "398" Parameter: CONF_N -> "8002" Comparing "398" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "399" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759792 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762069 ATOM PAIRS WERE FOUND FOR ATOM LIST 41861 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29488 from a total of 762069 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 399 -71.88453 -2.80796 0.77040 INTE EXTERN> -25.92636 -45.95817 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8845" Parameter: A <- "-71.8845" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9264" Parameter: B <- "-25.9264" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9582" Parameter: C <- "-45.9582" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 399 TOTAL ENERGY = -71.8845 RDTITL> * VAN DER WAALS = -25.9264 ELECTROSTATIC = -45.9582 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "399" Parameter: CONF_N -> "8002" Comparing "399" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "400" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762069 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767119 ATOM PAIRS WERE FOUND FOR ATOM LIST 42264 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29515 from a total of 767119 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 400 -85.25199 13.36747 0.72799 INTE EXTERN> -28.25944 -56.99256 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.252" Parameter: A <- "-85.252" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2594" Parameter: B <- "-28.2594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.9926" Parameter: C <- "-56.9926" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 400 TOTAL ENERGY = -85.252 RDTITL> * VAN DER WAALS = -28.2594 ELECTROSTATIC = -56.9926 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "400" Parameter: CONF_N -> "8002" Comparing "400" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "401" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767119 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762832 ATOM PAIRS WERE FOUND FOR ATOM LIST 42117 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29420 from a total of 762832 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 401 -89.12413 3.87214 0.71527 INTE EXTERN> -30.01426 -59.10987 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-89.1241" Parameter: A <- "-89.1241" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0143" Parameter: B <- "-30.0143" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.1099" Parameter: C <- "-59.1099" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 401 TOTAL ENERGY = -89.1241 RDTITL> * VAN DER WAALS = -30.0143 ELECTROSTATIC = -59.1099 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "401" Parameter: CONF_N -> "8002" Comparing "401" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "402" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762832 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766847 ATOM PAIRS WERE FOUND FOR ATOM LIST 42176 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29579 from a total of 766847 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 402 -74.45987 -14.66426 0.68615 INTE EXTERN> -28.85678 -45.60309 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4599" Parameter: A <- "-74.4599" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8568" Parameter: B <- "-28.8568" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6031" Parameter: C <- "-45.6031" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 402 TOTAL ENERGY = -74.4599 RDTITL> * VAN DER WAALS = -28.8568 ELECTROSTATIC = -45.6031 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "402" Parameter: CONF_N -> "8002" Comparing "402" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "403" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766847 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765917 ATOM PAIRS WERE FOUND FOR ATOM LIST 42183 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29957 from a total of 765917 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 403 -72.83588 -1.62398 0.63065 INTE EXTERN> -31.02025 -41.81563 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8359" Parameter: A <- "-72.8359" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0203" Parameter: B <- "-31.0203" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8156" Parameter: C <- "-41.8156" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 403 TOTAL ENERGY = -72.8359 RDTITL> * VAN DER WAALS = -31.0203 ELECTROSTATIC = -41.8156 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "403" Parameter: CONF_N -> "8002" Comparing "403" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "404" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765917 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766473 ATOM PAIRS WERE FOUND FOR ATOM LIST 42197 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29680 from a total of 766473 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 404 -71.67981 -1.15607 0.61886 INTE EXTERN> -32.50317 -39.17664 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6798" Parameter: A <- "-71.6798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5032" Parameter: B <- "-32.5032" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1766" Parameter: C <- "-39.1766" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 404 TOTAL ENERGY = -71.6798 RDTITL> * VAN DER WAALS = -32.5032 ELECTROSTATIC = -39.1766 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "404" Parameter: CONF_N -> "8002" Comparing "404" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "405" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766473 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762834 ATOM PAIRS WERE FOUND FOR ATOM LIST 42169 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29371 from a total of 762834 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 405 -76.84945 5.16964 0.59657 INTE EXTERN> -32.74652 -44.10293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8495" Parameter: A <- "-76.8495" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7465" Parameter: B <- "-32.7465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1029" Parameter: C <- "-44.1029" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 405 TOTAL ENERGY = -76.8495 RDTITL> * VAN DER WAALS = -32.7465 ELECTROSTATIC = -44.1029 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "405" Parameter: CONF_N -> "8002" Comparing "405" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "406" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762834 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769957 ATOM PAIRS WERE FOUND FOR ATOM LIST 42494 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29882 from a total of 769957 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 406 -78.61830 1.76885 0.62402 INTE EXTERN> -32.70578 -45.91252 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6183" Parameter: A <- "-78.6183" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7058" Parameter: B <- "-32.7058" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9125" Parameter: C <- "-45.9125" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 406 TOTAL ENERGY = -78.6183 RDTITL> * VAN DER WAALS = -32.7058 ELECTROSTATIC = -45.9125 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "406" Parameter: CONF_N -> "8002" Comparing "406" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "407" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769957 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768832 ATOM PAIRS WERE FOUND FOR ATOM LIST 42435 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29922 from a total of 768832 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 407 -77.06599 -1.55232 0.68028 INTE EXTERN> -30.91042 -46.15557 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.066" Parameter: A <- "-77.066" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9104" Parameter: B <- "-30.9104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1556" Parameter: C <- "-46.1556" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 407 TOTAL ENERGY = -77.066 RDTITL> * VAN DER WAALS = -30.9104 ELECTROSTATIC = -46.1556 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "407" Parameter: CONF_N -> "8002" Comparing "407" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "408" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768832 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769479 ATOM PAIRS WERE FOUND FOR ATOM LIST 42116 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30012 from a total of 769479 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 408 -77.66043 0.59444 0.65045 INTE EXTERN> -33.19707 -44.46337 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6604" Parameter: A <- "-77.6604" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1971" Parameter: B <- "-33.1971" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4634" Parameter: C <- "-44.4634" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 408 TOTAL ENERGY = -77.6604 RDTITL> * VAN DER WAALS = -33.1971 ELECTROSTATIC = -44.4634 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "408" Parameter: CONF_N -> "8002" Comparing "408" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "409" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769479 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766604 ATOM PAIRS WERE FOUND FOR ATOM LIST 42333 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29477 from a total of 766604 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 409 -70.74451 -6.91593 0.65465 INTE EXTERN> -30.55935 -40.18516 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7445" Parameter: A <- "-70.7445" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5593" Parameter: B <- "-30.5593" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1852" Parameter: C <- "-40.1852" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 409 TOTAL ENERGY = -70.7445 RDTITL> * VAN DER WAALS = -30.5593 ELECTROSTATIC = -40.1852 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "409" Parameter: CONF_N -> "8002" Comparing "409" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "410" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766604 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769654 ATOM PAIRS WERE FOUND FOR ATOM LIST 42283 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29922 from a total of 769654 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 410 -73.35741 2.61291 0.61276 INTE EXTERN> -31.36743 -41.98998 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3574" Parameter: A <- "-73.3574" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3674" Parameter: B <- "-31.3674" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.99" Parameter: C <- "-41.99" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 410 TOTAL ENERGY = -73.3574 RDTITL> * VAN DER WAALS = -31.3674 ELECTROSTATIC = -41.99 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "410" Parameter: CONF_N -> "8002" Comparing "410" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "411" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769654 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766703 ATOM PAIRS WERE FOUND FOR ATOM LIST 42159 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29818 from a total of 766703 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 411 -76.37524 3.01782 0.61490 INTE EXTERN> -32.45713 -43.91810 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3752" Parameter: A <- "-76.3752" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4571" Parameter: B <- "-32.4571" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9181" Parameter: C <- "-43.9181" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 411 TOTAL ENERGY = -76.3752 RDTITL> * VAN DER WAALS = -32.4571 ELECTROSTATIC = -43.9181 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "411" Parameter: CONF_N -> "8002" Comparing "411" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "412" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766703 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765277 ATOM PAIRS WERE FOUND FOR ATOM LIST 42076 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30038 from a total of 765277 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 412 -72.91280 -3.46243 0.58465 INTE EXTERN> -30.72702 -42.18578 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9128" Parameter: A <- "-72.9128" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.727" Parameter: B <- "-30.727" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1858" Parameter: C <- "-42.1858" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 412 TOTAL ENERGY = -72.9128 RDTITL> * VAN DER WAALS = -30.727 ELECTROSTATIC = -42.1858 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "412" Parameter: CONF_N -> "8002" Comparing "412" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "413" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765277 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764787 ATOM PAIRS WERE FOUND FOR ATOM LIST 42053 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29862 from a total of 764787 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 413 -74.33676 1.42396 0.75109 INTE EXTERN> -28.07664 -46.26012 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3368" Parameter: A <- "-74.3368" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0766" Parameter: B <- "-28.0766" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2601" Parameter: C <- "-46.2601" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 413 TOTAL ENERGY = -74.3368 RDTITL> * VAN DER WAALS = -28.0766 ELECTROSTATIC = -46.2601 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "413" Parameter: CONF_N -> "8002" Comparing "413" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "414" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764787 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764870 ATOM PAIRS WERE FOUND FOR ATOM LIST 42038 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29606 from a total of 764870 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 414 -74.05369 -0.28307 0.63327 INTE EXTERN> -30.80913 -43.24456 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0537" Parameter: A <- "-74.0537" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8091" Parameter: B <- "-30.8091" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2446" Parameter: C <- "-43.2446" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 414 TOTAL ENERGY = -74.0537 RDTITL> * VAN DER WAALS = -30.8091 ELECTROSTATIC = -43.2446 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "414" Parameter: CONF_N -> "8002" Comparing "414" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "415" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764870 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768377 ATOM PAIRS WERE FOUND FOR ATOM LIST 42255 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29967 from a total of 768377 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 415 -72.68027 -1.37342 0.67042 INTE EXTERN> -30.35311 -42.32716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6803" Parameter: A <- "-72.6803" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3531" Parameter: B <- "-30.3531" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3272" Parameter: C <- "-42.3272" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 415 TOTAL ENERGY = -72.6803 RDTITL> * VAN DER WAALS = -30.3531 ELECTROSTATIC = -42.3272 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "415" Parameter: CONF_N -> "8002" Comparing "415" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "416" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768377 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765673 ATOM PAIRS WERE FOUND FOR ATOM LIST 42005 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29267 from a total of 765673 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 416 -73.41894 0.73867 0.60323 INTE EXTERN> -31.16547 -42.25347 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4189" Parameter: A <- "-73.4189" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1655" Parameter: B <- "-31.1655" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2535" Parameter: C <- "-42.2535" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 416 TOTAL ENERGY = -73.4189 RDTITL> * VAN DER WAALS = -31.1655 ELECTROSTATIC = -42.2535 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "416" Parameter: CONF_N -> "8002" Comparing "416" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "417" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765673 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768819 ATOM PAIRS WERE FOUND FOR ATOM LIST 42258 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29417 from a total of 768819 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 417 -73.23764 -0.18130 0.53662 INTE EXTERN> -32.90629 -40.33135 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2376" Parameter: A <- "-73.2376" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9063" Parameter: B <- "-32.9063" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3313" Parameter: C <- "-40.3313" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 417 TOTAL ENERGY = -73.2376 RDTITL> * VAN DER WAALS = -32.9063 ELECTROSTATIC = -40.3313 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "417" Parameter: CONF_N -> "8002" Comparing "417" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "418" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768819 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761088 ATOM PAIRS WERE FOUND FOR ATOM LIST 41933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29744 from a total of 761088 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 418 -67.71763 -5.52001 0.56504 INTE EXTERN> -31.18693 -36.53070 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7176" Parameter: A <- "-67.7176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1869" Parameter: B <- "-31.1869" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5307" Parameter: C <- "-36.5307" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 418 TOTAL ENERGY = -67.7176 RDTITL> * VAN DER WAALS = -31.1869 ELECTROSTATIC = -36.5307 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "418" Parameter: CONF_N -> "8002" Comparing "418" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "419" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761088 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763534 ATOM PAIRS WERE FOUND FOR ATOM LIST 42002 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29121 from a total of 763534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 419 -76.42778 8.71015 0.63583 INTE EXTERN> -30.67589 -45.75189 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4278" Parameter: A <- "-76.4278" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6759" Parameter: B <- "-30.6759" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7519" Parameter: C <- "-45.7519" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 419 TOTAL ENERGY = -76.4278 RDTITL> * VAN DER WAALS = -30.6759 ELECTROSTATIC = -45.7519 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "419" Parameter: CONF_N -> "8002" Comparing "419" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "420" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765166 ATOM PAIRS WERE FOUND FOR ATOM LIST 42097 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29156 from a total of 765166 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 420 -74.49482 -1.93296 0.79314 INTE EXTERN> -24.59504 -49.89978 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4948" Parameter: A <- "-74.4948" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.595" Parameter: B <- "-24.595" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8998" Parameter: C <- "-49.8998" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 420 TOTAL ENERGY = -74.4948 RDTITL> * VAN DER WAALS = -24.595 ELECTROSTATIC = -49.8998 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "420" Parameter: CONF_N -> "8002" Comparing "420" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "421" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765166 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768649 ATOM PAIRS WERE FOUND FOR ATOM LIST 41956 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29791 from a total of 768649 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 421 -71.18599 -3.30883 0.65848 INTE EXTERN> -30.19677 -40.98922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.186" Parameter: A <- "-71.186" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1968" Parameter: B <- "-30.1968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9892" Parameter: C <- "-40.9892" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 421 TOTAL ENERGY = -71.186 RDTITL> * VAN DER WAALS = -30.1968 ELECTROSTATIC = -40.9892 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "421" Parameter: CONF_N -> "8002" Comparing "421" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "422" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768649 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762136 ATOM PAIRS WERE FOUND FOR ATOM LIST 41769 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29193 from a total of 762136 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 422 -70.99954 -0.18645 0.69539 INTE EXTERN> -25.37444 -45.62510 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9995" Parameter: A <- "-70.9995" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3744" Parameter: B <- "-25.3744" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6251" Parameter: C <- "-45.6251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 422 TOTAL ENERGY = -70.9995 RDTITL> * VAN DER WAALS = -25.3744 ELECTROSTATIC = -45.6251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "422" Parameter: CONF_N -> "8002" Comparing "422" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "423" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762136 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759457 ATOM PAIRS WERE FOUND FOR ATOM LIST 41685 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29190 from a total of 759457 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 423 -74.98692 3.98737 0.61836 INTE EXTERN> -31.05460 -43.93232 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9869" Parameter: A <- "-74.9869" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0546" Parameter: B <- "-31.0546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9323" Parameter: C <- "-43.9323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 423 TOTAL ENERGY = -74.9869 RDTITL> * VAN DER WAALS = -31.0546 ELECTROSTATIC = -43.9323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "423" Parameter: CONF_N -> "8002" Comparing "423" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "424" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759457 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764526 ATOM PAIRS WERE FOUND FOR ATOM LIST 42082 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29232 from a total of 764526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 424 -79.94110 4.95418 0.76380 INTE EXTERN> -25.84892 -54.09218 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9411" Parameter: A <- "-79.9411" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8489" Parameter: B <- "-25.8489" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0922" Parameter: C <- "-54.0922" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 424 TOTAL ENERGY = -79.9411 RDTITL> * VAN DER WAALS = -25.8489 ELECTROSTATIC = -54.0922 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "424" Parameter: CONF_N -> "8002" Comparing "424" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "425" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763359 ATOM PAIRS WERE FOUND FOR ATOM LIST 42000 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29413 from a total of 763359 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 425 -74.73275 -5.20835 0.73723 INTE EXTERN> -27.95287 -46.77988 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7328" Parameter: A <- "-74.7328" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9529" Parameter: B <- "-27.9529" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7799" Parameter: C <- "-46.7799" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 425 TOTAL ENERGY = -74.7328 RDTITL> * VAN DER WAALS = -27.9529 ELECTROSTATIC = -46.7799 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "425" Parameter: CONF_N -> "8002" Comparing "425" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "426" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763359 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763439 ATOM PAIRS WERE FOUND FOR ATOM LIST 41781 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29315 from a total of 763439 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 426 -76.54031 1.80756 0.59675 INTE EXTERN> -34.04733 -42.49298 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5403" Parameter: A <- "-76.5403" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0473" Parameter: B <- "-34.0473" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.493" Parameter: C <- "-42.493" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 426 TOTAL ENERGY = -76.5403 RDTITL> * VAN DER WAALS = -34.0473 ELECTROSTATIC = -42.493 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "426" Parameter: CONF_N -> "8002" Comparing "426" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "427" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763439 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766533 ATOM PAIRS WERE FOUND FOR ATOM LIST 42049 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29489 from a total of 766533 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 427 -75.10194 -1.43837 0.62701 INTE EXTERN> -31.28849 -43.81345 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1019" Parameter: A <- "-75.1019" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2885" Parameter: B <- "-31.2885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8134" Parameter: C <- "-43.8134" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 427 TOTAL ENERGY = -75.1019 RDTITL> * VAN DER WAALS = -31.2885 ELECTROSTATIC = -43.8134 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "427" Parameter: CONF_N -> "8002" Comparing "427" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "428" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766533 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767405 ATOM PAIRS WERE FOUND FOR ATOM LIST 42110 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29630 from a total of 767405 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 428 -71.86747 -3.23447 0.56993 INTE EXTERN> -35.13873 -36.72874 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8675" Parameter: A <- "-71.8675" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.1387" Parameter: B <- "-35.1387" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7287" Parameter: C <- "-36.7287" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 428 TOTAL ENERGY = -71.8675 RDTITL> * VAN DER WAALS = -35.1387 ELECTROSTATIC = -36.7287 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "428" Parameter: CONF_N -> "8002" Comparing "428" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "429" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767405 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766355 ATOM PAIRS WERE FOUND FOR ATOM LIST 41952 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29556 from a total of 766355 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 429 -85.82228 13.95481 0.67551 INTE EXTERN> -30.52767 -55.29461 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.8223" Parameter: A <- "-85.8223" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5277" Parameter: B <- "-30.5277" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.2946" Parameter: C <- "-55.2946" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 429 TOTAL ENERGY = -85.8223 RDTITL> * VAN DER WAALS = -30.5277 ELECTROSTATIC = -55.2946 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "429" Parameter: CONF_N -> "8002" Comparing "429" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "430" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766355 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771645 ATOM PAIRS WERE FOUND FOR ATOM LIST 42584 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30244 from a total of 771645 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 430 -84.21423 -1.60805 0.60460 INTE EXTERN> -35.31025 -48.90398 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.2142" Parameter: A <- "-84.2142" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.3102" Parameter: B <- "-35.3102" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.904" Parameter: C <- "-48.904" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 430 TOTAL ENERGY = -84.2142 RDTITL> * VAN DER WAALS = -35.3102 ELECTROSTATIC = -48.904 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "430" Parameter: CONF_N -> "8002" Comparing "430" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "431" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771645 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763933 ATOM PAIRS WERE FOUND FOR ATOM LIST 42177 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30015 from a total of 763933 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 431 -82.38686 -1.82737 0.65647 INTE EXTERN> -31.77808 -50.60878 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3869" Parameter: A <- "-82.3869" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7781" Parameter: B <- "-31.7781" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6088" Parameter: C <- "-50.6088" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 431 TOTAL ENERGY = -82.3869 RDTITL> * VAN DER WAALS = -31.7781 ELECTROSTATIC = -50.6088 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "431" Parameter: CONF_N -> "8002" Comparing "431" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "432" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763933 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768724 ATOM PAIRS WERE FOUND FOR ATOM LIST 42236 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29689 from a total of 768724 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 432 -83.14037 0.75351 0.64743 INTE EXTERN> -32.35377 -50.78659 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.1404" Parameter: A <- "-83.1404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3538" Parameter: B <- "-32.3538" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7866" Parameter: C <- "-50.7866" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 432 TOTAL ENERGY = -83.1404 RDTITL> * VAN DER WAALS = -32.3538 ELECTROSTATIC = -50.7866 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "432" Parameter: CONF_N -> "8002" Comparing "432" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "433" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768724 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767506 ATOM PAIRS WERE FOUND FOR ATOM LIST 42145 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30235 from a total of 767506 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 433 -90.32777 7.18741 0.72296 INTE EXTERN> -32.26266 -58.06511 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-90.3278" Parameter: A <- "-90.3278" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2627" Parameter: B <- "-32.2627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.0651" Parameter: C <- "-58.0651" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 433 TOTAL ENERGY = -90.3278 RDTITL> * VAN DER WAALS = -32.2627 ELECTROSTATIC = -58.0651 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "433" Parameter: CONF_N -> "8002" Comparing "433" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "434" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767506 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764736 ATOM PAIRS WERE FOUND FOR ATOM LIST 42204 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30123 from a total of 764736 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 434 -82.91107 -7.41670 0.64518 INTE EXTERN> -32.32477 -50.58630 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9111" Parameter: A <- "-82.9111" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3248" Parameter: B <- "-32.3248" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5863" Parameter: C <- "-50.5863" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 434 TOTAL ENERGY = -82.9111 RDTITL> * VAN DER WAALS = -32.3248 ELECTROSTATIC = -50.5863 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "434" Parameter: CONF_N -> "8002" Comparing "434" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "435" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764736 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765693 ATOM PAIRS WERE FOUND FOR ATOM LIST 42231 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30113 from a total of 765693 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 435 -85.50944 2.59836 0.76074 INTE EXTERN> -27.34100 -58.16844 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.5094" Parameter: A <- "-85.5094" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.341" Parameter: B <- "-27.341" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.1684" Parameter: C <- "-58.1684" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 435 TOTAL ENERGY = -85.5094 RDTITL> * VAN DER WAALS = -27.341 ELECTROSTATIC = -58.1684 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "435" Parameter: CONF_N -> "8002" Comparing "435" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "436" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765693 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768403 ATOM PAIRS WERE FOUND FOR ATOM LIST 42138 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29888 from a total of 768403 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 436 -91.03199 5.52255 0.72430 INTE EXTERN> -30.32078 -60.71122 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-91.032" Parameter: A <- "-91.032" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3208" Parameter: B <- "-30.3208" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-60.7112" Parameter: C <- "-60.7112" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 436 TOTAL ENERGY = -91.032 RDTITL> * VAN DER WAALS = -30.3208 ELECTROSTATIC = -60.7112 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "436" Parameter: CONF_N -> "8002" Comparing "436" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "437" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768403 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770297 ATOM PAIRS WERE FOUND FOR ATOM LIST 42254 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30287 from a total of 770297 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 437 -75.17284 -15.85916 0.55743 INTE EXTERN> -34.95063 -40.22220 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1728" Parameter: A <- "-75.1728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9506" Parameter: B <- "-34.9506" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2222" Parameter: C <- "-40.2222" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 437 TOTAL ENERGY = -75.1728 RDTITL> * VAN DER WAALS = -34.9506 ELECTROSTATIC = -40.2222 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "437" Parameter: CONF_N -> "8002" Comparing "437" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "438" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770297 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762490 ATOM PAIRS WERE FOUND FOR ATOM LIST 41910 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29662 from a total of 762490 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 438 -80.22315 5.05031 0.60862 INTE EXTERN> -33.03200 -47.19115 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2232" Parameter: A <- "-80.2232" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.032" Parameter: B <- "-33.032" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1911" Parameter: C <- "-47.1911" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 438 TOTAL ENERGY = -80.2232 RDTITL> * VAN DER WAALS = -33.032 ELECTROSTATIC = -47.1911 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "438" Parameter: CONF_N -> "8002" Comparing "438" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "439" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762490 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769155 ATOM PAIRS WERE FOUND FOR ATOM LIST 42179 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29796 from a total of 769155 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 439 -74.85923 -5.36392 0.61045 INTE EXTERN> -31.94237 -42.91686 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8592" Parameter: A <- "-74.8592" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9424" Parameter: B <- "-31.9424" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9169" Parameter: C <- "-42.9169" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 439 TOTAL ENERGY = -74.8592 RDTITL> * VAN DER WAALS = -31.9424 ELECTROSTATIC = -42.9169 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "439" Parameter: CONF_N -> "8002" Comparing "439" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "440" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769155 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772875 ATOM PAIRS WERE FOUND FOR ATOM LIST 42246 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29318 from a total of 772875 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 440 -81.63077 6.77154 0.72106 INTE EXTERN> -31.91435 -49.71641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6308" Parameter: A <- "-81.6308" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9144" Parameter: B <- "-31.9144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7164" Parameter: C <- "-49.7164" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 440 TOTAL ENERGY = -81.6308 RDTITL> * VAN DER WAALS = -31.9144 ELECTROSTATIC = -49.7164 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "440" Parameter: CONF_N -> "8002" Comparing "440" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "441" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772875 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769968 ATOM PAIRS WERE FOUND FOR ATOM LIST 42410 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29732 from a total of 769968 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 441 -82.46608 0.83532 0.61018 INTE EXTERN> -34.92403 -47.54205 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.4661" Parameter: A <- "-82.4661" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.924" Parameter: B <- "-34.924" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5421" Parameter: C <- "-47.5421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 441 TOTAL ENERGY = -82.4661 RDTITL> * VAN DER WAALS = -34.924 ELECTROSTATIC = -47.5421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "441" Parameter: CONF_N -> "8002" Comparing "441" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "442" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769968 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765049 ATOM PAIRS WERE FOUND FOR ATOM LIST 42156 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29463 from a total of 765049 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 442 -72.70409 -9.76199 0.74087 INTE EXTERN> -27.23507 -45.46903 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7041" Parameter: A <- "-72.7041" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2351" Parameter: B <- "-27.2351" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.469" Parameter: C <- "-45.469" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 442 TOTAL ENERGY = -72.7041 RDTITL> * VAN DER WAALS = -27.2351 ELECTROSTATIC = -45.469 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "442" Parameter: CONF_N -> "8002" Comparing "442" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "443" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765049 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764943 ATOM PAIRS WERE FOUND FOR ATOM LIST 42045 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29500 from a total of 764943 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 443 -76.12446 3.42037 0.56905 INTE EXTERN> -33.48213 -42.64233 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1245" Parameter: A <- "-76.1245" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4821" Parameter: B <- "-33.4821" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6423" Parameter: C <- "-42.6423" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 443 TOTAL ENERGY = -76.1245 RDTITL> * VAN DER WAALS = -33.4821 ELECTROSTATIC = -42.6423 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "443" Parameter: CONF_N -> "8002" Comparing "443" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "444" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764943 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 773397 ATOM PAIRS WERE FOUND FOR ATOM LIST 42352 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29575 from a total of 773397 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 444 -92.59819 16.47373 0.65670 INTE EXTERN> -30.87781 -61.72037 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-92.5982" Parameter: A <- "-92.5982" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8778" Parameter: B <- "-30.8778" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-61.7204" Parameter: C <- "-61.7204" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 444 TOTAL ENERGY = -92.5982 RDTITL> * VAN DER WAALS = -30.8778 ELECTROSTATIC = -61.7204 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "444" Parameter: CONF_N -> "8002" Comparing "444" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "445" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 773397 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764770 ATOM PAIRS WERE FOUND FOR ATOM LIST 42085 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30298 from a total of 764770 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 445 -74.30773 -18.29046 0.66353 INTE EXTERN> -29.22421 -45.08352 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3077" Parameter: A <- "-74.3077" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2242" Parameter: B <- "-29.2242" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0835" Parameter: C <- "-45.0835" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 445 TOTAL ENERGY = -74.3077 RDTITL> * VAN DER WAALS = -29.2242 ELECTROSTATIC = -45.0835 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "445" Parameter: CONF_N -> "8002" Comparing "445" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "446" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764770 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771693 ATOM PAIRS WERE FOUND FOR ATOM LIST 42355 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30023 from a total of 771693 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 446 -87.02044 12.71272 0.62996 INTE EXTERN> -32.23264 -54.78780 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.0204" Parameter: A <- "-87.0204" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2326" Parameter: B <- "-32.2326" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.7878" Parameter: C <- "-54.7878" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 446 TOTAL ENERGY = -87.0204 RDTITL> * VAN DER WAALS = -32.2326 ELECTROSTATIC = -54.7878 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "446" Parameter: CONF_N -> "8002" Comparing "446" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "447" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771693 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767970 ATOM PAIRS WERE FOUND FOR ATOM LIST 42398 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29628 from a total of 767970 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 447 -82.55892 -4.46153 0.71775 INTE EXTERN> -28.24482 -54.31410 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5589" Parameter: A <- "-82.5589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2448" Parameter: B <- "-28.2448" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.3141" Parameter: C <- "-54.3141" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 447 TOTAL ENERGY = -82.5589 RDTITL> * VAN DER WAALS = -28.2448 ELECTROSTATIC = -54.3141 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "447" Parameter: CONF_N -> "8002" Comparing "447" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "448" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767970 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768027 ATOM PAIRS WERE FOUND FOR ATOM LIST 42351 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29721 from a total of 768027 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 448 -92.68648 10.12756 0.65073 INTE EXTERN> -32.72221 -59.96427 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-92.6865" Parameter: A <- "-92.6865" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7222" Parameter: B <- "-32.7222" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.9643" Parameter: C <- "-59.9643" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 448 TOTAL ENERGY = -92.6865 RDTITL> * VAN DER WAALS = -32.7222 ELECTROSTATIC = -59.9643 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "448" Parameter: CONF_N -> "8002" Comparing "448" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "449" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768027 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 773266 ATOM PAIRS WERE FOUND FOR ATOM LIST 42549 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30158 from a total of 773266 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 449 -80.38406 -12.30242 0.73278 INTE EXTERN> -28.73127 -51.65279 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3841" Parameter: A <- "-80.3841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7313" Parameter: B <- "-28.7313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6528" Parameter: C <- "-51.6528" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 449 TOTAL ENERGY = -80.3841 RDTITL> * VAN DER WAALS = -28.7313 ELECTROSTATIC = -51.6528 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "449" Parameter: CONF_N -> "8002" Comparing "449" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "450" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 773266 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767391 ATOM PAIRS WERE FOUND FOR ATOM LIST 42317 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29758 from a total of 767391 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 450 -83.28881 2.90475 0.60215 INTE EXTERN> -33.54817 -49.74064 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.2888" Parameter: A <- "-83.2888" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5482" Parameter: B <- "-33.5482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7406" Parameter: C <- "-49.7406" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 450 TOTAL ENERGY = -83.2888 RDTITL> * VAN DER WAALS = -33.5482 ELECTROSTATIC = -49.7406 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "450" Parameter: CONF_N -> "8002" Comparing "450" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "451" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767391 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771321 ATOM PAIRS WERE FOUND FOR ATOM LIST 42461 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30046 from a total of 771321 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 451 -90.82199 7.53318 0.63345 INTE EXTERN> -31.30855 -59.51344 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-90.822" Parameter: A <- "-90.822" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3086" Parameter: B <- "-31.3086" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.5134" Parameter: C <- "-59.5134" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 451 TOTAL ENERGY = -90.822 RDTITL> * VAN DER WAALS = -31.3086 ELECTROSTATIC = -59.5134 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "451" Parameter: CONF_N -> "8002" Comparing "451" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "452" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771321 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772621 ATOM PAIRS WERE FOUND FOR ATOM LIST 42552 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29353 from a total of 772621 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 452 -82.13137 -8.69062 0.64200 INTE EXTERN> -32.34120 -49.79017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.1314" Parameter: A <- "-82.1314" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3412" Parameter: B <- "-32.3412" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7902" Parameter: C <- "-49.7902" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 452 TOTAL ENERGY = -82.1314 RDTITL> * VAN DER WAALS = -32.3412 ELECTROSTATIC = -49.7902 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "452" Parameter: CONF_N -> "8002" Comparing "452" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "453" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772621 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771291 ATOM PAIRS WERE FOUND FOR ATOM LIST 42333 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29640 from a total of 771291 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 453 -78.85898 -3.27239 0.56313 INTE EXTERN> -35.10388 -43.75510 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.859" Parameter: A <- "-78.859" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.1039" Parameter: B <- "-35.1039" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7551" Parameter: C <- "-43.7551" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 453 TOTAL ENERGY = -78.859 RDTITL> * VAN DER WAALS = -35.1039 ELECTROSTATIC = -43.7551 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "453" Parameter: CONF_N -> "8002" Comparing "453" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "454" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771291 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 773002 ATOM PAIRS WERE FOUND FOR ATOM LIST 42295 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29889 from a total of 773002 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 454 -83.58579 4.72681 0.60871 INTE EXTERN> -35.37711 -48.20868 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.5858" Parameter: A <- "-83.5858" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.3771" Parameter: B <- "-35.3771" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2087" Parameter: C <- "-48.2087" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 454 TOTAL ENERGY = -83.5858 RDTITL> * VAN DER WAALS = -35.3771 ELECTROSTATIC = -48.2087 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "454" Parameter: CONF_N -> "8002" Comparing "454" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "455" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 773002 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769352 ATOM PAIRS WERE FOUND FOR ATOM LIST 42232 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29872 from a total of 769352 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 455 -77.71301 -5.87278 0.72293 INTE EXTERN> -27.57341 -50.13959 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.713" Parameter: A <- "-77.713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5734" Parameter: B <- "-27.5734" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1396" Parameter: C <- "-50.1396" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 455 TOTAL ENERGY = -77.713 RDTITL> * VAN DER WAALS = -27.5734 ELECTROSTATIC = -50.1396 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "455" Parameter: CONF_N -> "8002" Comparing "455" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "456" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769352 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770490 ATOM PAIRS WERE FOUND FOR ATOM LIST 42171 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29665 from a total of 770490 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 456 -71.88030 -5.83270 0.84177 INTE EXTERN> -25.08948 -46.79083 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8803" Parameter: A <- "-71.8803" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0895" Parameter: B <- "-25.0895" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7908" Parameter: C <- "-46.7908" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 456 TOTAL ENERGY = -71.8803 RDTITL> * VAN DER WAALS = -25.0895 ELECTROSTATIC = -46.7908 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "456" Parameter: CONF_N -> "8002" Comparing "456" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "457" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770490 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767774 ATOM PAIRS WERE FOUND FOR ATOM LIST 42145 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29757 from a total of 767774 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 457 -78.72255 6.84224 0.74602 INTE EXTERN> -27.73375 -50.98879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7225" Parameter: A <- "-78.7225" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7338" Parameter: B <- "-27.7338" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9888" Parameter: C <- "-50.9888" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 457 TOTAL ENERGY = -78.7225 RDTITL> * VAN DER WAALS = -27.7338 ELECTROSTATIC = -50.9888 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "457" Parameter: CONF_N -> "8002" Comparing "457" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "458" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767774 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768906 ATOM PAIRS WERE FOUND FOR ATOM LIST 42238 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30576 from a total of 768906 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 458 -80.23601 1.51346 0.60068 INTE EXTERN> -32.49488 -47.74113 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.236" Parameter: A <- "-80.236" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4949" Parameter: B <- "-32.4949" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7411" Parameter: C <- "-47.7411" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 458 TOTAL ENERGY = -80.236 RDTITL> * VAN DER WAALS = -32.4949 ELECTROSTATIC = -47.7411 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "458" Parameter: CONF_N -> "8002" Comparing "458" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "459" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768906 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764978 ATOM PAIRS WERE FOUND FOR ATOM LIST 42107 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29975 from a total of 764978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 459 -80.44136 0.20535 0.69300 INTE EXTERN> -29.40663 -51.03472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4414" Parameter: A <- "-80.4414" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4066" Parameter: B <- "-29.4066" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0347" Parameter: C <- "-51.0347" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 459 TOTAL ENERGY = -80.4414 RDTITL> * VAN DER WAALS = -29.4066 ELECTROSTATIC = -51.0347 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "459" Parameter: CONF_N -> "8002" Comparing "459" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "460" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768375 ATOM PAIRS WERE FOUND FOR ATOM LIST 42298 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29774 from a total of 768375 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 460 -83.21262 2.77126 0.64959 INTE EXTERN> -31.92827 -51.28435 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.2126" Parameter: A <- "-83.2126" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9283" Parameter: B <- "-31.9283" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2843" Parameter: C <- "-51.2843" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 460 TOTAL ENERGY = -83.2126 RDTITL> * VAN DER WAALS = -31.9283 ELECTROSTATIC = -51.2843 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "460" Parameter: CONF_N -> "8002" Comparing "460" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "461" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768375 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766317 ATOM PAIRS WERE FOUND FOR ATOM LIST 42086 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29176 from a total of 766317 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 461 -77.36702 -5.84559 0.61973 INTE EXTERN> -32.92812 -44.43890 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.367" Parameter: A <- "-77.367" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9281" Parameter: B <- "-32.9281" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4389" Parameter: C <- "-44.4389" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 461 TOTAL ENERGY = -77.367 RDTITL> * VAN DER WAALS = -32.9281 ELECTROSTATIC = -44.4389 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "461" Parameter: CONF_N -> "8002" Comparing "461" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "462" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766317 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763744 ATOM PAIRS WERE FOUND FOR ATOM LIST 41782 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29344 from a total of 763744 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 462 -78.11300 0.74598 0.73246 INTE EXTERN> -29.43778 -48.67522 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.113" Parameter: A <- "-78.113" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4378" Parameter: B <- "-29.4378" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6752" Parameter: C <- "-48.6752" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 462 TOTAL ENERGY = -78.113 RDTITL> * VAN DER WAALS = -29.4378 ELECTROSTATIC = -48.6752 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "462" Parameter: CONF_N -> "8002" Comparing "462" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "463" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763744 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764890 ATOM PAIRS WERE FOUND FOR ATOM LIST 42246 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29184 from a total of 764890 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 463 -83.13587 5.02287 0.64374 INTE EXTERN> -33.63851 -49.49735 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.1359" Parameter: A <- "-83.1359" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6385" Parameter: B <- "-33.6385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4974" Parameter: C <- "-49.4974" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 463 TOTAL ENERGY = -83.1359 RDTITL> * VAN DER WAALS = -33.6385 ELECTROSTATIC = -49.4974 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "463" Parameter: CONF_N -> "8002" Comparing "463" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "464" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764890 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763374 ATOM PAIRS WERE FOUND FOR ATOM LIST 42094 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29212 from a total of 763374 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 464 -68.99913 -14.13674 0.72137 INTE EXTERN> -27.14396 -41.85517 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9991" Parameter: A <- "-68.9991" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.144" Parameter: B <- "-27.144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8552" Parameter: C <- "-41.8552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 464 TOTAL ENERGY = -68.9991 RDTITL> * VAN DER WAALS = -27.144 ELECTROSTATIC = -41.8552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "464" Parameter: CONF_N -> "8002" Comparing "464" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "465" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763374 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764032 ATOM PAIRS WERE FOUND FOR ATOM LIST 41965 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29988 from a total of 764032 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 465 -68.16746 -0.83166 0.71439 INTE EXTERN> -25.79832 -42.36914 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1675" Parameter: A <- "-68.1675" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7983" Parameter: B <- "-25.7983" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3691" Parameter: C <- "-42.3691" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 465 TOTAL ENERGY = -68.1675 RDTITL> * VAN DER WAALS = -25.7983 ELECTROSTATIC = -42.3691 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "465" Parameter: CONF_N -> "8002" Comparing "465" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "466" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764032 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763210 ATOM PAIRS WERE FOUND FOR ATOM LIST 41952 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28698 from a total of 763210 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 466 -69.43809 1.27063 0.56321 INTE EXTERN> -31.79993 -37.63817 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4381" Parameter: A <- "-69.4381" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7999" Parameter: B <- "-31.7999" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6382" Parameter: C <- "-37.6382" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 466 TOTAL ENERGY = -69.4381 RDTITL> * VAN DER WAALS = -31.7999 ELECTROSTATIC = -37.6382 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "466" Parameter: CONF_N -> "8002" Comparing "466" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "467" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763210 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764654 ATOM PAIRS WERE FOUND FOR ATOM LIST 42195 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28872 from a total of 764654 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 467 -71.03490 1.59680 0.78165 INTE EXTERN> -27.21574 -43.81916 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0349" Parameter: A <- "-71.0349" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2157" Parameter: B <- "-27.2157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8192" Parameter: C <- "-43.8192" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 467 TOTAL ENERGY = -71.0349 RDTITL> * VAN DER WAALS = -27.2157 ELECTROSTATIC = -43.8192 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "467" Parameter: CONF_N -> "8002" Comparing "467" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "468" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764654 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763338 ATOM PAIRS WERE FOUND FOR ATOM LIST 41891 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28704 from a total of 763338 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 468 -65.57691 -5.45798 0.66698 INTE EXTERN> -26.18856 -39.38835 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5769" Parameter: A <- "-65.5769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1886" Parameter: B <- "-26.1886" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3884" Parameter: C <- "-39.3884" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 468 TOTAL ENERGY = -65.5769 RDTITL> * VAN DER WAALS = -26.1886 ELECTROSTATIC = -39.3884 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "468" Parameter: CONF_N -> "8002" Comparing "468" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "469" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763338 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764506 ATOM PAIRS WERE FOUND FOR ATOM LIST 41919 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29728 from a total of 764506 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 469 -81.23100 15.65409 0.65357 INTE EXTERN> -29.75110 -51.47991 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.231" Parameter: A <- "-81.231" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7511" Parameter: B <- "-29.7511" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4799" Parameter: C <- "-51.4799" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 469 TOTAL ENERGY = -81.231 RDTITL> * VAN DER WAALS = -29.7511 ELECTROSTATIC = -51.4799 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "469" Parameter: CONF_N -> "8002" Comparing "469" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "470" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764506 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762355 ATOM PAIRS WERE FOUND FOR ATOM LIST 41826 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29677 from a total of 762355 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 470 -69.39151 -11.83949 0.63171 INTE EXTERN> -28.56737 -40.82414 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3915" Parameter: A <- "-69.3915" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5674" Parameter: B <- "-28.5674" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8241" Parameter: C <- "-40.8241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 470 TOTAL ENERGY = -69.3915 RDTITL> * VAN DER WAALS = -28.5674 ELECTROSTATIC = -40.8241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "470" Parameter: CONF_N -> "8002" Comparing "470" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "471" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762355 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764099 ATOM PAIRS WERE FOUND FOR ATOM LIST 41983 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29226 from a total of 764099 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 471 -66.33031 -3.06120 0.72937 INTE EXTERN> -26.29831 -40.03200 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3303" Parameter: A <- "-66.3303" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2983" Parameter: B <- "-26.2983" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.032" Parameter: C <- "-40.032" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 471 TOTAL ENERGY = -66.3303 RDTITL> * VAN DER WAALS = -26.2983 ELECTROSTATIC = -40.032 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "471" Parameter: CONF_N -> "8002" Comparing "471" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "472" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764099 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766031 ATOM PAIRS WERE FOUND FOR ATOM LIST 42068 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29471 from a total of 766031 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 472 -68.22954 1.89923 0.56303 INTE EXTERN> -30.85395 -37.37559 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2295" Parameter: A <- "-68.2295" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8539" Parameter: B <- "-30.8539" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3756" Parameter: C <- "-37.3756" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 472 TOTAL ENERGY = -68.2295 RDTITL> * VAN DER WAALS = -30.8539 ELECTROSTATIC = -37.3756 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "472" Parameter: CONF_N -> "8002" Comparing "472" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "473" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766031 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766509 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29760 from a total of 766509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 473 -61.52799 -6.70155 0.66088 INTE EXTERN> -28.57361 -32.95438 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.528" Parameter: A <- "-61.528" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5736" Parameter: B <- "-28.5736" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.9544" Parameter: C <- "-32.9544" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 473 TOTAL ENERGY = -61.528 RDTITL> * VAN DER WAALS = -28.5736 ELECTROSTATIC = -32.9544 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "473" Parameter: CONF_N -> "8002" Comparing "473" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "474" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764037 ATOM PAIRS WERE FOUND FOR ATOM LIST 41978 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29611 from a total of 764037 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 474 -69.63824 8.11025 0.56238 INTE EXTERN> -33.41401 -36.22424 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6382" Parameter: A <- "-69.6382" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.414" Parameter: B <- "-33.414" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2242" Parameter: C <- "-36.2242" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 474 TOTAL ENERGY = -69.6382 RDTITL> * VAN DER WAALS = -33.414 ELECTROSTATIC = -36.2242 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "474" Parameter: CONF_N -> "8002" Comparing "474" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "475" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764037 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771822 ATOM PAIRS WERE FOUND FOR ATOM LIST 42172 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29242 from a total of 771822 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 475 -71.38075 1.74250 0.63484 INTE EXTERN> -30.31776 -41.06298 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3807" Parameter: A <- "-71.3807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3178" Parameter: B <- "-30.3178" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.063" Parameter: C <- "-41.063" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 475 TOTAL ENERGY = -71.3807 RDTITL> * VAN DER WAALS = -30.3178 ELECTROSTATIC = -41.063 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "475" Parameter: CONF_N -> "8002" Comparing "475" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "476" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771822 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767571 ATOM PAIRS WERE FOUND FOR ATOM LIST 42158 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29622 from a total of 767571 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 476 -73.51087 2.13012 0.60621 INTE EXTERN> -31.45480 -42.05606 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5109" Parameter: A <- "-73.5109" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4548" Parameter: B <- "-31.4548" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0561" Parameter: C <- "-42.0561" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 476 TOTAL ENERGY = -73.5109 RDTITL> * VAN DER WAALS = -31.4548 ELECTROSTATIC = -42.0561 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "476" Parameter: CONF_N -> "8002" Comparing "476" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "477" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767571 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762417 ATOM PAIRS WERE FOUND FOR ATOM LIST 41926 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29622 from a total of 762417 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 477 -67.52562 -5.98525 0.63075 INTE EXTERN> -30.94778 -36.57784 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5256" Parameter: A <- "-67.5256" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9478" Parameter: B <- "-30.9478" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5778" Parameter: C <- "-36.5778" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 477 TOTAL ENERGY = -67.5256 RDTITL> * VAN DER WAALS = -30.9478 ELECTROSTATIC = -36.5778 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "477" Parameter: CONF_N -> "8002" Comparing "477" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "478" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762417 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 773164 ATOM PAIRS WERE FOUND FOR ATOM LIST 42237 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30051 from a total of 773164 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 478 -66.81799 -0.70763 0.65086 INTE EXTERN> -30.03725 -36.78073 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.818" Parameter: A <- "-66.818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0373" Parameter: B <- "-30.0373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7807" Parameter: C <- "-36.7807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 478 TOTAL ENERGY = -66.818 RDTITL> * VAN DER WAALS = -30.0373 ELECTROSTATIC = -36.7807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "478" Parameter: CONF_N -> "8002" Comparing "478" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "479" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 773164 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768054 ATOM PAIRS WERE FOUND FOR ATOM LIST 42135 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29849 from a total of 768054 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 479 -75.86684 9.04886 0.65634 INTE EXTERN> -29.99501 -45.87184 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8668" Parameter: A <- "-75.8668" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.995" Parameter: B <- "-29.995" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8718" Parameter: C <- "-45.8718" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 479 TOTAL ENERGY = -75.8668 RDTITL> * VAN DER WAALS = -29.995 ELECTROSTATIC = -45.8718 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "479" Parameter: CONF_N -> "8002" Comparing "479" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "480" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768054 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766040 ATOM PAIRS WERE FOUND FOR ATOM LIST 42119 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29663 from a total of 766040 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 480 -78.14732 2.28048 0.66641 INTE EXTERN> -31.01492 -47.13240 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1473" Parameter: A <- "-78.1473" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0149" Parameter: B <- "-31.0149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1324" Parameter: C <- "-47.1324" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 480 TOTAL ENERGY = -78.1473 RDTITL> * VAN DER WAALS = -31.0149 ELECTROSTATIC = -47.1324 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "480" Parameter: CONF_N -> "8002" Comparing "480" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "481" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766040 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768377 ATOM PAIRS WERE FOUND FOR ATOM LIST 42270 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30298 from a total of 768377 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 481 -73.95887 -4.18845 0.55544 INTE EXTERN> -35.04581 -38.91306 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9589" Parameter: A <- "-73.9589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.0458" Parameter: B <- "-35.0458" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9131" Parameter: C <- "-38.9131" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 481 TOTAL ENERGY = -73.9589 RDTITL> * VAN DER WAALS = -35.0458 ELECTROSTATIC = -38.9131 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "481" Parameter: CONF_N -> "8002" Comparing "481" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "482" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768377 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 773021 ATOM PAIRS WERE FOUND FOR ATOM LIST 42159 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29721 from a total of 773021 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 482 -73.14093 -0.81794 0.62760 INTE EXTERN> -31.73919 -41.40174 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1409" Parameter: A <- "-73.1409" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7392" Parameter: B <- "-31.7392" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4017" Parameter: C <- "-41.4017" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 482 TOTAL ENERGY = -73.1409 RDTITL> * VAN DER WAALS = -31.7392 ELECTROSTATIC = -41.4017 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "482" Parameter: CONF_N -> "8002" Comparing "482" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "483" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 773021 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 773260 ATOM PAIRS WERE FOUND FOR ATOM LIST 42326 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29582 from a total of 773260 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 483 -75.80108 2.66015 0.71279 INTE EXTERN> -26.76654 -49.03454 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8011" Parameter: A <- "-75.8011" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7665" Parameter: B <- "-26.7665" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0345" Parameter: C <- "-49.0345" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 483 TOTAL ENERGY = -75.8011 RDTITL> * VAN DER WAALS = -26.7665 ELECTROSTATIC = -49.0345 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "483" Parameter: CONF_N -> "8002" Comparing "483" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "484" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 773260 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762991 ATOM PAIRS WERE FOUND FOR ATOM LIST 41813 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29405 from a total of 762991 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 484 -73.03653 -2.76455 0.71139 INTE EXTERN> -27.68959 -45.34694 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0365" Parameter: A <- "-73.0365" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6896" Parameter: B <- "-27.6896" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3469" Parameter: C <- "-45.3469" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 484 TOTAL ENERGY = -73.0365 RDTITL> * VAN DER WAALS = -27.6896 ELECTROSTATIC = -45.3469 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "484" Parameter: CONF_N -> "8002" Comparing "484" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "485" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762991 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769058 ATOM PAIRS WERE FOUND FOR ATOM LIST 42278 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29876 from a total of 769058 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 485 -78.52318 5.48665 0.75016 INTE EXTERN> -27.35513 -51.16805 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5232" Parameter: A <- "-78.5232" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3551" Parameter: B <- "-27.3551" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1681" Parameter: C <- "-51.1681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 485 TOTAL ENERGY = -78.5232 RDTITL> * VAN DER WAALS = -27.3551 ELECTROSTATIC = -51.1681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "485" Parameter: CONF_N -> "8002" Comparing "485" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "486" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769058 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768250 ATOM PAIRS WERE FOUND FOR ATOM LIST 42161 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29585 from a total of 768250 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 486 -85.11808 6.59490 0.71579 INTE EXTERN> -26.78121 -58.33688 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.1181" Parameter: A <- "-85.1181" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7812" Parameter: B <- "-26.7812" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.3369" Parameter: C <- "-58.3369" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 486 TOTAL ENERGY = -85.1181 RDTITL> * VAN DER WAALS = -26.7812 ELECTROSTATIC = -58.3369 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "486" Parameter: CONF_N -> "8002" Comparing "486" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "487" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768250 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772920 ATOM PAIRS WERE FOUND FOR ATOM LIST 42412 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29793 from a total of 772920 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 487 -77.05983 -8.05826 0.63355 INTE EXTERN> -30.06924 -46.99059 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0598" Parameter: A <- "-77.0598" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0692" Parameter: B <- "-30.0692" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9906" Parameter: C <- "-46.9906" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 487 TOTAL ENERGY = -77.0598 RDTITL> * VAN DER WAALS = -30.0692 ELECTROSTATIC = -46.9906 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "487" Parameter: CONF_N -> "8002" Comparing "487" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "488" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772920 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 775799 ATOM PAIRS WERE FOUND FOR ATOM LIST 42633 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30225 from a total of 775799 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 488 -77.59835 0.53852 0.62559 INTE EXTERN> -29.92583 -47.67252 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5983" Parameter: A <- "-77.5983" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9258" Parameter: B <- "-29.9258" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6725" Parameter: C <- "-47.6725" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 488 TOTAL ENERGY = -77.5983 RDTITL> * VAN DER WAALS = -29.9258 ELECTROSTATIC = -47.6725 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "488" Parameter: CONF_N -> "8002" Comparing "488" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "489" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 775799 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770276 ATOM PAIRS WERE FOUND FOR ATOM LIST 42254 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30082 from a total of 770276 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 489 -71.28952 -6.30883 0.57050 INTE EXTERN> -32.27886 -39.01066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2895" Parameter: A <- "-71.2895" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2789" Parameter: B <- "-32.2789" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0107" Parameter: C <- "-39.0107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 489 TOTAL ENERGY = -71.2895 RDTITL> * VAN DER WAALS = -32.2789 ELECTROSTATIC = -39.0107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "489" Parameter: CONF_N -> "8002" Comparing "489" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "490" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770276 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771381 ATOM PAIRS WERE FOUND FOR ATOM LIST 42317 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29709 from a total of 771381 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 490 -74.24655 2.95703 0.59328 INTE EXTERN> -30.28196 -43.96458 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2465" Parameter: A <- "-74.2465" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.282" Parameter: B <- "-30.282" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9646" Parameter: C <- "-43.9646" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 490 TOTAL ENERGY = -74.2465 RDTITL> * VAN DER WAALS = -30.282 ELECTROSTATIC = -43.9646 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "490" Parameter: CONF_N -> "8002" Comparing "490" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "491" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771381 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767872 ATOM PAIRS WERE FOUND FOR ATOM LIST 42255 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30282 from a total of 767872 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 491 -79.73384 5.48729 0.66911 INTE EXTERN> -30.89462 -48.83922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7338" Parameter: A <- "-79.7338" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8946" Parameter: B <- "-30.8946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8392" Parameter: C <- "-48.8392" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 491 TOTAL ENERGY = -79.7338 RDTITL> * VAN DER WAALS = -30.8946 ELECTROSTATIC = -48.8392 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "491" Parameter: CONF_N -> "8002" Comparing "491" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "492" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767872 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770130 ATOM PAIRS WERE FOUND FOR ATOM LIST 42398 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29555 from a total of 770130 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 492 -74.86100 -4.87284 0.58431 INTE EXTERN> -34.12594 -40.73506 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.861" Parameter: A <- "-74.861" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1259" Parameter: B <- "-34.1259" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7351" Parameter: C <- "-40.7351" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 492 TOTAL ENERGY = -74.861 RDTITL> * VAN DER WAALS = -34.1259 ELECTROSTATIC = -40.7351 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "492" Parameter: CONF_N -> "8002" Comparing "492" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "493" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770130 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765366 ATOM PAIRS WERE FOUND FOR ATOM LIST 42123 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29728 from a total of 765366 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 493 -78.95660 4.09559 0.57588 INTE EXTERN> -33.11131 -45.84528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9566" Parameter: A <- "-78.9566" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1113" Parameter: B <- "-33.1113" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8453" Parameter: C <- "-45.8453" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 493 TOTAL ENERGY = -78.9566 RDTITL> * VAN DER WAALS = -33.1113 ELECTROSTATIC = -45.8453 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "493" Parameter: CONF_N -> "8002" Comparing "493" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "494" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765366 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765787 ATOM PAIRS WERE FOUND FOR ATOM LIST 42092 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29831 from a total of 765787 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 494 -71.89435 -7.06225 0.57468 INTE EXTERN> -31.24569 -40.64866 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8944" Parameter: A <- "-71.8944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2457" Parameter: B <- "-31.2457" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6487" Parameter: C <- "-40.6487" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 494 TOTAL ENERGY = -71.8944 RDTITL> * VAN DER WAALS = -31.2457 ELECTROSTATIC = -40.6487 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "494" Parameter: CONF_N -> "8002" Comparing "494" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "495" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765787 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771373 ATOM PAIRS WERE FOUND FOR ATOM LIST 42365 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30279 from a total of 771373 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 495 -77.91302 6.01867 0.88567 INTE EXTERN> -24.50739 -53.40563 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.913" Parameter: A <- "-77.913" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5074" Parameter: B <- "-24.5074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4056" Parameter: C <- "-53.4056" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 495 TOTAL ENERGY = -77.913 RDTITL> * VAN DER WAALS = -24.5074 ELECTROSTATIC = -53.4056 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "495" Parameter: CONF_N -> "8002" Comparing "495" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "496" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771373 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770437 ATOM PAIRS WERE FOUND FOR ATOM LIST 42084 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30149 from a total of 770437 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 496 -76.68688 -1.22614 0.60614 INTE EXTERN> -33.42579 -43.26108 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6869" Parameter: A <- "-76.6869" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4258" Parameter: B <- "-33.4258" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2611" Parameter: C <- "-43.2611" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 496 TOTAL ENERGY = -76.6869 RDTITL> * VAN DER WAALS = -33.4258 ELECTROSTATIC = -43.2611 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "496" Parameter: CONF_N -> "8002" Comparing "496" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "497" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770437 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767752 ATOM PAIRS WERE FOUND FOR ATOM LIST 42209 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29657 from a total of 767752 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 497 -77.45672 0.76984 0.63135 INTE EXTERN> -32.80553 -44.65119 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4567" Parameter: A <- "-77.4567" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8055" Parameter: B <- "-32.8055" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6512" Parameter: C <- "-44.6512" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 497 TOTAL ENERGY = -77.4567 RDTITL> * VAN DER WAALS = -32.8055 ELECTROSTATIC = -44.6512 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "497" Parameter: CONF_N -> "8002" Comparing "497" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "498" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767752 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772352 ATOM PAIRS WERE FOUND FOR ATOM LIST 42462 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29882 from a total of 772352 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 498 -74.20598 -3.25074 0.61441 INTE EXTERN> -33.30782 -40.89816 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.206" Parameter: A <- "-74.206" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3078" Parameter: B <- "-33.3078" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8982" Parameter: C <- "-40.8982" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 498 TOTAL ENERGY = -74.206 RDTITL> * VAN DER WAALS = -33.3078 ELECTROSTATIC = -40.8982 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "498" Parameter: CONF_N -> "8002" Comparing "498" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "499" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772352 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764697 ATOM PAIRS WERE FOUND FOR ATOM LIST 42001 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29779 from a total of 764697 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 499 -74.83571 0.62973 0.65118 INTE EXTERN> -30.23059 -44.60512 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8357" Parameter: A <- "-74.8357" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2306" Parameter: B <- "-30.2306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6051" Parameter: C <- "-44.6051" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 499 TOTAL ENERGY = -74.8357 RDTITL> * VAN DER WAALS = -30.2306 ELECTROSTATIC = -44.6051 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "499" Parameter: CONF_N -> "8002" Comparing "499" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "500" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764697 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761070 ATOM PAIRS WERE FOUND FOR ATOM LIST 41823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29531 from a total of 761070 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 500 -73.01945 -1.81626 0.55061 INTE EXTERN> -34.10437 -38.91509 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0195" Parameter: A <- "-73.0195" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1044" Parameter: B <- "-34.1044" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9151" Parameter: C <- "-38.9151" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 500 TOTAL ENERGY = -73.0195 RDTITL> * VAN DER WAALS = -34.1044 ELECTROSTATIC = -38.9151 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "500" Parameter: CONF_N -> "8002" Comparing "500" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "501" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761070 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763299 ATOM PAIRS WERE FOUND FOR ATOM LIST 41785 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29972 from a total of 763299 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 501 -79.22658 6.20713 0.61797 INTE EXTERN> -33.79391 -45.43267 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2266" Parameter: A <- "-79.2266" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7939" Parameter: B <- "-33.7939" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4327" Parameter: C <- "-45.4327" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 501 TOTAL ENERGY = -79.2266 RDTITL> * VAN DER WAALS = -33.7939 ELECTROSTATIC = -45.4327 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "501" Parameter: CONF_N -> "8002" Comparing "501" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "502" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763299 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765503 ATOM PAIRS WERE FOUND FOR ATOM LIST 42207 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29432 from a total of 765503 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 502 -77.63444 -1.59214 0.59248 INTE EXTERN> -33.88876 -43.74568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6344" Parameter: A <- "-77.6344" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8888" Parameter: B <- "-33.8888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7457" Parameter: C <- "-43.7457" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 502 TOTAL ENERGY = -77.6344 RDTITL> * VAN DER WAALS = -33.8888 ELECTROSTATIC = -43.7457 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "502" Parameter: CONF_N -> "8002" Comparing "502" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "503" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765503 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765454 ATOM PAIRS WERE FOUND FOR ATOM LIST 42126 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29284 from a total of 765454 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 503 -80.73329 3.09885 0.75359 INTE EXTERN> -28.55018 -52.18311 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7333" Parameter: A <- "-80.7333" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5502" Parameter: B <- "-28.5502" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1831" Parameter: C <- "-52.1831" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 503 TOTAL ENERGY = -80.7333 RDTITL> * VAN DER WAALS = -28.5502 ELECTROSTATIC = -52.1831 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "503" Parameter: CONF_N -> "8002" Comparing "503" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "504" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765454 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766629 ATOM PAIRS WERE FOUND FOR ATOM LIST 42056 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29198 from a total of 766629 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 504 -81.32309 0.58980 0.61099 INTE EXTERN> -33.36967 -47.95342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.3231" Parameter: A <- "-81.3231" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3697" Parameter: B <- "-33.3697" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9534" Parameter: C <- "-47.9534" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 504 TOTAL ENERGY = -81.3231 RDTITL> * VAN DER WAALS = -33.3697 ELECTROSTATIC = -47.9534 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "504" Parameter: CONF_N -> "8002" Comparing "504" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "505" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766629 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764229 ATOM PAIRS WERE FOUND FOR ATOM LIST 42084 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30133 from a total of 764229 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 505 -77.56088 -3.76221 0.73209 INTE EXTERN> -28.05557 -49.50531 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5609" Parameter: A <- "-77.5609" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0556" Parameter: B <- "-28.0556" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5053" Parameter: C <- "-49.5053" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 505 TOTAL ENERGY = -77.5609 RDTITL> * VAN DER WAALS = -28.0556 ELECTROSTATIC = -49.5053 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "505" Parameter: CONF_N -> "8002" Comparing "505" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "506" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764229 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764338 ATOM PAIRS WERE FOUND FOR ATOM LIST 41977 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29792 from a total of 764338 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 506 -71.20449 -6.35639 0.74332 INTE EXTERN> -28.08550 -43.11900 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2045" Parameter: A <- "-71.2045" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0855" Parameter: B <- "-28.0855" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.119" Parameter: C <- "-43.119" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 506 TOTAL ENERGY = -71.2045 RDTITL> * VAN DER WAALS = -28.0855 ELECTROSTATIC = -43.119 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "506" Parameter: CONF_N -> "8002" Comparing "506" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "507" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764338 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764544 ATOM PAIRS WERE FOUND FOR ATOM LIST 42184 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29705 from a total of 764544 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 507 -80.80199 9.59749 0.54139 INTE EXTERN> -33.13145 -47.67054 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.802" Parameter: A <- "-80.802" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1314" Parameter: B <- "-33.1314" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6705" Parameter: C <- "-47.6705" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 507 TOTAL ENERGY = -80.802 RDTITL> * VAN DER WAALS = -33.1314 ELECTROSTATIC = -47.6705 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "507" Parameter: CONF_N -> "8002" Comparing "507" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "508" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764544 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771426 ATOM PAIRS WERE FOUND FOR ATOM LIST 42402 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30323 from a total of 771426 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 508 -74.98694 -5.81505 0.71643 INTE EXTERN> -30.40701 -44.57993 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9869" Parameter: A <- "-74.9869" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.407" Parameter: B <- "-30.407" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5799" Parameter: C <- "-44.5799" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 508 TOTAL ENERGY = -74.9869 RDTITL> * VAN DER WAALS = -30.407 ELECTROSTATIC = -44.5799 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "508" Parameter: CONF_N -> "8002" Comparing "508" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "509" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771426 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768770 ATOM PAIRS WERE FOUND FOR ATOM LIST 42393 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29821 from a total of 768770 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 509 -78.04161 3.05466 0.75305 INTE EXTERN> -28.01572 -50.02589 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0416" Parameter: A <- "-78.0416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0157" Parameter: B <- "-28.0157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0259" Parameter: C <- "-50.0259" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 509 TOTAL ENERGY = -78.0416 RDTITL> * VAN DER WAALS = -28.0157 ELECTROSTATIC = -50.0259 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "509" Parameter: CONF_N -> "8002" Comparing "509" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "510" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768770 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770723 ATOM PAIRS WERE FOUND FOR ATOM LIST 42150 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30176 from a total of 770723 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 510 -81.21394 3.17234 0.64916 INTE EXTERN> -34.08909 -47.12486 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.2139" Parameter: A <- "-81.2139" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0891" Parameter: B <- "-34.0891" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1249" Parameter: C <- "-47.1249" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 510 TOTAL ENERGY = -81.2139 RDTITL> * VAN DER WAALS = -34.0891 ELECTROSTATIC = -47.1249 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "510" Parameter: CONF_N -> "8002" Comparing "510" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "511" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770723 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767792 ATOM PAIRS WERE FOUND FOR ATOM LIST 42189 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29726 from a total of 767792 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 511 -77.19845 -4.01549 0.61544 INTE EXTERN> -33.92038 -43.27806 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1984" Parameter: A <- "-77.1984" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9204" Parameter: B <- "-33.9204" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2781" Parameter: C <- "-43.2781" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 511 TOTAL ENERGY = -77.1984 RDTITL> * VAN DER WAALS = -33.9204 ELECTROSTATIC = -43.2781 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "511" Parameter: CONF_N -> "8002" Comparing "511" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "512" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767792 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765245 ATOM PAIRS WERE FOUND FOR ATOM LIST 42006 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29691 from a total of 765245 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 512 -79.13859 1.94015 0.68362 INTE EXTERN> -30.81205 -48.32654 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1386" Parameter: A <- "-79.1386" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8121" Parameter: B <- "-30.8121" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3265" Parameter: C <- "-48.3265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 512 TOTAL ENERGY = -79.1386 RDTITL> * VAN DER WAALS = -30.8121 ELECTROSTATIC = -48.3265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "512" Parameter: CONF_N -> "8002" Comparing "512" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "513" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765245 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768360 ATOM PAIRS WERE FOUND FOR ATOM LIST 42224 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30019 from a total of 768360 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 513 -79.29963 0.16103 0.65895 INTE EXTERN> -32.41948 -46.88015 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2996" Parameter: A <- "-79.2996" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4195" Parameter: B <- "-32.4195" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8801" Parameter: C <- "-46.8801" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 513 TOTAL ENERGY = -79.2996 RDTITL> * VAN DER WAALS = -32.4195 ELECTROSTATIC = -46.8801 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "513" Parameter: CONF_N -> "8002" Comparing "513" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "514" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768360 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766986 ATOM PAIRS WERE FOUND FOR ATOM LIST 42258 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30472 from a total of 766986 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 514 -83.48471 4.18508 0.71869 INTE EXTERN> -30.83295 -52.65175 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.4847" Parameter: A <- "-83.4847" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.833" Parameter: B <- "-30.833" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6518" Parameter: C <- "-52.6518" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 514 TOTAL ENERGY = -83.4847 RDTITL> * VAN DER WAALS = -30.833 ELECTROSTATIC = -52.6518 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "514" Parameter: CONF_N -> "8002" Comparing "514" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "515" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766986 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41975 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29258 from a total of 762118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 515 -86.22586 2.74115 0.75632 INTE EXTERN> -30.55376 -55.67210 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.2259" Parameter: A <- "-86.2259" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5538" Parameter: B <- "-30.5538" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.6721" Parameter: C <- "-55.6721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 515 TOTAL ENERGY = -86.2259 RDTITL> * VAN DER WAALS = -30.5538 ELECTROSTATIC = -55.6721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "515" Parameter: CONF_N -> "8002" Comparing "515" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "516" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762400 ATOM PAIRS WERE FOUND FOR ATOM LIST 42032 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30287 from a total of 762400 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 516 -76.92008 -9.30578 0.73129 INTE EXTERN> -28.12253 -48.79755 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9201" Parameter: A <- "-76.9201" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1225" Parameter: B <- "-28.1225" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7976" Parameter: C <- "-48.7976" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 516 TOTAL ENERGY = -76.9201 RDTITL> * VAN DER WAALS = -28.1225 ELECTROSTATIC = -48.7976 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "516" Parameter: CONF_N -> "8002" Comparing "516" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "517" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762400 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766207 ATOM PAIRS WERE FOUND FOR ATOM LIST 42153 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30555 from a total of 766207 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 517 -85.80405 8.88396 0.71349 INTE EXTERN> -30.47303 -55.33102 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.804" Parameter: A <- "-85.804" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.473" Parameter: B <- "-30.473" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.331" Parameter: C <- "-55.331" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 517 TOTAL ENERGY = -85.804 RDTITL> * VAN DER WAALS = -30.473 ELECTROSTATIC = -55.331 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "517" Parameter: CONF_N -> "8002" Comparing "517" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "518" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766207 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765705 ATOM PAIRS WERE FOUND FOR ATOM LIST 41921 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30488 from a total of 765705 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 518 -84.41209 -1.39196 0.81011 INTE EXTERN> -29.22258 -55.18950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.4121" Parameter: A <- "-84.4121" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2226" Parameter: B <- "-29.2226" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.1895" Parameter: C <- "-55.1895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 518 TOTAL ENERGY = -84.4121 RDTITL> * VAN DER WAALS = -29.2226 ELECTROSTATIC = -55.1895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "518" Parameter: CONF_N -> "8002" Comparing "518" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "519" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765705 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767265 ATOM PAIRS WERE FOUND FOR ATOM LIST 42344 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30569 from a total of 767265 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 519 -82.27784 -2.13425 0.73917 INTE EXTERN> -31.06918 -51.20865 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.2778" Parameter: A <- "-82.2778" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0692" Parameter: B <- "-31.0692" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2087" Parameter: C <- "-51.2087" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 519 TOTAL ENERGY = -82.2778 RDTITL> * VAN DER WAALS = -31.0692 ELECTROSTATIC = -51.2087 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "519" Parameter: CONF_N -> "8002" Comparing "519" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "520" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767265 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771672 ATOM PAIRS WERE FOUND FOR ATOM LIST 42650 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30732 from a total of 771672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 520 -78.38223 -3.89560 0.60024 INTE EXTERN> -34.95464 -43.42759 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3822" Parameter: A <- "-78.3822" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9546" Parameter: B <- "-34.9546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4276" Parameter: C <- "-43.4276" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 520 TOTAL ENERGY = -78.3822 RDTITL> * VAN DER WAALS = -34.9546 ELECTROSTATIC = -43.4276 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "520" Parameter: CONF_N -> "8002" Comparing "520" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "521" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768716 ATOM PAIRS WERE FOUND FOR ATOM LIST 42427 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30372 from a total of 768716 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 521 -85.26133 6.87910 0.64416 INTE EXTERN> -33.60077 -51.66057 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.2613" Parameter: A <- "-85.2613" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6008" Parameter: B <- "-33.6008" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6606" Parameter: C <- "-51.6606" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 521 TOTAL ENERGY = -85.2613 RDTITL> * VAN DER WAALS = -33.6008 ELECTROSTATIC = -51.6606 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "521" Parameter: CONF_N -> "8002" Comparing "521" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "522" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768716 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769108 ATOM PAIRS WERE FOUND FOR ATOM LIST 42274 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30506 from a total of 769108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 522 -74.95594 -10.30539 0.59458 INTE EXTERN> -33.62567 -41.33027 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9559" Parameter: A <- "-74.9559" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6257" Parameter: B <- "-33.6257" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3303" Parameter: C <- "-41.3303" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 522 TOTAL ENERGY = -74.9559 RDTITL> * VAN DER WAALS = -33.6257 ELECTROSTATIC = -41.3303 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "522" Parameter: CONF_N -> "8002" Comparing "522" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "523" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769430 ATOM PAIRS WERE FOUND FOR ATOM LIST 42363 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30456 from a total of 769430 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 523 -80.42834 5.47240 0.65137 INTE EXTERN> -31.36938 -49.05896 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4283" Parameter: A <- "-80.4283" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3694" Parameter: B <- "-31.3694" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.059" Parameter: C <- "-49.059" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 523 TOTAL ENERGY = -80.4283 RDTITL> * VAN DER WAALS = -31.3694 ELECTROSTATIC = -49.059 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "523" Parameter: CONF_N -> "8002" Comparing "523" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "524" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769430 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767807 ATOM PAIRS WERE FOUND FOR ATOM LIST 42325 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30268 from a total of 767807 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 524 -71.79496 -8.63338 0.61866 INTE EXTERN> -30.13719 -41.65778 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.795" Parameter: A <- "-71.795" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1372" Parameter: B <- "-30.1372" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6578" Parameter: C <- "-41.6578" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 524 TOTAL ENERGY = -71.795 RDTITL> * VAN DER WAALS = -30.1372 ELECTROSTATIC = -41.6578 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "524" Parameter: CONF_N -> "8002" Comparing "524" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "525" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767807 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761619 ATOM PAIRS WERE FOUND FOR ATOM LIST 42044 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29546 from a total of 761619 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 525 -74.82152 3.02656 0.57050 INTE EXTERN> -33.49883 -41.32269 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8215" Parameter: A <- "-74.8215" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4988" Parameter: B <- "-33.4988" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3227" Parameter: C <- "-41.3227" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 525 TOTAL ENERGY = -74.8215 RDTITL> * VAN DER WAALS = -33.4988 ELECTROSTATIC = -41.3227 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "525" Parameter: CONF_N -> "8002" Comparing "525" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "526" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761619 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769557 ATOM PAIRS WERE FOUND FOR ATOM LIST 42277 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30455 from a total of 769557 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 526 -76.20777 1.38625 0.65507 INTE EXTERN> -30.22377 -45.98400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2078" Parameter: A <- "-76.2078" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2238" Parameter: B <- "-30.2238" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.984" Parameter: C <- "-45.984" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 526 TOTAL ENERGY = -76.2078 RDTITL> * VAN DER WAALS = -30.2238 ELECTROSTATIC = -45.984 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "526" Parameter: CONF_N -> "8002" Comparing "526" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "527" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769557 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765419 ATOM PAIRS WERE FOUND FOR ATOM LIST 42226 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30101 from a total of 765419 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 527 -78.84433 2.63657 0.65442 INTE EXTERN> -28.16381 -50.68052 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8443" Parameter: A <- "-78.8443" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1638" Parameter: B <- "-28.1638" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6805" Parameter: C <- "-50.6805" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 527 TOTAL ENERGY = -78.8443 RDTITL> * VAN DER WAALS = -28.1638 ELECTROSTATIC = -50.6805 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "527" Parameter: CONF_N -> "8002" Comparing "527" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "528" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765419 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766583 ATOM PAIRS WERE FOUND FOR ATOM LIST 42059 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30236 from a total of 766583 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 528 -75.24790 -3.59643 0.67661 INTE EXTERN> -29.49030 -45.75761 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2479" Parameter: A <- "-75.2479" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4903" Parameter: B <- "-29.4903" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7576" Parameter: C <- "-45.7576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 528 TOTAL ENERGY = -75.2479 RDTITL> * VAN DER WAALS = -29.4903 ELECTROSTATIC = -45.7576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "528" Parameter: CONF_N -> "8002" Comparing "528" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "529" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766583 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765363 ATOM PAIRS WERE FOUND FOR ATOM LIST 42042 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30091 from a total of 765363 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 529 -76.85568 1.60778 0.73676 INTE EXTERN> -26.07303 -50.78265 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8557" Parameter: A <- "-76.8557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.073" Parameter: B <- "-26.073" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7826" Parameter: C <- "-50.7826" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 529 TOTAL ENERGY = -76.8557 RDTITL> * VAN DER WAALS = -26.073 ELECTROSTATIC = -50.7826 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "529" Parameter: CONF_N -> "8002" Comparing "529" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "530" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765363 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766170 ATOM PAIRS WERE FOUND FOR ATOM LIST 42204 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30178 from a total of 766170 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 530 -76.04848 -0.80720 0.58990 INTE EXTERN> -33.43181 -42.61667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0485" Parameter: A <- "-76.0485" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4318" Parameter: B <- "-33.4318" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6167" Parameter: C <- "-42.6167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 530 TOTAL ENERGY = -76.0485 RDTITL> * VAN DER WAALS = -33.4318 ELECTROSTATIC = -42.6167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "530" Parameter: CONF_N -> "8002" Comparing "530" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "531" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766170 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762509 ATOM PAIRS WERE FOUND FOR ATOM LIST 42150 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30018 from a total of 762509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 531 -76.33180 0.28332 0.83671 INTE EXTERN> -25.27132 -51.06048 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3318" Parameter: A <- "-76.3318" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2713" Parameter: B <- "-25.2713" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0605" Parameter: C <- "-51.0605" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 531 TOTAL ENERGY = -76.3318 RDTITL> * VAN DER WAALS = -25.2713 ELECTROSTATIC = -51.0605 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "531" Parameter: CONF_N -> "8002" Comparing "531" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "532" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758611 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29602 from a total of 758611 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 532 -76.15532 -0.17648 0.68800 INTE EXTERN> -30.15365 -46.00168 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1553" Parameter: A <- "-76.1553" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1536" Parameter: B <- "-30.1536" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0017" Parameter: C <- "-46.0017" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 532 TOTAL ENERGY = -76.1553 RDTITL> * VAN DER WAALS = -30.1536 ELECTROSTATIC = -46.0017 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "532" Parameter: CONF_N -> "8002" Comparing "532" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "533" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758611 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762542 ATOM PAIRS WERE FOUND FOR ATOM LIST 42070 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29289 from a total of 762542 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 533 -80.66359 4.50826 0.64189 INTE EXTERN> -32.18447 -48.47912 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6636" Parameter: A <- "-80.6636" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1845" Parameter: B <- "-32.1845" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4791" Parameter: C <- "-48.4791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 533 TOTAL ENERGY = -80.6636 RDTITL> * VAN DER WAALS = -32.1845 ELECTROSTATIC = -48.4791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "533" Parameter: CONF_N -> "8002" Comparing "533" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "534" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762542 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759943 ATOM PAIRS WERE FOUND FOR ATOM LIST 41919 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29631 from a total of 759943 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 534 -74.63875 -6.02484 0.59884 INTE EXTERN> -31.61939 -43.01936 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6387" Parameter: A <- "-74.6387" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6194" Parameter: B <- "-31.6194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0194" Parameter: C <- "-43.0194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 534 TOTAL ENERGY = -74.6387 RDTITL> * VAN DER WAALS = -31.6194 ELECTROSTATIC = -43.0194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "534" Parameter: CONF_N -> "8002" Comparing "534" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "535" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759943 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759828 ATOM PAIRS WERE FOUND FOR ATOM LIST 41692 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29673 from a total of 759828 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 535 -78.74188 4.10313 0.57802 INTE EXTERN> -34.39225 -44.34963 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7419" Parameter: A <- "-78.7419" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3923" Parameter: B <- "-34.3923" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3496" Parameter: C <- "-44.3496" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 535 TOTAL ENERGY = -78.7419 RDTITL> * VAN DER WAALS = -34.3923 ELECTROSTATIC = -44.3496 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "535" Parameter: CONF_N -> "8002" Comparing "535" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "536" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759828 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766598 ATOM PAIRS WERE FOUND FOR ATOM LIST 42291 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29644 from a total of 766598 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 536 -64.77324 -13.96864 0.53929 INTE EXTERN> -34.35859 -30.41465 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7732" Parameter: A <- "-64.7732" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3586" Parameter: B <- "-34.3586" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.4147" Parameter: C <- "-30.4147" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 536 TOTAL ENERGY = -64.7732 RDTITL> * VAN DER WAALS = -34.3586 ELECTROSTATIC = -30.4147 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "536" Parameter: CONF_N -> "8002" Comparing "536" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "537" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766598 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767356 ATOM PAIRS WERE FOUND FOR ATOM LIST 42114 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29832 from a total of 767356 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 537 -76.79563 12.02239 0.66765 INTE EXTERN> -30.58155 -46.21407 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7956" Parameter: A <- "-76.7956" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5816" Parameter: B <- "-30.5816" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2141" Parameter: C <- "-46.2141" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 537 TOTAL ENERGY = -76.7956 RDTITL> * VAN DER WAALS = -30.5816 ELECTROSTATIC = -46.2141 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "537" Parameter: CONF_N -> "8002" Comparing "537" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "538" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767356 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763927 ATOM PAIRS WERE FOUND FOR ATOM LIST 41994 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29497 from a total of 763927 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 538 -75.01518 -1.78044 0.67783 INTE EXTERN> -31.08909 -43.92610 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0152" Parameter: A <- "-75.0152" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0891" Parameter: B <- "-31.0891" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9261" Parameter: C <- "-43.9261" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 538 TOTAL ENERGY = -75.0152 RDTITL> * VAN DER WAALS = -31.0891 ELECTROSTATIC = -43.9261 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "538" Parameter: CONF_N -> "8002" Comparing "538" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "539" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763927 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766887 ATOM PAIRS WERE FOUND FOR ATOM LIST 42149 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29583 from a total of 766887 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 539 -64.96196 -10.05322 0.59650 INTE EXTERN> -28.77879 -36.18317 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.962" Parameter: A <- "-64.962" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7788" Parameter: B <- "-28.7788" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1832" Parameter: C <- "-36.1832" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 539 TOTAL ENERGY = -64.962 RDTITL> * VAN DER WAALS = -28.7788 ELECTROSTATIC = -36.1832 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "539" Parameter: CONF_N -> "8002" Comparing "539" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "540" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766887 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761824 ATOM PAIRS WERE FOUND FOR ATOM LIST 41926 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29537 from a total of 761824 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 540 -74.79204 9.83008 0.64146 INTE EXTERN> -31.32087 -43.47118 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.792" Parameter: A <- "-74.792" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3209" Parameter: B <- "-31.3209" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4712" Parameter: C <- "-43.4712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 540 TOTAL ENERGY = -74.792 RDTITL> * VAN DER WAALS = -31.3209 ELECTROSTATIC = -43.4712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "540" Parameter: CONF_N -> "8002" Comparing "540" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "541" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761824 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765672 ATOM PAIRS WERE FOUND FOR ATOM LIST 42123 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29775 from a total of 765672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 541 -72.95302 -1.83902 0.74892 INTE EXTERN> -28.77075 -44.18227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.953" Parameter: A <- "-72.953" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7708" Parameter: B <- "-28.7708" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1823" Parameter: C <- "-44.1823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 541 TOTAL ENERGY = -72.953 RDTITL> * VAN DER WAALS = -28.7708 ELECTROSTATIC = -44.1823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "541" Parameter: CONF_N -> "8002" Comparing "541" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "542" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768221 ATOM PAIRS WERE FOUND FOR ATOM LIST 42225 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29762 from a total of 768221 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 542 -80.34596 7.39294 0.71896 INTE EXTERN> -27.99624 -52.34972 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.346" Parameter: A <- "-80.346" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9962" Parameter: B <- "-27.9962" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3497" Parameter: C <- "-52.3497" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 542 TOTAL ENERGY = -80.346 RDTITL> * VAN DER WAALS = -27.9962 ELECTROSTATIC = -52.3497 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "542" Parameter: CONF_N -> "8002" Comparing "542" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "543" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768221 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767676 ATOM PAIRS WERE FOUND FOR ATOM LIST 42333 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29476 from a total of 767676 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 543 -74.93486 -5.41110 0.74648 INTE EXTERN> -25.75576 -49.17910 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9349" Parameter: A <- "-74.9349" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7558" Parameter: B <- "-25.7558" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1791" Parameter: C <- "-49.1791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 543 TOTAL ENERGY = -74.9349 RDTITL> * VAN DER WAALS = -25.7558 ELECTROSTATIC = -49.1791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "543" Parameter: CONF_N -> "8002" Comparing "543" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "544" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767676 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764987 ATOM PAIRS WERE FOUND FOR ATOM LIST 42066 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29235 from a total of 764987 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 544 -80.41312 5.47826 0.76753 INTE EXTERN> -29.57987 -50.83325 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4131" Parameter: A <- "-80.4131" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5799" Parameter: B <- "-29.5799" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8333" Parameter: C <- "-50.8333" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 544 TOTAL ENERGY = -80.4131 RDTITL> * VAN DER WAALS = -29.5799 ELECTROSTATIC = -50.8333 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "544" Parameter: CONF_N -> "8002" Comparing "544" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "545" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764987 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763239 ATOM PAIRS WERE FOUND FOR ATOM LIST 42062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30261 from a total of 763239 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 545 -73.76977 -6.64335 0.60427 INTE EXTERN> -33.29261 -40.47716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7698" Parameter: A <- "-73.7698" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2926" Parameter: B <- "-33.2926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4772" Parameter: C <- "-40.4772" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 545 TOTAL ENERGY = -73.7698 RDTITL> * VAN DER WAALS = -33.2926 ELECTROSTATIC = -40.4772 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "545" Parameter: CONF_N -> "8002" Comparing "545" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "546" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763239 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766195 ATOM PAIRS WERE FOUND FOR ATOM LIST 42291 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29613 from a total of 766195 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 546 -73.87646 0.10669 0.65918 INTE EXTERN> -30.16583 -43.71063 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8765" Parameter: A <- "-73.8765" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1658" Parameter: B <- "-30.1658" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7106" Parameter: C <- "-43.7106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 546 TOTAL ENERGY = -73.8765 RDTITL> * VAN DER WAALS = -30.1658 ELECTROSTATIC = -43.7106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "546" Parameter: CONF_N -> "8002" Comparing "546" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "547" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766195 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764093 ATOM PAIRS WERE FOUND FOR ATOM LIST 42136 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30176 from a total of 764093 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 547 -72.49877 -1.37770 0.67552 INTE EXTERN> -28.97612 -43.52265 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4988" Parameter: A <- "-72.4988" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9761" Parameter: B <- "-28.9761" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5226" Parameter: C <- "-43.5226" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 547 TOTAL ENERGY = -72.4988 RDTITL> * VAN DER WAALS = -28.9761 ELECTROSTATIC = -43.5226 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "547" Parameter: CONF_N -> "8002" Comparing "547" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "548" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764093 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763854 ATOM PAIRS WERE FOUND FOR ATOM LIST 42012 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30106 from a total of 763854 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 548 -72.58272 0.08395 0.67578 INTE EXTERN> -29.03146 -43.55126 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5827" Parameter: A <- "-72.5827" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0315" Parameter: B <- "-29.0315" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5513" Parameter: C <- "-43.5513" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 548 TOTAL ENERGY = -72.5827 RDTITL> * VAN DER WAALS = -29.0315 ELECTROSTATIC = -43.5513 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "548" Parameter: CONF_N -> "8002" Comparing "548" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "549" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763854 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761185 ATOM PAIRS WERE FOUND FOR ATOM LIST 42019 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29637 from a total of 761185 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 549 -74.48103 1.89831 0.57577 INTE EXTERN> -33.14725 -41.33378 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.481" Parameter: A <- "-74.481" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1472" Parameter: B <- "-33.1472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3338" Parameter: C <- "-41.3338" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 549 TOTAL ENERGY = -74.481 RDTITL> * VAN DER WAALS = -33.1472 ELECTROSTATIC = -41.3338 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "549" Parameter: CONF_N -> "8002" Comparing "549" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "550" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761185 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767405 ATOM PAIRS WERE FOUND FOR ATOM LIST 42094 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29711 from a total of 767405 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 550 -83.73883 9.25780 0.59293 INTE EXTERN> -33.19619 -50.54264 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.7388" Parameter: A <- "-83.7388" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1962" Parameter: B <- "-33.1962" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5426" Parameter: C <- "-50.5426" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 550 TOTAL ENERGY = -83.7388 RDTITL> * VAN DER WAALS = -33.1962 ELECTROSTATIC = -50.5426 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "550" Parameter: CONF_N -> "8002" Comparing "550" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "551" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767405 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766756 ATOM PAIRS WERE FOUND FOR ATOM LIST 42341 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29981 from a total of 766756 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 551 -78.68919 -5.04964 0.60854 INTE EXTERN> -33.22482 -45.46437 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6892" Parameter: A <- "-78.6892" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2248" Parameter: B <- "-33.2248" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4644" Parameter: C <- "-45.4644" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 551 TOTAL ENERGY = -78.6892 RDTITL> * VAN DER WAALS = -33.2248 ELECTROSTATIC = -45.4644 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "551" Parameter: CONF_N -> "8002" Comparing "551" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "552" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766756 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759663 ATOM PAIRS WERE FOUND FOR ATOM LIST 41744 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29764 from a total of 759663 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 552 -87.83704 9.14785 0.69386 INTE EXTERN> -30.35086 -57.48618 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.837" Parameter: A <- "-87.837" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3509" Parameter: B <- "-30.3509" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.4862" Parameter: C <- "-57.4862" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 552 TOTAL ENERGY = -87.837 RDTITL> * VAN DER WAALS = -30.3509 ELECTROSTATIC = -57.4862 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "552" Parameter: CONF_N -> "8002" Comparing "552" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "553" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759663 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760244 ATOM PAIRS WERE FOUND FOR ATOM LIST 41869 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29866 from a total of 760244 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 553 -77.20468 -10.63236 0.68958 INTE EXTERN> -31.45638 -45.74831 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2047" Parameter: A <- "-77.2047" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4564" Parameter: B <- "-31.4564" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7483" Parameter: C <- "-45.7483" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 553 TOTAL ENERGY = -77.2047 RDTITL> * VAN DER WAALS = -31.4564 ELECTROSTATIC = -45.7483 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "553" Parameter: CONF_N -> "8002" Comparing "553" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "554" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760244 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763971 ATOM PAIRS WERE FOUND FOR ATOM LIST 41811 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29908 from a total of 763971 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 554 -82.44623 5.24155 0.65575 INTE EXTERN> -33.04994 -49.39629 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.4462" Parameter: A <- "-82.4462" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0499" Parameter: B <- "-33.0499" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3963" Parameter: C <- "-49.3963" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 554 TOTAL ENERGY = -82.4462 RDTITL> * VAN DER WAALS = -33.0499 ELECTROSTATIC = -49.3963 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "554" Parameter: CONF_N -> "8002" Comparing "554" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "555" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763971 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761961 ATOM PAIRS WERE FOUND FOR ATOM LIST 41939 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29834 from a total of 761961 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 555 -79.54517 -2.90106 0.61591 INTE EXTERN> -33.98012 -45.56505 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5452" Parameter: A <- "-79.5452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9801" Parameter: B <- "-33.9801" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.565" Parameter: C <- "-45.565" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 555 TOTAL ENERGY = -79.5452 RDTITL> * VAN DER WAALS = -33.9801 ELECTROSTATIC = -45.565 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "555" Parameter: CONF_N -> "8002" Comparing "555" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "556" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761961 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759334 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28850 from a total of 759334 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 556 -89.35615 9.81098 0.72446 INTE EXTERN> -29.05172 -60.30444 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-89.3562" Parameter: A <- "-89.3562" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0517" Parameter: B <- "-29.0517" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-60.3044" Parameter: C <- "-60.3044" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 556 TOTAL ENERGY = -89.3562 RDTITL> * VAN DER WAALS = -29.0517 ELECTROSTATIC = -60.3044 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "556" Parameter: CONF_N -> "8002" Comparing "556" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "557" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759334 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758251 ATOM PAIRS WERE FOUND FOR ATOM LIST 41534 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30152 from a total of 758251 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 557 -71.37593 -17.98022 0.58461 INTE EXTERN> -32.11690 -39.25903 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3759" Parameter: A <- "-71.3759" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1169" Parameter: B <- "-32.1169" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.259" Parameter: C <- "-39.259" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 557 TOTAL ENERGY = -71.3759 RDTITL> * VAN DER WAALS = -32.1169 ELECTROSTATIC = -39.259 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "557" Parameter: CONF_N -> "8002" Comparing "557" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "558" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758251 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768278 ATOM PAIRS WERE FOUND FOR ATOM LIST 42074 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30038 from a total of 768278 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 558 -76.84925 5.47332 0.64921 INTE EXTERN> -31.73547 -45.11378 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8493" Parameter: A <- "-76.8493" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7355" Parameter: B <- "-31.7355" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1138" Parameter: C <- "-45.1138" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 558 TOTAL ENERGY = -76.8493 RDTITL> * VAN DER WAALS = -31.7355 ELECTROSTATIC = -45.1138 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "558" Parameter: CONF_N -> "8002" Comparing "558" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "559" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768278 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765894 ATOM PAIRS WERE FOUND FOR ATOM LIST 42100 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29938 from a total of 765894 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 559 -79.40474 2.55548 0.63475 INTE EXTERN> -30.84059 -48.56415 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4047" Parameter: A <- "-79.4047" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8406" Parameter: B <- "-30.8406" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5641" Parameter: C <- "-48.5641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 559 TOTAL ENERGY = -79.4047 RDTITL> * VAN DER WAALS = -30.8406 ELECTROSTATIC = -48.5641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "559" Parameter: CONF_N -> "8002" Comparing "559" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "560" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765894 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758735 ATOM PAIRS WERE FOUND FOR ATOM LIST 41784 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29933 from a total of 758735 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 560 -79.28072 -0.12402 0.61441 INTE EXTERN> -30.67649 -48.60422 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2807" Parameter: A <- "-79.2807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6765" Parameter: B <- "-30.6765" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6042" Parameter: C <- "-48.6042" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 560 TOTAL ENERGY = -79.2807 RDTITL> * VAN DER WAALS = -30.6765 ELECTROSTATIC = -48.6042 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "560" Parameter: CONF_N -> "8002" Comparing "560" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "561" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758735 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763196 ATOM PAIRS WERE FOUND FOR ATOM LIST 41924 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30041 from a total of 763196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 561 -78.33965 -0.94107 0.62278 INTE EXTERN> -31.22292 -47.11673 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3396" Parameter: A <- "-78.3396" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2229" Parameter: B <- "-31.2229" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1167" Parameter: C <- "-47.1167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 561 TOTAL ENERGY = -78.3396 RDTITL> * VAN DER WAALS = -31.2229 ELECTROSTATIC = -47.1167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "561" Parameter: CONF_N -> "8002" Comparing "561" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "562" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759829 ATOM PAIRS WERE FOUND FOR ATOM LIST 41874 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29811 from a total of 759829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 562 -71.28282 -7.05683 0.57448 INTE EXTERN> -32.95051 -38.33231 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2828" Parameter: A <- "-71.2828" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9505" Parameter: B <- "-32.9505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3323" Parameter: C <- "-38.3323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 562 TOTAL ENERGY = -71.2828 RDTITL> * VAN DER WAALS = -32.9505 ELECTROSTATIC = -38.3323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "562" Parameter: CONF_N -> "8002" Comparing "562" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "563" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770166 ATOM PAIRS WERE FOUND FOR ATOM LIST 42387 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30123 from a total of 770166 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 563 -77.24871 5.96590 0.75088 INTE EXTERN> -26.03981 -51.20891 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2487" Parameter: A <- "-77.2487" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0398" Parameter: B <- "-26.0398" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2089" Parameter: C <- "-51.2089" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 563 TOTAL ENERGY = -77.2487 RDTITL> * VAN DER WAALS = -26.0398 ELECTROSTATIC = -51.2089 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "563" Parameter: CONF_N -> "8002" Comparing "563" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "564" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770166 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763468 ATOM PAIRS WERE FOUND FOR ATOM LIST 41986 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29369 from a total of 763468 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 564 -68.94794 -8.30077 0.64931 INTE EXTERN> -30.82817 -38.11977 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9479" Parameter: A <- "-68.9479" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8282" Parameter: B <- "-30.8282" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1198" Parameter: C <- "-38.1198" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 564 TOTAL ENERGY = -68.9479 RDTITL> * VAN DER WAALS = -30.8282 ELECTROSTATIC = -38.1198 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "564" Parameter: CONF_N -> "8002" Comparing "564" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "565" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763468 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762518 ATOM PAIRS WERE FOUND FOR ATOM LIST 41724 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30046 from a total of 762518 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 565 -70.23136 1.28342 0.70251 INTE EXTERN> -27.21041 -43.02096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2314" Parameter: A <- "-70.2314" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2104" Parameter: B <- "-27.2104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.021" Parameter: C <- "-43.021" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 565 TOTAL ENERGY = -70.2314 RDTITL> * VAN DER WAALS = -27.2104 ELECTROSTATIC = -43.021 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "565" Parameter: CONF_N -> "8002" Comparing "565" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "566" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762518 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766433 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29526 from a total of 766433 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 566 -73.09183 2.86047 0.61744 INTE EXTERN> -29.60557 -43.48626 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0918" Parameter: A <- "-73.0918" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6056" Parameter: B <- "-29.6056" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4863" Parameter: C <- "-43.4863" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 566 TOTAL ENERGY = -73.0918 RDTITL> * VAN DER WAALS = -29.6056 ELECTROSTATIC = -43.4863 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "566" Parameter: CONF_N -> "8002" Comparing "566" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "567" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766433 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764973 ATOM PAIRS WERE FOUND FOR ATOM LIST 41914 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29227 from a total of 764973 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 567 -75.15939 2.06755 0.69789 INTE EXTERN> -25.98360 -49.17578 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1594" Parameter: A <- "-75.1594" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9836" Parameter: B <- "-25.9836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1758" Parameter: C <- "-49.1758" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 567 TOTAL ENERGY = -75.1594 RDTITL> * VAN DER WAALS = -25.9836 ELECTROSTATIC = -49.1758 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "567" Parameter: CONF_N -> "8002" Comparing "567" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "568" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764973 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760706 ATOM PAIRS WERE FOUND FOR ATOM LIST 41891 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29294 from a total of 760706 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 568 -70.65073 -4.50866 0.62403 INTE EXTERN> -29.98021 -40.67052 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6507" Parameter: A <- "-70.6507" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9802" Parameter: B <- "-29.9802" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6705" Parameter: C <- "-40.6705" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 568 TOTAL ENERGY = -70.6507 RDTITL> * VAN DER WAALS = -29.9802 ELECTROSTATIC = -40.6705 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "568" Parameter: CONF_N -> "8002" Comparing "568" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "569" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760706 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764716 ATOM PAIRS WERE FOUND FOR ATOM LIST 41951 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28955 from a total of 764716 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 569 -71.97153 1.32080 0.67591 INTE EXTERN> -26.31429 -45.65724 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9715" Parameter: A <- "-71.9715" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3143" Parameter: B <- "-26.3143" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6572" Parameter: C <- "-45.6572" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 569 TOTAL ENERGY = -71.9715 RDTITL> * VAN DER WAALS = -26.3143 ELECTROSTATIC = -45.6572 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "569" Parameter: CONF_N -> "8002" Comparing "569" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "570" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764716 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764957 ATOM PAIRS WERE FOUND FOR ATOM LIST 41991 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29726 from a total of 764957 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 570 -79.47772 7.50619 0.71842 INTE EXTERN> -27.41114 -52.06658 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4777" Parameter: A <- "-79.4777" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4111" Parameter: B <- "-27.4111" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0666" Parameter: C <- "-52.0666" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 570 TOTAL ENERGY = -79.4777 RDTITL> * VAN DER WAALS = -27.4111 ELECTROSTATIC = -52.0666 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "570" Parameter: CONF_N -> "8002" Comparing "570" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "571" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764957 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764478 ATOM PAIRS WERE FOUND FOR ATOM LIST 42040 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29858 from a total of 764478 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 571 -75.12788 -4.34984 0.68173 INTE EXTERN> -29.27131 -45.85657 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1279" Parameter: A <- "-75.1279" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2713" Parameter: B <- "-29.2713" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8566" Parameter: C <- "-45.8566" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 571 TOTAL ENERGY = -75.1279 RDTITL> * VAN DER WAALS = -29.2713 ELECTROSTATIC = -45.8566 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "571" Parameter: CONF_N -> "8002" Comparing "571" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "572" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764478 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769100 ATOM PAIRS WERE FOUND FOR ATOM LIST 42191 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30202 from a total of 769100 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 572 -74.12897 -0.99891 0.79452 INTE EXTERN> -24.08332 -50.04565 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.129" Parameter: A <- "-74.129" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0833" Parameter: B <- "-24.0833" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0456" Parameter: C <- "-50.0456" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 572 TOTAL ENERGY = -74.129 RDTITL> * VAN DER WAALS = -24.0833 ELECTROSTATIC = -50.0456 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "572" Parameter: CONF_N -> "8002" Comparing "572" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "573" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769100 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765622 ATOM PAIRS WERE FOUND FOR ATOM LIST 42125 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29839 from a total of 765622 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 573 -84.15545 10.02648 0.71266 INTE EXTERN> -30.33066 -53.82478 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.1554" Parameter: A <- "-84.1554" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3307" Parameter: B <- "-30.3307" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8248" Parameter: C <- "-53.8248" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 573 TOTAL ENERGY = -84.1554 RDTITL> * VAN DER WAALS = -30.3307 ELECTROSTATIC = -53.8248 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "573" Parameter: CONF_N -> "8002" Comparing "573" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "574" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765622 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768027 ATOM PAIRS WERE FOUND FOR ATOM LIST 42320 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30309 from a total of 768027 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 574 -74.63866 -9.51678 0.56653 INTE EXTERN> -34.54515 -40.09352 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6387" Parameter: A <- "-74.6387" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.5451" Parameter: B <- "-34.5451" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0935" Parameter: C <- "-40.0935" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 574 TOTAL ENERGY = -74.6387 RDTITL> * VAN DER WAALS = -34.5451 ELECTROSTATIC = -40.0935 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "574" Parameter: CONF_N -> "8002" Comparing "574" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "575" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768027 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766219 ATOM PAIRS WERE FOUND FOR ATOM LIST 41988 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29881 from a total of 766219 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 575 -75.30808 0.66942 0.62270 INTE EXTERN> -31.79768 -43.51041 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3081" Parameter: A <- "-75.3081" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7977" Parameter: B <- "-31.7977" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5104" Parameter: C <- "-43.5104" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 575 TOTAL ENERGY = -75.3081 RDTITL> * VAN DER WAALS = -31.7977 ELECTROSTATIC = -43.5104 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "575" Parameter: CONF_N -> "8002" Comparing "575" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "576" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766219 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758120 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29723 from a total of 758120 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 576 -83.98275 8.67467 0.70042 INTE EXTERN> -30.02397 -53.95878 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.9827" Parameter: A <- "-83.9827" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.024" Parameter: B <- "-30.024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.9588" Parameter: C <- "-53.9588" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 576 TOTAL ENERGY = -83.9827 RDTITL> * VAN DER WAALS = -30.024 ELECTROSTATIC = -53.9588 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "576" Parameter: CONF_N -> "8002" Comparing "576" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "577" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758120 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759073 ATOM PAIRS WERE FOUND FOR ATOM LIST 41703 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29653 from a total of 759073 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 577 -71.89072 -12.09203 0.73455 INTE EXTERN> -23.78370 -48.10702 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8907" Parameter: A <- "-71.8907" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7837" Parameter: B <- "-23.7837" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.107" Parameter: C <- "-48.107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 577 TOTAL ENERGY = -71.8907 RDTITL> * VAN DER WAALS = -23.7837 ELECTROSTATIC = -48.107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "577" Parameter: CONF_N -> "8002" Comparing "577" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "578" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759073 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763348 ATOM PAIRS WERE FOUND FOR ATOM LIST 41738 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30301 from a total of 763348 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 578 -76.25497 4.36425 0.73294 INTE EXTERN> -26.33854 -49.91642 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.255" Parameter: A <- "-76.255" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3385" Parameter: B <- "-26.3385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9164" Parameter: C <- "-49.9164" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 578 TOTAL ENERGY = -76.255 RDTITL> * VAN DER WAALS = -26.3385 ELECTROSTATIC = -49.9164 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "578" Parameter: CONF_N -> "8002" Comparing "578" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "579" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763348 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765741 ATOM PAIRS WERE FOUND FOR ATOM LIST 42088 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30054 from a total of 765741 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 579 -80.32556 4.07060 0.68968 INTE EXTERN> -29.38464 -50.94092 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3256" Parameter: A <- "-80.3256" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3846" Parameter: B <- "-29.3846" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9409" Parameter: C <- "-50.9409" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 579 TOTAL ENERGY = -80.3256 RDTITL> * VAN DER WAALS = -29.3846 ELECTROSTATIC = -50.9409 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "579" Parameter: CONF_N -> "8002" Comparing "579" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "580" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765741 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764627 ATOM PAIRS WERE FOUND FOR ATOM LIST 42026 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30011 from a total of 764627 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 580 -72.97453 -7.35104 0.61058 INTE EXTERN> -31.14247 -41.83205 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9745" Parameter: A <- "-72.9745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1425" Parameter: B <- "-31.1425" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8321" Parameter: C <- "-41.8321" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 580 TOTAL ENERGY = -72.9745 RDTITL> * VAN DER WAALS = -31.1425 ELECTROSTATIC = -41.8321 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "580" Parameter: CONF_N -> "8002" Comparing "580" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "581" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764627 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761221 ATOM PAIRS WERE FOUND FOR ATOM LIST 41900 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29866 from a total of 761221 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 581 -81.82866 8.85414 0.61888 INTE EXTERN> -33.80707 -48.02159 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8287" Parameter: A <- "-81.8287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8071" Parameter: B <- "-33.8071" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0216" Parameter: C <- "-48.0216" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 581 TOTAL ENERGY = -81.8287 RDTITL> * VAN DER WAALS = -33.8071 ELECTROSTATIC = -48.0216 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "581" Parameter: CONF_N -> "8002" Comparing "581" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "582" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761221 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765901 ATOM PAIRS WERE FOUND FOR ATOM LIST 42026 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30498 from a total of 765901 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 582 -73.36801 -8.46066 0.66978 INTE EXTERN> -27.41955 -45.94846 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.368" Parameter: A <- "-73.368" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4195" Parameter: B <- "-27.4195" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9485" Parameter: C <- "-45.9485" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 582 TOTAL ENERGY = -73.368 RDTITL> * VAN DER WAALS = -27.4195 ELECTROSTATIC = -45.9485 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "582" Parameter: CONF_N -> "8002" Comparing "582" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "583" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765901 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759565 ATOM PAIRS WERE FOUND FOR ATOM LIST 41854 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29135 from a total of 759565 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 583 -80.03192 6.66392 0.62044 INTE EXTERN> -31.34862 -48.68330 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0319" Parameter: A <- "-80.0319" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3486" Parameter: B <- "-31.3486" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6833" Parameter: C <- "-48.6833" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 583 TOTAL ENERGY = -80.0319 RDTITL> * VAN DER WAALS = -31.3486 ELECTROSTATIC = -48.6833 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "583" Parameter: CONF_N -> "8002" Comparing "583" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "584" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759565 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766056 ATOM PAIRS WERE FOUND FOR ATOM LIST 42003 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30009 from a total of 766056 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 584 -78.26306 -1.76886 0.66089 INTE EXTERN> -28.77053 -49.49253 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2631" Parameter: A <- "-78.2631" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7705" Parameter: B <- "-28.7705" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4925" Parameter: C <- "-49.4925" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 584 TOTAL ENERGY = -78.2631 RDTITL> * VAN DER WAALS = -28.7705 ELECTROSTATIC = -49.4925 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "584" Parameter: CONF_N -> "8002" Comparing "584" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "585" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766056 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764314 ATOM PAIRS WERE FOUND FOR ATOM LIST 42027 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28992 from a total of 764314 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 585 -69.14883 -9.11422 0.66805 INTE EXTERN> -27.94176 -41.20708 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1488" Parameter: A <- "-69.1488" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9418" Parameter: B <- "-27.9418" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2071" Parameter: C <- "-41.2071" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 585 TOTAL ENERGY = -69.1488 RDTITL> * VAN DER WAALS = -27.9418 ELECTROSTATIC = -41.2071 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "585" Parameter: CONF_N -> "8002" Comparing "585" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "586" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764314 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761403 ATOM PAIRS WERE FOUND FOR ATOM LIST 41932 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29772 from a total of 761403 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 586 -75.57624 6.42741 0.69052 INTE EXTERN> -26.11488 -49.46137 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5762" Parameter: A <- "-75.5762" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1149" Parameter: B <- "-26.1149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4614" Parameter: C <- "-49.4614" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 586 TOTAL ENERGY = -75.5762 RDTITL> * VAN DER WAALS = -26.1149 ELECTROSTATIC = -49.4614 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "586" Parameter: CONF_N -> "8002" Comparing "586" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "587" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761403 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768122 ATOM PAIRS WERE FOUND FOR ATOM LIST 42178 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30042 from a total of 768122 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 587 -70.20656 -5.36969 0.66552 INTE EXTERN> -26.70652 -43.50003 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2066" Parameter: A <- "-70.2066" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7065" Parameter: B <- "-26.7065" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5" Parameter: C <- "-43.5" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 587 TOTAL ENERGY = -70.2066 RDTITL> * VAN DER WAALS = -26.7065 ELECTROSTATIC = -43.5 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "587" Parameter: CONF_N -> "8002" Comparing "587" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "588" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768122 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761880 ATOM PAIRS WERE FOUND FOR ATOM LIST 41963 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29584 from a total of 761880 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 588 -80.05318 9.84662 0.73984 INTE EXTERN> -27.18806 -52.86511 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0532" Parameter: A <- "-80.0532" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1881" Parameter: B <- "-27.1881" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8651" Parameter: C <- "-52.8651" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 588 TOTAL ENERGY = -80.0532 RDTITL> * VAN DER WAALS = -27.1881 ELECTROSTATIC = -52.8651 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "588" Parameter: CONF_N -> "8002" Comparing "588" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "589" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761880 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760802 ATOM PAIRS WERE FOUND FOR ATOM LIST 41915 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29437 from a total of 760802 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 589 -76.53516 -3.51802 0.63279 INTE EXTERN> -31.94634 -44.58882 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5352" Parameter: A <- "-76.5352" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9463" Parameter: B <- "-31.9463" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5888" Parameter: C <- "-44.5888" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 589 TOTAL ENERGY = -76.5352 RDTITL> * VAN DER WAALS = -31.9463 ELECTROSTATIC = -44.5888 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "589" Parameter: CONF_N -> "8002" Comparing "589" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "590" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760802 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758741 ATOM PAIRS WERE FOUND FOR ATOM LIST 41459 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29852 from a total of 758741 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 590 -67.14650 -9.38866 0.72251 INTE EXTERN> -25.94503 -41.20148 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1465" Parameter: A <- "-67.1465" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.945" Parameter: B <- "-25.945" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2015" Parameter: C <- "-41.2015" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 590 TOTAL ENERGY = -67.1465 RDTITL> * VAN DER WAALS = -25.945 ELECTROSTATIC = -41.2015 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "590" Parameter: CONF_N -> "8002" Comparing "590" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "591" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758741 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764200 ATOM PAIRS WERE FOUND FOR ATOM LIST 41907 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29843 from a total of 764200 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 591 -72.86926 5.72275 0.62312 INTE EXTERN> -31.43678 -41.43248 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8693" Parameter: A <- "-72.8693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4368" Parameter: B <- "-31.4368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4325" Parameter: C <- "-41.4325" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 591 TOTAL ENERGY = -72.8693 RDTITL> * VAN DER WAALS = -31.4368 ELECTROSTATIC = -41.4325 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "591" Parameter: CONF_N -> "8002" Comparing "591" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "592" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764200 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769961 ATOM PAIRS WERE FOUND FOR ATOM LIST 42311 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30399 from a total of 769961 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 592 -70.97311 -1.89615 0.69229 INTE EXTERN> -28.23183 -42.74128 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9731" Parameter: A <- "-70.9731" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2318" Parameter: B <- "-28.2318" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7413" Parameter: C <- "-42.7413" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 592 TOTAL ENERGY = -70.9731 RDTITL> * VAN DER WAALS = -28.2318 ELECTROSTATIC = -42.7413 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "592" Parameter: CONF_N -> "8002" Comparing "592" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "593" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769961 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765281 ATOM PAIRS WERE FOUND FOR ATOM LIST 41955 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29913 from a total of 765281 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 593 -82.60390 11.63079 0.73812 INTE EXTERN> -28.15920 -54.44470 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.6039" Parameter: A <- "-82.6039" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1592" Parameter: B <- "-28.1592" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.4447" Parameter: C <- "-54.4447" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 593 TOTAL ENERGY = -82.6039 RDTITL> * VAN DER WAALS = -28.1592 ELECTROSTATIC = -54.4447 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "593" Parameter: CONF_N -> "8002" Comparing "593" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "594" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765281 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764550 ATOM PAIRS WERE FOUND FOR ATOM LIST 41932 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29933 from a total of 764550 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 594 -70.57438 -12.02952 0.69475 INTE EXTERN> -26.60336 -43.97102 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5744" Parameter: A <- "-70.5744" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6034" Parameter: B <- "-26.6034" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.971" Parameter: C <- "-43.971" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 594 TOTAL ENERGY = -70.5744 RDTITL> * VAN DER WAALS = -26.6034 ELECTROSTATIC = -43.971 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "594" Parameter: CONF_N -> "8002" Comparing "594" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "595" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764550 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762241 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29555 from a total of 762241 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 595 -70.40880 -0.16558 0.61380 INTE EXTERN> -30.04672 -40.36208 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4088" Parameter: A <- "-70.4088" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0467" Parameter: B <- "-30.0467" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3621" Parameter: C <- "-40.3621" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 595 TOTAL ENERGY = -70.4088 RDTITL> * VAN DER WAALS = -30.0467 ELECTROSTATIC = -40.3621 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "595" Parameter: CONF_N -> "8002" Comparing "595" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "596" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762241 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766306 ATOM PAIRS WERE FOUND FOR ATOM LIST 41841 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29754 from a total of 766306 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 596 -77.40201 6.99321 0.62904 INTE EXTERN> -31.37414 -46.02788 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.402" Parameter: A <- "-77.402" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3741" Parameter: B <- "-31.3741" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0279" Parameter: C <- "-46.0279" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 596 TOTAL ENERGY = -77.402 RDTITL> * VAN DER WAALS = -31.3741 ELECTROSTATIC = -46.0279 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "596" Parameter: CONF_N -> "8002" Comparing "596" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "597" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766306 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768453 ATOM PAIRS WERE FOUND FOR ATOM LIST 42147 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29373 from a total of 768453 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 597 -76.50540 -0.89661 0.63222 INTE EXTERN> -31.25117 -45.25423 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5054" Parameter: A <- "-76.5054" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2512" Parameter: B <- "-31.2512" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2542" Parameter: C <- "-45.2542" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 597 TOTAL ENERGY = -76.5054 RDTITL> * VAN DER WAALS = -31.2512 ELECTROSTATIC = -45.2542 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "597" Parameter: CONF_N -> "8002" Comparing "597" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "598" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768453 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761947 ATOM PAIRS WERE FOUND FOR ATOM LIST 41794 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29853 from a total of 761947 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 598 -79.04051 2.53511 0.67430 INTE EXTERN> -29.63116 -49.40935 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0405" Parameter: A <- "-79.0405" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6312" Parameter: B <- "-29.6312" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4093" Parameter: C <- "-49.4093" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 598 TOTAL ENERGY = -79.0405 RDTITL> * VAN DER WAALS = -29.6312 ELECTROSTATIC = -49.4093 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "598" Parameter: CONF_N -> "8002" Comparing "598" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "599" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761947 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762734 ATOM PAIRS WERE FOUND FOR ATOM LIST 41802 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29929 from a total of 762734 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 599 -84.99846 5.95795 0.69336 INTE EXTERN> -29.68300 -55.31546 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.9985" Parameter: A <- "-84.9985" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.683" Parameter: B <- "-29.683" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.3155" Parameter: C <- "-55.3155" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 599 TOTAL ENERGY = -84.9985 RDTITL> * VAN DER WAALS = -29.683 ELECTROSTATIC = -55.3155 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "599" Parameter: CONF_N -> "8002" Comparing "599" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "600" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762734 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764828 ATOM PAIRS WERE FOUND FOR ATOM LIST 41956 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30476 from a total of 764828 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 600 -82.84962 -2.14884 0.68571 INTE EXTERN> -29.45781 -53.39181 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.8496" Parameter: A <- "-82.8496" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4578" Parameter: B <- "-29.4578" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3918" Parameter: C <- "-53.3918" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 600 TOTAL ENERGY = -82.8496 RDTITL> * VAN DER WAALS = -29.4578 ELECTROSTATIC = -53.3918 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "600" Parameter: CONF_N -> "8002" Comparing "600" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "601" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764828 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763996 ATOM PAIRS WERE FOUND FOR ATOM LIST 41919 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30563 from a total of 763996 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 601 -86.55880 3.70918 0.80526 INTE EXTERN> -24.97019 -61.58861 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.5588" Parameter: A <- "-86.5588" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9702" Parameter: B <- "-24.9702" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-61.5886" Parameter: C <- "-61.5886" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 601 TOTAL ENERGY = -86.5588 RDTITL> * VAN DER WAALS = -24.9702 ELECTROSTATIC = -61.5886 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "601" Parameter: CONF_N -> "8002" Comparing "601" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "602" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763996 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758088 ATOM PAIRS WERE FOUND FOR ATOM LIST 41526 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29022 from a total of 758088 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 602 -85.43195 -1.12684 0.74519 INTE EXTERN> -27.31619 -58.11577 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.432" Parameter: A <- "-85.432" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3162" Parameter: B <- "-27.3162" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.1158" Parameter: C <- "-58.1158" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 602 TOTAL ENERGY = -85.432 RDTITL> * VAN DER WAALS = -27.3162 ELECTROSTATIC = -58.1158 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "602" Parameter: CONF_N -> "8002" Comparing "602" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "603" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758088 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761533 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29579 from a total of 761533 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 603 -85.87337 0.44141 0.70171 INTE EXTERN> -31.83625 -54.03712 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.8734" Parameter: A <- "-85.8734" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8363" Parameter: B <- "-31.8363" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0371" Parameter: C <- "-54.0371" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 603 TOTAL ENERGY = -85.8734 RDTITL> * VAN DER WAALS = -31.8363 ELECTROSTATIC = -54.0371 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "603" Parameter: CONF_N -> "8002" Comparing "603" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "604" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761533 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760619 ATOM PAIRS WERE FOUND FOR ATOM LIST 41614 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29308 from a total of 760619 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 604 -83.41831 -2.45506 0.71965 INTE EXTERN> -30.79185 -52.62645 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.4183" Parameter: A <- "-83.4183" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7919" Parameter: B <- "-30.7919" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6265" Parameter: C <- "-52.6265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 604 TOTAL ENERGY = -83.4183 RDTITL> * VAN DER WAALS = -30.7919 ELECTROSTATIC = -52.6265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "604" Parameter: CONF_N -> "8002" Comparing "604" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "605" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760619 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763203 ATOM PAIRS WERE FOUND FOR ATOM LIST 42014 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29439 from a total of 763203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 605 -72.03603 -11.38228 0.63202 INTE EXTERN> -29.76099 -42.27504 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.036" Parameter: A <- "-72.036" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.761" Parameter: B <- "-29.761" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.275" Parameter: C <- "-42.275" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 605 TOTAL ENERGY = -72.036 RDTITL> * VAN DER WAALS = -29.761 ELECTROSTATIC = -42.275 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "605" Parameter: CONF_N -> "8002" Comparing "605" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "606" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764234 ATOM PAIRS WERE FOUND FOR ATOM LIST 41921 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29692 from a total of 764234 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 606 -76.04036 4.00433 0.64945 INTE EXTERN> -31.92994 -44.11042 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0404" Parameter: A <- "-76.0404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9299" Parameter: B <- "-31.9299" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1104" Parameter: C <- "-44.1104" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 606 TOTAL ENERGY = -76.0404 RDTITL> * VAN DER WAALS = -31.9299 ELECTROSTATIC = -44.1104 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "606" Parameter: CONF_N -> "8002" Comparing "606" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "607" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764234 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762135 ATOM PAIRS WERE FOUND FOR ATOM LIST 41773 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29928 from a total of 762135 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 607 -85.51082 9.47047 0.72004 INTE EXTERN> -29.32339 -56.18743 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.5108" Parameter: A <- "-85.5108" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3234" Parameter: B <- "-29.3234" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.1874" Parameter: C <- "-56.1874" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 607 TOTAL ENERGY = -85.5108 RDTITL> * VAN DER WAALS = -29.3234 ELECTROSTATIC = -56.1874 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "607" Parameter: CONF_N -> "8002" Comparing "607" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "608" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762135 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762748 ATOM PAIRS WERE FOUND FOR ATOM LIST 41909 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29288 from a total of 762748 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 608 -83.80363 -1.70719 0.64619 INTE EXTERN> -30.77927 -53.02437 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.8036" Parameter: A <- "-83.8036" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7793" Parameter: B <- "-30.7793" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0244" Parameter: C <- "-53.0244" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 608 TOTAL ENERGY = -83.8036 RDTITL> * VAN DER WAALS = -30.7793 ELECTROSTATIC = -53.0244 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "608" Parameter: CONF_N -> "8002" Comparing "608" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "609" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762748 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761613 ATOM PAIRS WERE FOUND FOR ATOM LIST 41727 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29223 from a total of 761613 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 609 -82.98164 -0.82199 0.73402 INTE EXTERN> -26.83827 -56.14337 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9816" Parameter: A <- "-82.9816" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8383" Parameter: B <- "-26.8383" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.1434" Parameter: C <- "-56.1434" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 609 TOTAL ENERGY = -82.9816 RDTITL> * VAN DER WAALS = -26.8383 ELECTROSTATIC = -56.1434 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "609" Parameter: CONF_N -> "8002" Comparing "609" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "610" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761613 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756007 ATOM PAIRS WERE FOUND FOR ATOM LIST 41487 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29321 from a total of 756007 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 610 -73.71399 -9.26765 0.66462 INTE EXTERN> -29.66433 -44.04966 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.714" Parameter: A <- "-73.714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6643" Parameter: B <- "-29.6643" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0497" Parameter: C <- "-44.0497" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 610 TOTAL ENERGY = -73.714 RDTITL> * VAN DER WAALS = -29.6643 ELECTROSTATIC = -44.0497 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "610" Parameter: CONF_N -> "8002" Comparing "610" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "611" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756007 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759514 ATOM PAIRS WERE FOUND FOR ATOM LIST 41475 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29104 from a total of 759514 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 611 -75.75726 2.04327 0.65616 INTE EXTERN> -29.60589 -46.15137 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7573" Parameter: A <- "-75.7573" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6059" Parameter: B <- "-29.6059" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1514" Parameter: C <- "-46.1514" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 611 TOTAL ENERGY = -75.7573 RDTITL> * VAN DER WAALS = -29.6059 ELECTROSTATIC = -46.1514 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "611" Parameter: CONF_N -> "8002" Comparing "611" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "612" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759514 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764108 ATOM PAIRS WERE FOUND FOR ATOM LIST 41950 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29452 from a total of 764108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 612 -78.85879 3.10153 0.60916 INTE EXTERN> -32.04789 -46.81090 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8588" Parameter: A <- "-78.8588" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0479" Parameter: B <- "-32.0479" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8109" Parameter: C <- "-46.8109" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 612 TOTAL ENERGY = -78.8588 RDTITL> * VAN DER WAALS = -32.0479 ELECTROSTATIC = -46.8109 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "612" Parameter: CONF_N -> "8002" Comparing "612" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "613" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756121 ATOM PAIRS WERE FOUND FOR ATOM LIST 41589 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28883 from a total of 756121 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 613 -76.16272 -2.69608 0.61344 INTE EXTERN> -29.72138 -46.44134 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1627" Parameter: A <- "-76.1627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7214" Parameter: B <- "-29.7214" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4413" Parameter: C <- "-46.4413" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 613 TOTAL ENERGY = -76.1627 RDTITL> * VAN DER WAALS = -29.7214 ELECTROSTATIC = -46.4413 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "613" Parameter: CONF_N -> "8002" Comparing "613" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "614" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756121 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763316 ATOM PAIRS WERE FOUND FOR ATOM LIST 41929 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29701 from a total of 763316 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 614 -65.27532 -10.88739 0.62220 INTE EXTERN> -27.50330 -37.77202 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2753" Parameter: A <- "-65.2753" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5033" Parameter: B <- "-27.5033" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.772" Parameter: C <- "-37.772" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 614 TOTAL ENERGY = -65.2753 RDTITL> * VAN DER WAALS = -27.5033 ELECTROSTATIC = -37.772 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "614" Parameter: CONF_N -> "8002" Comparing "614" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "615" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763316 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763433 ATOM PAIRS WERE FOUND FOR ATOM LIST 42107 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29517 from a total of 763433 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 615 -72.79282 7.51750 0.59513 INTE EXTERN> -30.71993 -42.07290 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7928" Parameter: A <- "-72.7928" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7199" Parameter: B <- "-30.7199" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0729" Parameter: C <- "-42.0729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 615 TOTAL ENERGY = -72.7928 RDTITL> * VAN DER WAALS = -30.7199 ELECTROSTATIC = -42.0729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "615" Parameter: CONF_N -> "8002" Comparing "615" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "616" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763433 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764905 ATOM PAIRS WERE FOUND FOR ATOM LIST 41982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29035 from a total of 764905 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 616 -67.50224 -5.29059 0.64225 INTE EXTERN> -27.89918 -39.60306 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5022" Parameter: A <- "-67.5022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8992" Parameter: B <- "-27.8992" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6031" Parameter: C <- "-39.6031" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 616 TOTAL ENERGY = -67.5022 RDTITL> * VAN DER WAALS = -27.8992 ELECTROSTATIC = -39.6031 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "616" Parameter: CONF_N -> "8002" Comparing "616" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "617" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764905 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767872 ATOM PAIRS WERE FOUND FOR ATOM LIST 42199 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29027 from a total of 767872 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 617 -67.76926 0.26702 0.53600 INTE EXTERN> -33.24149 -34.52777 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7693" Parameter: A <- "-67.7693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2415" Parameter: B <- "-33.2415" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5278" Parameter: C <- "-34.5278" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 617 TOTAL ENERGY = -67.7693 RDTITL> * VAN DER WAALS = -33.2415 ELECTROSTATIC = -34.5278 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "617" Parameter: CONF_N -> "8002" Comparing "617" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "618" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767872 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766672 ATOM PAIRS WERE FOUND FOR ATOM LIST 42147 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29845 from a total of 766672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 618 -76.37449 8.60523 0.61702 INTE EXTERN> -32.28495 -44.08954 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3745" Parameter: A <- "-76.3745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.285" Parameter: B <- "-32.285" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0895" Parameter: C <- "-44.0895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 618 TOTAL ENERGY = -76.3745 RDTITL> * VAN DER WAALS = -32.285 ELECTROSTATIC = -44.0895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "618" Parameter: CONF_N -> "8002" Comparing "618" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "619" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763391 ATOM PAIRS WERE FOUND FOR ATOM LIST 41893 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30052 from a total of 763391 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 619 -78.61146 2.23697 0.73906 INTE EXTERN> -25.74039 -52.87107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6115" Parameter: A <- "-78.6115" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7404" Parameter: B <- "-25.7404" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8711" Parameter: C <- "-52.8711" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 619 TOTAL ENERGY = -78.6115 RDTITL> * VAN DER WAALS = -25.7404 ELECTROSTATIC = -52.8711 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "619" Parameter: CONF_N -> "8002" Comparing "619" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "620" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763391 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763921 ATOM PAIRS WERE FOUND FOR ATOM LIST 41887 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29918 from a total of 763921 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 620 -71.64521 -6.96625 0.59593 INTE EXTERN> -30.47805 -41.16716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6452" Parameter: A <- "-71.6452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.478" Parameter: B <- "-30.478" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1672" Parameter: C <- "-41.1672" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 620 TOTAL ENERGY = -71.6452 RDTITL> * VAN DER WAALS = -30.478 ELECTROSTATIC = -41.1672 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "620" Parameter: CONF_N -> "8002" Comparing "620" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "621" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763921 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758762 ATOM PAIRS WERE FOUND FOR ATOM LIST 41695 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29153 from a total of 758762 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 621 -71.88586 0.24065 0.67807 INTE EXTERN> -30.00650 -41.87936 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8859" Parameter: A <- "-71.8859" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0065" Parameter: B <- "-30.0065" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8794" Parameter: C <- "-41.8794" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 621 TOTAL ENERGY = -71.8859 RDTITL> * VAN DER WAALS = -30.0065 ELECTROSTATIC = -41.8794 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "621" Parameter: CONF_N -> "8002" Comparing "621" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "622" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758762 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757409 ATOM PAIRS WERE FOUND FOR ATOM LIST 41696 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28993 from a total of 757409 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 622 -81.87167 9.98581 0.62689 INTE EXTERN> -31.75915 -50.11252 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8717" Parameter: A <- "-81.8717" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7591" Parameter: B <- "-31.7591" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1125" Parameter: C <- "-50.1125" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 622 TOTAL ENERGY = -81.8717 RDTITL> * VAN DER WAALS = -31.7591 ELECTROSTATIC = -50.1125 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "622" Parameter: CONF_N -> "8002" Comparing "622" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "623" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757409 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761091 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30009 from a total of 761091 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 623 -74.46354 -7.40813 0.82158 INTE EXTERN> -23.56298 -50.90056 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4635" Parameter: A <- "-74.4635" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.563" Parameter: B <- "-23.563" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9006" Parameter: C <- "-50.9006" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 623 TOTAL ENERGY = -74.4635 RDTITL> * VAN DER WAALS = -23.563 ELECTROSTATIC = -50.9006 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "623" Parameter: CONF_N -> "8002" Comparing "623" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "624" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761091 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761898 ATOM PAIRS WERE FOUND FOR ATOM LIST 42126 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29413 from a total of 761898 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 624 -67.85085 -6.61269 0.66501 INTE EXTERN> -30.80473 -37.04612 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8509" Parameter: A <- "-67.8509" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8047" Parameter: B <- "-30.8047" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0461" Parameter: C <- "-37.0461" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 624 TOTAL ENERGY = -67.8509 RDTITL> * VAN DER WAALS = -30.8047 ELECTROSTATIC = -37.0461 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "624" Parameter: CONF_N -> "8002" Comparing "624" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "625" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761898 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760904 ATOM PAIRS WERE FOUND FOR ATOM LIST 42075 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29727 from a total of 760904 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 625 -69.20430 1.35344 0.69350 INTE EXTERN> -28.23124 -40.97305 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2043" Parameter: A <- "-69.2043" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2312" Parameter: B <- "-28.2312" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9731" Parameter: C <- "-40.9731" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 625 TOTAL ENERGY = -69.2043 RDTITL> * VAN DER WAALS = -28.2312 ELECTROSTATIC = -40.9731 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "625" Parameter: CONF_N -> "8002" Comparing "625" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "626" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760904 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758051 ATOM PAIRS WERE FOUND FOR ATOM LIST 41512 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29861 from a total of 758051 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 626 -75.20743 6.00313 0.73199 INTE EXTERN> -29.06218 -46.14525 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2074" Parameter: A <- "-75.2074" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0622" Parameter: B <- "-29.0622" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1452" Parameter: C <- "-46.1452" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 626 TOTAL ENERGY = -75.2074 RDTITL> * VAN DER WAALS = -29.0622 ELECTROSTATIC = -46.1452 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "626" Parameter: CONF_N -> "8002" Comparing "626" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "627" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758051 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764528 ATOM PAIRS WERE FOUND FOR ATOM LIST 41883 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29899 from a total of 764528 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 627 -71.21938 -3.98805 0.68494 INTE EXTERN> -30.02098 -41.19840 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2194" Parameter: A <- "-71.2194" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.021" Parameter: B <- "-30.021" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1984" Parameter: C <- "-41.1984" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 627 TOTAL ENERGY = -71.2194 RDTITL> * VAN DER WAALS = -30.021 ELECTROSTATIC = -41.1984 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "627" Parameter: CONF_N -> "8002" Comparing "627" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "628" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764528 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761481 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30186 from a total of 761481 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 628 -67.59365 -3.62573 0.64138 INTE EXTERN> -28.42572 -39.16793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5936" Parameter: A <- "-67.5936" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4257" Parameter: B <- "-28.4257" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1679" Parameter: C <- "-39.1679" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 628 TOTAL ENERGY = -67.5936 RDTITL> * VAN DER WAALS = -28.4257 ELECTROSTATIC = -39.1679 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "628" Parameter: CONF_N -> "8002" Comparing "628" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "629" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761481 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763023 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29841 from a total of 763023 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 629 -71.37461 3.78097 0.70817 INTE EXTERN> -25.37820 -45.99641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3746" Parameter: A <- "-71.3746" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3782" Parameter: B <- "-25.3782" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9964" Parameter: C <- "-45.9964" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 629 TOTAL ENERGY = -71.3746 RDTITL> * VAN DER WAALS = -25.3782 ELECTROSTATIC = -45.9964 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "629" Parameter: CONF_N -> "8002" Comparing "629" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "630" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763023 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761425 ATOM PAIRS WERE FOUND FOR ATOM LIST 41973 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29720 from a total of 761425 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 630 -79.69460 8.31999 0.65389 INTE EXTERN> -30.54199 -49.15261 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6946" Parameter: A <- "-79.6946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.542" Parameter: B <- "-30.542" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1526" Parameter: C <- "-49.1526" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 630 TOTAL ENERGY = -79.6946 RDTITL> * VAN DER WAALS = -30.542 ELECTROSTATIC = -49.1526 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "630" Parameter: CONF_N -> "8002" Comparing "630" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "631" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761425 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761475 ATOM PAIRS WERE FOUND FOR ATOM LIST 41815 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29765 from a total of 761475 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 631 -78.69240 -1.00220 0.71971 INTE EXTERN> -26.57149 -52.12091 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6924" Parameter: A <- "-78.6924" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5715" Parameter: B <- "-26.5715" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1209" Parameter: C <- "-52.1209" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 631 TOTAL ENERGY = -78.6924 RDTITL> * VAN DER WAALS = -26.5715 ELECTROSTATIC = -52.1209 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "631" Parameter: CONF_N -> "8002" Comparing "631" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "632" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761475 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765310 ATOM PAIRS WERE FOUND FOR ATOM LIST 42156 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30271 from a total of 765310 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 632 -75.73659 -2.95581 0.64736 INTE EXTERN> -30.89539 -44.84121 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7366" Parameter: A <- "-75.7366" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8954" Parameter: B <- "-30.8954" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8412" Parameter: C <- "-44.8412" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 632 TOTAL ENERGY = -75.7366 RDTITL> * VAN DER WAALS = -30.8954 ELECTROSTATIC = -44.8412 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "632" Parameter: CONF_N -> "8002" Comparing "632" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "633" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765310 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760205 ATOM PAIRS WERE FOUND FOR ATOM LIST 41936 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29600 from a total of 760205 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 633 -84.10941 8.37281 0.69625 INTE EXTERN> -28.64911 -55.46029 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.1094" Parameter: A <- "-84.1094" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6491" Parameter: B <- "-28.6491" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.4603" Parameter: C <- "-55.4603" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 633 TOTAL ENERGY = -84.1094 RDTITL> * VAN DER WAALS = -28.6491 ELECTROSTATIC = -55.4603 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "633" Parameter: CONF_N -> "8002" Comparing "633" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "634" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760205 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762212 ATOM PAIRS WERE FOUND FOR ATOM LIST 41867 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28691 from a total of 762212 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 634 -70.81131 -13.29810 0.58131 INTE EXTERN> -32.43032 -38.38098 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8113" Parameter: A <- "-70.8113" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4303" Parameter: B <- "-32.4303" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.381" Parameter: C <- "-38.381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 634 TOTAL ENERGY = -70.8113 RDTITL> * VAN DER WAALS = -32.4303 ELECTROSTATIC = -38.381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "634" Parameter: CONF_N -> "8002" Comparing "634" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "635" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762212 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761474 ATOM PAIRS WERE FOUND FOR ATOM LIST 41803 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29649 from a total of 761474 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 635 -80.23679 9.42549 0.72529 INTE EXTERN> -25.96803 -54.26876 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2368" Parameter: A <- "-80.2368" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.968" Parameter: B <- "-25.968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2688" Parameter: C <- "-54.2688" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 635 TOTAL ENERGY = -80.2368 RDTITL> * VAN DER WAALS = -25.968 ELECTROSTATIC = -54.2688 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "635" Parameter: CONF_N -> "8002" Comparing "635" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "636" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761474 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764898 ATOM PAIRS WERE FOUND FOR ATOM LIST 41942 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30005 from a total of 764898 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 636 -65.57324 -14.66356 0.66438 INTE EXTERN> -27.56769 -38.00555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5732" Parameter: A <- "-65.5732" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5677" Parameter: B <- "-27.5677" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0055" Parameter: C <- "-38.0055" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 636 TOTAL ENERGY = -65.5732 RDTITL> * VAN DER WAALS = -27.5677 ELECTROSTATIC = -38.0055 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "636" Parameter: CONF_N -> "8002" Comparing "636" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "637" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764898 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759932 ATOM PAIRS WERE FOUND FOR ATOM LIST 41651 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29482 from a total of 759932 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 637 -68.76028 3.18704 0.62397 INTE EXTERN> -30.12581 -38.63447 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7603" Parameter: A <- "-68.7603" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1258" Parameter: B <- "-30.1258" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6345" Parameter: C <- "-38.6345" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 637 TOTAL ENERGY = -68.7603 RDTITL> * VAN DER WAALS = -30.1258 ELECTROSTATIC = -38.6345 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "637" Parameter: CONF_N -> "8002" Comparing "637" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "638" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759932 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765235 ATOM PAIRS WERE FOUND FOR ATOM LIST 42021 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29947 from a total of 765235 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 638 -73.04473 4.28445 0.66911 INTE EXTERN> -28.75937 -44.28536 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0447" Parameter: A <- "-73.0447" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7594" Parameter: B <- "-28.7594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2854" Parameter: C <- "-44.2854" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 638 TOTAL ENERGY = -73.0447 RDTITL> * VAN DER WAALS = -28.7594 ELECTROSTATIC = -44.2854 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "638" Parameter: CONF_N -> "8002" Comparing "638" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "639" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765235 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762856 ATOM PAIRS WERE FOUND FOR ATOM LIST 42025 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30166 from a total of 762856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 639 -74.55114 1.50641 0.57384 INTE EXTERN> -33.20503 -41.34611 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5511" Parameter: A <- "-74.5511" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.205" Parameter: B <- "-33.205" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3461" Parameter: C <- "-41.3461" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 639 TOTAL ENERGY = -74.5511 RDTITL> * VAN DER WAALS = -33.205 ELECTROSTATIC = -41.3461 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "639" Parameter: CONF_N -> "8002" Comparing "639" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "640" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762976 ATOM PAIRS WERE FOUND FOR ATOM LIST 41935 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29325 from a total of 762976 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 640 -68.34852 -6.20261 0.66923 INTE EXTERN> -27.32228 -41.02624 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3485" Parameter: A <- "-68.3485" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3223" Parameter: B <- "-27.3223" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0262" Parameter: C <- "-41.0262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 640 TOTAL ENERGY = -68.3485 RDTITL> * VAN DER WAALS = -27.3223 ELECTROSTATIC = -41.0262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "640" Parameter: CONF_N -> "8002" Comparing "640" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "641" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762976 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761385 ATOM PAIRS WERE FOUND FOR ATOM LIST 41778 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29919 from a total of 761385 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 641 -75.28318 6.93466 0.62415 INTE EXTERN> -30.81330 -44.46988 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2832" Parameter: A <- "-75.2832" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8133" Parameter: B <- "-30.8133" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4699" Parameter: C <- "-44.4699" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 641 TOTAL ENERGY = -75.2832 RDTITL> * VAN DER WAALS = -30.8133 ELECTROSTATIC = -44.4699 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "641" Parameter: CONF_N -> "8002" Comparing "641" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "642" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761385 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764506 ATOM PAIRS WERE FOUND FOR ATOM LIST 42054 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29997 from a total of 764506 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 642 -69.45204 -5.83114 0.72042 INTE EXTERN> -26.42824 -43.02380 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.452" Parameter: A <- "-69.452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4282" Parameter: B <- "-26.4282" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0238" Parameter: C <- "-43.0238" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 642 TOTAL ENERGY = -69.452 RDTITL> * VAN DER WAALS = -26.4282 ELECTROSTATIC = -43.0238 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "642" Parameter: CONF_N -> "8002" Comparing "642" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "643" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764506 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766655 ATOM PAIRS WERE FOUND FOR ATOM LIST 42346 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29843 from a total of 766655 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 643 -65.58341 -3.86863 0.57900 INTE EXTERN> -31.12616 -34.45725 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5834" Parameter: A <- "-65.5834" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1262" Parameter: B <- "-31.1262" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4572" Parameter: C <- "-34.4572" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 643 TOTAL ENERGY = -65.5834 RDTITL> * VAN DER WAALS = -31.1262 ELECTROSTATIC = -34.4572 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "643" Parameter: CONF_N -> "8002" Comparing "643" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "644" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766655 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762462 ATOM PAIRS WERE FOUND FOR ATOM LIST 41853 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29653 from a total of 762462 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 644 -64.56043 -1.02298 0.53070 INTE EXTERN> -33.54745 -31.01297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5604" Parameter: A <- "-64.5604" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5475" Parameter: B <- "-33.5475" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.013" Parameter: C <- "-31.013" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 644 TOTAL ENERGY = -64.5604 RDTITL> * VAN DER WAALS = -33.5475 ELECTROSTATIC = -31.013 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "644" Parameter: CONF_N -> "8002" Comparing "644" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "645" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762462 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763982 ATOM PAIRS WERE FOUND FOR ATOM LIST 41999 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29662 from a total of 763982 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 645 -70.58140 6.02097 0.58182 INTE EXTERN> -30.60457 -39.97683 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5814" Parameter: A <- "-70.5814" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6046" Parameter: B <- "-30.6046" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9768" Parameter: C <- "-39.9768" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 645 TOTAL ENERGY = -70.5814 RDTITL> * VAN DER WAALS = -30.6046 ELECTROSTATIC = -39.9768 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "645" Parameter: CONF_N -> "8002" Comparing "645" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "646" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763982 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759668 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29661 from a total of 759668 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 646 -71.92867 1.34728 0.55306 INTE EXTERN> -30.44641 -41.48226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9287" Parameter: A <- "-71.9287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4464" Parameter: B <- "-30.4464" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4823" Parameter: C <- "-41.4823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 646 TOTAL ENERGY = -71.9287 RDTITL> * VAN DER WAALS = -30.4464 ELECTROSTATIC = -41.4823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "646" Parameter: CONF_N -> "8002" Comparing "646" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "647" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759668 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759497 ATOM PAIRS WERE FOUND FOR ATOM LIST 41721 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29986 from a total of 759497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 647 -72.90490 0.97622 0.61422 INTE EXTERN> -30.00957 -42.89533 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9049" Parameter: A <- "-72.9049" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0096" Parameter: B <- "-30.0096" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8953" Parameter: C <- "-42.8953" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 647 TOTAL ENERGY = -72.9049 RDTITL> * VAN DER WAALS = -30.0096 ELECTROSTATIC = -42.8953 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "647" Parameter: CONF_N -> "8002" Comparing "647" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "648" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762208 ATOM PAIRS WERE FOUND FOR ATOM LIST 41804 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30168 from a total of 762208 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 648 -77.26979 4.36489 0.61224 INTE EXTERN> -31.42741 -45.84238 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2698" Parameter: A <- "-77.2698" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4274" Parameter: B <- "-31.4274" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8424" Parameter: C <- "-45.8424" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 648 TOTAL ENERGY = -77.2698 RDTITL> * VAN DER WAALS = -31.4274 ELECTROSTATIC = -45.8424 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "648" Parameter: CONF_N -> "8002" Comparing "648" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "649" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762208 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761955 ATOM PAIRS WERE FOUND FOR ATOM LIST 41850 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30088 from a total of 761955 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 649 -71.67526 -5.59453 0.68879 INTE EXTERN> -27.36655 -44.30871 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6753" Parameter: A <- "-71.6753" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3665" Parameter: B <- "-27.3665" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3087" Parameter: C <- "-44.3087" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 649 TOTAL ENERGY = -71.6753 RDTITL> * VAN DER WAALS = -27.3665 ELECTROSTATIC = -44.3087 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "649" Parameter: CONF_N -> "8002" Comparing "649" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "650" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761955 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758583 ATOM PAIRS WERE FOUND FOR ATOM LIST 41595 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29711 from a total of 758583 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 650 -84.00250 12.32724 0.73444 INTE EXTERN> -25.66105 -58.34146 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.0025" Parameter: A <- "-84.0025" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.661" Parameter: B <- "-25.661" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.3415" Parameter: C <- "-58.3415" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 650 TOTAL ENERGY = -84.0025 RDTITL> * VAN DER WAALS = -25.661 ELECTROSTATIC = -58.3415 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "650" Parameter: CONF_N -> "8002" Comparing "650" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "651" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758583 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761139 ATOM PAIRS WERE FOUND FOR ATOM LIST 41995 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29621 from a total of 761139 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 651 -70.81114 -13.19136 0.54311 INTE EXTERN> -31.76532 -39.04582 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8111" Parameter: A <- "-70.8111" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7653" Parameter: B <- "-31.7653" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0458" Parameter: C <- "-39.0458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 651 TOTAL ENERGY = -70.8111 RDTITL> * VAN DER WAALS = -31.7653 ELECTROSTATIC = -39.0458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "651" Parameter: CONF_N -> "8002" Comparing "651" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "652" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761139 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757954 ATOM PAIRS WERE FOUND FOR ATOM LIST 41551 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29925 from a total of 757954 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 652 -64.75439 -6.05675 0.49372 INTE EXTERN> -33.71087 -31.04352 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7544" Parameter: A <- "-64.7544" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7109" Parameter: B <- "-33.7109" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.0435" Parameter: C <- "-31.0435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 652 TOTAL ENERGY = -64.7544 RDTITL> * VAN DER WAALS = -33.7109 ELECTROSTATIC = -31.0435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "652" Parameter: CONF_N -> "8002" Comparing "652" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "653" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757954 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764494 ATOM PAIRS WERE FOUND FOR ATOM LIST 41782 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29571 from a total of 764494 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 653 -68.69756 3.94317 0.60069 INTE EXTERN> -30.73562 -37.96195 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6976" Parameter: A <- "-68.6976" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7356" Parameter: B <- "-30.7356" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9619" Parameter: C <- "-37.9619" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 653 TOTAL ENERGY = -68.6976 RDTITL> * VAN DER WAALS = -30.7356 ELECTROSTATIC = -37.9619 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "653" Parameter: CONF_N -> "8002" Comparing "653" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "654" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764494 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755575 ATOM PAIRS WERE FOUND FOR ATOM LIST 41508 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29623 from a total of 755575 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 654 -75.82789 7.13032 0.55087 INTE EXTERN> -33.71122 -42.11667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8279" Parameter: A <- "-75.8279" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7112" Parameter: B <- "-33.7112" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1167" Parameter: C <- "-42.1167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 654 TOTAL ENERGY = -75.8279 RDTITL> * VAN DER WAALS = -33.7112 ELECTROSTATIC = -42.1167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "654" Parameter: CONF_N -> "8002" Comparing "654" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "655" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755575 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762191 ATOM PAIRS WERE FOUND FOR ATOM LIST 41744 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30059 from a total of 762191 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 655 -70.62408 -5.20381 0.62926 INTE EXTERN> -29.59165 -41.03243 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6241" Parameter: A <- "-70.6241" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5916" Parameter: B <- "-29.5916" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0324" Parameter: C <- "-41.0324" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 655 TOTAL ENERGY = -70.6241 RDTITL> * VAN DER WAALS = -29.5916 ELECTROSTATIC = -41.0324 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "655" Parameter: CONF_N -> "8002" Comparing "655" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "656" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762191 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760195 ATOM PAIRS WERE FOUND FOR ATOM LIST 41642 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29564 from a total of 760195 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 656 -68.80903 -1.81505 0.66156 INTE EXTERN> -28.74389 -40.06514 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.809" Parameter: A <- "-68.809" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7439" Parameter: B <- "-28.7439" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0651" Parameter: C <- "-40.0651" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 656 TOTAL ENERGY = -68.809 RDTITL> * VAN DER WAALS = -28.7439 ELECTROSTATIC = -40.0651 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "656" Parameter: CONF_N -> "8002" Comparing "656" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "657" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760195 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758194 ATOM PAIRS WERE FOUND FOR ATOM LIST 41564 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29265 from a total of 758194 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 657 -73.30743 4.49840 0.69701 INTE EXTERN> -28.18992 -45.11751 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3074" Parameter: A <- "-73.3074" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1899" Parameter: B <- "-28.1899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1175" Parameter: C <- "-45.1175" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 657 TOTAL ENERGY = -73.3074 RDTITL> * VAN DER WAALS = -28.1899 ELECTROSTATIC = -45.1175 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "657" Parameter: CONF_N -> "8002" Comparing "657" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "658" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758194 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757847 ATOM PAIRS WERE FOUND FOR ATOM LIST 41707 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29962 from a total of 757847 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 658 -67.44693 -5.86049 0.68874 INTE EXTERN> -28.20619 -39.24074 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4469" Parameter: A <- "-67.4469" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2062" Parameter: B <- "-28.2062" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2407" Parameter: C <- "-39.2407" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 658 TOTAL ENERGY = -67.4469 RDTITL> * VAN DER WAALS = -28.2062 ELECTROSTATIC = -39.2407 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "658" Parameter: CONF_N -> "8002" Comparing "658" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "659" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757847 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763530 ATOM PAIRS WERE FOUND FOR ATOM LIST 41679 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29927 from a total of 763530 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 659 -74.87507 7.42814 0.63763 INTE EXTERN> -30.94441 -43.93066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8751" Parameter: A <- "-74.8751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9444" Parameter: B <- "-30.9444" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9307" Parameter: C <- "-43.9307" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 659 TOTAL ENERGY = -74.8751 RDTITL> * VAN DER WAALS = -30.9444 ELECTROSTATIC = -43.9307 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "659" Parameter: CONF_N -> "8002" Comparing "659" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "660" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763530 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759786 ATOM PAIRS WERE FOUND FOR ATOM LIST 41789 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29317 from a total of 759786 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 660 -75.47906 0.60399 0.64480 INTE EXTERN> -30.79749 -44.68157 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4791" Parameter: A <- "-75.4791" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7975" Parameter: B <- "-30.7975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6816" Parameter: C <- "-44.6816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 660 TOTAL ENERGY = -75.4791 RDTITL> * VAN DER WAALS = -30.7975 ELECTROSTATIC = -44.6816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "660" Parameter: CONF_N -> "8002" Comparing "660" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "661" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759786 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761084 ATOM PAIRS WERE FOUND FOR ATOM LIST 41670 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29660 from a total of 761084 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 661 -76.09580 0.61674 0.64554 INTE EXTERN> -29.05209 -47.04371 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0958" Parameter: A <- "-76.0958" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0521" Parameter: B <- "-29.0521" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0437" Parameter: C <- "-47.0437" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 661 TOTAL ENERGY = -76.0958 RDTITL> * VAN DER WAALS = -29.0521 ELECTROSTATIC = -47.0437 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "661" Parameter: CONF_N -> "8002" Comparing "661" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "662" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761084 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756757 ATOM PAIRS WERE FOUND FOR ATOM LIST 41734 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28580 from a total of 756757 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 662 -65.18642 -10.90938 0.65939 INTE EXTERN> -28.74436 -36.44206 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1864" Parameter: A <- "-65.1864" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7444" Parameter: B <- "-28.7444" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4421" Parameter: C <- "-36.4421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 662 TOTAL ENERGY = -65.1864 RDTITL> * VAN DER WAALS = -28.7444 ELECTROSTATIC = -36.4421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "662" Parameter: CONF_N -> "8002" Comparing "662" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "663" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756757 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763078 ATOM PAIRS WERE FOUND FOR ATOM LIST 41791 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30233 from a total of 763078 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 663 -74.28809 9.10167 0.57833 INTE EXTERN> -30.65275 -43.63534 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2881" Parameter: A <- "-74.2881" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6528" Parameter: B <- "-30.6528" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6353" Parameter: C <- "-43.6353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 663 TOTAL ENERGY = -74.2881 RDTITL> * VAN DER WAALS = -30.6528 ELECTROSTATIC = -43.6353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "663" Parameter: CONF_N -> "8002" Comparing "663" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "664" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763078 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758535 ATOM PAIRS WERE FOUND FOR ATOM LIST 41615 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29776 from a total of 758535 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 664 -76.52076 2.23267 0.60559 INTE EXTERN> -30.95801 -45.56275 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5208" Parameter: A <- "-76.5208" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.958" Parameter: B <- "-30.958" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5627" Parameter: C <- "-45.5627" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 664 TOTAL ENERGY = -76.5208 RDTITL> * VAN DER WAALS = -30.958 ELECTROSTATIC = -45.5627 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "664" Parameter: CONF_N -> "8002" Comparing "664" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "665" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758535 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762098 ATOM PAIRS WERE FOUND FOR ATOM LIST 41975 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29991 from a total of 762098 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 665 -68.96136 -7.55939 0.57679 INTE EXTERN> -32.90427 -36.05709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9614" Parameter: A <- "-68.9614" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9043" Parameter: B <- "-32.9043" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0571" Parameter: C <- "-36.0571" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 665 TOTAL ENERGY = -68.9614 RDTITL> * VAN DER WAALS = -32.9043 ELECTROSTATIC = -36.0571 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "665" Parameter: CONF_N -> "8002" Comparing "665" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "666" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762098 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759566 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29780 from a total of 759566 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 666 -68.12833 -0.83303 0.55457 INTE EXTERN> -32.07307 -36.05527 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1283" Parameter: A <- "-68.1283" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0731" Parameter: B <- "-32.0731" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0553" Parameter: C <- "-36.0553" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 666 TOTAL ENERGY = -68.1283 RDTITL> * VAN DER WAALS = -32.0731 ELECTROSTATIC = -36.0553 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "666" Parameter: CONF_N -> "8002" Comparing "666" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "667" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759566 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762628 ATOM PAIRS WERE FOUND FOR ATOM LIST 42008 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30549 from a total of 762628 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 667 -69.94506 1.81673 0.64257 INTE EXTERN> -31.96824 -37.97683 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9451" Parameter: A <- "-69.9451" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9682" Parameter: B <- "-31.9682" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9768" Parameter: C <- "-37.9768" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 667 TOTAL ENERGY = -69.9451 RDTITL> * VAN DER WAALS = -31.9682 ELECTROSTATIC = -37.9768 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "667" Parameter: CONF_N -> "8002" Comparing "667" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "668" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762628 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759527 ATOM PAIRS WERE FOUND FOR ATOM LIST 41654 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30342 from a total of 759527 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 668 -70.14491 0.19985 0.58870 INTE EXTERN> -31.42315 -38.72177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1449" Parameter: A <- "-70.1449" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4231" Parameter: B <- "-31.4231" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7218" Parameter: C <- "-38.7218" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 668 TOTAL ENERGY = -70.1449 RDTITL> * VAN DER WAALS = -31.4231 ELECTROSTATIC = -38.7218 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "668" Parameter: CONF_N -> "8002" Comparing "668" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "669" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759527 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759574 ATOM PAIRS WERE FOUND FOR ATOM LIST 41582 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29857 from a total of 759574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 669 -65.23121 -4.91371 0.61210 INTE EXTERN> -28.41944 -36.81176 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2312" Parameter: A <- "-65.2312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4194" Parameter: B <- "-28.4194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8118" Parameter: C <- "-36.8118" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 669 TOTAL ENERGY = -65.2312 RDTITL> * VAN DER WAALS = -28.4194 ELECTROSTATIC = -36.8118 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "669" Parameter: CONF_N -> "8002" Comparing "669" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "670" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754699 ATOM PAIRS WERE FOUND FOR ATOM LIST 41286 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29104 from a total of 754699 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 670 -73.28077 8.04956 0.55479 INTE EXTERN> -32.99244 -40.28833 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2808" Parameter: A <- "-73.2808" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9924" Parameter: B <- "-32.9924" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2883" Parameter: C <- "-40.2883" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 670 TOTAL ENERGY = -73.2808 RDTITL> * VAN DER WAALS = -32.9924 ELECTROSTATIC = -40.2883 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "670" Parameter: CONF_N -> "8002" Comparing "670" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "671" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754699 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765486 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30058 from a total of 765486 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 671 -64.47501 -8.80576 0.58953 INTE EXTERN> -30.48565 -33.98935 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.475" Parameter: A <- "-64.475" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4857" Parameter: B <- "-30.4857" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9894" Parameter: C <- "-33.9894" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 671 TOTAL ENERGY = -64.475 RDTITL> * VAN DER WAALS = -30.4857 ELECTROSTATIC = -33.9894 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "671" Parameter: CONF_N -> "8002" Comparing "671" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "672" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765486 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767576 ATOM PAIRS WERE FOUND FOR ATOM LIST 42087 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29719 from a total of 767576 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 672 -71.57131 7.09631 0.61937 INTE EXTERN> -33.52731 -38.04401 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5713" Parameter: A <- "-71.5713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5273" Parameter: B <- "-33.5273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.044" Parameter: C <- "-38.044" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 672 TOTAL ENERGY = -71.5713 RDTITL> * VAN DER WAALS = -33.5273 ELECTROSTATIC = -38.044 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "672" Parameter: CONF_N -> "8002" Comparing "672" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "673" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767576 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758777 ATOM PAIRS WERE FOUND FOR ATOM LIST 41438 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29777 from a total of 758777 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 673 -78.83713 7.26582 0.66876 INTE EXTERN> -29.70269 -49.13444 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8371" Parameter: A <- "-78.8371" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7027" Parameter: B <- "-29.7027" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1344" Parameter: C <- "-49.1344" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 673 TOTAL ENERGY = -78.8371 RDTITL> * VAN DER WAALS = -29.7027 ELECTROSTATIC = -49.1344 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "673" Parameter: CONF_N -> "8002" Comparing "673" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "674" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758777 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758529 ATOM PAIRS WERE FOUND FOR ATOM LIST 41571 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29837 from a total of 758529 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 674 -89.59980 10.76267 0.70711 INTE EXTERN> -31.74180 -57.85800 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-89.5998" Parameter: A <- "-89.5998" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7418" Parameter: B <- "-31.7418" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.858" Parameter: C <- "-57.858" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 674 TOTAL ENERGY = -89.5998 RDTITL> * VAN DER WAALS = -31.7418 ELECTROSTATIC = -57.858 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "674" Parameter: CONF_N -> "8002" Comparing "674" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "675" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758529 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764626 ATOM PAIRS WERE FOUND FOR ATOM LIST 42081 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30147 from a total of 764626 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 675 -88.95485 -0.64495 0.78108 INTE EXTERN> -29.08189 -59.87296 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.9548" Parameter: A <- "-88.9548" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0819" Parameter: B <- "-29.0819" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.873" Parameter: C <- "-59.873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 675 TOTAL ENERGY = -88.9548 RDTITL> * VAN DER WAALS = -29.0819 ELECTROSTATIC = -59.873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "675" Parameter: CONF_N -> "8002" Comparing "675" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "676" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764626 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757475 ATOM PAIRS WERE FOUND FOR ATOM LIST 41509 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29322 from a total of 757475 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 676 -69.37735 -19.57749 0.62952 INTE EXTERN> -31.37196 -38.00540 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3774" Parameter: A <- "-69.3774" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.372" Parameter: B <- "-31.372" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0054" Parameter: C <- "-38.0054" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 676 TOTAL ENERGY = -69.3774 RDTITL> * VAN DER WAALS = -31.372 ELECTROSTATIC = -38.0054 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "676" Parameter: CONF_N -> "8002" Comparing "676" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "677" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757475 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762135 ATOM PAIRS WERE FOUND FOR ATOM LIST 41788 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28757 from a total of 762135 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 677 -69.45166 0.07431 0.56641 INTE EXTERN> -34.87151 -34.58015 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4517" Parameter: A <- "-69.4517" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.8715" Parameter: B <- "-34.8715" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5802" Parameter: C <- "-34.5802" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 677 TOTAL ENERGY = -69.4517 RDTITL> * VAN DER WAALS = -34.8715 ELECTROSTATIC = -34.5802 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "677" Parameter: CONF_N -> "8002" Comparing "677" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "678" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762135 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761035 ATOM PAIRS WERE FOUND FOR ATOM LIST 41723 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30124 from a total of 761035 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 678 -72.20350 2.75183 0.53824 INTE EXTERN> -35.76505 -36.43844 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2035" Parameter: A <- "-72.2035" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.7651" Parameter: B <- "-35.7651" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4384" Parameter: C <- "-36.4384" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 678 TOTAL ENERGY = -72.2035 RDTITL> * VAN DER WAALS = -35.7651 ELECTROSTATIC = -36.4384 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "678" Parameter: CONF_N -> "8002" Comparing "678" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "679" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761035 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770349 ATOM PAIRS WERE FOUND FOR ATOM LIST 42270 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30729 from a total of 770349 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 679 -71.63625 -0.56725 0.69813 INTE EXTERN> -28.48462 -43.15163 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6363" Parameter: A <- "-71.6363" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4846" Parameter: B <- "-28.4846" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1516" Parameter: C <- "-43.1516" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 679 TOTAL ENERGY = -71.6363 RDTITL> * VAN DER WAALS = -28.4846 ELECTROSTATIC = -43.1516 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "679" Parameter: CONF_N -> "8002" Comparing "679" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "680" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770349 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766518 ATOM PAIRS WERE FOUND FOR ATOM LIST 42029 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30388 from a total of 766518 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 680 -86.66179 15.02554 0.67074 INTE EXTERN> -31.80741 -54.85438 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.6618" Parameter: A <- "-86.6618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8074" Parameter: B <- "-31.8074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8544" Parameter: C <- "-54.8544" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 680 TOTAL ENERGY = -86.6618 RDTITL> * VAN DER WAALS = -31.8074 ELECTROSTATIC = -54.8544 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "680" Parameter: CONF_N -> "8002" Comparing "680" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "681" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766518 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763571 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30198 from a total of 763571 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 681 -79.74829 -6.91350 0.69794 INTE EXTERN> -30.17889 -49.56940 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7483" Parameter: A <- "-79.7483" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1789" Parameter: B <- "-30.1789" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5694" Parameter: C <- "-49.5694" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 681 TOTAL ENERGY = -79.7483 RDTITL> * VAN DER WAALS = -30.1789 ELECTROSTATIC = -49.5694 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "681" Parameter: CONF_N -> "8002" Comparing "681" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "682" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763571 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766080 ATOM PAIRS WERE FOUND FOR ATOM LIST 41930 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30924 from a total of 766080 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 682 -85.01519 5.26689 0.68636 INTE EXTERN> -33.19115 -51.82403 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.0152" Parameter: A <- "-85.0152" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1912" Parameter: B <- "-33.1912" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.824" Parameter: C <- "-51.824" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 682 TOTAL ENERGY = -85.0152 RDTITL> * VAN DER WAALS = -33.1912 ELECTROSTATIC = -51.824 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "682" Parameter: CONF_N -> "8002" Comparing "682" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "683" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766080 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764389 ATOM PAIRS WERE FOUND FOR ATOM LIST 42061 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30665 from a total of 764389 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 683 -80.14372 -4.87146 0.63401 INTE EXTERN> -34.06811 -46.07561 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1437" Parameter: A <- "-80.1437" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0681" Parameter: B <- "-34.0681" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0756" Parameter: C <- "-46.0756" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 683 TOTAL ENERGY = -80.1437 RDTITL> * VAN DER WAALS = -34.0681 ELECTROSTATIC = -46.0756 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "683" Parameter: CONF_N -> "8002" Comparing "683" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "684" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764389 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763718 ATOM PAIRS WERE FOUND FOR ATOM LIST 41897 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30133 from a total of 763718 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 684 -77.66012 -2.48361 0.69954 INTE EXTERN> -27.87996 -49.78016 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6601" Parameter: A <- "-77.6601" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.88" Parameter: B <- "-27.88" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7802" Parameter: C <- "-49.7802" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 684 TOTAL ENERGY = -77.6601 RDTITL> * VAN DER WAALS = -27.88 ELECTROSTATIC = -49.7802 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "684" Parameter: CONF_N -> "8002" Comparing "684" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "685" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763718 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766721 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30476 from a total of 766721 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 685 -83.94308 6.28296 0.70391 INTE EXTERN> -30.47516 -53.46792 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.9431" Parameter: A <- "-83.9431" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4752" Parameter: B <- "-30.4752" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4679" Parameter: C <- "-53.4679" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 685 TOTAL ENERGY = -83.9431 RDTITL> * VAN DER WAALS = -30.4752 ELECTROSTATIC = -53.4679 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "685" Parameter: CONF_N -> "8002" Comparing "685" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "686" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766721 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767273 ATOM PAIRS WERE FOUND FOR ATOM LIST 42124 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30244 from a total of 767273 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 686 -77.33495 -6.60813 0.71240 INTE EXTERN> -28.87703 -48.45792 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.335" Parameter: A <- "-77.335" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.877" Parameter: B <- "-28.877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4579" Parameter: C <- "-48.4579" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 686 TOTAL ENERGY = -77.335 RDTITL> * VAN DER WAALS = -28.877 ELECTROSTATIC = -48.4579 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "686" Parameter: CONF_N -> "8002" Comparing "686" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "687" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767273 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765543 ATOM PAIRS WERE FOUND FOR ATOM LIST 41940 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29623 from a total of 765543 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 687 -85.49452 8.15956 0.65279 INTE EXTERN> -30.44650 -55.04802 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.4945" Parameter: A <- "-85.4945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4465" Parameter: B <- "-30.4465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.048" Parameter: C <- "-55.048" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 687 TOTAL ENERGY = -85.4945 RDTITL> * VAN DER WAALS = -30.4465 ELECTROSTATIC = -55.048 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "687" Parameter: CONF_N -> "8002" Comparing "687" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "688" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765543 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770567 ATOM PAIRS WERE FOUND FOR ATOM LIST 42112 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30732 from a total of 770567 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 688 -70.15003 -15.34449 0.64586 INTE EXTERN> -30.65664 -39.49339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.15" Parameter: A <- "-70.15" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6566" Parameter: B <- "-30.6566" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4934" Parameter: C <- "-39.4934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 688 TOTAL ENERGY = -70.15 RDTITL> * VAN DER WAALS = -30.6566 ELECTROSTATIC = -39.4934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "688" Parameter: CONF_N -> "8002" Comparing "688" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "689" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770567 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760182 ATOM PAIRS WERE FOUND FOR ATOM LIST 41716 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29666 from a total of 760182 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 689 -79.29567 9.14564 0.65461 INTE EXTERN> -29.99662 -49.29905 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2957" Parameter: A <- "-79.2957" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9966" Parameter: B <- "-29.9966" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2991" Parameter: C <- "-49.2991" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 689 TOTAL ENERGY = -79.2957 RDTITL> * VAN DER WAALS = -29.9966 ELECTROSTATIC = -49.2991 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "689" Parameter: CONF_N -> "8002" Comparing "689" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "690" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760182 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759914 ATOM PAIRS WERE FOUND FOR ATOM LIST 41844 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29766 from a total of 759914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 690 -82.74853 3.45287 0.68305 INTE EXTERN> -31.29708 -51.45145 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7485" Parameter: A <- "-82.7485" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2971" Parameter: B <- "-31.2971" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4515" Parameter: C <- "-51.4515" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 690 TOTAL ENERGY = -82.7485 RDTITL> * VAN DER WAALS = -31.2971 ELECTROSTATIC = -51.4515 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "690" Parameter: CONF_N -> "8002" Comparing "690" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "691" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764789 ATOM PAIRS WERE FOUND FOR ATOM LIST 42076 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30055 from a total of 764789 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 691 -89.25545 6.50692 0.64466 INTE EXTERN> -32.66963 -56.58582 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-89.2555" Parameter: A <- "-89.2555" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6696" Parameter: B <- "-32.6696" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.5858" Parameter: C <- "-56.5858" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 691 TOTAL ENERGY = -89.2555 RDTITL> * VAN DER WAALS = -32.6696 ELECTROSTATIC = -56.5858 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "691" Parameter: CONF_N -> "8002" Comparing "691" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "692" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764789 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771485 ATOM PAIRS WERE FOUND FOR ATOM LIST 42261 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30685 from a total of 771485 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 692 -86.30293 -2.95253 0.70557 INTE EXTERN> -30.65235 -55.65058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.3029" Parameter: A <- "-86.3029" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6523" Parameter: B <- "-30.6523" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.6506" Parameter: C <- "-55.6506" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 692 TOTAL ENERGY = -86.3029 RDTITL> * VAN DER WAALS = -30.6523 ELECTROSTATIC = -55.6506 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "692" Parameter: CONF_N -> "8002" Comparing "692" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "693" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771485 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761054 ATOM PAIRS WERE FOUND FOR ATOM LIST 41799 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29550 from a total of 761054 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 693 -86.83990 0.53698 0.64894 INTE EXTERN> -32.62372 -54.21618 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.8399" Parameter: A <- "-86.8399" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6237" Parameter: B <- "-32.6237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2162" Parameter: C <- "-54.2162" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 693 TOTAL ENERGY = -86.8399 RDTITL> * VAN DER WAALS = -32.6237 ELECTROSTATIC = -54.2162 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "693" Parameter: CONF_N -> "8002" Comparing "693" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "694" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761054 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767364 ATOM PAIRS WERE FOUND FOR ATOM LIST 42130 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30312 from a total of 767364 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 694 -86.39909 -0.44081 0.68622 INTE EXTERN> -30.55887 -55.84021 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.3991" Parameter: A <- "-86.3991" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5589" Parameter: B <- "-30.5589" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.8402" Parameter: C <- "-55.8402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 694 TOTAL ENERGY = -86.3991 RDTITL> * VAN DER WAALS = -30.5589 ELECTROSTATIC = -55.8402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "694" Parameter: CONF_N -> "8002" Comparing "694" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "695" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767364 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760447 ATOM PAIRS WERE FOUND FOR ATOM LIST 41872 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29298 from a total of 760447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 695 -83.31752 -3.08156 0.71067 INTE EXTERN> -28.97784 -54.33968 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.3175" Parameter: A <- "-83.3175" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9778" Parameter: B <- "-28.9778" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.3397" Parameter: C <- "-54.3397" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 695 TOTAL ENERGY = -83.3175 RDTITL> * VAN DER WAALS = -28.9778 ELECTROSTATIC = -54.3397 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "695" Parameter: CONF_N -> "8002" Comparing "695" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "696" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761304 ATOM PAIRS WERE FOUND FOR ATOM LIST 41742 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29895 from a total of 761304 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 696 -81.72330 -1.59423 0.62613 INTE EXTERN> -31.23266 -50.49063 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.7233" Parameter: A <- "-81.7233" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2327" Parameter: B <- "-31.2327" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4906" Parameter: C <- "-50.4906" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 696 TOTAL ENERGY = -81.7233 RDTITL> * VAN DER WAALS = -31.2327 ELECTROSTATIC = -50.4906 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "696" Parameter: CONF_N -> "8002" Comparing "696" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "697" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761304 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764771 ATOM PAIRS WERE FOUND FOR ATOM LIST 41984 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30305 from a total of 764771 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 697 -72.48521 -9.23809 0.62031 INTE EXTERN> -29.37375 -43.11146 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4852" Parameter: A <- "-72.4852" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3738" Parameter: B <- "-29.3738" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1115" Parameter: C <- "-43.1115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 697 TOTAL ENERGY = -72.4852 RDTITL> * VAN DER WAALS = -29.3738 ELECTROSTATIC = -43.1115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "697" Parameter: CONF_N -> "8002" Comparing "697" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "698" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764771 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765983 ATOM PAIRS WERE FOUND FOR ATOM LIST 41932 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30059 from a total of 765983 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 698 -81.68004 9.19483 0.56626 INTE EXTERN> -36.23671 -45.44333 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.68" Parameter: A <- "-81.68" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.2367" Parameter: B <- "-36.2367" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4433" Parameter: C <- "-45.4433" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 698 TOTAL ENERGY = -81.68 RDTITL> * VAN DER WAALS = -36.2367 ELECTROSTATIC = -45.4433 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "698" Parameter: CONF_N -> "8002" Comparing "698" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "699" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765983 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763991 ATOM PAIRS WERE FOUND FOR ATOM LIST 42115 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29592 from a total of 763991 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 699 -75.80978 -5.87027 0.58057 INTE EXTERN> -33.32915 -42.48063 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8098" Parameter: A <- "-75.8098" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3291" Parameter: B <- "-33.3291" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4806" Parameter: C <- "-42.4806" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 699 TOTAL ENERGY = -75.8098 RDTITL> * VAN DER WAALS = -33.3291 ELECTROSTATIC = -42.4806 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "699" Parameter: CONF_N -> "8002" Comparing "699" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "700" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763991 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762524 ATOM PAIRS WERE FOUND FOR ATOM LIST 42035 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29887 from a total of 762524 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 700 -86.65499 10.84522 0.68109 INTE EXTERN> -30.59936 -56.05563 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.655" Parameter: A <- "-86.655" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5994" Parameter: B <- "-30.5994" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.0556" Parameter: C <- "-56.0556" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 700 TOTAL ENERGY = -86.655 RDTITL> * VAN DER WAALS = -30.5994 ELECTROSTATIC = -56.0556 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "700" Parameter: CONF_N -> "8002" Comparing "700" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "701" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762524 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758050 ATOM PAIRS WERE FOUND FOR ATOM LIST 41850 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29620 from a total of 758050 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 701 -81.80458 -4.85041 0.62543 INTE EXTERN> -34.19266 -47.61192 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8046" Parameter: A <- "-81.8046" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1927" Parameter: B <- "-34.1927" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6119" Parameter: C <- "-47.6119" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 701 TOTAL ENERGY = -81.8046 RDTITL> * VAN DER WAALS = -34.1927 ELECTROSTATIC = -47.6119 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "701" Parameter: CONF_N -> "8002" Comparing "701" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "702" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758050 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754473 ATOM PAIRS WERE FOUND FOR ATOM LIST 41410 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29186 from a total of 754473 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 702 -73.00690 -8.79768 0.63676 INTE EXTERN> -31.41518 -41.59173 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0069" Parameter: A <- "-73.0069" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4152" Parameter: B <- "-31.4152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5917" Parameter: C <- "-41.5917" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 702 TOTAL ENERGY = -73.0069 RDTITL> * VAN DER WAALS = -31.4152 ELECTROSTATIC = -41.5917 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "702" Parameter: CONF_N -> "8002" Comparing "702" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "703" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754473 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761108 ATOM PAIRS WERE FOUND FOR ATOM LIST 41766 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30134 from a total of 761108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 703 -74.27130 1.26440 0.64855 INTE EXTERN> -28.55279 -45.71851 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2713" Parameter: A <- "-74.2713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5528" Parameter: B <- "-28.5528" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7185" Parameter: C <- "-45.7185" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 703 TOTAL ENERGY = -74.2713 RDTITL> * VAN DER WAALS = -28.5528 ELECTROSTATIC = -45.7185 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "703" Parameter: CONF_N -> "8002" Comparing "703" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "704" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759560 ATOM PAIRS WERE FOUND FOR ATOM LIST 41741 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29415 from a total of 759560 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 704 -72.99149 -1.27980 0.67400 INTE EXTERN> -27.63289 -45.35860 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9915" Parameter: A <- "-72.9915" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6329" Parameter: B <- "-27.6329" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3586" Parameter: C <- "-45.3586" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 704 TOTAL ENERGY = -72.9915 RDTITL> * VAN DER WAALS = -27.6329 ELECTROSTATIC = -45.3586 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "704" Parameter: CONF_N -> "8002" Comparing "704" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "705" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759560 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758938 ATOM PAIRS WERE FOUND FOR ATOM LIST 41732 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29175 from a total of 758938 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 705 -86.36864 13.37715 0.66131 INTE EXTERN> -31.38622 -54.98242 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.3686" Parameter: A <- "-86.3686" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3862" Parameter: B <- "-31.3862" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.9824" Parameter: C <- "-54.9824" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 705 TOTAL ENERGY = -86.3686 RDTITL> * VAN DER WAALS = -31.3862 ELECTROSTATIC = -54.9824 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "705" Parameter: CONF_N -> "8002" Comparing "705" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "706" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758938 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763396 ATOM PAIRS WERE FOUND FOR ATOM LIST 41949 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29789 from a total of 763396 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 706 -76.47071 -9.89793 0.59977 INTE EXTERN> -32.28965 -44.18106 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4707" Parameter: A <- "-76.4707" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2897" Parameter: B <- "-32.2897" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1811" Parameter: C <- "-44.1811" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 706 TOTAL ENERGY = -76.4707 RDTITL> * VAN DER WAALS = -32.2897 ELECTROSTATIC = -44.1811 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "706" Parameter: CONF_N -> "8002" Comparing "706" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "707" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763396 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760654 ATOM PAIRS WERE FOUND FOR ATOM LIST 41801 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29875 from a total of 760654 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 707 -71.60861 -4.86210 0.65455 INTE EXTERN> -29.83273 -41.77588 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6086" Parameter: A <- "-71.6086" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8327" Parameter: B <- "-29.8327" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7759" Parameter: C <- "-41.7759" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 707 TOTAL ENERGY = -71.6086 RDTITL> * VAN DER WAALS = -29.8327 ELECTROSTATIC = -41.7759 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "707" Parameter: CONF_N -> "8002" Comparing "707" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "708" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760654 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761198 ATOM PAIRS WERE FOUND FOR ATOM LIST 41618 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30284 from a total of 761198 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 708 -74.33148 2.72286 0.67818 INTE EXTERN> -28.36480 -45.96668 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3315" Parameter: A <- "-74.3315" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3648" Parameter: B <- "-28.3648" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9667" Parameter: C <- "-45.9667" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 708 TOTAL ENERGY = -74.3315 RDTITL> * VAN DER WAALS = -28.3648 ELECTROSTATIC = -45.9667 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "708" Parameter: CONF_N -> "8002" Comparing "708" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "709" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761198 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756369 ATOM PAIRS WERE FOUND FOR ATOM LIST 41609 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30050 from a total of 756369 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 709 -88.53219 14.20071 0.77464 INTE EXTERN> -26.77424 -61.75795 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.5322" Parameter: A <- "-88.5322" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7742" Parameter: B <- "-26.7742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-61.7579" Parameter: C <- "-61.7579" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 709 TOTAL ENERGY = -88.5322 RDTITL> * VAN DER WAALS = -26.7742 ELECTROSTATIC = -61.7579 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "709" Parameter: CONF_N -> "8002" Comparing "709" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "710" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756369 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758949 ATOM PAIRS WERE FOUND FOR ATOM LIST 41617 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29761 from a total of 758949 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 710 -78.22458 -10.30761 0.80837 INTE EXTERN> -25.55221 -52.67237 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2246" Parameter: A <- "-78.2246" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5522" Parameter: B <- "-25.5522" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6724" Parameter: C <- "-52.6724" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 710 TOTAL ENERGY = -78.2246 RDTITL> * VAN DER WAALS = -25.5522 ELECTROSTATIC = -52.6724 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "710" Parameter: CONF_N -> "8002" Comparing "710" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "711" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758949 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765574 ATOM PAIRS WERE FOUND FOR ATOM LIST 42108 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30204 from a total of 765574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 711 -73.44662 -4.77796 0.68828 INTE EXTERN> -28.34895 -45.09767 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4466" Parameter: A <- "-73.4466" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.349" Parameter: B <- "-28.349" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0977" Parameter: C <- "-45.0977" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 711 TOTAL ENERGY = -73.4466 RDTITL> * VAN DER WAALS = -28.349 ELECTROSTATIC = -45.0977 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "711" Parameter: CONF_N -> "8002" Comparing "711" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "712" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762808 ATOM PAIRS WERE FOUND FOR ATOM LIST 41817 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29798 from a total of 762808 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 712 -66.47508 -6.97154 0.77556 INTE EXTERN> -25.37296 -41.10212 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4751" Parameter: A <- "-66.4751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.373" Parameter: B <- "-25.373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1021" Parameter: C <- "-41.1021" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 712 TOTAL ENERGY = -66.4751 RDTITL> * VAN DER WAALS = -25.373 ELECTROSTATIC = -41.1021 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "712" Parameter: CONF_N -> "8002" Comparing "712" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "713" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762808 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758347 ATOM PAIRS WERE FOUND FOR ATOM LIST 41511 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30441 from a total of 758347 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 713 -77.69668 11.22160 0.65963 INTE EXTERN> -28.30324 -49.39344 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6967" Parameter: A <- "-77.6967" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3032" Parameter: B <- "-28.3032" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3934" Parameter: C <- "-49.3934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 713 TOTAL ENERGY = -77.6967 RDTITL> * VAN DER WAALS = -28.3032 ELECTROSTATIC = -49.3934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "713" Parameter: CONF_N -> "8002" Comparing "713" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "714" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758347 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759707 ATOM PAIRS WERE FOUND FOR ATOM LIST 41635 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29702 from a total of 759707 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 714 -72.94117 -4.75551 0.74053 INTE EXTERN> -25.58109 -47.36008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9412" Parameter: A <- "-72.9412" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5811" Parameter: B <- "-25.5811" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3601" Parameter: C <- "-47.3601" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 714 TOTAL ENERGY = -72.9412 RDTITL> * VAN DER WAALS = -25.5811 ELECTROSTATIC = -47.3601 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "714" Parameter: CONF_N -> "8002" Comparing "714" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "715" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759707 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760059 ATOM PAIRS WERE FOUND FOR ATOM LIST 41777 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30370 from a total of 760059 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 715 -81.99935 9.05818 0.62489 INTE EXTERN> -32.01646 -49.98289 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9994" Parameter: A <- "-81.9994" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0165" Parameter: B <- "-32.0165" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9829" Parameter: C <- "-49.9829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 715 TOTAL ENERGY = -81.9994 RDTITL> * VAN DER WAALS = -32.0165 ELECTROSTATIC = -49.9829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "715" Parameter: CONF_N -> "8002" Comparing "715" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "716" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760059 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759932 ATOM PAIRS WERE FOUND FOR ATOM LIST 41665 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29852 from a total of 759932 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 716 -80.96690 -1.03245 0.70644 INTE EXTERN> -31.33365 -49.63325 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9669" Parameter: A <- "-80.9669" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3337" Parameter: B <- "-31.3337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6332" Parameter: C <- "-49.6332" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 716 TOTAL ENERGY = -80.9669 RDTITL> * VAN DER WAALS = -31.3337 ELECTROSTATIC = -49.6332 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "716" Parameter: CONF_N -> "8002" Comparing "716" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "717" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759932 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764394 ATOM PAIRS WERE FOUND FOR ATOM LIST 41959 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30005 from a total of 764394 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 717 -83.87694 2.91004 0.74342 INTE EXTERN> -29.34595 -54.53099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.8769" Parameter: A <- "-83.8769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3459" Parameter: B <- "-29.3459" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.531" Parameter: C <- "-54.531" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 717 TOTAL ENERGY = -83.8769 RDTITL> * VAN DER WAALS = -29.3459 ELECTROSTATIC = -54.531 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "717" Parameter: CONF_N -> "8002" Comparing "717" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "718" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764394 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762166 ATOM PAIRS WERE FOUND FOR ATOM LIST 41829 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30132 from a total of 762166 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 718 -87.73033 3.85339 0.66031 INTE EXTERN> -31.03183 -56.69850 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.7303" Parameter: A <- "-87.7303" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0318" Parameter: B <- "-31.0318" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.6985" Parameter: C <- "-56.6985" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 718 TOTAL ENERGY = -87.7303 RDTITL> * VAN DER WAALS = -31.0318 ELECTROSTATIC = -56.6985 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "718" Parameter: CONF_N -> "8002" Comparing "718" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "719" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762166 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763989 ATOM PAIRS WERE FOUND FOR ATOM LIST 41755 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29690 from a total of 763989 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 719 -78.84481 -8.88552 0.80880 INTE EXTERN> -27.72192 -51.12289 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8448" Parameter: A <- "-78.8448" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7219" Parameter: B <- "-27.7219" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1229" Parameter: C <- "-51.1229" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 719 TOTAL ENERGY = -78.8448 RDTITL> * VAN DER WAALS = -27.7219 ELECTROSTATIC = -51.1229 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "719" Parameter: CONF_N -> "8002" Comparing "719" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "720" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763989 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769393 ATOM PAIRS WERE FOUND FOR ATOM LIST 42316 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29145 from a total of 769393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 720 -86.11050 7.26569 0.63707 INTE EXTERN> -32.69089 -53.41960 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.1105" Parameter: A <- "-86.1105" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6909" Parameter: B <- "-32.6909" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4196" Parameter: C <- "-53.4196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 720 TOTAL ENERGY = -86.1105 RDTITL> * VAN DER WAALS = -32.6909 ELECTROSTATIC = -53.4196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "720" Parameter: CONF_N -> "8002" Comparing "720" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "721" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770556 ATOM PAIRS WERE FOUND FOR ATOM LIST 42276 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30018 from a total of 770556 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 721 -81.04856 -5.06194 0.72204 INTE EXTERN> -28.68881 -52.35975 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.0486" Parameter: A <- "-81.0486" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6888" Parameter: B <- "-28.6888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3597" Parameter: C <- "-52.3597" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 721 TOTAL ENERGY = -81.0486 RDTITL> * VAN DER WAALS = -28.6888 ELECTROSTATIC = -52.3597 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "721" Parameter: CONF_N -> "8002" Comparing "721" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "722" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770556 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765636 ATOM PAIRS WERE FOUND FOR ATOM LIST 41960 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30388 from a total of 765636 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 722 -84.70370 3.65514 0.61501 INTE EXTERN> -34.66220 -50.04150 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.7037" Parameter: A <- "-84.7037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6622" Parameter: B <- "-34.6622" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0415" Parameter: C <- "-50.0415" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 722 TOTAL ENERGY = -84.7037 RDTITL> * VAN DER WAALS = -34.6622 ELECTROSTATIC = -50.0415 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "722" Parameter: CONF_N -> "8002" Comparing "722" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "723" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765636 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765555 ATOM PAIRS WERE FOUND FOR ATOM LIST 42129 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30128 from a total of 765555 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 723 -88.47691 3.77322 0.60007 INTE EXTERN> -35.16639 -53.31052 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.4769" Parameter: A <- "-88.4769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.1664" Parameter: B <- "-35.1664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3105" Parameter: C <- "-53.3105" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 723 TOTAL ENERGY = -88.4769 RDTITL> * VAN DER WAALS = -35.1664 ELECTROSTATIC = -53.3105 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "723" Parameter: CONF_N -> "8002" Comparing "723" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "724" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765555 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770905 ATOM PAIRS WERE FOUND FOR ATOM LIST 42337 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30359 from a total of 770905 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 724 -75.69171 -12.78520 0.73798 INTE EXTERN> -26.83073 -48.86099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6917" Parameter: A <- "-75.6917" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8307" Parameter: B <- "-26.8307" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.861" Parameter: C <- "-48.861" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 724 TOTAL ENERGY = -75.6917 RDTITL> * VAN DER WAALS = -26.8307 ELECTROSTATIC = -48.861 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "724" Parameter: CONF_N -> "8002" Comparing "724" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "725" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770905 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763884 ATOM PAIRS WERE FOUND FOR ATOM LIST 41982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30127 from a total of 763884 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 725 -88.71726 13.02555 0.83436 INTE EXTERN> -25.45652 -63.26074 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.7173" Parameter: A <- "-88.7173" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4565" Parameter: B <- "-25.4565" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-63.2607" Parameter: C <- "-63.2607" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 725 TOTAL ENERGY = -88.7173 RDTITL> * VAN DER WAALS = -25.4565 ELECTROSTATIC = -63.2607 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "725" Parameter: CONF_N -> "8002" Comparing "725" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "726" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763884 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758408 ATOM PAIRS WERE FOUND FOR ATOM LIST 41606 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30303 from a total of 758408 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 726 -87.69693 -1.02033 0.77919 INTE EXTERN> -28.20994 -59.48699 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.6969" Parameter: A <- "-87.6969" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2099" Parameter: B <- "-28.2099" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.487" Parameter: C <- "-59.487" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 726 TOTAL ENERGY = -87.6969 RDTITL> * VAN DER WAALS = -28.2099 ELECTROSTATIC = -59.487 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "726" Parameter: CONF_N -> "8002" Comparing "726" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "727" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758408 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754967 ATOM PAIRS WERE FOUND FOR ATOM LIST 41550 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29842 from a total of 754967 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 727 -75.23814 -12.45878 0.71307 INTE EXTERN> -30.99858 -44.23956 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2381" Parameter: A <- "-75.2381" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9986" Parameter: B <- "-30.9986" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2396" Parameter: C <- "-44.2396" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 727 TOTAL ENERGY = -75.2381 RDTITL> * VAN DER WAALS = -30.9986 ELECTROSTATIC = -44.2396 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "727" Parameter: CONF_N -> "8002" Comparing "727" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "728" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754967 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756210 ATOM PAIRS WERE FOUND FOR ATOM LIST 41380 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29565 from a total of 756210 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 728 -71.98466 -3.25348 0.63999 INTE EXTERN> -31.09996 -40.88471 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9847" Parameter: A <- "-71.9847" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1" Parameter: B <- "-31.1" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8847" Parameter: C <- "-40.8847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 728 TOTAL ENERGY = -71.9847 RDTITL> * VAN DER WAALS = -31.1 ELECTROSTATIC = -40.8847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "728" Parameter: CONF_N -> "8002" Comparing "728" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "729" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756210 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759997 ATOM PAIRS WERE FOUND FOR ATOM LIST 41795 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30008 from a total of 759997 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 729 -69.68955 -2.29512 0.62686 INTE EXTERN> -30.34372 -39.34583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6895" Parameter: A <- "-69.6895" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3437" Parameter: B <- "-30.3437" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3458" Parameter: C <- "-39.3458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 729 TOTAL ENERGY = -69.6895 RDTITL> * VAN DER WAALS = -30.3437 ELECTROSTATIC = -39.3458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "729" Parameter: CONF_N -> "8002" Comparing "729" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "730" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759997 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768581 ATOM PAIRS WERE FOUND FOR ATOM LIST 42097 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30058 from a total of 768581 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 730 -72.35807 2.66853 0.56834 INTE EXTERN> -35.02345 -37.33462 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3581" Parameter: A <- "-72.3581" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.0235" Parameter: B <- "-35.0235" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3346" Parameter: C <- "-37.3346" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 730 TOTAL ENERGY = -72.3581 RDTITL> * VAN DER WAALS = -35.0235 ELECTROSTATIC = -37.3346 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "730" Parameter: CONF_N -> "8002" Comparing "730" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "731" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768581 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761876 ATOM PAIRS WERE FOUND FOR ATOM LIST 42007 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30142 from a total of 761876 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 731 -75.76286 3.40479 0.73568 INTE EXTERN> -29.69670 -46.06617 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7629" Parameter: A <- "-75.7629" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6967" Parameter: B <- "-29.6967" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0662" Parameter: C <- "-46.0662" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 731 TOTAL ENERGY = -75.7629 RDTITL> * VAN DER WAALS = -29.6967 ELECTROSTATIC = -46.0662 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "731" Parameter: CONF_N -> "8002" Comparing "731" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "732" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761876 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760350 ATOM PAIRS WERE FOUND FOR ATOM LIST 41847 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30238 from a total of 760350 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 732 -77.13009 1.36723 0.68341 INTE EXTERN> -28.24538 -48.88471 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1301" Parameter: A <- "-77.1301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2454" Parameter: B <- "-28.2454" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8847" Parameter: C <- "-48.8847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 732 TOTAL ENERGY = -77.1301 RDTITL> * VAN DER WAALS = -28.2454 ELECTROSTATIC = -48.8847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "732" Parameter: CONF_N -> "8002" Comparing "732" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "733" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760350 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762152 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30557 from a total of 762152 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 733 -58.25717 -18.87292 0.83214 INTE EXTERN> -22.26264 -35.99454 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.2572" Parameter: A <- "-58.2572" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.2626" Parameter: B <- "-22.2626" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9945" Parameter: C <- "-35.9945" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 733 TOTAL ENERGY = -58.2572 RDTITL> * VAN DER WAALS = -22.2626 ELECTROSTATIC = -35.9945 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "733" Parameter: CONF_N -> "8002" Comparing "733" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "734" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762152 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765569 ATOM PAIRS WERE FOUND FOR ATOM LIST 42169 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30556 from a total of 765569 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 734 -73.29458 15.03740 0.61895 INTE EXTERN> -32.63275 -40.66182 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2946" Parameter: A <- "-73.2946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6328" Parameter: B <- "-32.6328" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6618" Parameter: C <- "-40.6618" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 734 TOTAL ENERGY = -73.2946 RDTITL> * VAN DER WAALS = -32.6328 ELECTROSTATIC = -40.6618 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "734" Parameter: CONF_N -> "8002" Comparing "734" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "735" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765569 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770402 ATOM PAIRS WERE FOUND FOR ATOM LIST 42179 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30378 from a total of 770402 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 735 -87.57412 14.27954 0.68501 INTE EXTERN> -30.53369 -57.04043 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.5741" Parameter: A <- "-87.5741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5337" Parameter: B <- "-30.5337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.0404" Parameter: C <- "-57.0404" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 735 TOTAL ENERGY = -87.5741 RDTITL> * VAN DER WAALS = -30.5337 ELECTROSTATIC = -57.0404 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "735" Parameter: CONF_N -> "8002" Comparing "735" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "736" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770402 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768816 ATOM PAIRS WERE FOUND FOR ATOM LIST 42056 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30598 from a total of 768816 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 736 -75.12044 -12.45368 0.63807 INTE EXTERN> -34.41275 -40.70770 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1204" Parameter: A <- "-75.1204" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.4127" Parameter: B <- "-34.4127" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7077" Parameter: C <- "-40.7077" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 736 TOTAL ENERGY = -75.1204 RDTITL> * VAN DER WAALS = -34.4127 ELECTROSTATIC = -40.7077 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "736" Parameter: CONF_N -> "8002" Comparing "736" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "737" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768816 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764194 ATOM PAIRS WERE FOUND FOR ATOM LIST 42052 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30904 from a total of 764194 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 737 -78.04516 2.92472 0.62613 INTE EXTERN> -34.14131 -43.90385 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0452" Parameter: A <- "-78.0452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1413" Parameter: B <- "-34.1413" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9039" Parameter: C <- "-43.9039" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 737 TOTAL ENERGY = -78.0452 RDTITL> * VAN DER WAALS = -34.1413 ELECTROSTATIC = -43.9039 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "737" Parameter: CONF_N -> "8002" Comparing "737" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "738" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764194 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761984 ATOM PAIRS WERE FOUND FOR ATOM LIST 41910 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30349 from a total of 761984 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 738 -82.20527 4.16010 0.57067 INTE EXTERN> -35.66297 -46.54230 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.2053" Parameter: A <- "-82.2053" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.663" Parameter: B <- "-35.663" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5423" Parameter: C <- "-46.5423" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 738 TOTAL ENERGY = -82.2053 RDTITL> * VAN DER WAALS = -35.663 ELECTROSTATIC = -46.5423 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "738" Parameter: CONF_N -> "8002" Comparing "738" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "739" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761984 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765152 ATOM PAIRS WERE FOUND FOR ATOM LIST 42053 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30741 from a total of 765152 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 739 -81.42157 -0.78370 0.68851 INTE EXTERN> -31.49329 -49.92828 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4216" Parameter: A <- "-81.4216" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4933" Parameter: B <- "-31.4933" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9283" Parameter: C <- "-49.9283" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 739 TOTAL ENERGY = -81.4216 RDTITL> * VAN DER WAALS = -31.4933 ELECTROSTATIC = -49.9283 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "739" Parameter: CONF_N -> "8002" Comparing "739" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "740" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765152 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767048 ATOM PAIRS WERE FOUND FOR ATOM LIST 42058 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30744 from a total of 767048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 740 -72.24317 -9.17840 0.66529 INTE EXTERN> -31.88155 -40.36162 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2432" Parameter: A <- "-72.2432" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8816" Parameter: B <- "-31.8816" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3616" Parameter: C <- "-40.3616" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 740 TOTAL ENERGY = -72.2432 RDTITL> * VAN DER WAALS = -31.8816 ELECTROSTATIC = -40.3616 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "740" Parameter: CONF_N -> "8002" Comparing "740" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "741" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767168 ATOM PAIRS WERE FOUND FOR ATOM LIST 42127 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30578 from a total of 767168 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 741 -81.19939 8.95622 0.67611 INTE EXTERN> -29.01204 -52.18735 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1994" Parameter: A <- "-81.1994" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.012" Parameter: B <- "-29.012" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1873" Parameter: C <- "-52.1873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 741 TOTAL ENERGY = -81.1994 RDTITL> * VAN DER WAALS = -29.012 ELECTROSTATIC = -52.1873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "741" Parameter: CONF_N -> "8002" Comparing "741" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "742" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767168 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765368 ATOM PAIRS WERE FOUND FOR ATOM LIST 41760 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30662 from a total of 765368 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 742 -75.87116 -5.32823 0.84222 INTE EXTERN> -22.83018 -53.04097 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8712" Parameter: A <- "-75.8712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.8302" Parameter: B <- "-22.8302" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.041" Parameter: C <- "-53.041" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 742 TOTAL ENERGY = -75.8712 RDTITL> * VAN DER WAALS = -22.8302 ELECTROSTATIC = -53.041 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "742" Parameter: CONF_N -> "8002" Comparing "742" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "743" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765368 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766009 ATOM PAIRS WERE FOUND FOR ATOM LIST 42147 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30262 from a total of 766009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 743 -84.06636 8.19521 0.60345 INTE EXTERN> -34.01829 -50.04808 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.0664" Parameter: A <- "-84.0664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0183" Parameter: B <- "-34.0183" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0481" Parameter: C <- "-50.0481" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 743 TOTAL ENERGY = -84.0664 RDTITL> * VAN DER WAALS = -34.0183 ELECTROSTATIC = -50.0481 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "743" Parameter: CONF_N -> "8002" Comparing "743" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "744" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766941 ATOM PAIRS WERE FOUND FOR ATOM LIST 42151 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30468 from a total of 766941 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 744 -81.56533 -2.50104 0.65169 INTE EXTERN> -33.15188 -48.41345 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5653" Parameter: A <- "-81.5653" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1519" Parameter: B <- "-33.1519" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4135" Parameter: C <- "-48.4135" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 744 TOTAL ENERGY = -81.5653 RDTITL> * VAN DER WAALS = -33.1519 ELECTROSTATIC = -48.4135 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "744" Parameter: CONF_N -> "8002" Comparing "744" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "745" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766941 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766826 ATOM PAIRS WERE FOUND FOR ATOM LIST 42129 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30139 from a total of 766826 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 745 -79.96987 -1.59546 0.83763 INTE EXTERN> -22.67128 -57.29859 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9699" Parameter: A <- "-79.9699" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.6713" Parameter: B <- "-22.6713" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.2986" Parameter: C <- "-57.2986" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 745 TOTAL ENERGY = -79.9699 RDTITL> * VAN DER WAALS = -22.6713 ELECTROSTATIC = -57.2986 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "745" Parameter: CONF_N -> "8002" Comparing "745" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "746" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766826 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771363 ATOM PAIRS WERE FOUND FOR ATOM LIST 42218 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30624 from a total of 771363 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 746 -81.18471 1.21484 0.66273 INTE EXTERN> -32.24015 -48.94456 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1847" Parameter: A <- "-81.1847" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2401" Parameter: B <- "-32.2401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9446" Parameter: C <- "-48.9446" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 746 TOTAL ENERGY = -81.1847 RDTITL> * VAN DER WAALS = -32.2401 ELECTROSTATIC = -48.9446 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "746" Parameter: CONF_N -> "8002" Comparing "746" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "747" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771363 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771319 ATOM PAIRS WERE FOUND FOR ATOM LIST 42267 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 31163 from a total of 771319 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 747 -72.86156 -8.32315 0.61152 INTE EXTERN> -34.01607 -38.84549 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8616" Parameter: A <- "-72.8616" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0161" Parameter: B <- "-34.0161" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8455" Parameter: C <- "-38.8455" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 747 TOTAL ENERGY = -72.8616 RDTITL> * VAN DER WAALS = -34.0161 ELECTROSTATIC = -38.8455 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "747" Parameter: CONF_N -> "8002" Comparing "747" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "748" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771319 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763623 ATOM PAIRS WERE FOUND FOR ATOM LIST 41982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30608 from a total of 763623 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 748 -76.46702 3.60546 0.69107 INTE EXTERN> -33.38860 -43.07842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.467" Parameter: A <- "-76.467" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3886" Parameter: B <- "-33.3886" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0784" Parameter: C <- "-43.0784" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 748 TOTAL ENERGY = -76.467 RDTITL> * VAN DER WAALS = -33.3886 ELECTROSTATIC = -43.0784 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "748" Parameter: CONF_N -> "8002" Comparing "748" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "749" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763623 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763922 ATOM PAIRS WERE FOUND FOR ATOM LIST 41735 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30648 from a total of 763922 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 749 -76.74025 0.27323 0.68224 INTE EXTERN> -30.91186 -45.82839 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7402" Parameter: A <- "-76.7402" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9119" Parameter: B <- "-30.9119" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8284" Parameter: C <- "-45.8284" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 749 TOTAL ENERGY = -76.7402 RDTITL> * VAN DER WAALS = -30.9119 ELECTROSTATIC = -45.8284 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "749" Parameter: CONF_N -> "8002" Comparing "749" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "750" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763922 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766218 ATOM PAIRS WERE FOUND FOR ATOM LIST 42090 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30578 from a total of 766218 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 750 -74.64271 -2.09753 0.58636 INTE EXTERN> -33.25721 -41.38551 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6427" Parameter: A <- "-74.6427" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2572" Parameter: B <- "-33.2572" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3855" Parameter: C <- "-41.3855" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 750 TOTAL ENERGY = -74.6427 RDTITL> * VAN DER WAALS = -33.2572 ELECTROSTATIC = -41.3855 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "750" Parameter: CONF_N -> "8002" Comparing "750" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "751" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766218 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763068 ATOM PAIRS WERE FOUND FOR ATOM LIST 41754 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30776 from a total of 763068 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 751 -79.23619 4.59347 0.78321 INTE EXTERN> -26.25921 -52.97698 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2362" Parameter: A <- "-79.2362" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2592" Parameter: B <- "-26.2592" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.977" Parameter: C <- "-52.977" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 751 TOTAL ENERGY = -79.2362 RDTITL> * VAN DER WAALS = -26.2592 ELECTROSTATIC = -52.977 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "751" Parameter: CONF_N -> "8002" Comparing "751" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "752" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763068 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769767 ATOM PAIRS WERE FOUND FOR ATOM LIST 42170 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30315 from a total of 769767 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 752 -82.51616 3.27998 0.66774 INTE EXTERN> -31.93967 -50.57649 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5162" Parameter: A <- "-82.5162" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9397" Parameter: B <- "-31.9397" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5765" Parameter: C <- "-50.5765" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 752 TOTAL ENERGY = -82.5162 RDTITL> * VAN DER WAALS = -31.9397 ELECTROSTATIC = -50.5765 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "752" Parameter: CONF_N -> "8002" Comparing "752" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "753" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769767 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766558 ATOM PAIRS WERE FOUND FOR ATOM LIST 42280 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30729 from a total of 766558 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 753 -77.04161 -5.47455 0.61790 INTE EXTERN> -31.04592 -45.99570 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0416" Parameter: A <- "-77.0416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0459" Parameter: B <- "-31.0459" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9957" Parameter: C <- "-45.9957" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 753 TOTAL ENERGY = -77.0416 RDTITL> * VAN DER WAALS = -31.0459 ELECTROSTATIC = -45.9957 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "753" Parameter: CONF_N -> "8002" Comparing "753" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "754" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766558 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766338 ATOM PAIRS WERE FOUND FOR ATOM LIST 41905 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30306 from a total of 766338 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 754 -85.23593 8.19431 0.62043 INTE EXTERN> -34.19317 -51.04275 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.2359" Parameter: A <- "-85.2359" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1932" Parameter: B <- "-34.1932" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0428" Parameter: C <- "-51.0428" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 754 TOTAL ENERGY = -85.2359 RDTITL> * VAN DER WAALS = -34.1932 ELECTROSTATIC = -51.0428 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "754" Parameter: CONF_N -> "8002" Comparing "754" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "755" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766338 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768379 ATOM PAIRS WERE FOUND FOR ATOM LIST 42153 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30462 from a total of 768379 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 755 -82.11923 -3.11669 0.67271 INTE EXTERN> -30.93929 -51.17994 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.1192" Parameter: A <- "-82.1192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9393" Parameter: B <- "-30.9393" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1799" Parameter: C <- "-51.1799" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 755 TOTAL ENERGY = -82.1192 RDTITL> * VAN DER WAALS = -30.9393 ELECTROSTATIC = -51.1799 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "755" Parameter: CONF_N -> "8002" Comparing "755" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "756" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768379 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 774954 ATOM PAIRS WERE FOUND FOR ATOM LIST 42581 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30550 from a total of 774954 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 756 -67.17958 -14.93965 0.55115 INTE EXTERN> -33.33055 -33.84903 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1796" Parameter: A <- "-67.1796" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3306" Parameter: B <- "-33.3306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.849" Parameter: C <- "-33.849" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 756 TOTAL ENERGY = -67.1796 RDTITL> * VAN DER WAALS = -33.3306 ELECTROSTATIC = -33.849 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "756" Parameter: CONF_N -> "8002" Comparing "756" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "757" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 774954 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768659 ATOM PAIRS WERE FOUND FOR ATOM LIST 42225 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30745 from a total of 768659 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 757 -71.42767 4.24810 0.65543 INTE EXTERN> -30.46489 -40.96279 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4277" Parameter: A <- "-71.4277" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4649" Parameter: B <- "-30.4649" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9628" Parameter: C <- "-40.9628" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 757 TOTAL ENERGY = -71.4277 RDTITL> * VAN DER WAALS = -30.4649 ELECTROSTATIC = -40.9628 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "757" Parameter: CONF_N -> "8002" Comparing "757" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "758" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768659 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770933 ATOM PAIRS WERE FOUND FOR ATOM LIST 42201 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30093 from a total of 770933 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 758 -73.52491 2.09724 0.58802 INTE EXTERN> -32.60844 -40.91648 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5249" Parameter: A <- "-73.5249" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6084" Parameter: B <- "-32.6084" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9165" Parameter: C <- "-40.9165" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 758 TOTAL ENERGY = -73.5249 RDTITL> * VAN DER WAALS = -32.6084 ELECTROSTATIC = -40.9165 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "758" Parameter: CONF_N -> "8002" Comparing "758" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "759" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770933 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769065 ATOM PAIRS WERE FOUND FOR ATOM LIST 42258 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30511 from a total of 769065 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 759 -75.01735 1.49243 0.64162 INTE EXTERN> -29.73429 -45.28306 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0173" Parameter: A <- "-75.0173" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7343" Parameter: B <- "-29.7343" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2831" Parameter: C <- "-45.2831" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 759 TOTAL ENERGY = -75.0173 RDTITL> * VAN DER WAALS = -29.7343 ELECTROSTATIC = -45.2831 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "759" Parameter: CONF_N -> "8002" Comparing "759" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "760" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769065 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769968 ATOM PAIRS WERE FOUND FOR ATOM LIST 42443 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 31341 from a total of 769968 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 760 -80.21997 5.20262 0.64740 INTE EXTERN> -33.56239 -46.65758 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.22" Parameter: A <- "-80.22" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5624" Parameter: B <- "-33.5624" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6576" Parameter: C <- "-46.6576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 760 TOTAL ENERGY = -80.22 RDTITL> * VAN DER WAALS = -33.5624 ELECTROSTATIC = -46.6576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "760" Parameter: CONF_N -> "8002" Comparing "760" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "761" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769968 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768013 ATOM PAIRS WERE FOUND FOR ATOM LIST 42007 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30798 from a total of 768013 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 761 -83.81607 3.59610 0.63788 INTE EXTERN> -33.01801 -50.79806 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.8161" Parameter: A <- "-83.8161" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.018" Parameter: B <- "-33.018" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7981" Parameter: C <- "-50.7981" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 761 TOTAL ENERGY = -83.8161 RDTITL> * VAN DER WAALS = -33.018 ELECTROSTATIC = -50.7981 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "761" Parameter: CONF_N -> "8002" Comparing "761" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "762" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768013 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767479 ATOM PAIRS WERE FOUND FOR ATOM LIST 42043 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30517 from a total of 767479 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 762 -73.61097 -10.20510 0.65560 INTE EXTERN> -29.92474 -43.68623 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.611" Parameter: A <- "-73.611" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9247" Parameter: B <- "-29.9247" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6862" Parameter: C <- "-43.6862" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 762 TOTAL ENERGY = -73.611 RDTITL> * VAN DER WAALS = -29.9247 ELECTROSTATIC = -43.6862 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "762" Parameter: CONF_N -> "8002" Comparing "762" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "763" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767479 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764124 ATOM PAIRS WERE FOUND FOR ATOM LIST 41798 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29902 from a total of 764124 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 763 -82.50861 8.89763 0.69533 INTE EXTERN> -30.38523 -52.12337 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5086" Parameter: A <- "-82.5086" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3852" Parameter: B <- "-30.3852" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1234" Parameter: C <- "-52.1234" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 763 TOTAL ENERGY = -82.5086 RDTITL> * VAN DER WAALS = -30.3852 ELECTROSTATIC = -52.1234 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "763" Parameter: CONF_N -> "8002" Comparing "763" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "764" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764124 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762185 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29596 from a total of 762185 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 764 -76.38478 -6.12383 0.63211 INTE EXTERN> -33.17637 -43.20841 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3848" Parameter: A <- "-76.3848" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1764" Parameter: B <- "-33.1764" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2084" Parameter: C <- "-43.2084" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 764 TOTAL ENERGY = -76.3848 RDTITL> * VAN DER WAALS = -33.1764 ELECTROSTATIC = -43.2084 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "764" Parameter: CONF_N -> "8002" Comparing "764" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "765" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762185 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763672 ATOM PAIRS WERE FOUND FOR ATOM LIST 41879 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29659 from a total of 763672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 765 -86.79052 10.40574 0.62760 INTE EXTERN> -33.02785 -53.76268 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.7905" Parameter: A <- "-86.7905" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0278" Parameter: B <- "-33.0278" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.7627" Parameter: C <- "-53.7627" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 765 TOTAL ENERGY = -86.7905 RDTITL> * VAN DER WAALS = -33.0278 ELECTROSTATIC = -53.7627 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "765" Parameter: CONF_N -> "8002" Comparing "765" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "766" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760315 ATOM PAIRS WERE FOUND FOR ATOM LIST 41961 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29516 from a total of 760315 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 766 -78.31224 -8.47829 0.64947 INTE EXTERN> -28.89838 -49.41386 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3122" Parameter: A <- "-78.3122" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8984" Parameter: B <- "-28.8984" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4139" Parameter: C <- "-49.4139" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 766 TOTAL ENERGY = -78.3122 RDTITL> * VAN DER WAALS = -28.8984 ELECTROSTATIC = -49.4139 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "766" Parameter: CONF_N -> "8002" Comparing "766" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "767" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760315 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765480 ATOM PAIRS WERE FOUND FOR ATOM LIST 41933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30027 from a total of 765480 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 767 -83.09335 4.78112 0.85353 INTE EXTERN> -26.80540 -56.28795 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.0934" Parameter: A <- "-83.0934" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8054" Parameter: B <- "-26.8054" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.288" Parameter: C <- "-56.288" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 767 TOTAL ENERGY = -83.0934 RDTITL> * VAN DER WAALS = -26.8054 ELECTROSTATIC = -56.288 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "767" Parameter: CONF_N -> "8002" Comparing "767" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "768" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765480 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765235 ATOM PAIRS WERE FOUND FOR ATOM LIST 41935 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29855 from a total of 765235 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 768 -86.45893 3.36558 0.72869 INTE EXTERN> -29.53132 -56.92761 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.4589" Parameter: A <- "-86.4589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5313" Parameter: B <- "-29.5313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.9276" Parameter: C <- "-56.9276" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 768 TOTAL ENERGY = -86.4589 RDTITL> * VAN DER WAALS = -29.5313 ELECTROSTATIC = -56.9276 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "768" Parameter: CONF_N -> "8002" Comparing "768" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "769" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765235 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770903 ATOM PAIRS WERE FOUND FOR ATOM LIST 42332 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30137 from a total of 770903 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 769 -79.04815 -7.41079 0.64279 INTE EXTERN> -32.41452 -46.63363 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0481" Parameter: A <- "-79.0481" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4145" Parameter: B <- "-32.4145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6336" Parameter: C <- "-46.6336" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 769 TOTAL ENERGY = -79.0481 RDTITL> * VAN DER WAALS = -32.4145 ELECTROSTATIC = -46.6336 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "769" Parameter: CONF_N -> "8002" Comparing "769" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "770" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770903 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762037 ATOM PAIRS WERE FOUND FOR ATOM LIST 41915 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30020 from a total of 762037 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 770 -81.89478 2.84664 0.69124 INTE EXTERN> -30.52963 -51.36515 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8948" Parameter: A <- "-81.8948" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5296" Parameter: B <- "-30.5296" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3651" Parameter: C <- "-51.3651" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 770 TOTAL ENERGY = -81.8948 RDTITL> * VAN DER WAALS = -30.5296 ELECTROSTATIC = -51.3651 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "770" Parameter: CONF_N -> "8002" Comparing "770" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "771" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762037 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765383 ATOM PAIRS WERE FOUND FOR ATOM LIST 42106 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29876 from a total of 765383 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 771 -73.90218 -7.99261 0.70314 INTE EXTERN> -28.24995 -45.65223 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9022" Parameter: A <- "-73.9022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2499" Parameter: B <- "-28.2499" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6522" Parameter: C <- "-45.6522" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 771 TOTAL ENERGY = -73.9022 RDTITL> * VAN DER WAALS = -28.2499 ELECTROSTATIC = -45.6522 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "771" Parameter: CONF_N -> "8002" Comparing "771" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "772" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765383 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761897 ATOM PAIRS WERE FOUND FOR ATOM LIST 41717 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29728 from a total of 761897 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 772 -78.16928 4.26710 0.63092 INTE EXTERN> -32.76570 -45.40358 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1693" Parameter: A <- "-78.1693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7657" Parameter: B <- "-32.7657" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4036" Parameter: C <- "-45.4036" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 772 TOTAL ENERGY = -78.1693 RDTITL> * VAN DER WAALS = -32.7657 ELECTROSTATIC = -45.4036 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "772" Parameter: CONF_N -> "8002" Comparing "772" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "773" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761897 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767393 ATOM PAIRS WERE FOUND FOR ATOM LIST 42072 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29483 from a total of 767393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 773 -81.83591 3.66663 0.69917 INTE EXTERN> -31.95739 -49.87852 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8359" Parameter: A <- "-81.8359" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9574" Parameter: B <- "-31.9574" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8785" Parameter: C <- "-49.8785" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 773 TOTAL ENERGY = -81.8359 RDTITL> * VAN DER WAALS = -31.9574 ELECTROSTATIC = -49.8785 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "773" Parameter: CONF_N -> "8002" Comparing "773" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "774" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768512 ATOM PAIRS WERE FOUND FOR ATOM LIST 42288 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29984 from a total of 768512 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 774 -71.16176 -10.67415 0.72144 INTE EXTERN> -27.97649 -43.18527 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1618" Parameter: A <- "-71.1618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9765" Parameter: B <- "-27.9765" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1853" Parameter: C <- "-43.1853" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 774 TOTAL ENERGY = -71.1618 RDTITL> * VAN DER WAALS = -27.9765 ELECTROSTATIC = -43.1853 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "774" Parameter: CONF_N -> "8002" Comparing "774" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "775" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768512 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760261 ATOM PAIRS WERE FOUND FOR ATOM LIST 41875 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30041 from a total of 760261 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 775 -79.64691 8.48514 0.66058 INTE EXTERN> -29.27380 -50.37310 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6469" Parameter: A <- "-79.6469" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2738" Parameter: B <- "-29.2738" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3731" Parameter: C <- "-50.3731" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 775 TOTAL ENERGY = -79.6469 RDTITL> * VAN DER WAALS = -29.2738 ELECTROSTATIC = -50.3731 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "775" Parameter: CONF_N -> "8002" Comparing "775" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "776" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760261 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763894 ATOM PAIRS WERE FOUND FOR ATOM LIST 41931 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29604 from a total of 763894 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 776 -83.93745 4.29055 0.68634 INTE EXTERN> -32.40348 -51.53397 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.9375" Parameter: A <- "-83.9375" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4035" Parameter: B <- "-32.4035" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.534" Parameter: C <- "-51.534" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 776 TOTAL ENERGY = -83.9375 RDTITL> * VAN DER WAALS = -32.4035 ELECTROSTATIC = -51.534 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "776" Parameter: CONF_N -> "8002" Comparing "776" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "777" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763894 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755968 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29265 from a total of 755968 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 777 -81.52990 -2.40756 0.65826 INTE EXTERN> -32.20719 -49.32270 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5299" Parameter: A <- "-81.5299" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2072" Parameter: B <- "-32.2072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3227" Parameter: C <- "-49.3227" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 777 TOTAL ENERGY = -81.5299 RDTITL> * VAN DER WAALS = -32.2072 ELECTROSTATIC = -49.3227 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "777" Parameter: CONF_N -> "8002" Comparing "777" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "778" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755968 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756435 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29817 from a total of 756435 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 778 -76.71337 -4.81652 0.66888 INTE EXTERN> -31.37385 -45.33952 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7134" Parameter: A <- "-76.7134" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3738" Parameter: B <- "-31.3738" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3395" Parameter: C <- "-45.3395" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 778 TOTAL ENERGY = -76.7134 RDTITL> * VAN DER WAALS = -31.3738 ELECTROSTATIC = -45.3395 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "778" Parameter: CONF_N -> "8002" Comparing "778" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "779" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756435 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764187 ATOM PAIRS WERE FOUND FOR ATOM LIST 41932 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30424 from a total of 764187 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 779 -75.14941 -1.56396 0.79562 INTE EXTERN> -26.77175 -48.37766 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1494" Parameter: A <- "-75.1494" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7717" Parameter: B <- "-26.7717" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3777" Parameter: C <- "-48.3777" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 779 TOTAL ENERGY = -75.1494 RDTITL> * VAN DER WAALS = -26.7717 ELECTROSTATIC = -48.3777 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "779" Parameter: CONF_N -> "8002" Comparing "779" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "780" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764187 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766373 ATOM PAIRS WERE FOUND FOR ATOM LIST 42052 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30382 from a total of 766373 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 780 -73.49829 -1.65112 0.72502 INTE EXTERN> -28.38882 -45.10947 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4983" Parameter: A <- "-73.4983" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3888" Parameter: B <- "-28.3888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1095" Parameter: C <- "-45.1095" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 780 TOTAL ENERGY = -73.4983 RDTITL> * VAN DER WAALS = -28.3888 ELECTROSTATIC = -45.1095 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "780" Parameter: CONF_N -> "8002" Comparing "780" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "781" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766373 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765045 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30472 from a total of 765045 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 781 -69.58647 -3.91182 0.62863 INTE EXTERN> -31.26046 -38.32601 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5865" Parameter: A <- "-69.5865" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2605" Parameter: B <- "-31.2605" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.326" Parameter: C <- "-38.326" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 781 TOTAL ENERGY = -69.5865 RDTITL> * VAN DER WAALS = -31.2605 ELECTROSTATIC = -38.326 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "781" Parameter: CONF_N -> "8002" Comparing "781" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "782" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765045 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765526 ATOM PAIRS WERE FOUND FOR ATOM LIST 42077 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30102 from a total of 765526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 782 -79.14717 9.56069 0.65758 INTE EXTERN> -30.44900 -48.69817 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1472" Parameter: A <- "-79.1472" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.449" Parameter: B <- "-30.449" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6982" Parameter: C <- "-48.6982" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 782 TOTAL ENERGY = -79.1472 RDTITL> * VAN DER WAALS = -30.449 ELECTROSTATIC = -48.6982 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "782" Parameter: CONF_N -> "8002" Comparing "782" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "783" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761089 ATOM PAIRS WERE FOUND FOR ATOM LIST 42021 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30556 from a total of 761089 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 783 -68.69212 -10.45504 0.62752 INTE EXTERN> -32.76752 -35.92460 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6921" Parameter: A <- "-68.6921" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7675" Parameter: B <- "-32.7675" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9246" Parameter: C <- "-35.9246" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 783 TOTAL ENERGY = -68.6921 RDTITL> * VAN DER WAALS = -32.7675 ELECTROSTATIC = -35.9246 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "783" Parameter: CONF_N -> "8002" Comparing "783" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "784" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761089 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762371 ATOM PAIRS WERE FOUND FOR ATOM LIST 41782 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29835 from a total of 762371 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 784 -68.79350 0.10137 0.57893 INTE EXTERN> -28.10651 -40.68699 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7935" Parameter: A <- "-68.7935" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1065" Parameter: B <- "-28.1065" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.687" Parameter: C <- "-40.687" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 784 TOTAL ENERGY = -68.7935 RDTITL> * VAN DER WAALS = -28.1065 ELECTROSTATIC = -40.687 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "784" Parameter: CONF_N -> "8002" Comparing "784" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "785" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762371 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757269 ATOM PAIRS WERE FOUND FOR ATOM LIST 41639 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29828 from a total of 757269 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 785 -71.26284 2.46935 0.63979 INTE EXTERN> -30.61713 -40.64571 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2628" Parameter: A <- "-71.2628" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6171" Parameter: B <- "-30.6171" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6457" Parameter: C <- "-40.6457" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 785 TOTAL ENERGY = -71.2628 RDTITL> * VAN DER WAALS = -30.6171 ELECTROSTATIC = -40.6457 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "785" Parameter: CONF_N -> "8002" Comparing "785" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "786" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757269 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761499 ATOM PAIRS WERE FOUND FOR ATOM LIST 41704 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30231 from a total of 761499 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 786 -76.45207 5.18923 0.67944 INTE EXTERN> -30.47050 -45.98157 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4521" Parameter: A <- "-76.4521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4705" Parameter: B <- "-30.4705" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9816" Parameter: C <- "-45.9816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 786 TOTAL ENERGY = -76.4521 RDTITL> * VAN DER WAALS = -30.4705 ELECTROSTATIC = -45.9816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "786" Parameter: CONF_N -> "8002" Comparing "786" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "787" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761499 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762054 ATOM PAIRS WERE FOUND FOR ATOM LIST 41699 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29967 from a total of 762054 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 787 -82.76035 6.30828 0.84728 INTE EXTERN> -28.38654 -54.37382 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7604" Parameter: A <- "-82.7604" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3865" Parameter: B <- "-28.3865" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.3738" Parameter: C <- "-54.3738" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 787 TOTAL ENERGY = -82.7604 RDTITL> * VAN DER WAALS = -28.3865 ELECTROSTATIC = -54.3738 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "787" Parameter: CONF_N -> "8002" Comparing "787" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "788" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762054 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761349 ATOM PAIRS WERE FOUND FOR ATOM LIST 41787 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 761349 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 788 -78.33245 -4.42791 0.70908 INTE EXTERN> -31.00899 -47.32346 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3324" Parameter: A <- "-78.3324" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.009" Parameter: B <- "-31.009" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3235" Parameter: C <- "-47.3235" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 788 TOTAL ENERGY = -78.3324 RDTITL> * VAN DER WAALS = -31.009 ELECTROSTATIC = -47.3235 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "788" Parameter: CONF_N -> "8002" Comparing "788" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "789" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761349 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770431 ATOM PAIRS WERE FOUND FOR ATOM LIST 42232 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29961 from a total of 770431 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 789 -86.43327 8.10082 0.76495 INTE EXTERN> -29.99555 -56.43772 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.4333" Parameter: A <- "-86.4333" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9955" Parameter: B <- "-29.9955" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.4377" Parameter: C <- "-56.4377" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 789 TOTAL ENERGY = -86.4333 RDTITL> * VAN DER WAALS = -29.9955 ELECTROSTATIC = -56.4377 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "789" Parameter: CONF_N -> "8002" Comparing "789" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "790" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770431 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758598 ATOM PAIRS WERE FOUND FOR ATOM LIST 41548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29682 from a total of 758598 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 790 -77.30278 -9.13050 0.76333 INTE EXTERN> -27.83729 -49.46549 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3028" Parameter: A <- "-77.3028" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8373" Parameter: B <- "-27.8373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4655" Parameter: C <- "-49.4655" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 790 TOTAL ENERGY = -77.3028 RDTITL> * VAN DER WAALS = -27.8373 ELECTROSTATIC = -49.4655 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "790" Parameter: CONF_N -> "8002" Comparing "790" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "791" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758598 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762466 ATOM PAIRS WERE FOUND FOR ATOM LIST 41798 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30019 from a total of 762466 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 791 -75.12287 -2.17991 0.61122 INTE EXTERN> -31.97698 -43.14589 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1229" Parameter: A <- "-75.1229" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.977" Parameter: B <- "-31.977" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1459" Parameter: C <- "-43.1459" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 791 TOTAL ENERGY = -75.1229 RDTITL> * VAN DER WAALS = -31.977 ELECTROSTATIC = -43.1459 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "791" Parameter: CONF_N -> "8002" Comparing "791" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "792" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762466 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762831 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29970 from a total of 762831 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 792 -83.20465 8.08178 0.67356 INTE EXTERN> -32.40920 -50.79545 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.2046" Parameter: A <- "-83.2046" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4092" Parameter: B <- "-32.4092" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7954" Parameter: C <- "-50.7954" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 792 TOTAL ENERGY = -83.2046 RDTITL> * VAN DER WAALS = -32.4092 ELECTROSTATIC = -50.7954 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "792" Parameter: CONF_N -> "8002" Comparing "792" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "793" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762831 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757733 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29593 from a total of 757733 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 793 -80.94393 -2.26071 0.78692 INTE EXTERN> -25.71022 -55.23372 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9439" Parameter: A <- "-80.9439" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7102" Parameter: B <- "-25.7102" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.2337" Parameter: C <- "-55.2337" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 793 TOTAL ENERGY = -80.9439 RDTITL> * VAN DER WAALS = -25.7102 ELECTROSTATIC = -55.2337 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "793" Parameter: CONF_N -> "8002" Comparing "793" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "794" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757733 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761627 ATOM PAIRS WERE FOUND FOR ATOM LIST 41737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30063 from a total of 761627 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 794 -86.20802 5.26409 0.69470 INTE EXTERN> -27.81351 -58.39452 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.208" Parameter: A <- "-86.208" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8135" Parameter: B <- "-27.8135" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.3945" Parameter: C <- "-58.3945" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 794 TOTAL ENERGY = -86.208 RDTITL> * VAN DER WAALS = -27.8135 ELECTROSTATIC = -58.3945 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "794" Parameter: CONF_N -> "8002" Comparing "794" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "795" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761627 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761196 ATOM PAIRS WERE FOUND FOR ATOM LIST 41621 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30116 from a total of 761196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 795 -82.83473 -3.37329 0.69084 INTE EXTERN> -30.30563 -52.52910 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.8347" Parameter: A <- "-82.8347" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3056" Parameter: B <- "-30.3056" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5291" Parameter: C <- "-52.5291" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 795 TOTAL ENERGY = -82.8347 RDTITL> * VAN DER WAALS = -30.3056 ELECTROSTATIC = -52.5291 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "795" Parameter: CONF_N -> "8002" Comparing "795" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "796" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759853 ATOM PAIRS WERE FOUND FOR ATOM LIST 41761 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29487 from a total of 759853 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 796 -79.49390 -3.34083 0.73004 INTE EXTERN> -30.67707 -48.81683 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4939" Parameter: A <- "-79.4939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6771" Parameter: B <- "-30.6771" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8168" Parameter: C <- "-48.8168" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 796 TOTAL ENERGY = -79.4939 RDTITL> * VAN DER WAALS = -30.6771 ELECTROSTATIC = -48.8168 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "796" Parameter: CONF_N -> "8002" Comparing "796" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "797" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759853 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757264 ATOM PAIRS WERE FOUND FOR ATOM LIST 41554 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29560 from a total of 757264 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 797 -79.07239 -0.42151 0.75915 INTE EXTERN> -26.64336 -52.42903 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0724" Parameter: A <- "-79.0724" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6434" Parameter: B <- "-26.6434" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.429" Parameter: C <- "-52.429" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 797 TOTAL ENERGY = -79.0724 RDTITL> * VAN DER WAALS = -26.6434 ELECTROSTATIC = -52.429 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "797" Parameter: CONF_N -> "8002" Comparing "797" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "798" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757264 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764416 ATOM PAIRS WERE FOUND FOR ATOM LIST 41722 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29190 from a total of 764416 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 798 -86.96867 7.89627 0.71462 INTE EXTERN> -28.23223 -58.73643 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.9687" Parameter: A <- "-86.9687" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2322" Parameter: B <- "-28.2322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.7364" Parameter: C <- "-58.7364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 798 TOTAL ENERGY = -86.9687 RDTITL> * VAN DER WAALS = -28.2322 ELECTROSTATIC = -58.7364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "798" Parameter: CONF_N -> "8002" Comparing "798" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "799" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764416 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758178 ATOM PAIRS WERE FOUND FOR ATOM LIST 41493 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29023 from a total of 758178 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 799 -81.66948 -5.29919 0.60574 INTE EXTERN> -31.01043 -50.65905 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6695" Parameter: A <- "-81.6695" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0104" Parameter: B <- "-31.0104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6591" Parameter: C <- "-50.6591" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 799 TOTAL ENERGY = -81.6695 RDTITL> * VAN DER WAALS = -31.0104 ELECTROSTATIC = -50.6591 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "799" Parameter: CONF_N -> "8002" Comparing "799" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "800" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758178 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755884 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29170 from a total of 755884 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 800 -79.05852 -2.61096 0.63769 INTE EXTERN> -30.22622 -48.83230 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0585" Parameter: A <- "-79.0585" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2262" Parameter: B <- "-30.2262" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8323" Parameter: C <- "-48.8323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 800 TOTAL ENERGY = -79.0585 RDTITL> * VAN DER WAALS = -30.2262 ELECTROSTATIC = -48.8323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "800" Parameter: CONF_N -> "8002" Comparing "800" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "801" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755884 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760203 ATOM PAIRS WERE FOUND FOR ATOM LIST 41431 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29042 from a total of 760203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 801 -70.67649 -8.38203 0.52076 INTE EXTERN> -33.99110 -36.68539 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6765" Parameter: A <- "-70.6765" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9911" Parameter: B <- "-33.9911" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6854" Parameter: C <- "-36.6854" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 801 TOTAL ENERGY = -70.6765 RDTITL> * VAN DER WAALS = -33.9911 ELECTROSTATIC = -36.6854 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "801" Parameter: CONF_N -> "8002" Comparing "801" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "802" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756240 ATOM PAIRS WERE FOUND FOR ATOM LIST 41434 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29426 from a total of 756240 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 802 -77.48350 6.80701 0.66488 INTE EXTERN> -31.54528 -45.93822 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4835" Parameter: A <- "-77.4835" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5453" Parameter: B <- "-31.5453" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9382" Parameter: C <- "-45.9382" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 802 TOTAL ENERGY = -77.4835 RDTITL> * VAN DER WAALS = -31.5453 ELECTROSTATIC = -45.9382 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "802" Parameter: CONF_N -> "8002" Comparing "802" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "803" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756240 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759715 ATOM PAIRS WERE FOUND FOR ATOM LIST 41669 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29037 from a total of 759715 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 803 -74.46051 -3.02299 0.62495 INTE EXTERN> -30.44305 -44.01746 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4605" Parameter: A <- "-74.4605" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4431" Parameter: B <- "-30.4431" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0175" Parameter: C <- "-44.0175" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 803 TOTAL ENERGY = -74.4605 RDTITL> * VAN DER WAALS = -30.4431 ELECTROSTATIC = -44.0175 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "803" Parameter: CONF_N -> "8002" Comparing "803" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "804" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759715 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757763 ATOM PAIRS WERE FOUND FOR ATOM LIST 41539 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29723 from a total of 757763 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 804 -79.28819 4.82768 0.61852 INTE EXTERN> -31.74854 -47.53964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2882" Parameter: A <- "-79.2882" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7485" Parameter: B <- "-31.7485" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5396" Parameter: C <- "-47.5396" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 804 TOTAL ENERGY = -79.2882 RDTITL> * VAN DER WAALS = -31.7485 ELECTROSTATIC = -47.5396 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "804" Parameter: CONF_N -> "8002" Comparing "804" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "805" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757763 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755802 ATOM PAIRS WERE FOUND FOR ATOM LIST 41540 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29048 from a total of 755802 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 805 -70.24376 -9.04443 0.60752 INTE EXTERN> -30.68142 -39.56234 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2438" Parameter: A <- "-70.2438" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6814" Parameter: B <- "-30.6814" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5623" Parameter: C <- "-39.5623" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 805 TOTAL ENERGY = -70.2438 RDTITL> * VAN DER WAALS = -30.6814 ELECTROSTATIC = -39.5623 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "805" Parameter: CONF_N -> "8002" Comparing "805" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "806" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755802 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747128 ATOM PAIRS WERE FOUND FOR ATOM LIST 40935 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29149 from a total of 747128 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 806 -61.22788 -9.01588 0.63151 INTE EXTERN> -27.98510 -33.24278 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.2279" Parameter: A <- "-61.2279" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9851" Parameter: B <- "-27.9851" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2428" Parameter: C <- "-33.2428" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 806 TOTAL ENERGY = -61.2279 RDTITL> * VAN DER WAALS = -27.9851 ELECTROSTATIC = -33.2428 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "806" Parameter: CONF_N -> "8002" Comparing "806" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "807" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747128 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756998 ATOM PAIRS WERE FOUND FOR ATOM LIST 41382 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29048 from a total of 756998 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 807 -63.77700 2.54912 0.70564 INTE EXTERN> -26.05197 -37.72503 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.777" Parameter: A <- "-63.777" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.052" Parameter: B <- "-26.052" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.725" Parameter: C <- "-37.725" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 807 TOTAL ENERGY = -63.777 RDTITL> * VAN DER WAALS = -26.052 ELECTROSTATIC = -37.725 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "807" Parameter: CONF_N -> "8002" Comparing "807" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "808" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756998 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757782 ATOM PAIRS WERE FOUND FOR ATOM LIST 41296 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29336 from a total of 757782 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 808 -71.58179 7.80480 0.54132 INTE EXTERN> -33.86969 -37.71210 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5818" Parameter: A <- "-71.5818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8697" Parameter: B <- "-33.8697" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7121" Parameter: C <- "-37.7121" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 808 TOTAL ENERGY = -71.5818 RDTITL> * VAN DER WAALS = -33.8697 ELECTROSTATIC = -37.7121 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "808" Parameter: CONF_N -> "8002" Comparing "808" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "809" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757782 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758487 ATOM PAIRS WERE FOUND FOR ATOM LIST 41365 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29102 from a total of 758487 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 809 -71.49591 -0.08588 0.58665 INTE EXTERN> -31.66250 -39.83341 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4959" Parameter: A <- "-71.4959" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6625" Parameter: B <- "-31.6625" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8334" Parameter: C <- "-39.8334" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 809 TOTAL ENERGY = -71.4959 RDTITL> * VAN DER WAALS = -31.6625 ELECTROSTATIC = -39.8334 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "809" Parameter: CONF_N -> "8002" Comparing "809" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "810" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758487 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764411 ATOM PAIRS WERE FOUND FOR ATOM LIST 41669 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29132 from a total of 764411 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 810 -67.22382 -4.27209 0.57206 INTE EXTERN> -34.55089 -32.67293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2238" Parameter: A <- "-67.2238" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.5509" Parameter: B <- "-34.5509" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.6729" Parameter: C <- "-32.6729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 810 TOTAL ENERGY = -67.2238 RDTITL> * VAN DER WAALS = -34.5509 ELECTROSTATIC = -32.6729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "810" Parameter: CONF_N -> "8002" Comparing "810" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "811" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764411 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759473 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29489 from a total of 759473 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 811 -66.33551 -0.88831 0.57739 INTE EXTERN> -31.43820 -34.89731 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3355" Parameter: A <- "-66.3355" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4382" Parameter: B <- "-31.4382" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8973" Parameter: C <- "-34.8973" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 811 TOTAL ENERGY = -66.3355 RDTITL> * VAN DER WAALS = -31.4382 ELECTROSTATIC = -34.8973 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "811" Parameter: CONF_N -> "8002" Comparing "811" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "812" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759473 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762697 ATOM PAIRS WERE FOUND FOR ATOM LIST 41682 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29815 from a total of 762697 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 812 -69.25232 2.91680 0.74277 INTE EXTERN> -26.13565 -43.11667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2523" Parameter: A <- "-69.2523" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1356" Parameter: B <- "-26.1356" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1167" Parameter: C <- "-43.1167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 812 TOTAL ENERGY = -69.2523 RDTITL> * VAN DER WAALS = -26.1356 ELECTROSTATIC = -43.1167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "812" Parameter: CONF_N -> "8002" Comparing "812" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "813" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762697 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762602 ATOM PAIRS WERE FOUND FOR ATOM LIST 41980 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29409 from a total of 762602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 813 -77.03915 7.78683 0.62108 INTE EXTERN> -32.91831 -44.12084 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0391" Parameter: A <- "-77.0391" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9183" Parameter: B <- "-32.9183" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1208" Parameter: C <- "-44.1208" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 813 TOTAL ENERGY = -77.0391 RDTITL> * VAN DER WAALS = -32.9183 ELECTROSTATIC = -44.1208 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "813" Parameter: CONF_N -> "8002" Comparing "813" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "814" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759251 ATOM PAIRS WERE FOUND FOR ATOM LIST 41579 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29819 from a total of 759251 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 814 -71.59100 -5.44815 0.62194 INTE EXTERN> -31.91454 -39.67646 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.591" Parameter: A <- "-71.591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9145" Parameter: B <- "-31.9145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6765" Parameter: C <- "-39.6765" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 814 TOTAL ENERGY = -71.591 RDTITL> * VAN DER WAALS = -31.9145 ELECTROSTATIC = -39.6765 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "814" Parameter: CONF_N -> "8002" Comparing "814" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "815" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759251 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765461 ATOM PAIRS WERE FOUND FOR ATOM LIST 42118 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29999 from a total of 765461 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 815 -77.51753 5.92654 0.62257 INTE EXTERN> -34.09186 -43.42568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5175" Parameter: A <- "-77.5175" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0919" Parameter: B <- "-34.0919" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4257" Parameter: C <- "-43.4257" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 815 TOTAL ENERGY = -77.5175 RDTITL> * VAN DER WAALS = -34.0919 ELECTROSTATIC = -43.4257 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "815" Parameter: CONF_N -> "8002" Comparing "815" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "816" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765461 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763602 ATOM PAIRS WERE FOUND FOR ATOM LIST 41753 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29628 from a total of 763602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 816 -74.98296 -2.53458 0.70192 INTE EXTERN> -28.61985 -46.36311 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.983" Parameter: A <- "-74.983" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6199" Parameter: B <- "-28.6199" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3631" Parameter: C <- "-46.3631" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 816 TOTAL ENERGY = -74.983 RDTITL> * VAN DER WAALS = -28.6199 ELECTROSTATIC = -46.3631 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "816" Parameter: CONF_N -> "8002" Comparing "816" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "817" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755851 ATOM PAIRS WERE FOUND FOR ATOM LIST 41369 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29997 from a total of 755851 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 817 -72.89491 -2.08805 0.71650 INTE EXTERN> -27.64363 -45.25128 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8949" Parameter: A <- "-72.8949" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6436" Parameter: B <- "-27.6436" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2513" Parameter: C <- "-45.2513" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 817 TOTAL ENERGY = -72.8949 RDTITL> * VAN DER WAALS = -27.6436 ELECTROSTATIC = -45.2513 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "817" Parameter: CONF_N -> "8002" Comparing "817" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "818" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755851 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756077 ATOM PAIRS WERE FOUND FOR ATOM LIST 41625 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28915 from a total of 756077 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 818 -67.68881 -5.20611 0.53580 INTE EXTERN> -33.46407 -34.22474 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6888" Parameter: A <- "-67.6888" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4641" Parameter: B <- "-33.4641" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2247" Parameter: C <- "-34.2247" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 818 TOTAL ENERGY = -67.6888 RDTITL> * VAN DER WAALS = -33.4641 ELECTROSTATIC = -34.2247 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "818" Parameter: CONF_N -> "8002" Comparing "818" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "819" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756077 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756163 ATOM PAIRS WERE FOUND FOR ATOM LIST 41523 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29551 from a total of 756163 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 819 -65.65184 -2.03696 0.57505 INTE EXTERN> -32.60102 -33.05082 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6518" Parameter: A <- "-65.6518" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.601" Parameter: B <- "-32.601" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.0508" Parameter: C <- "-33.0508" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 819 TOTAL ENERGY = -65.6518 RDTITL> * VAN DER WAALS = -32.601 ELECTROSTATIC = -33.0508 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "819" Parameter: CONF_N -> "8002" Comparing "819" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "820" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756163 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759675 ATOM PAIRS WERE FOUND FOR ATOM LIST 41704 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29907 from a total of 759675 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 820 -70.10423 4.45239 0.72093 INTE EXTERN> -27.00180 -43.10243 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1042" Parameter: A <- "-70.1042" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0018" Parameter: B <- "-27.0018" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1024" Parameter: C <- "-43.1024" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 820 TOTAL ENERGY = -70.1042 RDTITL> * VAN DER WAALS = -27.0018 ELECTROSTATIC = -43.1024 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "820" Parameter: CONF_N -> "8002" Comparing "820" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "821" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759675 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758331 ATOM PAIRS WERE FOUND FOR ATOM LIST 41587 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29969 from a total of 758331 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 821 -71.75148 1.64725 0.81582 INTE EXTERN> -24.52941 -47.22207 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7515" Parameter: A <- "-71.7515" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5294" Parameter: B <- "-24.5294" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2221" Parameter: C <- "-47.2221" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 821 TOTAL ENERGY = -71.7515 RDTITL> * VAN DER WAALS = -24.5294 ELECTROSTATIC = -47.2221 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "821" Parameter: CONF_N -> "8002" Comparing "821" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "822" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758331 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752101 ATOM PAIRS WERE FOUND FOR ATOM LIST 41339 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28881 from a total of 752101 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 822 -73.72515 1.97367 0.66537 INTE EXTERN> -28.23835 -45.48680 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7252" Parameter: A <- "-73.7252" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2384" Parameter: B <- "-28.2384" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4868" Parameter: C <- "-45.4868" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 822 TOTAL ENERGY = -73.7252 RDTITL> * VAN DER WAALS = -28.2384 ELECTROSTATIC = -45.4868 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "822" Parameter: CONF_N -> "8002" Comparing "822" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "823" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752101 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761677 ATOM PAIRS WERE FOUND FOR ATOM LIST 41800 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29494 from a total of 761677 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 823 -73.80167 0.07651 0.72881 INTE EXTERN> -27.37134 -46.43032 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8017" Parameter: A <- "-73.8017" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3713" Parameter: B <- "-27.3713" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4303" Parameter: C <- "-46.4303" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 823 TOTAL ENERGY = -73.8017 RDTITL> * VAN DER WAALS = -27.3713 ELECTROSTATIC = -46.4303 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "823" Parameter: CONF_N -> "8002" Comparing "823" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "824" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761677 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754501 ATOM PAIRS WERE FOUND FOR ATOM LIST 41324 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28927 from a total of 754501 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 824 -70.30566 -3.49601 0.58865 INTE EXTERN> -32.22701 -38.07865 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3057" Parameter: A <- "-70.3057" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.227" Parameter: B <- "-32.227" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0786" Parameter: C <- "-38.0786" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 824 TOTAL ENERGY = -70.3057 RDTITL> * VAN DER WAALS = -32.227 ELECTROSTATIC = -38.0786 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "824" Parameter: CONF_N -> "8002" Comparing "824" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "825" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754501 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751683 ATOM PAIRS WERE FOUND FOR ATOM LIST 41231 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29068 from a total of 751683 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 825 -80.51541 10.20975 0.80864 INTE EXTERN> -26.50095 -54.01445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5154" Parameter: A <- "-80.5154" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.501" Parameter: B <- "-26.501" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0145" Parameter: C <- "-54.0145" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 825 TOTAL ENERGY = -80.5154 RDTITL> * VAN DER WAALS = -26.501 ELECTROSTATIC = -54.0145 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "825" Parameter: CONF_N -> "8002" Comparing "825" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "826" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751683 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750829 ATOM PAIRS WERE FOUND FOR ATOM LIST 40782 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29200 from a total of 750829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 826 -76.45723 -4.05818 0.73674 INTE EXTERN> -25.02627 -51.43096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4572" Parameter: A <- "-76.4572" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0263" Parameter: B <- "-25.0263" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.431" Parameter: C <- "-51.431" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 826 TOTAL ENERGY = -76.4572 RDTITL> * VAN DER WAALS = -25.0263 ELECTROSTATIC = -51.431 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "826" Parameter: CONF_N -> "8002" Comparing "826" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "827" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754477 ATOM PAIRS WERE FOUND FOR ATOM LIST 41258 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29279 from a total of 754477 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 827 -80.07130 3.61407 0.60714 INTE EXTERN> -33.55889 -46.51241 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0713" Parameter: A <- "-80.0713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5589" Parameter: B <- "-33.5589" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5124" Parameter: C <- "-46.5124" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 827 TOTAL ENERGY = -80.0713 RDTITL> * VAN DER WAALS = -33.5589 ELECTROSTATIC = -46.5124 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "827" Parameter: CONF_N -> "8002" Comparing "827" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "828" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754477 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756469 ATOM PAIRS WERE FOUND FOR ATOM LIST 41469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29289 from a total of 756469 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 828 -70.15071 -9.92060 0.66783 INTE EXTERN> -28.16555 -41.98516 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1507" Parameter: A <- "-70.1507" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1656" Parameter: B <- "-28.1656" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9852" Parameter: C <- "-41.9852" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 828 TOTAL ENERGY = -70.1507 RDTITL> * VAN DER WAALS = -28.1656 ELECTROSTATIC = -41.9852 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "828" Parameter: CONF_N -> "8002" Comparing "828" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "829" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756469 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752362 ATOM PAIRS WERE FOUND FOR ATOM LIST 41381 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29732 from a total of 752362 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 829 -70.50803 0.35733 0.82182 INTE EXTERN> -26.25323 -44.25481 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.508" Parameter: A <- "-70.508" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2532" Parameter: B <- "-26.2532" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2548" Parameter: C <- "-44.2548" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 829 TOTAL ENERGY = -70.508 RDTITL> * VAN DER WAALS = -26.2532 ELECTROSTATIC = -44.2548 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "829" Parameter: CONF_N -> "8002" Comparing "829" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "830" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752362 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755993 ATOM PAIRS WERE FOUND FOR ATOM LIST 41626 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29161 from a total of 755993 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 830 -74.36790 3.85986 0.80335 INTE EXTERN> -25.61604 -48.75185 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3679" Parameter: A <- "-74.3679" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.616" Parameter: B <- "-25.616" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7519" Parameter: C <- "-48.7519" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 830 TOTAL ENERGY = -74.3679 RDTITL> * VAN DER WAALS = -25.616 ELECTROSTATIC = -48.7519 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "830" Parameter: CONF_N -> "8002" Comparing "830" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "831" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755993 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752934 ATOM PAIRS WERE FOUND FOR ATOM LIST 41224 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29395 from a total of 752934 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 831 -78.29164 3.92374 0.69362 INTE EXTERN> -28.03921 -50.25243 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2916" Parameter: A <- "-78.2916" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0392" Parameter: B <- "-28.0392" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2524" Parameter: C <- "-50.2524" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 831 TOTAL ENERGY = -78.2916 RDTITL> * VAN DER WAALS = -28.0392 ELECTROSTATIC = -50.2524 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "831" Parameter: CONF_N -> "8002" Comparing "831" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "832" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752934 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758053 ATOM PAIRS WERE FOUND FOR ATOM LIST 41822 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29753 from a total of 758053 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 832 -71.88262 -6.40902 0.72966 INTE EXTERN> -27.08904 -44.79358 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8826" Parameter: A <- "-71.8826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.089" Parameter: B <- "-27.089" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7936" Parameter: C <- "-44.7936" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 832 TOTAL ENERGY = -71.8826 RDTITL> * VAN DER WAALS = -27.089 ELECTROSTATIC = -44.7936 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "832" Parameter: CONF_N -> "8002" Comparing "832" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "833" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758053 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758507 ATOM PAIRS WERE FOUND FOR ATOM LIST 41604 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29591 from a total of 758507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 833 -73.79357 1.91095 0.63855 INTE EXTERN> -30.93065 -42.86292 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7936" Parameter: A <- "-73.7936" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9306" Parameter: B <- "-30.9306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8629" Parameter: C <- "-42.8629" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 833 TOTAL ENERGY = -73.7936 RDTITL> * VAN DER WAALS = -30.9306 ELECTROSTATIC = -42.8629 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "833" Parameter: CONF_N -> "8002" Comparing "833" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "834" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754530 ATOM PAIRS WERE FOUND FOR ATOM LIST 41439 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29329 from a total of 754530 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 834 -74.83744 1.04387 0.70855 INTE EXTERN> -30.52681 -44.31064 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8374" Parameter: A <- "-74.8374" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5268" Parameter: B <- "-30.5268" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3106" Parameter: C <- "-44.3106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 834 TOTAL ENERGY = -74.8374 RDTITL> * VAN DER WAALS = -30.5268 ELECTROSTATIC = -44.3106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "834" Parameter: CONF_N -> "8002" Comparing "834" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "835" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754530 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753600 ATOM PAIRS WERE FOUND FOR ATOM LIST 41498 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28885 from a total of 753600 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 835 -68.77002 -6.06743 0.63785 INTE EXTERN> -28.43871 -40.33131 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.77" Parameter: A <- "-68.77" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4387" Parameter: B <- "-28.4387" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3313" Parameter: C <- "-40.3313" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 835 TOTAL ENERGY = -68.77 RDTITL> * VAN DER WAALS = -28.4387 ELECTROSTATIC = -40.3313 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "835" Parameter: CONF_N -> "8002" Comparing "835" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "836" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753600 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756215 ATOM PAIRS WERE FOUND FOR ATOM LIST 41592 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29114 from a total of 756215 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 836 -73.75487 4.98485 0.76482 INTE EXTERN> -26.38880 -47.36607 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7549" Parameter: A <- "-73.7549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3888" Parameter: B <- "-26.3888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3661" Parameter: C <- "-47.3661" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 836 TOTAL ENERGY = -73.7549 RDTITL> * VAN DER WAALS = -26.3888 ELECTROSTATIC = -47.3661 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "836" Parameter: CONF_N -> "8002" Comparing "836" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "837" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756215 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753478 ATOM PAIRS WERE FOUND FOR ATOM LIST 41505 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28892 from a total of 753478 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 837 -70.49292 -3.26195 0.74646 INTE EXTERN> -25.23547 -45.25745 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4929" Parameter: A <- "-70.4929" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2355" Parameter: B <- "-25.2355" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2574" Parameter: C <- "-45.2574" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 837 TOTAL ENERGY = -70.4929 RDTITL> * VAN DER WAALS = -25.2355 ELECTROSTATIC = -45.2574 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "837" Parameter: CONF_N -> "8002" Comparing "837" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "838" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753478 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748304 ATOM PAIRS WERE FOUND FOR ATOM LIST 41334 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29458 from a total of 748304 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 838 -77.57383 7.08091 0.79280 INTE EXTERN> -25.80171 -51.77212 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5738" Parameter: A <- "-77.5738" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8017" Parameter: B <- "-25.8017" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7721" Parameter: C <- "-51.7721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 838 TOTAL ENERGY = -77.5738 RDTITL> * VAN DER WAALS = -25.8017 ELECTROSTATIC = -51.7721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "838" Parameter: CONF_N -> "8002" Comparing "838" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "839" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748304 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755213 ATOM PAIRS WERE FOUND FOR ATOM LIST 41601 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29556 from a total of 755213 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 839 -76.56799 -1.00584 0.75555 INTE EXTERN> -28.67035 -47.89764 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.568" Parameter: A <- "-76.568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6703" Parameter: B <- "-28.6703" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8976" Parameter: C <- "-47.8976" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 839 TOTAL ENERGY = -76.568 RDTITL> * VAN DER WAALS = -28.6703 ELECTROSTATIC = -47.8976 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "839" Parameter: CONF_N -> "8002" Comparing "839" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "840" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755213 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754007 ATOM PAIRS WERE FOUND FOR ATOM LIST 41678 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28939 from a total of 754007 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 840 -76.28086 -0.28712 0.66538 INTE EXTERN> -33.30869 -42.97217 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2809" Parameter: A <- "-76.2809" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3087" Parameter: B <- "-33.3087" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9722" Parameter: C <- "-42.9722" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 840 TOTAL ENERGY = -76.2809 RDTITL> * VAN DER WAALS = -33.3087 ELECTROSTATIC = -42.9722 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "840" Parameter: CONF_N -> "8002" Comparing "840" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "841" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754007 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757764 ATOM PAIRS WERE FOUND FOR ATOM LIST 41743 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29725 from a total of 757764 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 841 -67.57129 -8.70957 0.63441 INTE EXTERN> -30.08446 -37.48684 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5713" Parameter: A <- "-67.5713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0845" Parameter: B <- "-30.0845" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4868" Parameter: C <- "-37.4868" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 841 TOTAL ENERGY = -67.5713 RDTITL> * VAN DER WAALS = -30.0845 ELECTROSTATIC = -37.4868 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "841" Parameter: CONF_N -> "8002" Comparing "841" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "842" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757764 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751122 ATOM PAIRS WERE FOUND FOR ATOM LIST 41402 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29353 from a total of 751122 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 842 -65.51460 -2.05669 0.60881 INTE EXTERN> -30.78745 -34.72716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5146" Parameter: A <- "-65.5146" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7874" Parameter: B <- "-30.7874" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7272" Parameter: C <- "-34.7272" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 842 TOTAL ENERGY = -65.5146 RDTITL> * VAN DER WAALS = -30.7874 ELECTROSTATIC = -34.7272 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "842" Parameter: CONF_N -> "8002" Comparing "842" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "843" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751122 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753347 ATOM PAIRS WERE FOUND FOR ATOM LIST 41314 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29487 from a total of 753347 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 843 -69.97565 4.46105 0.63418 INTE EXTERN> -30.72692 -39.24873 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9757" Parameter: A <- "-69.9757" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7269" Parameter: B <- "-30.7269" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2487" Parameter: C <- "-39.2487" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 843 TOTAL ENERGY = -69.9757 RDTITL> * VAN DER WAALS = -30.7269 ELECTROSTATIC = -39.2487 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "843" Parameter: CONF_N -> "8002" Comparing "843" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "844" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753347 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754676 ATOM PAIRS WERE FOUND FOR ATOM LIST 41676 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29564 from a total of 754676 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 844 -73.38884 3.41319 0.62159 INTE EXTERN> -30.70884 -42.68000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3888" Parameter: A <- "-73.3888" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7088" Parameter: B <- "-30.7088" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.68" Parameter: C <- "-42.68" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 844 TOTAL ENERGY = -73.3888 RDTITL> * VAN DER WAALS = -30.7088 ELECTROSTATIC = -42.68 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "844" Parameter: CONF_N -> "8002" Comparing "844" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "845" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754676 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753947 ATOM PAIRS WERE FOUND FOR ATOM LIST 41519 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29933 from a total of 753947 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 845 -73.34735 -0.04149 0.67738 INTE EXTERN> -29.82168 -43.52567 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3474" Parameter: A <- "-73.3474" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8217" Parameter: B <- "-29.8217" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5257" Parameter: C <- "-43.5257" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 845 TOTAL ENERGY = -73.3474 RDTITL> * VAN DER WAALS = -29.8217 ELECTROSTATIC = -43.5257 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "845" Parameter: CONF_N -> "8002" Comparing "845" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "846" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753947 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760921 ATOM PAIRS WERE FOUND FOR ATOM LIST 41585 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29925 from a total of 760921 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 846 -68.13539 -5.21196 0.61804 INTE EXTERN> -31.60297 -36.53242 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1354" Parameter: A <- "-68.1354" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.603" Parameter: B <- "-31.603" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5324" Parameter: C <- "-36.5324" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 846 TOTAL ENERGY = -68.1354 RDTITL> * VAN DER WAALS = -31.603 ELECTROSTATIC = -36.5324 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "846" Parameter: CONF_N -> "8002" Comparing "846" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "847" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760921 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756944 ATOM PAIRS WERE FOUND FOR ATOM LIST 41608 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29611 from a total of 756944 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 847 -66.14922 -1.98617 0.54696 INTE EXTERN> -32.52696 -33.62226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1492" Parameter: A <- "-66.1492" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.527" Parameter: B <- "-32.527" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6223" Parameter: C <- "-33.6223" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 847 TOTAL ENERGY = -66.1492 RDTITL> * VAN DER WAALS = -32.527 ELECTROSTATIC = -33.6223 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "847" Parameter: CONF_N -> "8002" Comparing "847" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "848" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756944 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757874 ATOM PAIRS WERE FOUND FOR ATOM LIST 41590 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29057 from a total of 757874 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 848 -75.86836 9.71914 0.74087 INTE EXTERN> -26.81448 -49.05387 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8684" Parameter: A <- "-75.8684" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8145" Parameter: B <- "-26.8145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0539" Parameter: C <- "-49.0539" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 848 TOTAL ENERGY = -75.8684 RDTITL> * VAN DER WAALS = -26.8145 ELECTROSTATIC = -49.0539 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "848" Parameter: CONF_N -> "8002" Comparing "848" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "849" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757874 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761920 ATOM PAIRS WERE FOUND FOR ATOM LIST 41908 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29863 from a total of 761920 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 849 -71.38369 -4.48467 0.65581 INTE EXTERN> -28.02885 -43.35484 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3837" Parameter: A <- "-71.3837" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0289" Parameter: B <- "-28.0289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3548" Parameter: C <- "-43.3548" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 849 TOTAL ENERGY = -71.3837 RDTITL> * VAN DER WAALS = -28.0289 ELECTROSTATIC = -43.3548 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "849" Parameter: CONF_N -> "8002" Comparing "849" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "850" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761920 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761558 ATOM PAIRS WERE FOUND FOR ATOM LIST 41803 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30032 from a total of 761558 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 850 -69.98925 -1.39444 0.63062 INTE EXTERN> -29.67456 -40.31469 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9893" Parameter: A <- "-69.9893" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6746" Parameter: B <- "-29.6746" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3147" Parameter: C <- "-40.3147" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 850 TOTAL ENERGY = -69.9893 RDTITL> * VAN DER WAALS = -29.6746 ELECTROSTATIC = -40.3147 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "850" Parameter: CONF_N -> "8002" Comparing "850" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "851" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761558 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758622 ATOM PAIRS WERE FOUND FOR ATOM LIST 41554 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29702 from a total of 758622 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 851 -75.34838 5.35913 0.78630 INTE EXTERN> -27.99816 -47.35022 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3484" Parameter: A <- "-75.3484" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9982" Parameter: B <- "-27.9982" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3502" Parameter: C <- "-47.3502" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 851 TOTAL ENERGY = -75.3484 RDTITL> * VAN DER WAALS = -27.9982 ELECTROSTATIC = -47.3502 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "851" Parameter: CONF_N -> "8002" Comparing "851" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "852" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758622 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764734 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29501 from a total of 764734 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 852 -71.33192 -4.01646 0.77282 INTE EXTERN> -23.50365 -47.82827 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3319" Parameter: A <- "-71.3319" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.5036" Parameter: B <- "-23.5036" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8283" Parameter: C <- "-47.8283" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 852 TOTAL ENERGY = -71.3319 RDTITL> * VAN DER WAALS = -23.5036 ELECTROSTATIC = -47.8283 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "852" Parameter: CONF_N -> "8002" Comparing "852" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "853" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764734 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764765 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29962 from a total of 764765 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 853 -73.40372 2.07180 0.67336 INTE EXTERN> -29.74449 -43.65922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4037" Parameter: A <- "-73.4037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7445" Parameter: B <- "-29.7445" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6592" Parameter: C <- "-43.6592" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 853 TOTAL ENERGY = -73.4037 RDTITL> * VAN DER WAALS = -29.7445 ELECTROSTATIC = -43.6592 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "853" Parameter: CONF_N -> "8002" Comparing "853" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "854" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764765 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761956 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29710 from a total of 761956 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 854 -75.16830 1.76458 0.60077 INTE EXTERN> -30.63049 -44.53781 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1683" Parameter: A <- "-75.1683" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6305" Parameter: B <- "-30.6305" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5378" Parameter: C <- "-44.5378" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 854 TOTAL ENERGY = -75.1683 RDTITL> * VAN DER WAALS = -30.6305 ELECTROSTATIC = -44.5378 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "854" Parameter: CONF_N -> "8002" Comparing "854" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "855" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761956 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765411 ATOM PAIRS WERE FOUND FOR ATOM LIST 42009 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30058 from a total of 765411 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 855 -67.40225 -7.76605 0.62177 INTE EXTERN> -30.38611 -37.01614 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4023" Parameter: A <- "-67.4023" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3861" Parameter: B <- "-30.3861" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0161" Parameter: C <- "-37.0161" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 855 TOTAL ENERGY = -67.4023 RDTITL> * VAN DER WAALS = -30.3861 ELECTROSTATIC = -37.0161 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "855" Parameter: CONF_N -> "8002" Comparing "855" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "856" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765411 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763680 ATOM PAIRS WERE FOUND FOR ATOM LIST 41949 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29401 from a total of 763680 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 856 -69.47741 2.07516 0.59005 INTE EXTERN> -31.76881 -37.70860 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4774" Parameter: A <- "-69.4774" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7688" Parameter: B <- "-31.7688" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7086" Parameter: C <- "-37.7086" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 856 TOTAL ENERGY = -69.4774 RDTITL> * VAN DER WAALS = -31.7688 ELECTROSTATIC = -37.7086 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "856" Parameter: CONF_N -> "8002" Comparing "856" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "857" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763680 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764513 ATOM PAIRS WERE FOUND FOR ATOM LIST 41922 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29287 from a total of 764513 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 857 -80.27507 10.79766 0.69525 INTE EXTERN> -29.31358 -50.96149 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2751" Parameter: A <- "-80.2751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3136" Parameter: B <- "-29.3136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9615" Parameter: C <- "-50.9615" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 857 TOTAL ENERGY = -80.2751 RDTITL> * VAN DER WAALS = -29.3136 ELECTROSTATIC = -50.9615 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "857" Parameter: CONF_N -> "8002" Comparing "857" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "858" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764513 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767181 ATOM PAIRS WERE FOUND FOR ATOM LIST 42100 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29410 from a total of 767181 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 858 -77.39853 -2.87654 0.65087 INTE EXTERN> -32.84520 -44.55334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3985" Parameter: A <- "-77.3985" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8452" Parameter: B <- "-32.8452" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5533" Parameter: C <- "-44.5533" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 858 TOTAL ENERGY = -77.3985 RDTITL> * VAN DER WAALS = -32.8452 ELECTROSTATIC = -44.5533 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "858" Parameter: CONF_N -> "8002" Comparing "858" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "859" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767181 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766863 ATOM PAIRS WERE FOUND FOR ATOM LIST 42018 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29984 from a total of 766863 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 859 -72.30133 -5.09720 0.68503 INTE EXTERN> -29.27568 -43.02565 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3013" Parameter: A <- "-72.3013" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2757" Parameter: B <- "-29.2757" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0257" Parameter: C <- "-43.0257" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 859 TOTAL ENERGY = -72.3013 RDTITL> * VAN DER WAALS = -29.2757 ELECTROSTATIC = -43.0257 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "859" Parameter: CONF_N -> "8002" Comparing "859" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "860" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766863 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765044 ATOM PAIRS WERE FOUND FOR ATOM LIST 41997 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29645 from a total of 765044 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 860 -75.01554 2.71421 0.75655 INTE EXTERN> -25.61279 -49.40276 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0155" Parameter: A <- "-75.0155" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6128" Parameter: B <- "-25.6128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4028" Parameter: C <- "-49.4028" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 860 TOTAL ENERGY = -75.0155 RDTITL> * VAN DER WAALS = -25.6128 ELECTROSTATIC = -49.4028 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "860" Parameter: CONF_N -> "8002" Comparing "860" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "861" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765044 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764956 ATOM PAIRS WERE FOUND FOR ATOM LIST 41764 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30102 from a total of 764956 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 861 -73.75019 -1.26535 0.69906 INTE EXTERN> -29.56697 -44.18321 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7502" Parameter: A <- "-73.7502" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.567" Parameter: B <- "-29.567" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1832" Parameter: C <- "-44.1832" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 861 TOTAL ENERGY = -73.7502 RDTITL> * VAN DER WAALS = -29.567 ELECTROSTATIC = -44.1832 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "861" Parameter: CONF_N -> "8002" Comparing "861" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "862" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764956 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756814 ATOM PAIRS WERE FOUND FOR ATOM LIST 41484 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29982 from a total of 756814 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 862 -72.71069 -1.03950 0.70435 INTE EXTERN> -27.43434 -45.27635 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7107" Parameter: A <- "-72.7107" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4343" Parameter: B <- "-27.4343" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2764" Parameter: C <- "-45.2764" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 862 TOTAL ENERGY = -72.7107 RDTITL> * VAN DER WAALS = -27.4343 ELECTROSTATIC = -45.2764 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "862" Parameter: CONF_N -> "8002" Comparing "862" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "863" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756814 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760672 ATOM PAIRS WERE FOUND FOR ATOM LIST 41567 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29658 from a total of 760672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 863 -76.81869 4.10800 0.71692 INTE EXTERN> -28.10581 -48.71288 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8187" Parameter: A <- "-76.8187" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1058" Parameter: B <- "-28.1058" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7129" Parameter: C <- "-48.7129" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 863 TOTAL ENERGY = -76.8187 RDTITL> * VAN DER WAALS = -28.1058 ELECTROSTATIC = -48.7129 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "863" Parameter: CONF_N -> "8002" Comparing "863" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "864" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762689 ATOM PAIRS WERE FOUND FOR ATOM LIST 41860 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30014 from a total of 762689 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 864 -69.60596 -7.21273 0.57358 INTE EXTERN> -33.35529 -36.25068 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.606" Parameter: A <- "-69.606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3553" Parameter: B <- "-33.3553" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2507" Parameter: C <- "-36.2507" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 864 TOTAL ENERGY = -69.606 RDTITL> * VAN DER WAALS = -33.3553 ELECTROSTATIC = -36.2507 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "864" Parameter: CONF_N -> "8002" Comparing "864" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "865" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762689 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763859 ATOM PAIRS WERE FOUND FOR ATOM LIST 41733 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29533 from a total of 763859 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 865 -67.26919 -2.33677 0.67116 INTE EXTERN> -27.80461 -39.46458 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2692" Parameter: A <- "-67.2692" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8046" Parameter: B <- "-27.8046" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4646" Parameter: C <- "-39.4646" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 865 TOTAL ENERGY = -67.2692 RDTITL> * VAN DER WAALS = -27.8046 ELECTROSTATIC = -39.4646 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "865" Parameter: CONF_N -> "8002" Comparing "865" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "866" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763859 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757476 ATOM PAIRS WERE FOUND FOR ATOM LIST 41409 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29875 from a total of 757476 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 866 -68.87952 1.61033 0.64967 INTE EXTERN> -26.41573 -42.46380 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8795" Parameter: A <- "-68.8795" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4157" Parameter: B <- "-26.4157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4638" Parameter: C <- "-42.4638" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 866 TOTAL ENERGY = -68.8795 RDTITL> * VAN DER WAALS = -26.4157 ELECTROSTATIC = -42.4638 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "866" Parameter: CONF_N -> "8002" Comparing "866" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "867" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757476 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761616 ATOM PAIRS WERE FOUND FOR ATOM LIST 41823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29723 from a total of 761616 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 867 -72.49426 3.61473 0.63484 INTE EXTERN> -30.26778 -42.22648 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4943" Parameter: A <- "-72.4943" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2678" Parameter: B <- "-30.2678" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2265" Parameter: C <- "-42.2265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 867 TOTAL ENERGY = -72.4943 RDTITL> * VAN DER WAALS = -30.2678 ELECTROSTATIC = -42.2265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "867" Parameter: CONF_N -> "8002" Comparing "867" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "868" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761616 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759964 ATOM PAIRS WERE FOUND FOR ATOM LIST 41867 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29625 from a total of 759964 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 868 -69.88012 -2.61413 0.79260 INTE EXTERN> -22.38954 -47.49059 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8801" Parameter: A <- "-69.8801" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.3895" Parameter: B <- "-22.3895" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4906" Parameter: C <- "-47.4906" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 868 TOTAL ENERGY = -69.8801 RDTITL> * VAN DER WAALS = -22.3895 ELECTROSTATIC = -47.4906 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "868" Parameter: CONF_N -> "8002" Comparing "868" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "869" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759964 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758546 ATOM PAIRS WERE FOUND FOR ATOM LIST 41677 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29763 from a total of 758546 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 869 -69.07915 -0.80097 0.77544 INTE EXTERN> -26.82857 -42.25058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0792" Parameter: A <- "-69.0792" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8286" Parameter: B <- "-26.8286" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2506" Parameter: C <- "-42.2506" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 869 TOTAL ENERGY = -69.0792 RDTITL> * VAN DER WAALS = -26.8286 ELECTROSTATIC = -42.2506 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "869" Parameter: CONF_N -> "8002" Comparing "869" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "870" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758546 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756509 ATOM PAIRS WERE FOUND FOR ATOM LIST 41554 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29936 from a total of 756509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 870 -69.17026 0.09111 0.88129 INTE EXTERN> -23.90069 -45.26958 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1703" Parameter: A <- "-69.1703" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9007" Parameter: B <- "-23.9007" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2696" Parameter: C <- "-45.2696" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 870 TOTAL ENERGY = -69.1703 RDTITL> * VAN DER WAALS = -23.9007 ELECTROSTATIC = -45.2696 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "870" Parameter: CONF_N -> "8002" Comparing "870" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "871" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757592 ATOM PAIRS WERE FOUND FOR ATOM LIST 41655 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29567 from a total of 757592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 871 -74.83275 5.66249 0.76357 INTE EXTERN> -25.92209 -48.91066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8328" Parameter: A <- "-74.8328" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9221" Parameter: B <- "-25.9221" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9107" Parameter: C <- "-48.9107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 871 TOTAL ENERGY = -74.8328 RDTITL> * VAN DER WAALS = -25.9221 ELECTROSTATIC = -48.9107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "871" Parameter: CONF_N -> "8002" Comparing "871" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "872" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762342 ATOM PAIRS WERE FOUND FOR ATOM LIST 41919 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29579 from a total of 762342 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 872 -73.89304 -0.93971 0.74392 INTE EXTERN> -26.36736 -47.52569 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.893" Parameter: A <- "-73.893" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3674" Parameter: B <- "-26.3674" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5257" Parameter: C <- "-47.5257" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 872 TOTAL ENERGY = -73.893 RDTITL> * VAN DER WAALS = -26.3674 ELECTROSTATIC = -47.5257 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "872" Parameter: CONF_N -> "8002" Comparing "872" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "873" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762342 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759744 ATOM PAIRS WERE FOUND FOR ATOM LIST 41666 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29540 from a total of 759744 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 873 -69.79952 -4.09352 0.57744 INTE EXTERN> -31.66130 -38.13822 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7995" Parameter: A <- "-69.7995" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6613" Parameter: B <- "-31.6613" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1382" Parameter: C <- "-38.1382" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 873 TOTAL ENERGY = -69.7995 RDTITL> * VAN DER WAALS = -31.6613 ELECTROSTATIC = -38.1382 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "873" Parameter: CONF_N -> "8002" Comparing "873" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "874" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759744 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761939 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29113 from a total of 761939 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 874 -70.58706 0.78754 0.82485 INTE EXTERN> -21.55581 -49.03125 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5871" Parameter: A <- "-70.5871" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.5558" Parameter: B <- "-21.5558" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0313" Parameter: C <- "-49.0313" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 874 TOTAL ENERGY = -70.5871 RDTITL> * VAN DER WAALS = -21.5558 ELECTROSTATIC = -49.0313 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "874" Parameter: CONF_N -> "8002" Comparing "874" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "875" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761939 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759050 ATOM PAIRS WERE FOUND FOR ATOM LIST 41691 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29647 from a total of 759050 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 875 -75.20443 4.61736 0.73935 INTE EXTERN> -28.14476 -47.05966 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2044" Parameter: A <- "-75.2044" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1448" Parameter: B <- "-28.1448" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0597" Parameter: C <- "-47.0597" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 875 TOTAL ENERGY = -75.2044 RDTITL> * VAN DER WAALS = -28.1448 ELECTROSTATIC = -47.0597 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "875" Parameter: CONF_N -> "8002" Comparing "875" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "876" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759050 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765898 ATOM PAIRS WERE FOUND FOR ATOM LIST 41869 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29709 from a total of 765898 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 876 -68.11252 -7.09191 0.81838 INTE EXTERN> -21.77704 -46.33547 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1125" Parameter: A <- "-68.1125" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.777" Parameter: B <- "-21.777" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3355" Parameter: C <- "-46.3355" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 876 TOTAL ENERGY = -68.1125 RDTITL> * VAN DER WAALS = -21.777 ELECTROSTATIC = -46.3355 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "876" Parameter: CONF_N -> "8002" Comparing "876" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "877" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765898 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763612 ATOM PAIRS WERE FOUND FOR ATOM LIST 41825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30135 from a total of 763612 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 877 -71.50976 3.39724 0.68452 INTE EXTERN> -31.95290 -39.55686 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5098" Parameter: A <- "-71.5098" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9529" Parameter: B <- "-31.9529" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5569" Parameter: C <- "-39.5569" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 877 TOTAL ENERGY = -71.5098 RDTITL> * VAN DER WAALS = -31.9529 ELECTROSTATIC = -39.5569 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "877" Parameter: CONF_N -> "8002" Comparing "877" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "878" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763612 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764897 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29664 from a total of 764897 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 878 -67.91116 -3.59860 0.69912 INTE EXTERN> -27.80751 -40.10365 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9112" Parameter: A <- "-67.9112" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8075" Parameter: B <- "-27.8075" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1036" Parameter: C <- "-40.1036" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 878 TOTAL ENERGY = -67.9112 RDTITL> * VAN DER WAALS = -27.8075 ELECTROSTATIC = -40.1036 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "878" Parameter: CONF_N -> "8002" Comparing "878" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "879" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764897 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766568 ATOM PAIRS WERE FOUND FOR ATOM LIST 42046 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29951 from a total of 766568 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 879 -69.62671 1.71555 0.66600 INTE EXTERN> -27.92363 -41.70309 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6267" Parameter: A <- "-69.6267" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9236" Parameter: B <- "-27.9236" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7031" Parameter: C <- "-41.7031" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 879 TOTAL ENERGY = -69.6267 RDTITL> * VAN DER WAALS = -27.9236 ELECTROSTATIC = -41.7031 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "879" Parameter: CONF_N -> "8002" Comparing "879" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "880" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766568 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765397 ATOM PAIRS WERE FOUND FOR ATOM LIST 42036 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29780 from a total of 765397 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 880 -71.35414 1.72743 0.83725 INTE EXTERN> -22.88600 -48.46814 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3541" Parameter: A <- "-71.3541" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.886" Parameter: B <- "-22.886" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4681" Parameter: C <- "-48.4681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 880 TOTAL ENERGY = -71.3541 RDTITL> * VAN DER WAALS = -22.886 ELECTROSTATIC = -48.4681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "880" Parameter: CONF_N -> "8002" Comparing "880" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "881" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765397 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762189 ATOM PAIRS WERE FOUND FOR ATOM LIST 41656 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29672 from a total of 762189 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 881 -75.09551 3.74136 0.59113 INTE EXTERN> -32.58812 -42.50739 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0955" Parameter: A <- "-75.0955" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5881" Parameter: B <- "-32.5881" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5074" Parameter: C <- "-42.5074" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 881 TOTAL ENERGY = -75.0955 RDTITL> * VAN DER WAALS = -32.5881 ELECTROSTATIC = -42.5074 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "881" Parameter: CONF_N -> "8002" Comparing "881" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "882" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762189 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760802 ATOM PAIRS WERE FOUND FOR ATOM LIST 41734 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30046 from a total of 760802 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 882 -71.68939 -3.40612 0.75334 INTE EXTERN> -26.55783 -45.13155 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6894" Parameter: A <- "-71.6894" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5578" Parameter: B <- "-26.5578" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1316" Parameter: C <- "-45.1316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 882 TOTAL ENERGY = -71.6894 RDTITL> * VAN DER WAALS = -26.5578 ELECTROSTATIC = -45.1316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "882" Parameter: CONF_N -> "8002" Comparing "882" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "883" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760802 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762322 ATOM PAIRS WERE FOUND FOR ATOM LIST 41707 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30259 from a total of 762322 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 883 -64.16246 -7.52693 0.72521 INTE EXTERN> -27.84333 -36.31912 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1625" Parameter: A <- "-64.1625" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8433" Parameter: B <- "-27.8433" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3191" Parameter: C <- "-36.3191" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 883 TOTAL ENERGY = -64.1625 RDTITL> * VAN DER WAALS = -27.8433 ELECTROSTATIC = -36.3191 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "883" Parameter: CONF_N -> "8002" Comparing "883" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "884" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762322 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755327 ATOM PAIRS WERE FOUND FOR ATOM LIST 41614 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29215 from a total of 755327 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 884 -70.24005 6.07759 0.63356 INTE EXTERN> -29.45456 -40.78549 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.24" Parameter: A <- "-70.24" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4546" Parameter: B <- "-29.4546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7855" Parameter: C <- "-40.7855" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 884 TOTAL ENERGY = -70.24 RDTITL> * VAN DER WAALS = -29.4546 ELECTROSTATIC = -40.7855 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "884" Parameter: CONF_N -> "8002" Comparing "884" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "885" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755327 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757893 ATOM PAIRS WERE FOUND FOR ATOM LIST 41480 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28997 from a total of 757893 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 885 -63.66397 -6.57608 0.57837 INTE EXTERN> -29.90898 -33.75499 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.664" Parameter: A <- "-63.664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.909" Parameter: B <- "-29.909" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.755" Parameter: C <- "-33.755" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 885 TOTAL ENERGY = -63.664 RDTITL> * VAN DER WAALS = -29.909 ELECTROSTATIC = -33.755 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "885" Parameter: CONF_N -> "8002" Comparing "885" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "886" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757893 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767582 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29411 from a total of 767582 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 886 -68.50653 4.84256 0.59883 INTE EXTERN> -33.68592 -34.82061 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5065" Parameter: A <- "-68.5065" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6859" Parameter: B <- "-33.6859" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8206" Parameter: C <- "-34.8206" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 886 TOTAL ENERGY = -68.5065 RDTITL> * VAN DER WAALS = -33.6859 ELECTROSTATIC = -34.8206 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "886" Parameter: CONF_N -> "8002" Comparing "886" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "887" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767582 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761569 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29928 from a total of 761569 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 887 -68.44348 -0.06305 0.73925 INTE EXTERN> -25.46077 -42.98272 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4435" Parameter: A <- "-68.4435" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4608" Parameter: B <- "-25.4608" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9827" Parameter: C <- "-42.9827" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 887 TOTAL ENERGY = -68.4435 RDTITL> * VAN DER WAALS = -25.4608 ELECTROSTATIC = -42.9827 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "887" Parameter: CONF_N -> "8002" Comparing "887" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "888" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761569 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767412 ATOM PAIRS WERE FOUND FOR ATOM LIST 42017 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29438 from a total of 767412 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 888 -65.96610 -2.47738 0.58243 INTE EXTERN> -32.15225 -33.81385 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9661" Parameter: A <- "-65.9661" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1522" Parameter: B <- "-32.1522" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8139" Parameter: C <- "-33.8139" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 888 TOTAL ENERGY = -65.9661 RDTITL> * VAN DER WAALS = -32.1522 ELECTROSTATIC = -33.8139 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "888" Parameter: CONF_N -> "8002" Comparing "888" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "889" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767412 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756778 ATOM PAIRS WERE FOUND FOR ATOM LIST 41632 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29136 from a total of 756778 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 889 -75.93609 9.96999 0.59542 INTE EXTERN> -33.36004 -42.57605 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9361" Parameter: A <- "-75.9361" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.36" Parameter: B <- "-33.36" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5761" Parameter: C <- "-42.5761" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 889 TOTAL ENERGY = -75.9361 RDTITL> * VAN DER WAALS = -33.36 ELECTROSTATIC = -42.5761 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "889" Parameter: CONF_N -> "8002" Comparing "889" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "890" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756778 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762406 ATOM PAIRS WERE FOUND FOR ATOM LIST 41783 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29395 from a total of 762406 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 890 -74.11130 -1.82480 0.71967 INTE EXTERN> -28.16432 -45.94698 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1113" Parameter: A <- "-74.1113" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1643" Parameter: B <- "-28.1643" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.947" Parameter: C <- "-45.947" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 890 TOTAL ENERGY = -74.1113 RDTITL> * VAN DER WAALS = -28.1643 ELECTROSTATIC = -45.947 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "890" Parameter: CONF_N -> "8002" Comparing "890" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "891" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762406 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762664 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29607 from a total of 762664 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 891 -65.63308 -8.47822 0.71077 INTE EXTERN> -27.81057 -37.82251 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6331" Parameter: A <- "-65.6331" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8106" Parameter: B <- "-27.8106" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8225" Parameter: C <- "-37.8225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 891 TOTAL ENERGY = -65.6331 RDTITL> * VAN DER WAALS = -27.8106 ELECTROSTATIC = -37.8225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "891" Parameter: CONF_N -> "8002" Comparing "891" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "892" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762664 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761149 ATOM PAIRS WERE FOUND FOR ATOM LIST 41762 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29463 from a total of 761149 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 892 -71.68611 6.05303 0.72170 INTE EXTERN> -26.07375 -45.61236 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6861" Parameter: A <- "-71.6861" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0737" Parameter: B <- "-26.0737" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6124" Parameter: C <- "-45.6124" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 892 TOTAL ENERGY = -71.6861 RDTITL> * VAN DER WAALS = -26.0737 ELECTROSTATIC = -45.6124 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "892" Parameter: CONF_N -> "8002" Comparing "892" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "893" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761149 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764209 ATOM PAIRS WERE FOUND FOR ATOM LIST 41683 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29647 from a total of 764209 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 893 -73.38455 1.69844 0.69023 INTE EXTERN> -29.22810 -44.15645 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3845" Parameter: A <- "-73.3845" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2281" Parameter: B <- "-29.2281" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1564" Parameter: C <- "-44.1564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 893 TOTAL ENERGY = -73.3845 RDTITL> * VAN DER WAALS = -29.2281 ELECTROSTATIC = -44.1564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "893" Parameter: CONF_N -> "8002" Comparing "893" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "894" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764209 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766596 ATOM PAIRS WERE FOUND FOR ATOM LIST 42089 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30067 from a total of 766596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 894 -69.28955 -4.09500 0.64114 INTE EXTERN> -29.35817 -39.93137 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2895" Parameter: A <- "-69.2895" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3582" Parameter: B <- "-29.3582" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9314" Parameter: C <- "-39.9314" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 894 TOTAL ENERGY = -69.2895 RDTITL> * VAN DER WAALS = -29.3582 ELECTROSTATIC = -39.9314 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "894" Parameter: CONF_N -> "8002" Comparing "894" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "895" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767958 ATOM PAIRS WERE FOUND FOR ATOM LIST 42180 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30157 from a total of 767958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 895 -68.00552 -1.28402 0.69186 INTE EXTERN> -27.05061 -40.95491 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0055" Parameter: A <- "-68.0055" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0506" Parameter: B <- "-27.0506" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9549" Parameter: C <- "-40.9549" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 895 TOTAL ENERGY = -68.0055 RDTITL> * VAN DER WAALS = -27.0506 ELECTROSTATIC = -40.9549 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "895" Parameter: CONF_N -> "8002" Comparing "895" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "896" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770657 ATOM PAIRS WERE FOUND FOR ATOM LIST 42157 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29922 from a total of 770657 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 896 -68.99878 0.99326 0.71993 INTE EXTERN> -24.51498 -44.48379 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9988" Parameter: A <- "-68.9988" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.515" Parameter: B <- "-24.515" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4838" Parameter: C <- "-44.4838" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 896 TOTAL ENERGY = -68.9988 RDTITL> * VAN DER WAALS = -24.515 ELECTROSTATIC = -44.4838 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "896" Parameter: CONF_N -> "8002" Comparing "896" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "897" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770657 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770507 ATOM PAIRS WERE FOUND FOR ATOM LIST 42390 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30342 from a total of 770507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 897 -72.74154 3.74276 0.61903 INTE EXTERN> -30.86853 -41.87301 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7415" Parameter: A <- "-72.7415" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8685" Parameter: B <- "-30.8685" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.873" Parameter: C <- "-41.873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 897 TOTAL ENERGY = -72.7415 RDTITL> * VAN DER WAALS = -30.8685 ELECTROSTATIC = -41.873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "897" Parameter: CONF_N -> "8002" Comparing "897" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "898" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764686 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29707 from a total of 764686 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 898 -69.14186 -3.59968 0.59203 INTE EXTERN> -32.23532 -36.90654 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1419" Parameter: A <- "-69.1419" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2353" Parameter: B <- "-32.2353" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9065" Parameter: C <- "-36.9065" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 898 TOTAL ENERGY = -69.1419 RDTITL> * VAN DER WAALS = -32.2353 ELECTROSTATIC = -36.9065 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "898" Parameter: CONF_N -> "8002" Comparing "898" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "899" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764686 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766715 ATOM PAIRS WERE FOUND FOR ATOM LIST 42002 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30049 from a total of 766715 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 899 -68.88155 -0.26031 0.61702 INTE EXTERN> -27.97055 -40.91099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8815" Parameter: A <- "-68.8815" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9706" Parameter: B <- "-27.9706" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.911" Parameter: C <- "-40.911" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 899 TOTAL ENERGY = -68.8815 RDTITL> * VAN DER WAALS = -27.9706 ELECTROSTATIC = -40.911 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "899" Parameter: CONF_N -> "8002" Comparing "899" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "900" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766715 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763212 ATOM PAIRS WERE FOUND FOR ATOM LIST 41615 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29718 from a total of 763212 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 900 -66.64972 -2.23183 0.56183 INTE EXTERN> -29.33186 -37.31786 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6497" Parameter: A <- "-66.6497" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3319" Parameter: B <- "-29.3319" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3179" Parameter: C <- "-37.3179" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 900 TOTAL ENERGY = -66.6497 RDTITL> * VAN DER WAALS = -29.3319 ELECTROSTATIC = -37.3179 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "900" Parameter: CONF_N -> "8002" Comparing "900" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "901" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763212 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769814 ATOM PAIRS WERE FOUND FOR ATOM LIST 42130 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30223 from a total of 769814 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 901 -75.72987 9.08015 0.63452 INTE EXTERN> -30.40882 -45.32105 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7299" Parameter: A <- "-75.7299" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4088" Parameter: B <- "-30.4088" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.321" Parameter: C <- "-45.321" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 901 TOTAL ENERGY = -75.7299 RDTITL> * VAN DER WAALS = -30.4088 ELECTROSTATIC = -45.321 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "901" Parameter: CONF_N -> "8002" Comparing "901" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "902" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769814 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770151 ATOM PAIRS WERE FOUND FOR ATOM LIST 42253 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30370 from a total of 770151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 902 -70.44420 -5.28567 0.63375 INTE EXTERN> -28.38586 -42.05834 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4442" Parameter: A <- "-70.4442" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3859" Parameter: B <- "-28.3859" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0583" Parameter: C <- "-42.0583" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 902 TOTAL ENERGY = -70.4442 RDTITL> * VAN DER WAALS = -28.3859 ELECTROSTATIC = -42.0583 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "902" Parameter: CONF_N -> "8002" Comparing "902" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "903" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763769 ATOM PAIRS WERE FOUND FOR ATOM LIST 42039 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29738 from a total of 763769 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 903 -68.66545 -1.77875 0.48146 INTE EXTERN> -33.89858 -34.76687 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6654" Parameter: A <- "-68.6654" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8986" Parameter: B <- "-33.8986" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7669" Parameter: C <- "-34.7669" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 903 TOTAL ENERGY = -68.6654 RDTITL> * VAN DER WAALS = -33.8986 ELECTROSTATIC = -34.7669 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "903" Parameter: CONF_N -> "8002" Comparing "903" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "904" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763769 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764579 ATOM PAIRS WERE FOUND FOR ATOM LIST 41730 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30215 from a total of 764579 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 904 -62.43201 -6.23344 0.54887 INTE EXTERN> -31.56951 -30.86250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.432" Parameter: A <- "-62.432" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5695" Parameter: B <- "-31.5695" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.8625" Parameter: C <- "-30.8625" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 904 TOTAL ENERGY = -62.432 RDTITL> * VAN DER WAALS = -31.5695 ELECTROSTATIC = -30.8625 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "904" Parameter: CONF_N -> "8002" Comparing "904" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "905" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764579 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766667 ATOM PAIRS WERE FOUND FOR ATOM LIST 41985 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30050 from a total of 766667 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 905 -72.08751 9.65550 0.60283 INTE EXTERN> -31.88992 -40.19759 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0875" Parameter: A <- "-72.0875" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8899" Parameter: B <- "-31.8899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1976" Parameter: C <- "-40.1976" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 905 TOTAL ENERGY = -72.0875 RDTITL> * VAN DER WAALS = -31.8899 ELECTROSTATIC = -40.1976 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "905" Parameter: CONF_N -> "8002" Comparing "905" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "906" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766667 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767556 ATOM PAIRS WERE FOUND FOR ATOM LIST 42127 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29638 from a total of 767556 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 906 -77.23620 5.14870 0.67197 INTE EXTERN> -29.40339 -47.83281 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2362" Parameter: A <- "-77.2362" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4034" Parameter: B <- "-29.4034" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8328" Parameter: C <- "-47.8328" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 906 TOTAL ENERGY = -77.2362 RDTITL> * VAN DER WAALS = -29.4034 ELECTROSTATIC = -47.8328 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "906" Parameter: CONF_N -> "8002" Comparing "906" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "907" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767556 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762198 ATOM PAIRS WERE FOUND FOR ATOM LIST 41578 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29556 from a total of 762198 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 907 -71.55338 -5.68283 0.69592 INTE EXTERN> -25.22416 -46.32922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5534" Parameter: A <- "-71.5534" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2242" Parameter: B <- "-25.2242" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3292" Parameter: C <- "-46.3292" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 907 TOTAL ENERGY = -71.5534 RDTITL> * VAN DER WAALS = -25.2242 ELECTROSTATIC = -46.3292 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "907" Parameter: CONF_N -> "8002" Comparing "907" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "908" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762198 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761056 ATOM PAIRS WERE FOUND FOR ATOM LIST 41965 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29544 from a total of 761056 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 908 -64.13208 -7.42129 0.67464 INTE EXTERN> -26.34598 -37.78610 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1321" Parameter: A <- "-64.1321" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.346" Parameter: B <- "-26.346" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7861" Parameter: C <- "-37.7861" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 908 TOTAL ENERGY = -64.1321 RDTITL> * VAN DER WAALS = -26.346 ELECTROSTATIC = -37.7861 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "908" Parameter: CONF_N -> "8002" Comparing "908" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "909" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761056 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772459 ATOM PAIRS WERE FOUND FOR ATOM LIST 42292 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29928 from a total of 772459 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 909 -66.77530 2.64321 0.73516 INTE EXTERN> -24.37533 -42.39996 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7753" Parameter: A <- "-66.7753" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3753" Parameter: B <- "-24.3753" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4" Parameter: C <- "-42.4" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 909 TOTAL ENERGY = -66.7753 RDTITL> * VAN DER WAALS = -24.3753 ELECTROSTATIC = -42.4 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "909" Parameter: CONF_N -> "8002" Comparing "909" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "910" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772459 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765400 ATOM PAIRS WERE FOUND FOR ATOM LIST 42019 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29820 from a total of 765400 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 910 -65.96829 -0.80701 0.49302 INTE EXTERN> -34.11032 -31.85797 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9683" Parameter: A <- "-65.9683" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1103" Parameter: B <- "-34.1103" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.858" Parameter: C <- "-31.858" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 910 TOTAL ENERGY = -65.9683 RDTITL> * VAN DER WAALS = -34.1103 ELECTROSTATIC = -31.858 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "910" Parameter: CONF_N -> "8002" Comparing "910" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "911" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765400 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768363 ATOM PAIRS WERE FOUND FOR ATOM LIST 42095 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29915 from a total of 768363 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 911 -67.95786 1.98957 0.52387 INTE EXTERN> -31.84686 -36.11101 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9579" Parameter: A <- "-67.9579" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8469" Parameter: B <- "-31.8469" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.111" Parameter: C <- "-36.111" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 911 TOTAL ENERGY = -67.9579 RDTITL> * VAN DER WAALS = -31.8469 ELECTROSTATIC = -36.111 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "911" Parameter: CONF_N -> "8002" Comparing "911" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "912" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768363 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768379 ATOM PAIRS WERE FOUND FOR ATOM LIST 42165 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29823 from a total of 768379 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 912 -74.85879 6.90092 0.72834 INTE EXTERN> -26.50923 -48.34956 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8588" Parameter: A <- "-74.8588" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5092" Parameter: B <- "-26.5092" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3496" Parameter: C <- "-48.3496" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 912 TOTAL ENERGY = -74.8588 RDTITL> * VAN DER WAALS = -26.5092 ELECTROSTATIC = -48.3496 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "912" Parameter: CONF_N -> "8002" Comparing "912" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "913" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768379 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763695 ATOM PAIRS WERE FOUND FOR ATOM LIST 41949 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29984 from a total of 763695 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 913 -66.26737 -8.59142 0.62973 INTE EXTERN> -27.86671 -38.40066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2674" Parameter: A <- "-66.2674" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8667" Parameter: B <- "-27.8667" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4007" Parameter: C <- "-38.4007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 913 TOTAL ENERGY = -66.2674 RDTITL> * VAN DER WAALS = -27.8667 ELECTROSTATIC = -38.4007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "913" Parameter: CONF_N -> "8002" Comparing "913" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "914" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763695 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764511 ATOM PAIRS WERE FOUND FOR ATOM LIST 41931 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30141 from a total of 764511 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 914 -72.63090 6.36353 0.64254 INTE EXTERN> -28.85994 -43.77096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6309" Parameter: A <- "-72.6309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8599" Parameter: B <- "-28.8599" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.771" Parameter: C <- "-43.771" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 914 TOTAL ENERGY = -72.6309 RDTITL> * VAN DER WAALS = -28.8599 ELECTROSTATIC = -43.771 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "914" Parameter: CONF_N -> "8002" Comparing "914" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "915" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764511 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772310 ATOM PAIRS WERE FOUND FOR ATOM LIST 42200 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30053 from a total of 772310 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 915 -64.45097 -8.17993 0.66405 INTE EXTERN> -25.12146 -39.32951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.451" Parameter: A <- "-64.451" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1215" Parameter: B <- "-25.1215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3295" Parameter: C <- "-39.3295" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 915 TOTAL ENERGY = -64.451 RDTITL> * VAN DER WAALS = -25.1215 ELECTROSTATIC = -39.3295 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "915" Parameter: CONF_N -> "8002" Comparing "915" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "916" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772310 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 774760 ATOM PAIRS WERE FOUND FOR ATOM LIST 42363 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30433 from a total of 774760 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 916 -67.29357 2.84260 0.53416 INTE EXTERN> -34.57390 -32.71967 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2936" Parameter: A <- "-67.2936" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.5739" Parameter: B <- "-34.5739" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.7197" Parameter: C <- "-32.7197" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 916 TOTAL ENERGY = -67.2936 RDTITL> * VAN DER WAALS = -34.5739 ELECTROSTATIC = -32.7197 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "916" Parameter: CONF_N -> "8002" Comparing "916" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "917" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 774760 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 774104 ATOM PAIRS WERE FOUND FOR ATOM LIST 42354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30442 from a total of 774104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 917 -61.83392 -5.45965 0.63112 INTE EXTERN> -28.93652 -32.89740 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.8339" Parameter: A <- "-61.8339" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9365" Parameter: B <- "-28.9365" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.8974" Parameter: C <- "-32.8974" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 917 TOTAL ENERGY = -61.8339 RDTITL> * VAN DER WAALS = -28.9365 ELECTROSTATIC = -32.8974 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "917" Parameter: CONF_N -> "8002" Comparing "917" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "918" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 774104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769796 ATOM PAIRS WERE FOUND FOR ATOM LIST 42023 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30005 from a total of 769796 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 918 -74.51914 12.68522 0.69682 INTE EXTERN> -29.62699 -44.89215 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5191" Parameter: A <- "-74.5191" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.627" Parameter: B <- "-29.627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8922" Parameter: C <- "-44.8922" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 918 TOTAL ENERGY = -74.5191 RDTITL> * VAN DER WAALS = -29.627 ELECTROSTATIC = -44.8922 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "918" Parameter: CONF_N -> "8002" Comparing "918" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "919" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769796 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767039 ATOM PAIRS WERE FOUND FOR ATOM LIST 41856 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29714 from a total of 767039 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 919 -72.70381 -1.81534 0.60309 INTE EXTERN> -32.63243 -40.07138 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7038" Parameter: A <- "-72.7038" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6324" Parameter: B <- "-32.6324" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0714" Parameter: C <- "-40.0714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 919 TOTAL ENERGY = -72.7038 RDTITL> * VAN DER WAALS = -32.6324 ELECTROSTATIC = -40.0714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "919" Parameter: CONF_N -> "8002" Comparing "919" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "920" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767039 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763986 ATOM PAIRS WERE FOUND FOR ATOM LIST 41958 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29738 from a total of 763986 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 920 -72.64871 -0.05509 0.64192 INTE EXTERN> -29.28111 -43.36760 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6487" Parameter: A <- "-72.6487" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2811" Parameter: B <- "-29.2811" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3676" Parameter: C <- "-43.3676" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 920 TOTAL ENERGY = -72.6487 RDTITL> * VAN DER WAALS = -29.2811 ELECTROSTATIC = -43.3676 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "920" Parameter: CONF_N -> "8002" Comparing "920" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "921" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763986 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770125 ATOM PAIRS WERE FOUND FOR ATOM LIST 41988 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30433 from a total of 770125 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 921 -68.81729 -3.83142 0.63134 INTE EXTERN> -30.09972 -38.71757 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8173" Parameter: A <- "-68.8173" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0997" Parameter: B <- "-30.0997" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7176" Parameter: C <- "-38.7176" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 921 TOTAL ENERGY = -68.8173 RDTITL> * VAN DER WAALS = -30.0997 ELECTROSTATIC = -38.7176 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "921" Parameter: CONF_N -> "8002" Comparing "921" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "922" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770125 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771290 ATOM PAIRS WERE FOUND FOR ATOM LIST 42064 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29698 from a total of 771290 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 922 -70.05872 1.24143 0.61017 INTE EXTERN> -29.85482 -40.20390 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0587" Parameter: A <- "-70.0587" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8548" Parameter: B <- "-29.8548" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2039" Parameter: C <- "-40.2039" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 922 TOTAL ENERGY = -70.0587 RDTITL> * VAN DER WAALS = -29.8548 ELECTROSTATIC = -40.2039 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "922" Parameter: CONF_N -> "8002" Comparing "922" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "923" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771290 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771765 ATOM PAIRS WERE FOUND FOR ATOM LIST 42097 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29923 from a total of 771765 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 923 -72.06439 2.00567 0.74902 INTE EXTERN> -26.66767 -45.39672 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0644" Parameter: A <- "-72.0644" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6677" Parameter: B <- "-26.6677" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3967" Parameter: C <- "-45.3967" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 923 TOTAL ENERGY = -72.0644 RDTITL> * VAN DER WAALS = -26.6677 ELECTROSTATIC = -45.3967 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "923" Parameter: CONF_N -> "8002" Comparing "923" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "924" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771765 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764824 ATOM PAIRS WERE FOUND FOR ATOM LIST 41981 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29874 from a total of 764824 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 924 -65.59069 -6.47370 0.81308 INTE EXTERN> -22.36573 -43.22497 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5907" Parameter: A <- "-65.5907" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.3657" Parameter: B <- "-22.3657" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.225" Parameter: C <- "-43.225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 924 TOTAL ENERGY = -65.5907 RDTITL> * VAN DER WAALS = -22.3657 ELECTROSTATIC = -43.225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "924" Parameter: CONF_N -> "8002" Comparing "924" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "925" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764824 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764527 ATOM PAIRS WERE FOUND FOR ATOM LIST 41806 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29931 from a total of 764527 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 925 -72.44082 6.85013 0.69371 INTE EXTERN> -28.87294 -43.56788 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4408" Parameter: A <- "-72.4408" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8729" Parameter: B <- "-28.8729" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5679" Parameter: C <- "-43.5679" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 925 TOTAL ENERGY = -72.4408 RDTITL> * VAN DER WAALS = -28.8729 ELECTROSTATIC = -43.5679 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "925" Parameter: CONF_N -> "8002" Comparing "925" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "926" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764527 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764380 ATOM PAIRS WERE FOUND FOR ATOM LIST 41973 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29493 from a total of 764380 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 926 -71.97750 -0.46332 0.53868 INTE EXTERN> -33.39277 -38.58473 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9775" Parameter: A <- "-71.9775" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3928" Parameter: B <- "-33.3928" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5847" Parameter: C <- "-38.5847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 926 TOTAL ENERGY = -71.9775 RDTITL> * VAN DER WAALS = -33.3928 ELECTROSTATIC = -38.5847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "926" Parameter: CONF_N -> "8002" Comparing "926" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "927" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764380 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772116 ATOM PAIRS WERE FOUND FOR ATOM LIST 42250 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30262 from a total of 772116 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 927 -70.54766 -1.42984 0.73086 INTE EXTERN> -26.38443 -44.16323 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5477" Parameter: A <- "-70.5477" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3844" Parameter: B <- "-26.3844" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1632" Parameter: C <- "-44.1632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 927 TOTAL ENERGY = -70.5477 RDTITL> * VAN DER WAALS = -26.3844 ELECTROSTATIC = -44.1632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "927" Parameter: CONF_N -> "8002" Comparing "927" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "928" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772116 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763575 ATOM PAIRS WERE FOUND FOR ATOM LIST 41861 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29769 from a total of 763575 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 928 -72.94460 2.39694 0.66048 INTE EXTERN> -29.17361 -43.77099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9446" Parameter: A <- "-72.9446" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1736" Parameter: B <- "-29.1736" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.771" Parameter: C <- "-43.771" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 928 TOTAL ENERGY = -72.9446 RDTITL> * VAN DER WAALS = -29.1736 ELECTROSTATIC = -43.771 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "928" Parameter: CONF_N -> "8002" Comparing "928" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "929" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763575 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766050 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29463 from a total of 766050 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 929 -72.37720 -0.56740 0.58704 INTE EXTERN> -32.16331 -40.21389 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3772" Parameter: A <- "-72.3772" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1633" Parameter: B <- "-32.1633" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2139" Parameter: C <- "-40.2139" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 929 TOTAL ENERGY = -72.3772 RDTITL> * VAN DER WAALS = -32.1633 ELECTROSTATIC = -40.2139 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "929" Parameter: CONF_N -> "8002" Comparing "929" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "930" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766050 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763844 ATOM PAIRS WERE FOUND FOR ATOM LIST 41842 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29771 from a total of 763844 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 930 -70.26933 -2.10787 0.76833 INTE EXTERN> -27.34391 -42.92543 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2693" Parameter: A <- "-70.2693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3439" Parameter: B <- "-27.3439" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9254" Parameter: C <- "-42.9254" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 930 TOTAL ENERGY = -70.2693 RDTITL> * VAN DER WAALS = -27.3439 ELECTROSTATIC = -42.9254 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "930" Parameter: CONF_N -> "8002" Comparing "930" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "931" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763844 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766855 ATOM PAIRS WERE FOUND FOR ATOM LIST 42041 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29817 from a total of 766855 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 931 -70.17901 -0.09032 0.60441 INTE EXTERN> -31.32515 -38.85386 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.179" Parameter: A <- "-70.179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3252" Parameter: B <- "-31.3252" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8539" Parameter: C <- "-38.8539" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 931 TOTAL ENERGY = -70.179 RDTITL> * VAN DER WAALS = -31.3252 ELECTROSTATIC = -38.8539 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "931" Parameter: CONF_N -> "8002" Comparing "931" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "932" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766855 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766073 ATOM PAIRS WERE FOUND FOR ATOM LIST 42019 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29868 from a total of 766073 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 932 -66.51981 -3.65920 0.66026 INTE EXTERN> -28.89934 -37.62047 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5198" Parameter: A <- "-66.5198" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8993" Parameter: B <- "-28.8993" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6205" Parameter: C <- "-37.6205" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 932 TOTAL ENERGY = -66.5198 RDTITL> * VAN DER WAALS = -28.8993 ELECTROSTATIC = -37.6205 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "932" Parameter: CONF_N -> "8002" Comparing "932" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "933" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766073 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761895 ATOM PAIRS WERE FOUND FOR ATOM LIST 41655 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29701 from a total of 761895 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 933 -71.46626 4.94645 0.63927 INTE EXTERN> -28.56107 -42.90519 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4663" Parameter: A <- "-71.4663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5611" Parameter: B <- "-28.5611" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9052" Parameter: C <- "-42.9052" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 933 TOTAL ENERGY = -71.4663 RDTITL> * VAN DER WAALS = -28.5611 ELECTROSTATIC = -42.9052 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "933" Parameter: CONF_N -> "8002" Comparing "933" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "934" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761895 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769780 ATOM PAIRS WERE FOUND FOR ATOM LIST 42027 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30127 from a total of 769780 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 934 -71.16077 -0.30549 0.55044 INTE EXTERN> -33.07426 -38.08651 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1608" Parameter: A <- "-71.1608" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0743" Parameter: B <- "-33.0743" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0865" Parameter: C <- "-38.0865" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 934 TOTAL ENERGY = -71.1608 RDTITL> * VAN DER WAALS = -33.0743 ELECTROSTATIC = -38.0865 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "934" Parameter: CONF_N -> "8002" Comparing "934" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "935" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769780 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772092 ATOM PAIRS WERE FOUND FOR ATOM LIST 42350 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29935 from a total of 772092 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 935 -74.45314 3.29237 0.65108 INTE EXTERN> -28.98996 -45.46318 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4531" Parameter: A <- "-74.4531" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.99" Parameter: B <- "-28.99" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4632" Parameter: C <- "-45.4632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 935 TOTAL ENERGY = -74.4531 RDTITL> * VAN DER WAALS = -28.99 ELECTROSTATIC = -45.4632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "935" Parameter: CONF_N -> "8002" Comparing "935" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "936" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772092 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 775108 ATOM PAIRS WERE FOUND FOR ATOM LIST 42350 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30382 from a total of 775108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 936 -69.98515 -4.46799 0.74111 INTE EXTERN> -27.61461 -42.37054 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9852" Parameter: A <- "-69.9852" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6146" Parameter: B <- "-27.6146" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3705" Parameter: C <- "-42.3705" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 936 TOTAL ENERGY = -69.9852 RDTITL> * VAN DER WAALS = -27.6146 ELECTROSTATIC = -42.3705 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "936" Parameter: CONF_N -> "8002" Comparing "936" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "937" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 775108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 774476 ATOM PAIRS WERE FOUND FOR ATOM LIST 42311 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30120 from a total of 774476 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 937 -76.32244 6.33728 0.67455 INTE EXTERN> -30.55542 -45.76701 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3224" Parameter: A <- "-76.3224" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5554" Parameter: B <- "-30.5554" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.767" Parameter: C <- "-45.767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 937 TOTAL ENERGY = -76.3224 RDTITL> * VAN DER WAALS = -30.5554 ELECTROSTATIC = -45.767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "937" Parameter: CONF_N -> "8002" Comparing "937" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "938" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 774476 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767736 ATOM PAIRS WERE FOUND FOR ATOM LIST 41828 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29768 from a total of 767736 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 938 -72.29390 -4.02853 0.59536 INTE EXTERN> -31.97164 -40.32227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2939" Parameter: A <- "-72.2939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9716" Parameter: B <- "-31.9716" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3223" Parameter: C <- "-40.3223" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 938 TOTAL ENERGY = -72.2939 RDTITL> * VAN DER WAALS = -31.9716 ELECTROSTATIC = -40.3223 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "938" Parameter: CONF_N -> "8002" Comparing "938" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "939" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767736 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770653 ATOM PAIRS WERE FOUND FOR ATOM LIST 42244 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30128 from a total of 770653 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 939 -75.27462 2.98072 0.70462 INTE EXTERN> -28.59808 -46.67654 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2746" Parameter: A <- "-75.2746" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5981" Parameter: B <- "-28.5981" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6765" Parameter: C <- "-46.6765" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 939 TOTAL ENERGY = -75.2746 RDTITL> * VAN DER WAALS = -28.5981 ELECTROSTATIC = -46.6765 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "939" Parameter: CONF_N -> "8002" Comparing "939" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "940" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770653 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763779 ATOM PAIRS WERE FOUND FOR ATOM LIST 41730 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29802 from a total of 763779 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 940 -70.77865 -4.49598 0.67718 INTE EXTERN> -27.53517 -43.24348 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7786" Parameter: A <- "-70.7786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5352" Parameter: B <- "-27.5352" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2435" Parameter: C <- "-43.2435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 940 TOTAL ENERGY = -70.7786 RDTITL> * VAN DER WAALS = -27.5352 ELECTROSTATIC = -43.2435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "940" Parameter: CONF_N -> "8002" Comparing "940" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "941" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763779 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767840 ATOM PAIRS WERE FOUND FOR ATOM LIST 42182 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29739 from a total of 767840 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 941 -69.87998 -0.89867 0.58664 INTE EXTERN> -31.51338 -38.36660 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.88" Parameter: A <- "-69.88" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5134" Parameter: B <- "-31.5134" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3666" Parameter: C <- "-38.3666" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 941 TOTAL ENERGY = -69.88 RDTITL> * VAN DER WAALS = -31.5134 ELECTROSTATIC = -38.3666 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "941" Parameter: CONF_N -> "8002" Comparing "941" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "942" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767840 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769287 ATOM PAIRS WERE FOUND FOR ATOM LIST 42149 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30085 from a total of 769287 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 942 -75.28529 5.40532 0.64614 INTE EXTERN> -29.59736 -45.68793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2853" Parameter: A <- "-75.2853" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5974" Parameter: B <- "-29.5974" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6879" Parameter: C <- "-45.6879" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 942 TOTAL ENERGY = -75.2853 RDTITL> * VAN DER WAALS = -29.5974 ELECTROSTATIC = -45.6879 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "942" Parameter: CONF_N -> "8002" Comparing "942" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "943" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769287 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766361 ATOM PAIRS WERE FOUND FOR ATOM LIST 41949 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29951 from a total of 766361 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 943 -68.50011 -6.78519 0.72644 INTE EXTERN> -24.95839 -43.54171 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5001" Parameter: A <- "-68.5001" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9584" Parameter: B <- "-24.9584" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5417" Parameter: C <- "-43.5417" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 943 TOTAL ENERGY = -68.5001 RDTITL> * VAN DER WAALS = -24.9584 ELECTROSTATIC = -43.5417 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "943" Parameter: CONF_N -> "8002" Comparing "943" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "944" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766361 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41989 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30041 from a total of 765009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 944 -62.53491 -5.96520 0.72282 INTE EXTERN> -25.92349 -36.61141 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5349" Parameter: A <- "-62.5349" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9235" Parameter: B <- "-25.9235" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6114" Parameter: C <- "-36.6114" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 944 TOTAL ENERGY = -62.5349 RDTITL> * VAN DER WAALS = -25.9235 ELECTROSTATIC = -36.6114 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "944" Parameter: CONF_N -> "8002" Comparing "944" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "945" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766395 ATOM PAIRS WERE FOUND FOR ATOM LIST 41834 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29563 from a total of 766395 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 945 -72.36788 9.83298 0.73352 INTE EXTERN> -24.97881 -47.38907 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3679" Parameter: A <- "-72.3679" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9788" Parameter: B <- "-24.9788" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3891" Parameter: C <- "-47.3891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 945 TOTAL ENERGY = -72.3679 RDTITL> * VAN DER WAALS = -24.9788 ELECTROSTATIC = -47.3891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "945" Parameter: CONF_N -> "8002" Comparing "945" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "946" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766395 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762546 ATOM PAIRS WERE FOUND FOR ATOM LIST 41564 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29934 from a total of 762546 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 946 -68.19475 -4.17313 0.56392 INTE EXTERN> -32.04055 -36.15420 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1947" Parameter: A <- "-68.1947" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0406" Parameter: B <- "-32.0406" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1542" Parameter: C <- "-36.1542" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 946 TOTAL ENERGY = -68.1947 RDTITL> * VAN DER WAALS = -32.0406 ELECTROSTATIC = -36.1542 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "946" Parameter: CONF_N -> "8002" Comparing "946" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "947" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762546 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770994 ATOM PAIRS WERE FOUND FOR ATOM LIST 42106 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30125 from a total of 770994 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 947 -64.81324 -3.38151 0.51437 INTE EXTERN> -33.26145 -31.55179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8132" Parameter: A <- "-64.8132" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2614" Parameter: B <- "-33.2614" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.5518" Parameter: C <- "-31.5518" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 947 TOTAL ENERGY = -64.8132 RDTITL> * VAN DER WAALS = -33.2614 ELECTROSTATIC = -31.5518 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "947" Parameter: CONF_N -> "8002" Comparing "947" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "948" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770994 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765473 ATOM PAIRS WERE FOUND FOR ATOM LIST 41898 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29636 from a total of 765473 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 948 -60.41306 -4.40018 0.58279 INTE EXTERN> -27.07793 -33.33512 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.4131" Parameter: A <- "-60.4131" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0779" Parameter: B <- "-27.0779" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.3351" Parameter: C <- "-33.3351" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 948 TOTAL ENERGY = -60.4131 RDTITL> * VAN DER WAALS = -27.0779 ELECTROSTATIC = -33.3351 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "948" Parameter: CONF_N -> "8002" Comparing "948" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "949" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765473 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763649 ATOM PAIRS WERE FOUND FOR ATOM LIST 41827 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28909 from a total of 763649 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 949 -62.41003 1.99698 0.52574 INTE EXTERN> -31.88738 -30.52265 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.41" Parameter: A <- "-62.41" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8874" Parameter: B <- "-31.8874" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.5227" Parameter: C <- "-30.5227" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 949 TOTAL ENERGY = -62.41 RDTITL> * VAN DER WAALS = -31.8874 ELECTROSTATIC = -30.5227 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "949" Parameter: CONF_N -> "8002" Comparing "949" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "950" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763649 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768370 ATOM PAIRS WERE FOUND FOR ATOM LIST 42066 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29387 from a total of 768370 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 950 -62.03929 -0.37074 0.71744 INTE EXTERN> -24.42587 -37.61342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.0393" Parameter: A <- "-62.0393" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4259" Parameter: B <- "-24.4259" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6134" Parameter: C <- "-37.6134" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 950 TOTAL ENERGY = -62.0393 RDTITL> * VAN DER WAALS = -24.4259 ELECTROSTATIC = -37.6134 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "950" Parameter: CONF_N -> "8002" Comparing "950" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "951" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768370 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769722 ATOM PAIRS WERE FOUND FOR ATOM LIST 41897 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29039 from a total of 769722 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 951 -71.35260 9.31330 0.59971 INTE EXTERN> -29.97913 -41.37347 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3526" Parameter: A <- "-71.3526" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9791" Parameter: B <- "-29.9791" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3735" Parameter: C <- "-41.3735" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 951 TOTAL ENERGY = -71.3526 RDTITL> * VAN DER WAALS = -29.9791 ELECTROSTATIC = -41.3735 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "951" Parameter: CONF_N -> "8002" Comparing "951" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "952" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769722 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765353 ATOM PAIRS WERE FOUND FOR ATOM LIST 41797 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29766 from a total of 765353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 952 -66.05803 -5.29457 0.63430 INTE EXTERN> -29.24752 -36.81051 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.058" Parameter: A <- "-66.058" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2475" Parameter: B <- "-29.2475" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8105" Parameter: C <- "-36.8105" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 952 TOTAL ENERGY = -66.058 RDTITL> * VAN DER WAALS = -29.2475 ELECTROSTATIC = -36.8105 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "952" Parameter: CONF_N -> "8002" Comparing "952" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "953" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762293 ATOM PAIRS WERE FOUND FOR ATOM LIST 41609 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29385 from a total of 762293 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 953 -71.32470 5.26667 0.60826 INTE EXTERN> -30.36877 -40.95593 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3247" Parameter: A <- "-71.3247" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3688" Parameter: B <- "-30.3688" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9559" Parameter: C <- "-40.9559" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 953 TOTAL ENERGY = -71.3247 RDTITL> * VAN DER WAALS = -30.3688 ELECTROSTATIC = -40.9559 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "953" Parameter: CONF_N -> "8002" Comparing "953" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "954" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762293 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758596 ATOM PAIRS WERE FOUND FOR ATOM LIST 41814 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29628 from a total of 758596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 954 -76.51704 5.19234 0.67691 INTE EXTERN> -29.34969 -47.16735 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.517" Parameter: A <- "-76.517" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3497" Parameter: B <- "-29.3497" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1673" Parameter: C <- "-47.1673" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 954 TOTAL ENERGY = -76.517 RDTITL> * VAN DER WAALS = -29.3497 ELECTROSTATIC = -47.1673 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "954" Parameter: CONF_N -> "8002" Comparing "954" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "955" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767342 ATOM PAIRS WERE FOUND FOR ATOM LIST 41945 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29933 from a total of 767342 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 955 -67.69947 -8.81757 0.67690 INTE EXTERN> -30.11448 -37.58499 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6995" Parameter: A <- "-67.6995" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1145" Parameter: B <- "-30.1145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.585" Parameter: C <- "-37.585" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 955 TOTAL ENERGY = -67.6995 RDTITL> * VAN DER WAALS = -30.1145 ELECTROSTATIC = -37.585 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "955" Parameter: CONF_N -> "8002" Comparing "955" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "956" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767342 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767915 ATOM PAIRS WERE FOUND FOR ATOM LIST 41958 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30149 from a total of 767915 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 956 -65.65907 -2.04040 0.69371 INTE EXTERN> -26.64007 -39.01900 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6591" Parameter: A <- "-65.6591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6401" Parameter: B <- "-26.6401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.019" Parameter: C <- "-39.019" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 956 TOTAL ENERGY = -65.6591 RDTITL> * VAN DER WAALS = -26.6401 ELECTROSTATIC = -39.019 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "956" Parameter: CONF_N -> "8002" Comparing "956" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "957" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767915 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770102 ATOM PAIRS WERE FOUND FOR ATOM LIST 41980 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29731 from a total of 770102 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 957 -64.37607 -1.28300 0.60061 INTE EXTERN> -29.81956 -34.55651 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3761" Parameter: A <- "-64.3761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8196" Parameter: B <- "-29.8196" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5565" Parameter: C <- "-34.5565" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 957 TOTAL ENERGY = -64.3761 RDTITL> * VAN DER WAALS = -29.8196 ELECTROSTATIC = -34.5565 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "957" Parameter: CONF_N -> "8002" Comparing "957" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "958" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770102 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762276 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29572 from a total of 762276 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 958 -61.84412 -2.53195 0.75383 INTE EXTERN> -23.47263 -38.37149 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.8441" Parameter: A <- "-61.8441" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4726" Parameter: B <- "-23.4726" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3715" Parameter: C <- "-38.3715" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 958 TOTAL ENERGY = -61.8441 RDTITL> * VAN DER WAALS = -23.4726 ELECTROSTATIC = -38.3715 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "958" Parameter: CONF_N -> "8002" Comparing "958" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "959" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762276 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760046 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29441 from a total of 760046 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 959 -69.36673 7.52262 0.65931 INTE EXTERN> -28.28799 -41.07874 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3667" Parameter: A <- "-69.3667" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.288" Parameter: B <- "-28.288" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0787" Parameter: C <- "-41.0787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 959 TOTAL ENERGY = -69.3667 RDTITL> * VAN DER WAALS = -28.288 ELECTROSTATIC = -41.0787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "959" Parameter: CONF_N -> "8002" Comparing "959" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "960" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760046 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764651 ATOM PAIRS WERE FOUND FOR ATOM LIST 41985 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30267 from a total of 764651 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 960 -63.62931 -5.73743 0.50489 INTE EXTERN> -32.17041 -31.45890 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6293" Parameter: A <- "-63.6293" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1704" Parameter: B <- "-32.1704" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4589" Parameter: C <- "-31.4589" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 960 TOTAL ENERGY = -63.6293 RDTITL> * VAN DER WAALS = -32.1704 ELECTROSTATIC = -31.4589 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "960" Parameter: CONF_N -> "8002" Comparing "960" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "961" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764651 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767040 ATOM PAIRS WERE FOUND FOR ATOM LIST 42090 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30262 from a total of 767040 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 961 -70.49972 6.87041 0.73969 INTE EXTERN> -26.87059 -43.62913 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4997" Parameter: A <- "-70.4997" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8706" Parameter: B <- "-26.8706" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6291" Parameter: C <- "-43.6291" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 961 TOTAL ENERGY = -70.4997 RDTITL> * VAN DER WAALS = -26.8706 ELECTROSTATIC = -43.6291 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "961" Parameter: CONF_N -> "8002" Comparing "961" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "962" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767040 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762822 ATOM PAIRS WERE FOUND FOR ATOM LIST 41955 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29964 from a total of 762822 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 962 -68.02613 -2.47358 0.60084 INTE EXTERN> -32.59182 -35.43432 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0261" Parameter: A <- "-68.0261" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5918" Parameter: B <- "-32.5918" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4343" Parameter: C <- "-35.4343" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 962 TOTAL ENERGY = -68.0261 RDTITL> * VAN DER WAALS = -32.5918 ELECTROSTATIC = -35.4343 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "962" Parameter: CONF_N -> "8002" Comparing "962" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "963" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762822 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766362 ATOM PAIRS WERE FOUND FOR ATOM LIST 42020 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29791 from a total of 766362 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 963 -66.00094 -2.02519 0.68961 INTE EXTERN> -28.38241 -37.61853 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0009" Parameter: A <- "-66.0009" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3824" Parameter: B <- "-28.3824" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6185" Parameter: C <- "-37.6185" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 963 TOTAL ENERGY = -66.0009 RDTITL> * VAN DER WAALS = -28.3824 ELECTROSTATIC = -37.6185 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "963" Parameter: CONF_N -> "8002" Comparing "963" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "964" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766362 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767334 ATOM PAIRS WERE FOUND FOR ATOM LIST 41909 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29991 from a total of 767334 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 964 -64.22917 -1.77177 0.59662 INTE EXTERN> -30.91751 -33.31165 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2292" Parameter: A <- "-64.2292" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9175" Parameter: B <- "-30.9175" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.3117" Parameter: C <- "-33.3117" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 964 TOTAL ENERGY = -64.2292 RDTITL> * VAN DER WAALS = -30.9175 ELECTROSTATIC = -33.3117 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "964" Parameter: CONF_N -> "8002" Comparing "964" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "965" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767334 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768664 ATOM PAIRS WERE FOUND FOR ATOM LIST 42043 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30250 from a total of 768664 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 965 -66.44249 2.21332 0.70501 INTE EXTERN> -27.89339 -38.54910 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4425" Parameter: A <- "-66.4425" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8934" Parameter: B <- "-27.8934" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5491" Parameter: C <- "-38.5491" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 965 TOTAL ENERGY = -66.4425 RDTITL> * VAN DER WAALS = -27.8934 ELECTROSTATIC = -38.5491 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "965" Parameter: CONF_N -> "8002" Comparing "965" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "966" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768664 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769172 ATOM PAIRS WERE FOUND FOR ATOM LIST 41922 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30465 from a total of 769172 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 966 -66.20705 -0.23544 0.57664 INTE EXTERN> -32.46089 -33.74616 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2071" Parameter: A <- "-66.2071" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4609" Parameter: B <- "-32.4609" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7462" Parameter: C <- "-33.7462" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 966 TOTAL ENERGY = -66.2071 RDTITL> * VAN DER WAALS = -32.4609 ELECTROSTATIC = -33.7462 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "966" Parameter: CONF_N -> "8002" Comparing "966" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "967" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769172 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770357 ATOM PAIRS WERE FOUND FOR ATOM LIST 42209 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30089 from a total of 770357 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 967 -70.77141 4.56436 0.60124 INTE EXTERN> -31.65969 -39.11172 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7714" Parameter: A <- "-70.7714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6597" Parameter: B <- "-31.6597" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1117" Parameter: C <- "-39.1117" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 967 TOTAL ENERGY = -70.7714 RDTITL> * VAN DER WAALS = -31.6597 ELECTROSTATIC = -39.1117 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "967" Parameter: CONF_N -> "8002" Comparing "967" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "968" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770357 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766832 ATOM PAIRS WERE FOUND FOR ATOM LIST 42003 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30566 from a total of 766832 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 968 -65.87673 -4.89468 0.69136 INTE EXTERN> -27.03679 -38.83993 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8767" Parameter: A <- "-65.8767" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0368" Parameter: B <- "-27.0368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8399" Parameter: C <- "-38.8399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 968 TOTAL ENERGY = -65.8767 RDTITL> * VAN DER WAALS = -27.0368 ELECTROSTATIC = -38.8399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "968" Parameter: CONF_N -> "8002" Comparing "968" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "969" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766832 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762182 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30000 from a total of 762182 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 969 -67.83020 1.95347 0.60049 INTE EXTERN> -31.46637 -36.36383 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8302" Parameter: A <- "-67.8302" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4664" Parameter: B <- "-31.4664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3638" Parameter: C <- "-36.3638" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 969 TOTAL ENERGY = -67.8302 RDTITL> * VAN DER WAALS = -31.4664 ELECTROSTATIC = -36.3638 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "969" Parameter: CONF_N -> "8002" Comparing "969" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "970" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762182 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765905 ATOM PAIRS WERE FOUND FOR ATOM LIST 41802 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30579 from a total of 765905 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 970 -69.02538 1.19518 0.67061 INTE EXTERN> -27.63856 -41.38681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0254" Parameter: A <- "-69.0254" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6386" Parameter: B <- "-27.6386" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3868" Parameter: C <- "-41.3868" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 970 TOTAL ENERGY = -69.0254 RDTITL> * VAN DER WAALS = -27.6386 ELECTROSTATIC = -41.3868 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "970" Parameter: CONF_N -> "8002" Comparing "970" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "971" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765905 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761150 ATOM PAIRS WERE FOUND FOR ATOM LIST 41616 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30100 from a total of 761150 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 971 -63.48969 -5.53569 0.66531 INTE EXTERN> -26.96691 -36.52278 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4897" Parameter: A <- "-63.4897" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9669" Parameter: B <- "-26.9669" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5228" Parameter: C <- "-36.5228" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 971 TOTAL ENERGY = -63.4897 RDTITL> * VAN DER WAALS = -26.9669 ELECTROSTATIC = -36.5228 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "971" Parameter: CONF_N -> "8002" Comparing "971" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "972" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761150 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760316 ATOM PAIRS WERE FOUND FOR ATOM LIST 41875 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29914 from a total of 760316 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 972 -72.83500 9.34531 0.59988 INTE EXTERN> -32.36088 -40.47413 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.835" Parameter: A <- "-72.835" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3609" Parameter: B <- "-32.3609" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4741" Parameter: C <- "-40.4741" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 972 TOTAL ENERGY = -72.835 RDTITL> * VAN DER WAALS = -32.3609 ELECTROSTATIC = -40.4741 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "972" Parameter: CONF_N -> "8002" Comparing "972" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "973" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760316 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765382 ATOM PAIRS WERE FOUND FOR ATOM LIST 41957 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29624 from a total of 765382 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 973 -62.69870 -10.13630 0.80854 INTE EXTERN> -22.60213 -40.09657 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.6987" Parameter: A <- "-62.6987" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.6021" Parameter: B <- "-22.6021" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0966" Parameter: C <- "-40.0966" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 973 TOTAL ENERGY = -62.6987 RDTITL> * VAN DER WAALS = -22.6021 ELECTROSTATIC = -40.0966 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "973" Parameter: CONF_N -> "8002" Comparing "973" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "974" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765382 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761983 ATOM PAIRS WERE FOUND FOR ATOM LIST 41796 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29825 from a total of 761983 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 974 -62.12303 -0.57567 0.69910 INTE EXTERN> -27.13470 -34.98833 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.123" Parameter: A <- "-62.123" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1347" Parameter: B <- "-27.1347" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9883" Parameter: C <- "-34.9883" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 974 TOTAL ENERGY = -62.123 RDTITL> * VAN DER WAALS = -27.1347 ELECTROSTATIC = -34.9883 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "974" Parameter: CONF_N -> "8002" Comparing "974" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "975" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761983 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764231 ATOM PAIRS WERE FOUND FOR ATOM LIST 41896 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30281 from a total of 764231 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 975 -62.39692 0.27388 0.67398 INTE EXTERN> -25.52271 -36.87421 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3969" Parameter: A <- "-62.3969" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5227" Parameter: B <- "-25.5227" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8742" Parameter: C <- "-36.8742" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 975 TOTAL ENERGY = -62.3969 RDTITL> * VAN DER WAALS = -25.5227 ELECTROSTATIC = -36.8742 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "975" Parameter: CONF_N -> "8002" Comparing "975" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "976" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764231 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760391 ATOM PAIRS WERE FOUND FOR ATOM LIST 41713 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29557 from a total of 760391 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 976 -67.04365 4.64673 0.85362 INTE EXTERN> -24.09902 -42.94462 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0436" Parameter: A <- "-67.0436" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.099" Parameter: B <- "-24.099" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9446" Parameter: C <- "-42.9446" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 976 TOTAL ENERGY = -67.0436 RDTITL> * VAN DER WAALS = -24.099 ELECTROSTATIC = -42.9446 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "976" Parameter: CONF_N -> "8002" Comparing "976" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "977" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760391 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762162 ATOM PAIRS WERE FOUND FOR ATOM LIST 41830 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29953 from a total of 762162 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 977 -67.99035 0.94670 0.74478 INTE EXTERN> -23.39709 -44.59325 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9903" Parameter: A <- "-67.9903" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.3971" Parameter: B <- "-23.3971" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5933" Parameter: C <- "-44.5933" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 977 TOTAL ENERGY = -67.9903 RDTITL> * VAN DER WAALS = -23.3971 ELECTROSTATIC = -44.5933 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "977" Parameter: CONF_N -> "8002" Comparing "977" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "978" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762162 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768605 ATOM PAIRS WERE FOUND FOR ATOM LIST 42052 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29924 from a total of 768605 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 978 -66.76140 -1.22895 0.65696 INTE EXTERN> -29.17219 -37.58921 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7614" Parameter: A <- "-66.7614" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1722" Parameter: B <- "-29.1722" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5892" Parameter: C <- "-37.5892" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 978 TOTAL ENERGY = -66.7614 RDTITL> * VAN DER WAALS = -29.1722 ELECTROSTATIC = -37.5892 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "978" Parameter: CONF_N -> "8002" Comparing "978" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "979" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768605 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766089 ATOM PAIRS WERE FOUND FOR ATOM LIST 41939 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30410 from a total of 766089 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 979 -65.29107 -1.47033 0.67506 INTE EXTERN> -26.70521 -38.58586 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2911" Parameter: A <- "-65.2911" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7052" Parameter: B <- "-26.7052" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5859" Parameter: C <- "-38.5859" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 979 TOTAL ENERGY = -65.2911 RDTITL> * VAN DER WAALS = -26.7052 ELECTROSTATIC = -38.5859 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "979" Parameter: CONF_N -> "8002" Comparing "979" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "980" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766089 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770356 ATOM PAIRS WERE FOUND FOR ATOM LIST 42132 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30105 from a total of 770356 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 980 -66.25903 0.96796 0.61454 INTE EXTERN> -29.95569 -36.30334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.259" Parameter: A <- "-66.259" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9557" Parameter: B <- "-29.9557" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3033" Parameter: C <- "-36.3033" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 980 TOTAL ENERGY = -66.259 RDTITL> * VAN DER WAALS = -29.9557 ELECTROSTATIC = -36.3033 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "980" Parameter: CONF_N -> "8002" Comparing "980" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "981" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770356 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768762 ATOM PAIRS WERE FOUND FOR ATOM LIST 42133 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30116 from a total of 768762 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 981 -55.75863 -10.50040 0.45191 INTE EXTERN> -33.64239 -22.11623 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.7586" Parameter: A <- "-55.7586" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6424" Parameter: B <- "-33.6424" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-22.1162" Parameter: C <- "-22.1162" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 981 TOTAL ENERGY = -55.7586 RDTITL> * VAN DER WAALS = -33.6424 ELECTROSTATIC = -22.1162 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "981" Parameter: CONF_N -> "8002" Comparing "981" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "982" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768762 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759890 ATOM PAIRS WERE FOUND FOR ATOM LIST 41680 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29359 from a total of 759890 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 982 -67.87388 12.11525 0.63111 INTE EXTERN> -30.42707 -37.44681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8739" Parameter: A <- "-67.8739" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4271" Parameter: B <- "-30.4271" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4468" Parameter: C <- "-37.4468" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 982 TOTAL ENERGY = -67.8739 RDTITL> * VAN DER WAALS = -30.4271 ELECTROSTATIC = -37.4468 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "982" Parameter: CONF_N -> "8002" Comparing "982" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "983" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759890 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763426 ATOM PAIRS WERE FOUND FOR ATOM LIST 41544 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29585 from a total of 763426 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 983 -71.85406 3.98018 0.61980 INTE EXTERN> -28.98542 -42.86864 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8541" Parameter: A <- "-71.8541" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9854" Parameter: B <- "-28.9854" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8686" Parameter: C <- "-42.8686" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 983 TOTAL ENERGY = -71.8541 RDTITL> * VAN DER WAALS = -28.9854 ELECTROSTATIC = -42.8686 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "983" Parameter: CONF_N -> "8002" Comparing "983" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "984" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763426 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756580 ATOM PAIRS WERE FOUND FOR ATOM LIST 41461 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29432 from a total of 756580 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 984 -65.00003 -6.85403 0.57262 INTE EXTERN> -30.95476 -34.04528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65" Parameter: A <- "-65" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9548" Parameter: B <- "-30.9548" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.0453" Parameter: C <- "-34.0453" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 984 TOTAL ENERGY = -65 RDTITL> * VAN DER WAALS = -30.9548 ELECTROSTATIC = -34.0453 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "984" Parameter: CONF_N -> "8002" Comparing "984" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "985" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756580 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758714 ATOM PAIRS WERE FOUND FOR ATOM LIST 41618 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29904 from a total of 758714 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 985 -68.43051 3.43048 0.70394 INTE EXTERN> -26.95801 -41.47250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4305" Parameter: A <- "-68.4305" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.958" Parameter: B <- "-26.958" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4725" Parameter: C <- "-41.4725" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 985 TOTAL ENERGY = -68.4305 RDTITL> * VAN DER WAALS = -26.958 ELECTROSTATIC = -41.4725 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "985" Parameter: CONF_N -> "8002" Comparing "985" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "986" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758714 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767504 ATOM PAIRS WERE FOUND FOR ATOM LIST 41946 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30254 from a total of 767504 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 986 -64.47903 -3.95148 0.70168 INTE EXTERN> -29.75301 -34.72601 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.479" Parameter: A <- "-64.479" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.753" Parameter: B <- "-29.753" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.726" Parameter: C <- "-34.726" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 986 TOTAL ENERGY = -64.479 RDTITL> * VAN DER WAALS = -29.753 ELECTROSTATIC = -34.726 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "986" Parameter: CONF_N -> "8002" Comparing "986" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "987" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767504 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770204 ATOM PAIRS WERE FOUND FOR ATOM LIST 42164 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30436 from a total of 770204 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 987 -69.02826 4.54923 0.71513 INTE EXTERN> -27.82652 -41.20173 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0283" Parameter: A <- "-69.0283" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8265" Parameter: B <- "-27.8265" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2017" Parameter: C <- "-41.2017" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 987 TOTAL ENERGY = -69.0283 RDTITL> * VAN DER WAALS = -27.8265 ELECTROSTATIC = -41.2017 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "987" Parameter: CONF_N -> "8002" Comparing "987" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "988" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770204 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760852 ATOM PAIRS WERE FOUND FOR ATOM LIST 41535 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30446 from a total of 760852 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 988 -70.36954 1.34128 0.64414 INTE EXTERN> -29.87929 -40.49026 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3695" Parameter: A <- "-70.3695" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8793" Parameter: B <- "-29.8793" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4903" Parameter: C <- "-40.4903" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 988 TOTAL ENERGY = -70.3695 RDTITL> * VAN DER WAALS = -29.8793 ELECTROSTATIC = -40.4903 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "988" Parameter: CONF_N -> "8002" Comparing "988" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "989" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760852 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761780 ATOM PAIRS WERE FOUND FOR ATOM LIST 41474 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30276 from a total of 761780 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 989 -72.97569 2.60615 0.68077 INTE EXTERN> -27.32370 -45.65199 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9757" Parameter: A <- "-72.9757" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3237" Parameter: B <- "-27.3237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.652" Parameter: C <- "-45.652" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 989 TOTAL ENERGY = -72.9757 RDTITL> * VAN DER WAALS = -27.3237 ELECTROSTATIC = -45.652 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "989" Parameter: CONF_N -> "8002" Comparing "989" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "990" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761780 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766812 ATOM PAIRS WERE FOUND FOR ATOM LIST 41933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30485 from a total of 766812 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 990 -75.26590 2.29022 0.74806 INTE EXTERN> -27.21575 -48.05015 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2659" Parameter: A <- "-75.2659" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2158" Parameter: B <- "-27.2158" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0502" Parameter: C <- "-48.0502" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 990 TOTAL ENERGY = -75.2659 RDTITL> * VAN DER WAALS = -27.2158 ELECTROSTATIC = -48.0502 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "990" Parameter: CONF_N -> "8002" Comparing "990" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "991" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766812 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757585 ATOM PAIRS WERE FOUND FOR ATOM LIST 41560 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29912 from a total of 757585 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 991 -69.48539 -5.78051 0.73986 INTE EXTERN> -27.79592 -41.68947 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4854" Parameter: A <- "-69.4854" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7959" Parameter: B <- "-27.7959" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6895" Parameter: C <- "-41.6895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 991 TOTAL ENERGY = -69.4854 RDTITL> * VAN DER WAALS = -27.7959 ELECTROSTATIC = -41.6895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "991" Parameter: CONF_N -> "8002" Comparing "991" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "992" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757585 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759940 ATOM PAIRS WERE FOUND FOR ATOM LIST 41457 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29385 from a total of 759940 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 992 -70.47127 0.98587 0.64153 INTE EXTERN> -28.51684 -41.95442 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4713" Parameter: A <- "-70.4713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5168" Parameter: B <- "-28.5168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9544" Parameter: C <- "-41.9544" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 992 TOTAL ENERGY = -70.4713 RDTITL> * VAN DER WAALS = -28.5168 ELECTROSTATIC = -41.9544 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "992" Parameter: CONF_N -> "8002" Comparing "992" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "993" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759940 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760468 ATOM PAIRS WERE FOUND FOR ATOM LIST 41781 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29931 from a total of 760468 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 993 -69.54896 -0.92231 0.67313 INTE EXTERN> -29.39886 -40.15010 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.549" Parameter: A <- "-69.549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3989" Parameter: B <- "-29.3989" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1501" Parameter: C <- "-40.1501" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 993 TOTAL ENERGY = -69.549 RDTITL> * VAN DER WAALS = -29.3989 ELECTROSTATIC = -40.1501 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "993" Parameter: CONF_N -> "8002" Comparing "993" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "994" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760468 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757968 ATOM PAIRS WERE FOUND FOR ATOM LIST 41443 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30106 from a total of 757968 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 994 -73.58857 4.03961 0.65047 INTE EXTERN> -28.80444 -44.78414 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5886" Parameter: A <- "-73.5886" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8044" Parameter: B <- "-28.8044" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7841" Parameter: C <- "-44.7841" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 994 TOTAL ENERGY = -73.5886 RDTITL> * VAN DER WAALS = -28.8044 ELECTROSTATIC = -44.7841 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "994" Parameter: CONF_N -> "8002" Comparing "994" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "995" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757968 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759276 ATOM PAIRS WERE FOUND FOR ATOM LIST 41670 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29818 from a total of 759276 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 995 -69.37506 -4.21351 0.79694 INTE EXTERN> -24.65097 -44.72409 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3751" Parameter: A <- "-69.3751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.651" Parameter: B <- "-24.651" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7241" Parameter: C <- "-44.7241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 995 TOTAL ENERGY = -69.3751 RDTITL> * VAN DER WAALS = -24.651 ELECTROSTATIC = -44.7241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "995" Parameter: CONF_N -> "8002" Comparing "995" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "996" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759276 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757157 ATOM PAIRS WERE FOUND FOR ATOM LIST 41350 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29738 from a total of 757157 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 996 -68.63040 -0.74466 0.52507 INTE EXTERN> -35.31742 -33.31298 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6304" Parameter: A <- "-68.6304" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.3174" Parameter: B <- "-35.3174" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.313" Parameter: C <- "-33.313" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 996 TOTAL ENERGY = -68.6304 RDTITL> * VAN DER WAALS = -35.3174 ELECTROSTATIC = -33.313 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "996" Parameter: CONF_N -> "8002" Comparing "996" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "997" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757157 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757830 ATOM PAIRS WERE FOUND FOR ATOM LIST 41451 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29567 from a total of 757830 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 997 -66.86010 -1.77031 0.68903 INTE EXTERN> -27.62999 -39.23011 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8601" Parameter: A <- "-66.8601" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.63" Parameter: B <- "-27.63" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2301" Parameter: C <- "-39.2301" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 997 TOTAL ENERGY = -66.8601 RDTITL> * VAN DER WAALS = -27.63 ELECTROSTATIC = -39.2301 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "997" Parameter: CONF_N -> "8002" Comparing "997" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "998" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757830 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757537 ATOM PAIRS WERE FOUND FOR ATOM LIST 41527 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29935 from a total of 757537 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 998 -62.62929 -4.23081 0.63025 INTE EXTERN> -28.70470 -33.92459 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.6293" Parameter: A <- "-62.6293" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7047" Parameter: B <- "-28.7047" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9246" Parameter: C <- "-33.9246" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 998 TOTAL ENERGY = -62.6293 RDTITL> * VAN DER WAALS = -28.7047 ELECTROSTATIC = -33.9246 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "998" Parameter: CONF_N -> "8002" Comparing "998" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "999" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757537 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41563 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29514 from a total of 756118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 999 -68.25288 5.62359 0.61980 INTE EXTERN> -30.91853 -37.33434 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2529" Parameter: A <- "-68.2529" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9185" Parameter: B <- "-30.9185" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3343" Parameter: C <- "-37.3343" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 999 TOTAL ENERGY = -68.2529 RDTITL> * VAN DER WAALS = -30.9185 ELECTROSTATIC = -37.3343 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "999" Parameter: CONF_N -> "8002" Comparing "999" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1000" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753085 ATOM PAIRS WERE FOUND FOR ATOM LIST 41312 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29299 from a total of 753085 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1000 -64.68632 -3.56655 0.58879 INTE EXTERN> -29.04418 -35.64215 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6863" Parameter: A <- "-64.6863" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0442" Parameter: B <- "-29.0442" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6421" Parameter: C <- "-35.6421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1000 TOTAL ENERGY = -64.6863 RDTITL> * VAN DER WAALS = -29.0442 ELECTROSTATIC = -35.6421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1000" Parameter: CONF_N -> "8002" Comparing "1000" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1001" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753085 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750975 ATOM PAIRS WERE FOUND FOR ATOM LIST 41217 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29332 from a total of 750975 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1001 -65.32007 0.63374 0.61252 INTE EXTERN> -29.95036 -35.36971 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3201" Parameter: A <- "-65.3201" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9504" Parameter: B <- "-29.9504" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3697" Parameter: C <- "-35.3697" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1001 TOTAL ENERGY = -65.3201 RDTITL> * VAN DER WAALS = -29.9504 ELECTROSTATIC = -35.3697 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1001" Parameter: CONF_N -> "8002" Comparing "1001" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1002" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750975 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754557 ATOM PAIRS WERE FOUND FOR ATOM LIST 41436 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29595 from a total of 754557 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1002 -72.91193 7.59186 0.66302 INTE EXTERN> -29.39704 -43.51489 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9119" Parameter: A <- "-72.9119" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.397" Parameter: B <- "-29.397" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5149" Parameter: C <- "-43.5149" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1002 TOTAL ENERGY = -72.9119 RDTITL> * VAN DER WAALS = -29.397 ELECTROSTATIC = -43.5149 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1002" Parameter: CONF_N -> "8002" Comparing "1002" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1003" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754557 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758769 ATOM PAIRS WERE FOUND FOR ATOM LIST 41707 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29464 from a total of 758769 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1003 -68.88739 -4.02454 0.72754 INTE EXTERN> -25.44995 -43.43744 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8874" Parameter: A <- "-68.8874" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.45" Parameter: B <- "-25.45" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4374" Parameter: C <- "-43.4374" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1003 TOTAL ENERGY = -68.8874 RDTITL> * VAN DER WAALS = -25.45 ELECTROSTATIC = -43.4374 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1003" Parameter: CONF_N -> "8002" Comparing "1003" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1004" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758769 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760966 ATOM PAIRS WERE FOUND FOR ATOM LIST 41687 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29761 from a total of 760966 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1004 -74.13606 5.24867 0.60621 INTE EXTERN> -32.19681 -41.93925 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1361" Parameter: A <- "-74.1361" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1968" Parameter: B <- "-32.1968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9392" Parameter: C <- "-41.9392" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1004 TOTAL ENERGY = -74.1361 RDTITL> * VAN DER WAALS = -32.1968 ELECTROSTATIC = -41.9392 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1004" Parameter: CONF_N -> "8002" Comparing "1004" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1005" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760966 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755861 ATOM PAIRS WERE FOUND FOR ATOM LIST 41348 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29375 from a total of 755861 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1005 -60.73908 -13.39697 0.59150 INTE EXTERN> -30.71338 -30.02571 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.7391" Parameter: A <- "-60.7391" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7134" Parameter: B <- "-30.7134" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.0257" Parameter: C <- "-30.0257" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1005 TOTAL ENERGY = -60.7391 RDTITL> * VAN DER WAALS = -30.7134 ELECTROSTATIC = -30.0257 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1005" Parameter: CONF_N -> "8002" Comparing "1005" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1006" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755861 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756473 ATOM PAIRS WERE FOUND FOR ATOM LIST 41317 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30159 from a total of 756473 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1006 -65.59513 4.85604 0.65436 INTE EXTERN> -28.61283 -36.98229 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5951" Parameter: A <- "-65.5951" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6128" Parameter: B <- "-28.6128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9823" Parameter: C <- "-36.9823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1006 TOTAL ENERGY = -65.5951 RDTITL> * VAN DER WAALS = -28.6128 ELECTROSTATIC = -36.9823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1006" Parameter: CONF_N -> "8002" Comparing "1006" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1007" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756473 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753080 ATOM PAIRS WERE FOUND FOR ATOM LIST 41452 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29178 from a total of 753080 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1007 -69.00722 3.41209 0.61398 INTE EXTERN> -32.31131 -36.69591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0072" Parameter: A <- "-69.0072" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3113" Parameter: B <- "-32.3113" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6959" Parameter: C <- "-36.6959" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1007 TOTAL ENERGY = -69.0072 RDTITL> * VAN DER WAALS = -32.3113 ELECTROSTATIC = -36.6959 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1007" Parameter: CONF_N -> "8002" Comparing "1007" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1008" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753080 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758524 ATOM PAIRS WERE FOUND FOR ATOM LIST 41667 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29557 from a total of 758524 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1008 -74.06231 5.05509 0.70427 INTE EXTERN> -26.35946 -47.70285 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0623" Parameter: A <- "-74.0623" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3595" Parameter: B <- "-26.3595" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7028" Parameter: C <- "-47.7028" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1008 TOTAL ENERGY = -74.0623 RDTITL> * VAN DER WAALS = -26.3595 ELECTROSTATIC = -47.7028 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1008" Parameter: CONF_N -> "8002" Comparing "1008" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1009" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758524 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760114 ATOM PAIRS WERE FOUND FOR ATOM LIST 41739 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29804 from a total of 760114 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1009 -70.10677 -3.95554 0.62863 INTE EXTERN> -29.73971 -40.36707 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1068" Parameter: A <- "-70.1068" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7397" Parameter: B <- "-29.7397" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3671" Parameter: C <- "-40.3671" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1009 TOTAL ENERGY = -70.1068 RDTITL> * VAN DER WAALS = -29.7397 ELECTROSTATIC = -40.3671 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1009" Parameter: CONF_N -> "8002" Comparing "1009" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1010" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760114 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761577 ATOM PAIRS WERE FOUND FOR ATOM LIST 41649 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29144 from a total of 761577 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1010 -70.03138 -0.07539 0.79418 INTE EXTERN> -23.69754 -46.33385 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0314" Parameter: A <- "-70.0314" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6975" Parameter: B <- "-23.6975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3338" Parameter: C <- "-46.3338" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1010 TOTAL ENERGY = -70.0314 RDTITL> * VAN DER WAALS = -23.6975 ELECTROSTATIC = -46.3338 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1010" Parameter: CONF_N -> "8002" Comparing "1010" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1011" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761577 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761044 ATOM PAIRS WERE FOUND FOR ATOM LIST 41571 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29630 from a total of 761044 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1011 -64.94530 -5.08608 0.57468 INTE EXTERN> -32.24928 -32.69601 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9453" Parameter: A <- "-64.9453" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2493" Parameter: B <- "-32.2493" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.696" Parameter: C <- "-32.696" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1011 TOTAL ENERGY = -64.9453 RDTITL> * VAN DER WAALS = -32.2493 ELECTROSTATIC = -32.696 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1011" Parameter: CONF_N -> "8002" Comparing "1011" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1012" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761044 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754013 ATOM PAIRS WERE FOUND FOR ATOM LIST 41226 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29252 from a total of 754013 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1012 -64.63435 -0.31095 0.69891 INTE EXTERN> -26.59993 -38.03442 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6343" Parameter: A <- "-64.6343" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5999" Parameter: B <- "-26.5999" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0344" Parameter: C <- "-38.0344" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1012 TOTAL ENERGY = -64.6343 RDTITL> * VAN DER WAALS = -26.5999 ELECTROSTATIC = -38.0344 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1012" Parameter: CONF_N -> "8002" Comparing "1012" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1013" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754013 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760181 ATOM PAIRS WERE FOUND FOR ATOM LIST 41695 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29254 from a total of 760181 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1013 -64.48754 -0.14680 0.73304 INTE EXTERN> -24.73629 -39.75126 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.4875" Parameter: A <- "-64.4875" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7363" Parameter: B <- "-24.7363" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7513" Parameter: C <- "-39.7513" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1013 TOTAL ENERGY = -64.4875 RDTITL> * VAN DER WAALS = -24.7363 ELECTROSTATIC = -39.7513 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1013" Parameter: CONF_N -> "8002" Comparing "1013" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1014" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760181 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759525 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28804 from a total of 759525 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1014 -68.65802 4.17048 0.57796 INTE EXTERN> -30.78967 -37.86835 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.658" Parameter: A <- "-68.658" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7897" Parameter: B <- "-30.7897" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8683" Parameter: C <- "-37.8683" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1014 TOTAL ENERGY = -68.658 RDTITL> * VAN DER WAALS = -30.7897 ELECTROSTATIC = -37.8683 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1014" Parameter: CONF_N -> "8002" Comparing "1014" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1015" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759525 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759811 ATOM PAIRS WERE FOUND FOR ATOM LIST 41519 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29326 from a total of 759811 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1015 -65.46699 -3.19103 0.51518 INTE EXTERN> -33.89067 -31.57633 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.467" Parameter: A <- "-65.467" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8907" Parameter: B <- "-33.8907" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.5763" Parameter: C <- "-31.5763" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1015 TOTAL ENERGY = -65.467 RDTITL> * VAN DER WAALS = -33.8907 ELECTROSTATIC = -31.5763 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1015" Parameter: CONF_N -> "8002" Comparing "1015" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1016" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759811 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762402 ATOM PAIRS WERE FOUND FOR ATOM LIST 41800 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30152 from a total of 762402 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1016 -62.25086 -3.21613 0.58530 INTE EXTERN> -31.78276 -30.46810 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.2509" Parameter: A <- "-62.2509" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7828" Parameter: B <- "-31.7828" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.4681" Parameter: C <- "-30.4681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1016 TOTAL ENERGY = -62.2509 RDTITL> * VAN DER WAALS = -31.7828 ELECTROSTATIC = -30.4681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1016" Parameter: CONF_N -> "8002" Comparing "1016" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1017" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762402 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764912 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29792 from a total of 764912 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1017 -64.21025 1.95938 0.66145 INTE EXTERN> -29.38722 -34.82302 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2102" Parameter: A <- "-64.2102" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3872" Parameter: B <- "-29.3872" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.823" Parameter: C <- "-34.823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1017 TOTAL ENERGY = -64.2102 RDTITL> * VAN DER WAALS = -29.3872 ELECTROSTATIC = -34.823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1017" Parameter: CONF_N -> "8002" Comparing "1017" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1018" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764912 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763085 ATOM PAIRS WERE FOUND FOR ATOM LIST 41883 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29714 from a total of 763085 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1018 -64.64826 0.43802 0.62239 INTE EXTERN> -29.79390 -34.85436 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6483" Parameter: A <- "-64.6483" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7939" Parameter: B <- "-29.7939" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8544" Parameter: C <- "-34.8544" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1018 TOTAL ENERGY = -64.6483 RDTITL> * VAN DER WAALS = -29.7939 ELECTROSTATIC = -34.8544 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1018" Parameter: CONF_N -> "8002" Comparing "1018" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1019" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763085 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762518 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29757 from a total of 762518 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1019 -64.35586 -0.29240 0.55241 INTE EXTERN> -31.38119 -32.97466 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3559" Parameter: A <- "-64.3559" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3812" Parameter: B <- "-31.3812" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.9747" Parameter: C <- "-32.9747" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1019 TOTAL ENERGY = -64.3559 RDTITL> * VAN DER WAALS = -31.3812 ELECTROSTATIC = -32.9747 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1019" Parameter: CONF_N -> "8002" Comparing "1019" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1020" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762518 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766201 ATOM PAIRS WERE FOUND FOR ATOM LIST 42049 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30243 from a total of 766201 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1020 -65.11006 0.75420 0.52693 INTE EXTERN> -34.33526 -30.77480 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1101" Parameter: A <- "-65.1101" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3353" Parameter: B <- "-34.3353" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.7748" Parameter: C <- "-30.7748" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1020 TOTAL ENERGY = -65.1101 RDTITL> * VAN DER WAALS = -34.3353 ELECTROSTATIC = -30.7748 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1020" Parameter: CONF_N -> "8002" Comparing "1020" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1021" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766201 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763302 ATOM PAIRS WERE FOUND FOR ATOM LIST 41755 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30097 from a total of 763302 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1021 -69.17962 4.06956 0.62651 INTE EXTERN> -28.06514 -41.11448 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1796" Parameter: A <- "-69.1796" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0651" Parameter: B <- "-28.0651" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1145" Parameter: C <- "-41.1145" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1021 TOTAL ENERGY = -69.1796 RDTITL> * VAN DER WAALS = -28.0651 ELECTROSTATIC = -41.1145 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1021" Parameter: CONF_N -> "8002" Comparing "1021" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1022" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763302 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762681 ATOM PAIRS WERE FOUND FOR ATOM LIST 41875 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29407 from a total of 762681 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1022 -70.59053 1.41091 0.64053 INTE EXTERN> -30.48670 -40.10383 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5905" Parameter: A <- "-70.5905" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4867" Parameter: B <- "-30.4867" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1038" Parameter: C <- "-40.1038" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1022 TOTAL ENERGY = -70.5905 RDTITL> * VAN DER WAALS = -30.4867 ELECTROSTATIC = -40.1038 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1022" Parameter: CONF_N -> "8002" Comparing "1022" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1023" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762681 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764439 ATOM PAIRS WERE FOUND FOR ATOM LIST 41930 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30324 from a total of 764439 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1023 -69.14800 -1.44253 0.59181 INTE EXTERN> -33.39429 -35.75370 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.148" Parameter: A <- "-69.148" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3943" Parameter: B <- "-33.3943" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7537" Parameter: C <- "-35.7537" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1023 TOTAL ENERGY = -69.148 RDTITL> * VAN DER WAALS = -33.3943 ELECTROSTATIC = -35.7537 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1023" Parameter: CONF_N -> "8002" Comparing "1023" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1024" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764439 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761394 ATOM PAIRS WERE FOUND FOR ATOM LIST 41681 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30102 from a total of 761394 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1024 -65.21890 -3.92910 0.58458 INTE EXTERN> -30.33424 -34.88466 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2189" Parameter: A <- "-65.2189" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3342" Parameter: B <- "-30.3342" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8847" Parameter: C <- "-34.8847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1024 TOTAL ENERGY = -65.2189 RDTITL> * VAN DER WAALS = -30.3342 ELECTROSTATIC = -34.8847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1024" Parameter: CONF_N -> "8002" Comparing "1024" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1025" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761394 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760539 ATOM PAIRS WERE FOUND FOR ATOM LIST 41744 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30212 from a total of 760539 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1025 -67.01102 1.79212 0.53333 INTE EXTERN> -34.47439 -32.53663 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.011" Parameter: A <- "-67.011" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.4744" Parameter: B <- "-34.4744" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5366" Parameter: C <- "-32.5366" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1025 TOTAL ENERGY = -67.011 RDTITL> * VAN DER WAALS = -34.4744 ELECTROSTATIC = -32.5366 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1025" Parameter: CONF_N -> "8002" Comparing "1025" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1026" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760539 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765600 ATOM PAIRS WERE FOUND FOR ATOM LIST 41981 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30162 from a total of 765600 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1026 -67.80653 0.79551 0.51117 INTE EXTERN> -33.49179 -34.31474 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8065" Parameter: A <- "-67.8065" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4918" Parameter: B <- "-33.4918" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3147" Parameter: C <- "-34.3147" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1026 TOTAL ENERGY = -67.8065 RDTITL> * VAN DER WAALS = -33.4918 ELECTROSTATIC = -34.3147 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1026" Parameter: CONF_N -> "8002" Comparing "1026" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1027" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765600 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765374 ATOM PAIRS WERE FOUND FOR ATOM LIST 41965 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30316 from a total of 765374 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1027 -70.87047 3.06394 0.59661 INTE EXTERN> -32.97720 -37.89327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8705" Parameter: A <- "-70.8705" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9772" Parameter: B <- "-32.9772" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8933" Parameter: C <- "-37.8933" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1027 TOTAL ENERGY = -70.8705 RDTITL> * VAN DER WAALS = -32.9772 ELECTROSTATIC = -37.8933 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1027" Parameter: CONF_N -> "8002" Comparing "1027" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1028" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765374 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763307 ATOM PAIRS WERE FOUND FOR ATOM LIST 41716 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29874 from a total of 763307 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1028 -67.73826 -3.13221 0.61452 INTE EXTERN> -31.10904 -36.62922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7383" Parameter: A <- "-67.7383" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.109" Parameter: B <- "-31.109" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6292" Parameter: C <- "-36.6292" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1028 TOTAL ENERGY = -67.7383 RDTITL> * VAN DER WAALS = -31.109 ELECTROSTATIC = -36.6292 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1028" Parameter: CONF_N -> "8002" Comparing "1028" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1029" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763307 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760455 ATOM PAIRS WERE FOUND FOR ATOM LIST 41791 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29935 from a total of 760455 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1029 -61.11372 -6.62454 0.62175 INTE EXTERN> -30.47626 -30.63746 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.1137" Parameter: A <- "-61.1137" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4763" Parameter: B <- "-30.4763" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.6375" Parameter: C <- "-30.6375" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1029 TOTAL ENERGY = -61.1137 RDTITL> * VAN DER WAALS = -30.4763 ELECTROSTATIC = -30.6375 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1029" Parameter: CONF_N -> "8002" Comparing "1029" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1030" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760455 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763688 ATOM PAIRS WERE FOUND FOR ATOM LIST 41736 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30185 from a total of 763688 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1030 -71.69069 10.57697 0.61553 INTE EXTERN> -30.08152 -41.60917 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6907" Parameter: A <- "-71.6907" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0815" Parameter: B <- "-30.0815" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6092" Parameter: C <- "-41.6092" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1030 TOTAL ENERGY = -71.6907 RDTITL> * VAN DER WAALS = -30.0815 ELECTROSTATIC = -41.6092 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1030" Parameter: CONF_N -> "8002" Comparing "1030" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1031" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763688 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762704 ATOM PAIRS WERE FOUND FOR ATOM LIST 41810 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29245 from a total of 762704 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1031 -66.83135 -4.85934 0.75051 INTE EXTERN> -27.57691 -39.25444 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8314" Parameter: A <- "-66.8314" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5769" Parameter: B <- "-27.5769" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2544" Parameter: C <- "-39.2544" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1031 TOTAL ENERGY = -66.8314 RDTITL> * VAN DER WAALS = -27.5769 ELECTROSTATIC = -39.2544 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1031" Parameter: CONF_N -> "8002" Comparing "1031" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1032" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762704 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761158 ATOM PAIRS WERE FOUND FOR ATOM LIST 41651 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29646 from a total of 761158 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1032 -63.77013 -3.06122 0.57078 INTE EXTERN> -31.45364 -32.31649 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7701" Parameter: A <- "-63.7701" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4536" Parameter: B <- "-31.4536" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.3165" Parameter: C <- "-32.3165" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1032 TOTAL ENERGY = -63.7701 RDTITL> * VAN DER WAALS = -31.4536 ELECTROSTATIC = -32.3165 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1032" Parameter: CONF_N -> "8002" Comparing "1032" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1033" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761158 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757203 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29450 from a total of 757203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1033 -64.88321 1.11307 0.74913 INTE EXTERN> -24.01157 -40.87163 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8832" Parameter: A <- "-64.8832" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0116" Parameter: B <- "-24.0116" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8716" Parameter: C <- "-40.8716" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1033 TOTAL ENERGY = -64.8832 RDTITL> * VAN DER WAALS = -24.0116 ELECTROSTATIC = -40.8716 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1033" Parameter: CONF_N -> "8002" Comparing "1033" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1034" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758849 ATOM PAIRS WERE FOUND FOR ATOM LIST 41555 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30034 from a total of 758849 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1034 -62.27979 -2.60341 0.52122 INTE EXTERN> -32.50497 -29.77483 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.2798" Parameter: A <- "-62.2798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.505" Parameter: B <- "-32.505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.7748" Parameter: C <- "-29.7748" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1034 TOTAL ENERGY = -62.2798 RDTITL> * VAN DER WAALS = -32.505 ELECTROSTATIC = -29.7748 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1034" Parameter: CONF_N -> "8002" Comparing "1034" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1035" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758849 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762973 ATOM PAIRS WERE FOUND FOR ATOM LIST 41994 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30028 from a total of 762973 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1035 -64.94539 2.66559 0.57615 INTE EXTERN> -30.53960 -34.40578 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9454" Parameter: A <- "-64.9454" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5396" Parameter: B <- "-30.5396" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4058" Parameter: C <- "-34.4058" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1035 TOTAL ENERGY = -64.9454 RDTITL> * VAN DER WAALS = -30.5396 ELECTROSTATIC = -34.4058 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1035" Parameter: CONF_N -> "8002" Comparing "1035" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1036" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762973 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764361 ATOM PAIRS WERE FOUND FOR ATOM LIST 41944 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30788 from a total of 764361 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1036 -68.82891 3.88352 0.68857 INTE EXTERN> -25.47796 -43.35095 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8289" Parameter: A <- "-68.8289" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.478" Parameter: B <- "-25.478" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.351" Parameter: C <- "-43.351" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1036 TOTAL ENERGY = -68.8289 RDTITL> * VAN DER WAALS = -25.478 ELECTROSTATIC = -43.351 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1036" Parameter: CONF_N -> "8002" Comparing "1036" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1037" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764361 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759307 ATOM PAIRS WERE FOUND FOR ATOM LIST 41854 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29486 from a total of 759307 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1037 -55.37571 -13.45320 0.50844 INTE EXTERN> -33.44356 -21.93215 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.3757" Parameter: A <- "-55.3757" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4436" Parameter: B <- "-33.4436" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-21.9322" Parameter: C <- "-21.9322" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1037 TOTAL ENERGY = -55.3757 RDTITL> * VAN DER WAALS = -33.4436 ELECTROSTATIC = -21.9322 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1037" Parameter: CONF_N -> "8002" Comparing "1037" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1038" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759307 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765847 ATOM PAIRS WERE FOUND FOR ATOM LIST 41933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30299 from a total of 765847 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1038 -62.12116 6.74545 0.68864 INTE EXTERN> -25.29477 -36.82639 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.1212" Parameter: A <- "-62.1212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2948" Parameter: B <- "-25.2948" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8264" Parameter: C <- "-36.8264" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1038 TOTAL ENERGY = -62.1212 RDTITL> * VAN DER WAALS = -25.2948 ELECTROSTATIC = -36.8264 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1038" Parameter: CONF_N -> "8002" Comparing "1038" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1039" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765847 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765787 ATOM PAIRS WERE FOUND FOR ATOM LIST 41983 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30079 from a total of 765787 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1039 -68.61917 6.49801 0.61628 INTE EXTERN> -33.42525 -35.19392 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6192" Parameter: A <- "-68.6192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4252" Parameter: B <- "-33.4252" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1939" Parameter: C <- "-35.1939" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1039 TOTAL ENERGY = -68.6192 RDTITL> * VAN DER WAALS = -33.4252 ELECTROSTATIC = -35.1939 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1039" Parameter: CONF_N -> "8002" Comparing "1039" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1040" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765787 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760081 ATOM PAIRS WERE FOUND FOR ATOM LIST 41555 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30101 from a total of 760081 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1040 -72.23929 3.62012 0.62571 INTE EXTERN> -31.65544 -40.58385 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2393" Parameter: A <- "-72.2393" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6554" Parameter: B <- "-31.6554" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5838" Parameter: C <- "-40.5838" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1040 TOTAL ENERGY = -72.2393 RDTITL> * VAN DER WAALS = -31.6554 ELECTROSTATIC = -40.5838 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1040" Parameter: CONF_N -> "8002" Comparing "1040" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1041" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760081 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763321 ATOM PAIRS WERE FOUND FOR ATOM LIST 41823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30051 from a total of 763321 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1041 -60.36710 -11.87219 0.69092 INTE EXTERN> -23.78552 -36.58158 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.3671" Parameter: A <- "-60.3671" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7855" Parameter: B <- "-23.7855" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5816" Parameter: C <- "-36.5816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1041 TOTAL ENERGY = -60.3671 RDTITL> * VAN DER WAALS = -23.7855 ELECTROSTATIC = -36.5816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1041" Parameter: CONF_N -> "8002" Comparing "1041" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1042" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763321 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764359 ATOM PAIRS WERE FOUND FOR ATOM LIST 41941 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30507 from a total of 764359 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1042 -70.32587 9.95877 0.65479 INTE EXTERN> -30.09025 -40.23562 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3259" Parameter: A <- "-70.3259" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0903" Parameter: B <- "-30.0903" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2356" Parameter: C <- "-40.2356" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1042 TOTAL ENERGY = -70.3259 RDTITL> * VAN DER WAALS = -30.0903 ELECTROSTATIC = -40.2356 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1042" Parameter: CONF_N -> "8002" Comparing "1042" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1043" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764359 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760377 ATOM PAIRS WERE FOUND FOR ATOM LIST 41740 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30158 from a total of 760377 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1043 -62.71367 -7.61220 0.66644 INTE EXTERN> -28.64703 -34.06665 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7137" Parameter: A <- "-62.7137" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.647" Parameter: B <- "-28.647" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.0666" Parameter: C <- "-34.0666" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1043 TOTAL ENERGY = -62.7137 RDTITL> * VAN DER WAALS = -28.647 ELECTROSTATIC = -34.0666 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1043" Parameter: CONF_N -> "8002" Comparing "1043" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1044" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760377 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763206 ATOM PAIRS WERE FOUND FOR ATOM LIST 41773 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30327 from a total of 763206 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1044 -69.27684 6.56317 0.62597 INTE EXTERN> -31.70371 -37.57313 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2768" Parameter: A <- "-69.2768" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7037" Parameter: B <- "-31.7037" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5731" Parameter: C <- "-37.5731" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1044 TOTAL ENERGY = -69.2768 RDTITL> * VAN DER WAALS = -31.7037 ELECTROSTATIC = -37.5731 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1044" Parameter: CONF_N -> "8002" Comparing "1044" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1045" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763206 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769212 ATOM PAIRS WERE FOUND FOR ATOM LIST 42283 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30423 from a total of 769212 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1045 -66.62266 -2.65419 0.64139 INTE EXTERN> -30.29438 -36.32827 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6227" Parameter: A <- "-66.6227" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2944" Parameter: B <- "-30.2944" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3283" Parameter: C <- "-36.3283" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1045 TOTAL ENERGY = -66.6227 RDTITL> * VAN DER WAALS = -30.2944 ELECTROSTATIC = -36.3283 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1045" Parameter: CONF_N -> "8002" Comparing "1045" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1046" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769212 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764132 ATOM PAIRS WERE FOUND FOR ATOM LIST 41928 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30534 from a total of 764132 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1046 -64.89336 -1.72930 0.56815 INTE EXTERN> -31.11549 -33.77787 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8934" Parameter: A <- "-64.8934" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1155" Parameter: B <- "-31.1155" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7779" Parameter: C <- "-33.7779" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1046 TOTAL ENERGY = -64.8934 RDTITL> * VAN DER WAALS = -31.1155 ELECTROSTATIC = -33.7779 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1046" Parameter: CONF_N -> "8002" Comparing "1046" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1047" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764132 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761716 ATOM PAIRS WERE FOUND FOR ATOM LIST 41974 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30013 from a total of 761716 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1047 -71.56757 6.67421 0.63215 INTE EXTERN> -31.92499 -39.64258 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5676" Parameter: A <- "-71.5676" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.925" Parameter: B <- "-31.925" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6426" Parameter: C <- "-39.6426" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1047 TOTAL ENERGY = -71.5676 RDTITL> * VAN DER WAALS = -31.925 ELECTROSTATIC = -39.6426 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1047" Parameter: CONF_N -> "8002" Comparing "1047" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1048" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761716 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761981 ATOM PAIRS WERE FOUND FOR ATOM LIST 41892 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30023 from a total of 761981 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1048 -62.99304 -8.57452 0.63531 INTE EXTERN> -29.35983 -33.63321 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.993" Parameter: A <- "-62.993" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3598" Parameter: B <- "-29.3598" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6332" Parameter: C <- "-33.6332" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1048 TOTAL ENERGY = -62.993 RDTITL> * VAN DER WAALS = -29.3598 ELECTROSTATIC = -33.6332 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1048" Parameter: CONF_N -> "8002" Comparing "1048" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1049" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761981 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755773 ATOM PAIRS WERE FOUND FOR ATOM LIST 41525 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29411 from a total of 755773 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1049 -67.26929 4.27624 0.61732 INTE EXTERN> -28.98822 -38.28107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2693" Parameter: A <- "-67.2693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9882" Parameter: B <- "-28.9882" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2811" Parameter: C <- "-38.2811" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1049 TOTAL ENERGY = -67.2693 RDTITL> * VAN DER WAALS = -28.9882 ELECTROSTATIC = -38.2811 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1049" Parameter: CONF_N -> "8002" Comparing "1049" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1050" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755773 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761011 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29761 from a total of 761011 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1050 -66.32764 -0.94165 0.56146 INTE EXTERN> -31.85753 -34.47011 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3276" Parameter: A <- "-66.3276" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8575" Parameter: B <- "-31.8575" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4701" Parameter: C <- "-34.4701" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1050 TOTAL ENERGY = -66.3276 RDTITL> * VAN DER WAALS = -31.8575 ELECTROSTATIC = -34.4701 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1050" Parameter: CONF_N -> "8002" Comparing "1050" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1051" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761011 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761020 ATOM PAIRS WERE FOUND FOR ATOM LIST 41756 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29590 from a total of 761020 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1051 -72.96660 6.63897 0.59701 INTE EXTERN> -32.07685 -40.88976 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9666" Parameter: A <- "-72.9666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0768" Parameter: B <- "-32.0768" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8898" Parameter: C <- "-40.8898" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1051 TOTAL ENERGY = -72.9666 RDTITL> * VAN DER WAALS = -32.0768 ELECTROSTATIC = -40.8898 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1051" Parameter: CONF_N -> "8002" Comparing "1051" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1052" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761020 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759511 ATOM PAIRS WERE FOUND FOR ATOM LIST 41658 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29231 from a total of 759511 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1052 -66.91851 -6.04809 0.67876 INTE EXTERN> -28.02578 -38.89272 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9185" Parameter: A <- "-66.9185" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0258" Parameter: B <- "-28.0258" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8927" Parameter: C <- "-38.8927" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1052 TOTAL ENERGY = -66.9185 RDTITL> * VAN DER WAALS = -28.0258 ELECTROSTATIC = -38.8927 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1052" Parameter: CONF_N -> "8002" Comparing "1052" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1053" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759511 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762196 ATOM PAIRS WERE FOUND FOR ATOM LIST 41872 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30261 from a total of 762196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1053 -70.18774 3.26924 0.63825 INTE EXTERN> -28.98449 -41.20326 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1877" Parameter: A <- "-70.1877" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9845" Parameter: B <- "-28.9845" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2033" Parameter: C <- "-41.2033" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1053 TOTAL ENERGY = -70.1877 RDTITL> * VAN DER WAALS = -28.9845 ELECTROSTATIC = -41.2033 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1053" Parameter: CONF_N -> "8002" Comparing "1053" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1054" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758901 ATOM PAIRS WERE FOUND FOR ATOM LIST 41652 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29373 from a total of 758901 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1054 -62.76075 -7.42699 0.49552 INTE EXTERN> -34.39186 -28.36889 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7608" Parameter: A <- "-62.7608" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3919" Parameter: B <- "-34.3919" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.3689" Parameter: C <- "-28.3689" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1054 TOTAL ENERGY = -62.7608 RDTITL> * VAN DER WAALS = -34.3919 ELECTROSTATIC = -28.3689 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1054" Parameter: CONF_N -> "8002" Comparing "1054" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1055" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758901 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762015 ATOM PAIRS WERE FOUND FOR ATOM LIST 41972 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30031 from a total of 762015 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1055 -61.31686 -1.44389 0.53803 INTE EXTERN> -33.47524 -27.84162 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.3169" Parameter: A <- "-61.3169" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4752" Parameter: B <- "-33.4752" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.8416" Parameter: C <- "-27.8416" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1055 TOTAL ENERGY = -61.3169 RDTITL> * VAN DER WAALS = -33.4752 ELECTROSTATIC = -27.8416 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1055" Parameter: CONF_N -> "8002" Comparing "1055" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1056" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762015 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762076 ATOM PAIRS WERE FOUND FOR ATOM LIST 41931 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30408 from a total of 762076 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1056 -67.56833 6.25147 0.64439 INTE EXTERN> -31.42595 -36.14238 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5683" Parameter: A <- "-67.5683" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4259" Parameter: B <- "-31.4259" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1424" Parameter: C <- "-36.1424" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1056 TOTAL ENERGY = -67.5683 RDTITL> * VAN DER WAALS = -31.4259 ELECTROSTATIC = -36.1424 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1056" Parameter: CONF_N -> "8002" Comparing "1056" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1057" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762076 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763349 ATOM PAIRS WERE FOUND FOR ATOM LIST 41828 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29645 from a total of 763349 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1057 -65.93609 -1.63224 0.70238 INTE EXTERN> -29.05964 -36.87646 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9361" Parameter: A <- "-65.9361" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0596" Parameter: B <- "-29.0596" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8765" Parameter: C <- "-36.8765" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1057 TOTAL ENERGY = -65.9361 RDTITL> * VAN DER WAALS = -29.0596 ELECTROSTATIC = -36.8765 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1057" Parameter: CONF_N -> "8002" Comparing "1057" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1058" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763349 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765755 ATOM PAIRS WERE FOUND FOR ATOM LIST 41919 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29921 from a total of 765755 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1058 -64.27044 -1.66565 0.52502 INTE EXTERN> -34.19905 -30.07139 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2704" Parameter: A <- "-64.2704" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1991" Parameter: B <- "-34.1991" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.0714" Parameter: C <- "-30.0714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1058 TOTAL ENERGY = -64.2704 RDTITL> * VAN DER WAALS = -34.1991 ELECTROSTATIC = -30.0714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1058" Parameter: CONF_N -> "8002" Comparing "1058" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1059" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765755 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761346 ATOM PAIRS WERE FOUND FOR ATOM LIST 41715 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29656 from a total of 761346 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1059 -62.40160 -1.86884 0.56141 INTE EXTERN> -31.74873 -30.65287 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.4016" Parameter: A <- "-62.4016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7487" Parameter: B <- "-31.7487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.6529" Parameter: C <- "-30.6529" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1059 TOTAL ENERGY = -62.4016 RDTITL> * VAN DER WAALS = -31.7487 ELECTROSTATIC = -30.6529 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1059" Parameter: CONF_N -> "8002" Comparing "1059" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1060" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761346 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763386 ATOM PAIRS WERE FOUND FOR ATOM LIST 41842 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29830 from a total of 763386 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1060 -60.01120 -2.39040 0.72504 INTE EXTERN> -28.70976 -31.30144 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.0112" Parameter: A <- "-60.0112" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7098" Parameter: B <- "-28.7098" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.3014" Parameter: C <- "-31.3014" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1060 TOTAL ENERGY = -60.0112 RDTITL> * VAN DER WAALS = -28.7098 ELECTROSTATIC = -31.3014 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1060" Parameter: CONF_N -> "8002" Comparing "1060" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1061" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763386 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760185 ATOM PAIRS WERE FOUND FOR ATOM LIST 41736 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29924 from a total of 760185 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1061 -63.64530 3.63411 0.62209 INTE EXTERN> -31.14296 -32.50235 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6453" Parameter: A <- "-63.6453" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.143" Parameter: B <- "-31.143" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5023" Parameter: C <- "-32.5023" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1061 TOTAL ENERGY = -63.6453 RDTITL> * VAN DER WAALS = -31.143 ELECTROSTATIC = -32.5023 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1061" Parameter: CONF_N -> "8002" Comparing "1061" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1062" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760185 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762209 ATOM PAIRS WERE FOUND FOR ATOM LIST 41707 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30020 from a total of 762209 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1062 -69.45729 5.81199 0.68573 INTE EXTERN> -29.06924 -40.38805 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4573" Parameter: A <- "-69.4573" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0692" Parameter: B <- "-29.0692" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.388" Parameter: C <- "-40.388" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1062 TOTAL ENERGY = -69.4573 RDTITL> * VAN DER WAALS = -29.0692 ELECTROSTATIC = -40.388 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1062" Parameter: CONF_N -> "8002" Comparing "1062" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1063" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762209 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759150 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29684 from a total of 759150 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1063 -64.13659 -5.32071 0.58077 INTE EXTERN> -31.31494 -32.82165 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1366" Parameter: A <- "-64.1366" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3149" Parameter: B <- "-31.3149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.8216" Parameter: C <- "-32.8216" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1063 TOTAL ENERGY = -64.1366 RDTITL> * VAN DER WAALS = -31.3149 ELECTROSTATIC = -32.8216 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1063" Parameter: CONF_N -> "8002" Comparing "1063" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1064" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759150 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758034 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29174 from a total of 758034 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1064 -65.61171 1.47512 0.62334 INTE EXTERN> -28.04478 -37.56693 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6117" Parameter: A <- "-65.6117" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0448" Parameter: B <- "-28.0448" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5669" Parameter: C <- "-37.5669" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1064 TOTAL ENERGY = -65.6117 RDTITL> * VAN DER WAALS = -28.0448 ELECTROSTATIC = -37.5669 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1064" Parameter: CONF_N -> "8002" Comparing "1064" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1065" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758034 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766256 ATOM PAIRS WERE FOUND FOR ATOM LIST 41999 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29837 from a total of 766256 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1065 -65.25431 -0.35740 0.65996 INTE EXTERN> -27.62896 -37.62535 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2543" Parameter: A <- "-65.2543" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.629" Parameter: B <- "-27.629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6254" Parameter: C <- "-37.6254" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1065 TOTAL ENERGY = -65.2543 RDTITL> * VAN DER WAALS = -27.629 ELECTROSTATIC = -37.6254 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1065" Parameter: CONF_N -> "8002" Comparing "1065" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1066" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766256 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762066 ATOM PAIRS WERE FOUND FOR ATOM LIST 41936 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29615 from a total of 762066 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1066 -67.80806 2.55375 0.57864 INTE EXTERN> -31.51514 -36.29292 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8081" Parameter: A <- "-67.8081" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5151" Parameter: B <- "-31.5151" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2929" Parameter: C <- "-36.2929" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1066 TOTAL ENERGY = -67.8081 RDTITL> * VAN DER WAALS = -31.5151 ELECTROSTATIC = -36.2929 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1066" Parameter: CONF_N -> "8002" Comparing "1066" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1067" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762066 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758889 ATOM PAIRS WERE FOUND FOR ATOM LIST 41625 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28802 from a total of 758889 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1067 -61.56920 -6.23886 0.59044 INTE EXTERN> -28.06411 -33.50509 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.5692" Parameter: A <- "-61.5692" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0641" Parameter: B <- "-28.0641" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.5051" Parameter: C <- "-33.5051" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1067 TOTAL ENERGY = -61.5692 RDTITL> * VAN DER WAALS = -28.0641 ELECTROSTATIC = -33.5051 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1067" Parameter: CONF_N -> "8002" Comparing "1067" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1068" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758889 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760785 ATOM PAIRS WERE FOUND FOR ATOM LIST 41545 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29637 from a total of 760785 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1068 -68.73144 7.16224 0.57882 INTE EXTERN> -30.12684 -38.60460 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7314" Parameter: A <- "-68.7314" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1268" Parameter: B <- "-30.1268" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6046" Parameter: C <- "-38.6046" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1068 TOTAL ENERGY = -68.7314 RDTITL> * VAN DER WAALS = -30.1268 ELECTROSTATIC = -38.6046 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1068" Parameter: CONF_N -> "8002" Comparing "1068" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1069" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760785 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764934 ATOM PAIRS WERE FOUND FOR ATOM LIST 42061 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29632 from a total of 764934 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1069 -67.28618 -1.44526 0.65689 INTE EXTERN> -28.10920 -39.17698 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2862" Parameter: A <- "-67.2862" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1092" Parameter: B <- "-28.1092" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.177" Parameter: C <- "-39.177" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1069 TOTAL ENERGY = -67.2862 RDTITL> * VAN DER WAALS = -28.1092 ELECTROSTATIC = -39.177 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1069" Parameter: CONF_N -> "8002" Comparing "1069" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1070" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764934 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764386 ATOM PAIRS WERE FOUND FOR ATOM LIST 42026 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29981 from a total of 764386 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1070 -62.84532 -4.44086 0.58062 INTE EXTERN> -30.27016 -32.57516 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.8453" Parameter: A <- "-62.8453" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2702" Parameter: B <- "-30.2702" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5752" Parameter: C <- "-32.5752" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1070 TOTAL ENERGY = -62.8453 RDTITL> * VAN DER WAALS = -30.2702 ELECTROSTATIC = -32.5752 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1070" Parameter: CONF_N -> "8002" Comparing "1070" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1071" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764386 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759544 ATOM PAIRS WERE FOUND FOR ATOM LIST 41901 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29757 from a total of 759544 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1071 -67.97941 5.13409 0.67600 INTE EXTERN> -28.76922 -39.21019 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9794" Parameter: A <- "-67.9794" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7692" Parameter: B <- "-28.7692" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2102" Parameter: C <- "-39.2102" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1071 TOTAL ENERGY = -67.9794 RDTITL> * VAN DER WAALS = -28.7692 ELECTROSTATIC = -39.2102 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1071" Parameter: CONF_N -> "8002" Comparing "1071" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1072" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759544 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761782 ATOM PAIRS WERE FOUND FOR ATOM LIST 41785 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29377 from a total of 761782 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1072 -67.24908 -0.73033 0.71835 INTE EXTERN> -26.82496 -40.42412 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2491" Parameter: A <- "-67.2491" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.825" Parameter: B <- "-26.825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4241" Parameter: C <- "-40.4241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1072 TOTAL ENERGY = -67.2491 RDTITL> * VAN DER WAALS = -26.825 ELECTROSTATIC = -40.4241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1072" Parameter: CONF_N -> "8002" Comparing "1072" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1073" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761782 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762249 ATOM PAIRS WERE FOUND FOR ATOM LIST 42041 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29780 from a total of 762249 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1073 -60.00890 -7.24019 0.54712 INTE EXTERN> -33.09119 -26.91771 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.0089" Parameter: A <- "-60.0089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0912" Parameter: B <- "-33.0912" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-26.9177" Parameter: C <- "-26.9177" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1073 TOTAL ENERGY = -60.0089 RDTITL> * VAN DER WAALS = -33.0912 ELECTROSTATIC = -26.9177 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1073" Parameter: CONF_N -> "8002" Comparing "1073" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1074" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762249 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768221 ATOM PAIRS WERE FOUND FOR ATOM LIST 42220 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30128 from a total of 768221 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1074 -65.16077 5.15187 0.81352 INTE EXTERN> -24.62549 -40.53528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1608" Parameter: A <- "-65.1608" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6255" Parameter: B <- "-24.6255" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5353" Parameter: C <- "-40.5353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1074 TOTAL ENERGY = -65.1608 RDTITL> * VAN DER WAALS = -24.6255 ELECTROSTATIC = -40.5353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1074" Parameter: CONF_N -> "8002" Comparing "1074" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1075" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768221 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763334 ATOM PAIRS WERE FOUND FOR ATOM LIST 41916 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29171 from a total of 763334 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1075 -64.85111 -0.30966 0.58802 INTE EXTERN> -28.31634 -36.53477 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8511" Parameter: A <- "-64.8511" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3163" Parameter: B <- "-28.3163" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5348" Parameter: C <- "-36.5348" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1075 TOTAL ENERGY = -64.8511 RDTITL> * VAN DER WAALS = -28.3163 ELECTROSTATIC = -36.5348 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1075" Parameter: CONF_N -> "8002" Comparing "1075" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1076" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763334 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765855 ATOM PAIRS WERE FOUND FOR ATOM LIST 41954 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29402 from a total of 765855 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1076 -63.81468 -1.03643 0.64117 INTE EXTERN> -27.60370 -36.21099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.8147" Parameter: A <- "-63.8147" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6037" Parameter: B <- "-27.6037" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.211" Parameter: C <- "-36.211" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1076 TOTAL ENERGY = -63.8147 RDTITL> * VAN DER WAALS = -27.6037 ELECTROSTATIC = -36.211 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1076" Parameter: CONF_N -> "8002" Comparing "1076" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1077" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765855 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764900 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29668 from a total of 764900 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1077 -65.17886 1.36418 0.54152 INTE EXTERN> -32.38313 -32.79574 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1789" Parameter: A <- "-65.1789" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3831" Parameter: B <- "-32.3831" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.7957" Parameter: C <- "-32.7957" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1077 TOTAL ENERGY = -65.1789 RDTITL> * VAN DER WAALS = -32.3831 ELECTROSTATIC = -32.7957 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1077" Parameter: CONF_N -> "8002" Comparing "1077" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1078" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764900 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761879 ATOM PAIRS WERE FOUND FOR ATOM LIST 41851 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29227 from a total of 761879 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1078 -64.05498 -1.12389 0.62424 INTE EXTERN> -27.93070 -36.12427 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.055" Parameter: A <- "-64.055" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9307" Parameter: B <- "-27.9307" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1243" Parameter: C <- "-36.1243" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1078 TOTAL ENERGY = -64.055 RDTITL> * VAN DER WAALS = -27.9307 ELECTROSTATIC = -36.1243 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1078" Parameter: CONF_N -> "8002" Comparing "1078" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1079" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761879 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764350 ATOM PAIRS WERE FOUND FOR ATOM LIST 42050 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29953 from a total of 764350 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1079 -64.84517 0.79020 0.60351 INTE EXTERN> -27.06448 -37.78070 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8452" Parameter: A <- "-64.8452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0645" Parameter: B <- "-27.0645" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7807" Parameter: C <- "-37.7807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1079 TOTAL ENERGY = -64.8452 RDTITL> * VAN DER WAALS = -27.0645 ELECTROSTATIC = -37.7807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1079" Parameter: CONF_N -> "8002" Comparing "1079" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1080" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764350 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760816 ATOM PAIRS WERE FOUND FOR ATOM LIST 41642 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30362 from a total of 760816 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1080 -65.69639 0.85122 0.58978 INTE EXTERN> -29.00167 -36.69472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6964" Parameter: A <- "-65.6964" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0017" Parameter: B <- "-29.0017" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6947" Parameter: C <- "-36.6947" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1080 TOTAL ENERGY = -65.6964 RDTITL> * VAN DER WAALS = -29.0017 ELECTROSTATIC = -36.6947 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1080" Parameter: CONF_N -> "8002" Comparing "1080" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1081" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760816 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754245 ATOM PAIRS WERE FOUND FOR ATOM LIST 41539 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29510 from a total of 754245 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1081 -61.83172 -3.86466 0.61188 INTE EXTERN> -28.08171 -33.75001 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.8317" Parameter: A <- "-61.8317" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0817" Parameter: B <- "-28.0817" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.75" Parameter: C <- "-33.75" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1081 TOTAL ENERGY = -61.8317 RDTITL> * VAN DER WAALS = -28.0817 ELECTROSTATIC = -33.75 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1081" Parameter: CONF_N -> "8002" Comparing "1081" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1082" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754245 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759222 ATOM PAIRS WERE FOUND FOR ATOM LIST 41739 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29585 from a total of 759222 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1082 -66.97551 5.14378 0.52300 INTE EXTERN> -33.57312 -33.40239 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9755" Parameter: A <- "-66.9755" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5731" Parameter: B <- "-33.5731" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.4024" Parameter: C <- "-33.4024" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1082 TOTAL ENERGY = -66.9755 RDTITL> * VAN DER WAALS = -33.5731 ELECTROSTATIC = -33.4024 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1082" Parameter: CONF_N -> "8002" Comparing "1082" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1083" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759222 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760309 ATOM PAIRS WERE FOUND FOR ATOM LIST 41590 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29684 from a total of 760309 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1083 -66.73420 -0.24130 0.52471 INTE EXTERN> -34.55817 -32.17603 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7342" Parameter: A <- "-66.7342" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.5582" Parameter: B <- "-34.5582" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.176" Parameter: C <- "-32.176" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1083 TOTAL ENERGY = -66.7342 RDTITL> * VAN DER WAALS = -34.5582 ELECTROSTATIC = -32.176 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1083" Parameter: CONF_N -> "8002" Comparing "1083" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1084" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760309 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761765 ATOM PAIRS WERE FOUND FOR ATOM LIST 41856 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29621 from a total of 761765 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1084 -70.92869 4.19449 0.67797 INTE EXTERN> -28.53642 -42.39227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9287" Parameter: A <- "-70.9287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5364" Parameter: B <- "-28.5364" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3923" Parameter: C <- "-42.3923" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1084 TOTAL ENERGY = -70.9287 RDTITL> * VAN DER WAALS = -28.5364 ELECTROSTATIC = -42.3923 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1084" Parameter: CONF_N -> "8002" Comparing "1084" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1085" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761765 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765266 ATOM PAIRS WERE FOUND FOR ATOM LIST 41932 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29426 from a total of 765266 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1085 -68.93480 -1.99389 0.64520 INTE EXTERN> -28.42800 -40.50680 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9348" Parameter: A <- "-68.9348" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.428" Parameter: B <- "-28.428" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5068" Parameter: C <- "-40.5068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1085 TOTAL ENERGY = -68.9348 RDTITL> * VAN DER WAALS = -28.428 ELECTROSTATIC = -40.5068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1085" Parameter: CONF_N -> "8002" Comparing "1085" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1086" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765266 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766542 ATOM PAIRS WERE FOUND FOR ATOM LIST 42227 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29536 from a total of 766542 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1086 -67.89870 -1.03610 0.79713 INTE EXTERN> -23.83712 -44.06158 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8987" Parameter: A <- "-67.8987" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8371" Parameter: B <- "-23.8371" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0616" Parameter: C <- "-44.0616" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1086 TOTAL ENERGY = -67.8987 RDTITL> * VAN DER WAALS = -23.8371 ELECTROSTATIC = -44.0616 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1086" Parameter: CONF_N -> "8002" Comparing "1086" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1087" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766542 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760799 ATOM PAIRS WERE FOUND FOR ATOM LIST 41709 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29355 from a total of 760799 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1087 -76.15053 8.25183 0.72946 INTE EXTERN> -30.01903 -46.13150 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1505" Parameter: A <- "-76.1505" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.019" Parameter: B <- "-30.019" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1315" Parameter: C <- "-46.1315" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1087 TOTAL ENERGY = -76.1505 RDTITL> * VAN DER WAALS = -30.019 ELECTROSTATIC = -46.1315 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1087" Parameter: CONF_N -> "8002" Comparing "1087" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1088" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760799 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762107 ATOM PAIRS WERE FOUND FOR ATOM LIST 42019 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30009 from a total of 762107 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1088 -65.22595 -10.92458 0.67279 INTE EXTERN> -27.61917 -37.60678 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.226" Parameter: A <- "-65.226" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6192" Parameter: B <- "-27.6192" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6068" Parameter: C <- "-37.6068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1088 TOTAL ENERGY = -65.226 RDTITL> * VAN DER WAALS = -27.6192 ELECTROSTATIC = -37.6068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1088" Parameter: CONF_N -> "8002" Comparing "1088" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1089" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762107 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759883 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29531 from a total of 759883 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1089 -71.48965 6.26370 0.56336 INTE EXTERN> -33.97450 -37.51515 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4897" Parameter: A <- "-71.4897" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9745" Parameter: B <- "-33.9745" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5151" Parameter: C <- "-37.5151" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1089 TOTAL ENERGY = -71.4897 RDTITL> * VAN DER WAALS = -33.9745 ELECTROSTATIC = -37.5151 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1089" Parameter: CONF_N -> "8002" Comparing "1089" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1090" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759883 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760352 ATOM PAIRS WERE FOUND FOR ATOM LIST 41811 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29041 from a total of 760352 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1090 -62.38703 -9.10262 0.56406 INTE EXTERN> -31.61163 -30.77540 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.387" Parameter: A <- "-62.387" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6116" Parameter: B <- "-31.6116" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.7754" Parameter: C <- "-30.7754" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1090 TOTAL ENERGY = -62.387 RDTITL> * VAN DER WAALS = -31.6116 ELECTROSTATIC = -30.7754 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1090" Parameter: CONF_N -> "8002" Comparing "1090" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1091" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760352 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756728 ATOM PAIRS WERE FOUND FOR ATOM LIST 41346 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29362 from a total of 756728 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1091 -70.12731 7.74028 0.63766 INTE EXTERN> -30.95444 -39.17287 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1273" Parameter: A <- "-70.1273" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9544" Parameter: B <- "-30.9544" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1729" Parameter: C <- "-39.1729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1091 TOTAL ENERGY = -70.1273 RDTITL> * VAN DER WAALS = -30.9544 ELECTROSTATIC = -39.1729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1091" Parameter: CONF_N -> "8002" Comparing "1091" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1092" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756728 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760015 ATOM PAIRS WERE FOUND FOR ATOM LIST 41781 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29604 from a total of 760015 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1092 -67.00908 -3.11823 0.60020 INTE EXTERN> -30.75167 -36.25742 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0091" Parameter: A <- "-67.0091" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7517" Parameter: B <- "-30.7517" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2574" Parameter: C <- "-36.2574" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1092 TOTAL ENERGY = -67.0091 RDTITL> * VAN DER WAALS = -30.7517 ELECTROSTATIC = -36.2574 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1092" Parameter: CONF_N -> "8002" Comparing "1092" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1093" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760015 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763730 ATOM PAIRS WERE FOUND FOR ATOM LIST 41931 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30132 from a total of 763730 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1093 -73.93228 6.92319 0.72558 INTE EXTERN> -29.24573 -44.68654 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9323" Parameter: A <- "-73.9323" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2457" Parameter: B <- "-29.2457" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6865" Parameter: C <- "-44.6865" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1093 TOTAL ENERGY = -73.9323 RDTITL> * VAN DER WAALS = -29.2457 ELECTROSTATIC = -44.6865 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1093" Parameter: CONF_N -> "8002" Comparing "1093" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1094" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763730 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761917 ATOM PAIRS WERE FOUND FOR ATOM LIST 41643 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30447 from a total of 761917 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1094 -67.86136 -6.07092 0.54235 INTE EXTERN> -33.19796 -34.66341 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8614" Parameter: A <- "-67.8614" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.198" Parameter: B <- "-33.198" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.6634" Parameter: C <- "-34.6634" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1094 TOTAL ENERGY = -67.8614 RDTITL> * VAN DER WAALS = -33.198 ELECTROSTATIC = -34.6634 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1094" Parameter: CONF_N -> "8002" Comparing "1094" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1095" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761917 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761585 ATOM PAIRS WERE FOUND FOR ATOM LIST 41909 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30035 from a total of 761585 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1095 -69.38398 1.52262 0.66851 INTE EXTERN> -30.38443 -38.99955 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.384" Parameter: A <- "-69.384" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3844" Parameter: B <- "-30.3844" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9995" Parameter: C <- "-38.9995" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1095 TOTAL ENERGY = -69.384 RDTITL> * VAN DER WAALS = -30.3844 ELECTROSTATIC = -38.9995 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1095" Parameter: CONF_N -> "8002" Comparing "1095" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1096" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761585 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767680 ATOM PAIRS WERE FOUND FOR ATOM LIST 42245 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30018 from a total of 767680 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1096 -67.83789 -1.54609 0.63014 INTE EXTERN> -28.57763 -39.26026 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8379" Parameter: A <- "-67.8379" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5776" Parameter: B <- "-28.5776" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2603" Parameter: C <- "-39.2603" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1096 TOTAL ENERGY = -67.8379 RDTITL> * VAN DER WAALS = -28.5776 ELECTROSTATIC = -39.2603 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1096" Parameter: CONF_N -> "8002" Comparing "1096" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1097" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767680 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761609 ATOM PAIRS WERE FOUND FOR ATOM LIST 41841 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30529 from a total of 761609 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1097 -64.83984 -2.99805 0.74728 INTE EXTERN> -26.69205 -38.14779 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8398" Parameter: A <- "-64.8398" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6921" Parameter: B <- "-26.6921" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1478" Parameter: C <- "-38.1478" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1097 TOTAL ENERGY = -64.8398 RDTITL> * VAN DER WAALS = -26.6921 ELECTROSTATIC = -38.1478 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1097" Parameter: CONF_N -> "8002" Comparing "1097" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1098" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761609 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763494 ATOM PAIRS WERE FOUND FOR ATOM LIST 41918 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30083 from a total of 763494 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1098 -67.41711 2.57727 0.60074 INTE EXTERN> -30.98916 -36.42796 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4171" Parameter: A <- "-67.4171" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9892" Parameter: B <- "-30.9892" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.428" Parameter: C <- "-36.428" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1098 TOTAL ENERGY = -67.4171 RDTITL> * VAN DER WAALS = -30.9892 ELECTROSTATIC = -36.428 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1098" Parameter: CONF_N -> "8002" Comparing "1098" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1099" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763494 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762252 ATOM PAIRS WERE FOUND FOR ATOM LIST 41770 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30088 from a total of 762252 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1099 -73.18111 5.76400 0.65619 INTE EXTERN> -30.08402 -43.09709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1811" Parameter: A <- "-73.1811" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.084" Parameter: B <- "-30.084" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0971" Parameter: C <- "-43.0971" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1099 TOTAL ENERGY = -73.1811 RDTITL> * VAN DER WAALS = -30.084 ELECTROSTATIC = -43.0971 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1099" Parameter: CONF_N -> "8002" Comparing "1099" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1100" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762252 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760212 ATOM PAIRS WERE FOUND FOR ATOM LIST 41994 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30377 from a total of 760212 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1100 -67.42845 -5.75266 0.62365 INTE EXTERN> -30.48658 -36.94187 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4285" Parameter: A <- "-67.4285" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4866" Parameter: B <- "-30.4866" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9419" Parameter: C <- "-36.9419" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1100 TOTAL ENERGY = -67.4285 RDTITL> * VAN DER WAALS = -30.4866 ELECTROSTATIC = -36.9419 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1100" Parameter: CONF_N -> "8002" Comparing "1100" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1101" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760212 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760539 ATOM PAIRS WERE FOUND FOR ATOM LIST 41729 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30298 from a total of 760539 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1101 -71.55398 4.12552 0.82682 INTE EXTERN> -24.82237 -46.73161 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.554" Parameter: A <- "-71.554" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8224" Parameter: B <- "-24.8224" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7316" Parameter: C <- "-46.7316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1101 TOTAL ENERGY = -71.554 RDTITL> * VAN DER WAALS = -24.8224 ELECTROSTATIC = -46.7316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1101" Parameter: CONF_N -> "8002" Comparing "1101" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1102" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760539 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761680 ATOM PAIRS WERE FOUND FOR ATOM LIST 41823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30659 from a total of 761680 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1102 -69.13920 -2.41478 0.63782 INTE EXTERN> -29.74160 -39.39760 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1392" Parameter: A <- "-69.1392" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7416" Parameter: B <- "-29.7416" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3976" Parameter: C <- "-39.3976" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1102 TOTAL ENERGY = -69.1392 RDTITL> * VAN DER WAALS = -29.7416 ELECTROSTATIC = -39.3976 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1102" Parameter: CONF_N -> "8002" Comparing "1102" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1103" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761680 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41914 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30268 from a total of 761601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1103 -70.56052 1.42132 0.61467 INTE EXTERN> -29.90859 -40.65193 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5605" Parameter: A <- "-70.5605" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9086" Parameter: B <- "-29.9086" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6519" Parameter: C <- "-40.6519" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1103 TOTAL ENERGY = -70.5605 RDTITL> * VAN DER WAALS = -29.9086 ELECTROSTATIC = -40.6519 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1103" Parameter: CONF_N -> "8002" Comparing "1103" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1104" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760439 ATOM PAIRS WERE FOUND FOR ATOM LIST 41777 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29869 from a total of 760439 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1104 -66.15093 -4.40959 0.55373 INTE EXTERN> -30.89759 -35.25334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1509" Parameter: A <- "-66.1509" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8976" Parameter: B <- "-30.8976" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2533" Parameter: C <- "-35.2533" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1104 TOTAL ENERGY = -66.1509 RDTITL> * VAN DER WAALS = -30.8976 ELECTROSTATIC = -35.2533 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1104" Parameter: CONF_N -> "8002" Comparing "1104" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1105" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760439 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761925 ATOM PAIRS WERE FOUND FOR ATOM LIST 41856 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30186 from a total of 761925 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1105 -70.84529 4.69436 0.63171 INTE EXTERN> -29.95206 -40.89323 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8453" Parameter: A <- "-70.8453" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9521" Parameter: B <- "-29.9521" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8932" Parameter: C <- "-40.8932" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1105 TOTAL ENERGY = -70.8453 RDTITL> * VAN DER WAALS = -29.9521 ELECTROSTATIC = -40.8932 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1105" Parameter: CONF_N -> "8002" Comparing "1105" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1106" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761925 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751913 ATOM PAIRS WERE FOUND FOR ATOM LIST 41512 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29198 from a total of 751913 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1106 -65.19052 -5.65477 0.51902 INTE EXTERN> -32.57499 -32.61553 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1905" Parameter: A <- "-65.1905" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.575" Parameter: B <- "-32.575" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.6155" Parameter: C <- "-32.6155" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1106 TOTAL ENERGY = -65.1905 RDTITL> * VAN DER WAALS = -32.575 ELECTROSTATIC = -32.6155 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1106" Parameter: CONF_N -> "8002" Comparing "1106" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1107" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751913 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765315 ATOM PAIRS WERE FOUND FOR ATOM LIST 41942 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29743 from a total of 765315 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1107 -66.74167 1.55115 0.65152 INTE EXTERN> -29.55780 -37.18388 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7417" Parameter: A <- "-66.7417" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5578" Parameter: B <- "-29.5578" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1839" Parameter: C <- "-37.1839" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1107 TOTAL ENERGY = -66.7417 RDTITL> * VAN DER WAALS = -29.5578 ELECTROSTATIC = -37.1839 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1107" Parameter: CONF_N -> "8002" Comparing "1107" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1108" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765315 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761152 ATOM PAIRS WERE FOUND FOR ATOM LIST 41860 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30248 from a total of 761152 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1108 -62.43144 -4.31024 0.60258 INTE EXTERN> -27.37774 -35.05370 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.4314" Parameter: A <- "-62.4314" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3777" Parameter: B <- "-27.3777" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0537" Parameter: C <- "-35.0537" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1108 TOTAL ENERGY = -62.4314 RDTITL> * VAN DER WAALS = -27.3777 ELECTROSTATIC = -35.0537 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1108" Parameter: CONF_N -> "8002" Comparing "1108" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1109" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761152 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764135 ATOM PAIRS WERE FOUND FOR ATOM LIST 41838 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30301 from a total of 764135 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1109 -65.88510 3.45366 0.68582 INTE EXTERN> -28.48390 -37.40120 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8851" Parameter: A <- "-65.8851" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4839" Parameter: B <- "-28.4839" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4012" Parameter: C <- "-37.4012" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1109 TOTAL ENERGY = -65.8851 RDTITL> * VAN DER WAALS = -28.4839 ELECTROSTATIC = -37.4012 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1109" Parameter: CONF_N -> "8002" Comparing "1109" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1110" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764135 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767068 ATOM PAIRS WERE FOUND FOR ATOM LIST 42016 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30802 from a total of 767068 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1110 -64.82048 -1.06462 0.54197 INTE EXTERN> -32.58824 -32.23223 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8205" Parameter: A <- "-64.8205" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5882" Parameter: B <- "-32.5882" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2322" Parameter: C <- "-32.2322" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1110 TOTAL ENERGY = -64.8205 RDTITL> * VAN DER WAALS = -32.5882 ELECTROSTATIC = -32.2322 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1110" Parameter: CONF_N -> "8002" Comparing "1110" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1111" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767068 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766316 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30965 from a total of 766316 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1111 -66.51457 1.69410 0.66823 INTE EXTERN> -26.56152 -39.95306 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5146" Parameter: A <- "-66.5146" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5615" Parameter: B <- "-26.5615" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9531" Parameter: C <- "-39.9531" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1111 TOTAL ENERGY = -66.5146 RDTITL> * VAN DER WAALS = -26.5615 ELECTROSTATIC = -39.9531 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1111" Parameter: CONF_N -> "8002" Comparing "1111" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1112" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766316 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760232 ATOM PAIRS WERE FOUND FOR ATOM LIST 41785 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30524 from a total of 760232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1112 -63.77851 -2.73606 0.63070 INTE EXTERN> -26.70269 -37.07582 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7785" Parameter: A <- "-63.7785" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7027" Parameter: B <- "-26.7027" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0758" Parameter: C <- "-37.0758" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1112 TOTAL ENERGY = -63.7785 RDTITL> * VAN DER WAALS = -26.7027 ELECTROSTATIC = -37.0758 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1112" Parameter: CONF_N -> "8002" Comparing "1112" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1113" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767136 ATOM PAIRS WERE FOUND FOR ATOM LIST 42128 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30166 from a total of 767136 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1113 -61.21920 -2.55931 0.57086 INTE EXTERN> -29.03887 -32.18033 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.2192" Parameter: A <- "-61.2192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0389" Parameter: B <- "-29.0389" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.1803" Parameter: C <- "-32.1803" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1113 TOTAL ENERGY = -61.2192 RDTITL> * VAN DER WAALS = -29.0389 ELECTROSTATIC = -32.1803 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1113" Parameter: CONF_N -> "8002" Comparing "1113" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1114" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767136 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764358 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29990 from a total of 764358 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1114 -68.46056 7.24137 0.76149 INTE EXTERN> -24.11138 -44.34918 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4606" Parameter: A <- "-68.4606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1114" Parameter: B <- "-24.1114" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3492" Parameter: C <- "-44.3492" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1114 TOTAL ENERGY = -68.4606 RDTITL> * VAN DER WAALS = -24.1114 ELECTROSTATIC = -44.3492 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1114" Parameter: CONF_N -> "8002" Comparing "1114" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1115" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764358 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762398 ATOM PAIRS WERE FOUND FOR ATOM LIST 41990 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29707 from a total of 762398 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1115 -65.60569 -2.85488 0.54687 INTE EXTERN> -31.08043 -34.52525 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6057" Parameter: A <- "-65.6057" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0804" Parameter: B <- "-31.0804" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5253" Parameter: C <- "-34.5253" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1115 TOTAL ENERGY = -65.6057 RDTITL> * VAN DER WAALS = -31.0804 ELECTROSTATIC = -34.5253 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1115" Parameter: CONF_N -> "8002" Comparing "1115" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1116" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762398 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769829 ATOM PAIRS WERE FOUND FOR ATOM LIST 42396 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30436 from a total of 769829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1116 -70.58263 4.97694 0.72794 INTE EXTERN> -25.65216 -44.93047 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5826" Parameter: A <- "-70.5826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6522" Parameter: B <- "-25.6522" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9305" Parameter: C <- "-44.9305" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1116 TOTAL ENERGY = -70.5826 RDTITL> * VAN DER WAALS = -25.6522 ELECTROSTATIC = -44.9305 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1116" Parameter: CONF_N -> "8002" Comparing "1116" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1117" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756270 ATOM PAIRS WERE FOUND FOR ATOM LIST 41656 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29786 from a total of 756270 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1117 -64.35127 -6.23135 0.52568 INTE EXTERN> -33.71896 -30.63232 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3513" Parameter: A <- "-64.3513" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.719" Parameter: B <- "-33.719" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.6323" Parameter: C <- "-30.6323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1117 TOTAL ENERGY = -64.3513 RDTITL> * VAN DER WAALS = -33.719 ELECTROSTATIC = -30.6323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1117" Parameter: CONF_N -> "8002" Comparing "1117" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1118" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756270 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763310 ATOM PAIRS WERE FOUND FOR ATOM LIST 41878 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29215 from a total of 763310 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1118 -65.55122 1.19994 0.64531 INTE EXTERN> -25.05558 -40.49563 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5512" Parameter: A <- "-65.5512" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0556" Parameter: B <- "-25.0556" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4956" Parameter: C <- "-40.4956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1118 TOTAL ENERGY = -65.5512 RDTITL> * VAN DER WAALS = -25.0556 ELECTROSTATIC = -40.4956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1118" Parameter: CONF_N -> "8002" Comparing "1118" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1119" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763310 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760056 ATOM PAIRS WERE FOUND FOR ATOM LIST 41612 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29721 from a total of 760056 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1119 -62.91650 -2.63472 0.73934 INTE EXTERN> -26.25923 -36.65727 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9165" Parameter: A <- "-62.9165" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2592" Parameter: B <- "-26.2592" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6573" Parameter: C <- "-36.6573" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1119 TOTAL ENERGY = -62.9165 RDTITL> * VAN DER WAALS = -26.2592 ELECTROSTATIC = -36.6573 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1119" Parameter: CONF_N -> "8002" Comparing "1119" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1120" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760056 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765363 ATOM PAIRS WERE FOUND FOR ATOM LIST 41945 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29844 from a total of 765363 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1120 -68.00052 5.08402 0.57976 INTE EXTERN> -31.78563 -36.21489 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0005" Parameter: A <- "-68.0005" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7856" Parameter: B <- "-31.7856" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2149" Parameter: C <- "-36.2149" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1120 TOTAL ENERGY = -68.0005 RDTITL> * VAN DER WAALS = -31.7856 ELECTROSTATIC = -36.2149 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1120" Parameter: CONF_N -> "8002" Comparing "1120" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1121" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765363 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762411 ATOM PAIRS WERE FOUND FOR ATOM LIST 41979 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30084 from a total of 762411 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1121 -58.71996 -9.28056 0.64690 INTE EXTERN> -27.47836 -31.24160 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.72" Parameter: A <- "-58.72" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4784" Parameter: B <- "-27.4784" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.2416" Parameter: C <- "-31.2416" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1121 TOTAL ENERGY = -58.72 RDTITL> * VAN DER WAALS = -27.4784 ELECTROSTATIC = -31.2416 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1121" Parameter: CONF_N -> "8002" Comparing "1121" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1122" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762411 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762615 ATOM PAIRS WERE FOUND FOR ATOM LIST 41740 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30604 from a total of 762615 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1122 -62.53538 3.81542 0.60286 INTE EXTERN> -28.86331 -33.67207 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5354" Parameter: A <- "-62.5354" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8633" Parameter: B <- "-28.8633" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6721" Parameter: C <- "-33.6721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1122 TOTAL ENERGY = -62.5354 RDTITL> * VAN DER WAALS = -28.8633 ELECTROSTATIC = -33.6721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1122" Parameter: CONF_N -> "8002" Comparing "1122" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1123" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762615 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763044 ATOM PAIRS WERE FOUND FOR ATOM LIST 41929 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29861 from a total of 763044 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1123 -63.99182 1.45644 0.67592 INTE EXTERN> -26.70479 -37.28704 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.9918" Parameter: A <- "-63.9918" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7048" Parameter: B <- "-26.7048" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.287" Parameter: C <- "-37.287" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1123 TOTAL ENERGY = -63.9918 RDTITL> * VAN DER WAALS = -26.7048 ELECTROSTATIC = -37.287 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1123" Parameter: CONF_N -> "8002" Comparing "1123" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1124" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763044 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762234 ATOM PAIRS WERE FOUND FOR ATOM LIST 41773 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29957 from a total of 762234 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1124 -68.37999 4.38816 0.63648 INTE EXTERN> -30.14158 -38.23841 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.38" Parameter: A <- "-68.38" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1416" Parameter: B <- "-30.1416" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2384" Parameter: C <- "-38.2384" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1124 TOTAL ENERGY = -68.38 RDTITL> * VAN DER WAALS = -30.1416 ELECTROSTATIC = -38.2384 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1124" Parameter: CONF_N -> "8002" Comparing "1124" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1125" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762234 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761379 ATOM PAIRS WERE FOUND FOR ATOM LIST 41974 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30186 from a total of 761379 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1125 -58.40270 -9.97728 0.59503 INTE EXTERN> -28.67708 -29.72562 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.4027" Parameter: A <- "-58.4027" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6771" Parameter: B <- "-28.6771" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.7256" Parameter: C <- "-29.7256" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1125 TOTAL ENERGY = -58.4027 RDTITL> * VAN DER WAALS = -28.6771 ELECTROSTATIC = -29.7256 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1125" Parameter: CONF_N -> "8002" Comparing "1125" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1126" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761379 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757052 ATOM PAIRS WERE FOUND FOR ATOM LIST 41644 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29539 from a total of 757052 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1126 -64.88163 6.47893 0.53469 INTE EXTERN> -32.01620 -32.86543 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8816" Parameter: A <- "-64.8816" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0162" Parameter: B <- "-32.0162" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.8654" Parameter: C <- "-32.8654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1126 TOTAL ENERGY = -64.8816 RDTITL> * VAN DER WAALS = -32.0162 ELECTROSTATIC = -32.8654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1126" Parameter: CONF_N -> "8002" Comparing "1126" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1127" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757052 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759072 ATOM PAIRS WERE FOUND FOR ATOM LIST 41799 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30373 from a total of 759072 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1127 -65.24383 0.36219 0.76562 INTE EXTERN> -26.32776 -38.91607 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2438" Parameter: A <- "-65.2438" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3278" Parameter: B <- "-26.3278" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9161" Parameter: C <- "-38.9161" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1127 TOTAL ENERGY = -65.2438 RDTITL> * VAN DER WAALS = -26.3278 ELECTROSTATIC = -38.9161 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1127" Parameter: CONF_N -> "8002" Comparing "1127" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1128" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759072 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762548 ATOM PAIRS WERE FOUND FOR ATOM LIST 41906 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30043 from a total of 762548 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1128 -68.20177 2.95795 0.80332 INTE EXTERN> -24.38596 -43.81581 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2018" Parameter: A <- "-68.2018" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.386" Parameter: B <- "-24.386" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8158" Parameter: C <- "-43.8158" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1128 TOTAL ENERGY = -68.2018 RDTITL> * VAN DER WAALS = -24.386 ELECTROSTATIC = -43.8158 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1128" Parameter: CONF_N -> "8002" Comparing "1128" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1129" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762548 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758468 ATOM PAIRS WERE FOUND FOR ATOM LIST 41775 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29401 from a total of 758468 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1129 -68.23593 0.03416 0.61453 INTE EXTERN> -31.24295 -36.99298 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2359" Parameter: A <- "-68.2359" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2429" Parameter: B <- "-31.2429" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.993" Parameter: C <- "-36.993" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1129 TOTAL ENERGY = -68.2359 RDTITL> * VAN DER WAALS = -31.2429 ELECTROSTATIC = -36.993 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1129" Parameter: CONF_N -> "8002" Comparing "1129" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1130" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758468 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757514 ATOM PAIRS WERE FOUND FOR ATOM LIST 41777 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29287 from a total of 757514 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1130 -59.85871 -8.37722 0.69650 INTE EXTERN> -26.59256 -33.26615 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.8587" Parameter: A <- "-59.8587" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5926" Parameter: B <- "-26.5926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2662" Parameter: C <- "-33.2662" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1130 TOTAL ENERGY = -59.8587 RDTITL> * VAN DER WAALS = -26.5926 ELECTROSTATIC = -33.2662 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1130" Parameter: CONF_N -> "8002" Comparing "1130" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1131" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757514 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757564 ATOM PAIRS WERE FOUND FOR ATOM LIST 41667 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29498 from a total of 757564 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1131 -63.30319 3.44448 0.56659 INTE EXTERN> -30.44111 -32.86208 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3032" Parameter: A <- "-63.3032" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4411" Parameter: B <- "-30.4411" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.8621" Parameter: C <- "-32.8621" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1131 TOTAL ENERGY = -63.3032 RDTITL> * VAN DER WAALS = -30.4411 ELECTROSTATIC = -32.8621 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1131" Parameter: CONF_N -> "8002" Comparing "1131" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1132" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757564 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758280 ATOM PAIRS WERE FOUND FOR ATOM LIST 41878 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30404 from a total of 758280 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1132 -62.04240 -1.26079 0.59721 INTE EXTERN> -27.79618 -34.24623 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.0424" Parameter: A <- "-62.0424" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7962" Parameter: B <- "-27.7962" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2462" Parameter: C <- "-34.2462" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1132 TOTAL ENERGY = -62.0424 RDTITL> * VAN DER WAALS = -27.7962 ELECTROSTATIC = -34.2462 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1132" Parameter: CONF_N -> "8002" Comparing "1132" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1133" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758280 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762834 ATOM PAIRS WERE FOUND FOR ATOM LIST 42040 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30405 from a total of 762834 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1133 -70.83320 8.79080 0.55291 INTE EXTERN> -33.66912 -37.16408 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8332" Parameter: A <- "-70.8332" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6691" Parameter: B <- "-33.6691" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1641" Parameter: C <- "-37.1641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1133 TOTAL ENERGY = -70.8332 RDTITL> * VAN DER WAALS = -33.6691 ELECTROSTATIC = -37.1641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1133" Parameter: CONF_N -> "8002" Comparing "1133" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1134" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762834 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764901 ATOM PAIRS WERE FOUND FOR ATOM LIST 42075 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29871 from a total of 764901 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1134 -69.30075 -1.53245 0.70117 INTE EXTERN> -28.57459 -40.72616 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3008" Parameter: A <- "-69.3008" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5746" Parameter: B <- "-28.5746" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7262" Parameter: C <- "-40.7262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1134 TOTAL ENERGY = -69.3008 RDTITL> * VAN DER WAALS = -28.5746 ELECTROSTATIC = -40.7262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1134" Parameter: CONF_N -> "8002" Comparing "1134" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1135" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764901 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764762 ATOM PAIRS WERE FOUND FOR ATOM LIST 42119 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29815 from a total of 764762 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1135 -61.69533 -7.60542 0.64591 INTE EXTERN> -29.01467 -32.68066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.6953" Parameter: A <- "-61.6953" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0147" Parameter: B <- "-29.0147" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.6807" Parameter: C <- "-32.6807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1135 TOTAL ENERGY = -61.6953 RDTITL> * VAN DER WAALS = -29.0147 ELECTROSTATIC = -32.6807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1135" Parameter: CONF_N -> "8002" Comparing "1135" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1136" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764762 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765022 ATOM PAIRS WERE FOUND FOR ATOM LIST 42136 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29589 from a total of 765022 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1136 -66.89677 5.20144 0.57749 INTE EXTERN> -33.02282 -33.87395 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8968" Parameter: A <- "-66.8968" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0228" Parameter: B <- "-33.0228" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8739" Parameter: C <- "-33.8739" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1136 TOTAL ENERGY = -66.8968 RDTITL> * VAN DER WAALS = -33.0228 ELECTROSTATIC = -33.8739 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1136" Parameter: CONF_N -> "8002" Comparing "1136" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1137" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765022 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766147 ATOM PAIRS WERE FOUND FOR ATOM LIST 42134 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29835 from a total of 766147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1137 -59.25452 -7.64225 0.55084 INTE EXTERN> -30.11288 -29.14164 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.2545" Parameter: A <- "-59.2545" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1129" Parameter: B <- "-30.1129" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.1416" Parameter: C <- "-29.1416" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1137 TOTAL ENERGY = -59.2545 RDTITL> * VAN DER WAALS = -30.1129 ELECTROSTATIC = -29.1416 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1137" Parameter: CONF_N -> "8002" Comparing "1137" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1138" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763759 ATOM PAIRS WERE FOUND FOR ATOM LIST 41977 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30307 from a total of 763759 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1138 -58.91862 -0.33590 0.57528 INTE EXTERN> -30.98088 -27.93774 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.9186" Parameter: A <- "-58.9186" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9809" Parameter: B <- "-30.9809" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.9377" Parameter: C <- "-27.9377" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1138 TOTAL ENERGY = -58.9186 RDTITL> * VAN DER WAALS = -30.9809 ELECTROSTATIC = -27.9377 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1138" Parameter: CONF_N -> "8002" Comparing "1138" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1139" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763759 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756712 ATOM PAIRS WERE FOUND FOR ATOM LIST 41493 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29674 from a total of 756712 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1139 -64.33101 5.41239 0.68757 INTE EXTERN> -25.91509 -38.41592 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.331" Parameter: A <- "-64.331" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9151" Parameter: B <- "-25.9151" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4159" Parameter: C <- "-38.4159" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1139 TOTAL ENERGY = -64.331 RDTITL> * VAN DER WAALS = -25.9151 ELECTROSTATIC = -38.4159 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1139" Parameter: CONF_N -> "8002" Comparing "1139" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1140" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756712 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759141 ATOM PAIRS WERE FOUND FOR ATOM LIST 41874 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29645 from a total of 759141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1140 -61.90086 -2.43015 0.62896 INTE EXTERN> -27.80482 -34.09604 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.9009" Parameter: A <- "-61.9009" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8048" Parameter: B <- "-27.8048" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.096" Parameter: C <- "-34.096" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1140 TOTAL ENERGY = -61.9009 RDTITL> * VAN DER WAALS = -27.8048 ELECTROSTATIC = -34.096 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1140" Parameter: CONF_N -> "8002" Comparing "1140" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1141" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759156 ATOM PAIRS WERE FOUND FOR ATOM LIST 41759 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29245 from a total of 759156 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1141 -62.32466 0.42380 0.72850 INTE EXTERN> -25.20134 -37.12332 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3247" Parameter: A <- "-62.3247" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2013" Parameter: B <- "-25.2013" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1233" Parameter: C <- "-37.1233" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1141 TOTAL ENERGY = -62.3247 RDTITL> * VAN DER WAALS = -25.2013 ELECTROSTATIC = -37.1233 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1141" Parameter: CONF_N -> "8002" Comparing "1141" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1142" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759156 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761472 ATOM PAIRS WERE FOUND FOR ATOM LIST 41961 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29365 from a total of 761472 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1142 -63.60983 1.28517 0.65218 INTE EXTERN> -25.87905 -37.73078 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6098" Parameter: A <- "-63.6098" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.879" Parameter: B <- "-25.879" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7308" Parameter: C <- "-37.7308" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1142 TOTAL ENERGY = -63.6098 RDTITL> * VAN DER WAALS = -25.879 ELECTROSTATIC = -37.7308 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1142" Parameter: CONF_N -> "8002" Comparing "1142" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1143" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761472 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768618 ATOM PAIRS WERE FOUND FOR ATOM LIST 42370 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30274 from a total of 768618 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1143 -62.55034 -1.05949 0.56061 INTE EXTERN> -28.49168 -34.05866 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5503" Parameter: A <- "-62.5503" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4917" Parameter: B <- "-28.4917" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.0587" Parameter: C <- "-34.0587" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1143 TOTAL ENERGY = -62.5503 RDTITL> * VAN DER WAALS = -28.4917 ELECTROSTATIC = -34.0587 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1143" Parameter: CONF_N -> "8002" Comparing "1143" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1144" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768618 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766682 ATOM PAIRS WERE FOUND FOR ATOM LIST 42177 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29999 from a total of 766682 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1144 -57.28066 -5.26968 0.79348 INTE EXTERN> -21.20946 -36.07120 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.2807" Parameter: A <- "-57.2807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.2095" Parameter: B <- "-21.2095" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0712" Parameter: C <- "-36.0712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1144 TOTAL ENERGY = -57.2807 RDTITL> * VAN DER WAALS = -21.2095 ELECTROSTATIC = -36.0712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1144" Parameter: CONF_N -> "8002" Comparing "1144" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1145" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766682 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756161 ATOM PAIRS WERE FOUND FOR ATOM LIST 41750 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28847 from a total of 756161 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1145 -57.20645 -0.07421 0.55091 INTE EXTERN> -28.18855 -29.01790 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.2064" Parameter: A <- "-57.2064" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1885" Parameter: B <- "-28.1885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.0179" Parameter: C <- "-29.0179" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1145 TOTAL ENERGY = -57.2064 RDTITL> * VAN DER WAALS = -28.1885 ELECTROSTATIC = -29.0179 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1145" Parameter: CONF_N -> "8002" Comparing "1145" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1146" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756161 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762886 ATOM PAIRS WERE FOUND FOR ATOM LIST 41908 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29906 from a total of 762886 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1146 -61.56907 4.36262 0.80479 INTE EXTERN> -19.90184 -41.66723 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.5691" Parameter: A <- "-61.5691" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-19.9018" Parameter: B <- "-19.9018" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6672" Parameter: C <- "-41.6672" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1146 TOTAL ENERGY = -61.5691 RDTITL> * VAN DER WAALS = -19.9018 ELECTROSTATIC = -41.6672 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1146" Parameter: CONF_N -> "8002" Comparing "1146" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1147" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762886 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765643 ATOM PAIRS WERE FOUND FOR ATOM LIST 42099 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30368 from a total of 765643 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1147 -62.55056 0.98149 0.68684 INTE EXTERN> -27.71752 -34.83304 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5506" Parameter: A <- "-62.5506" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7175" Parameter: B <- "-27.7175" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.833" Parameter: C <- "-34.833" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1147 TOTAL ENERGY = -62.5506 RDTITL> * VAN DER WAALS = -27.7175 ELECTROSTATIC = -34.833 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1147" Parameter: CONF_N -> "8002" Comparing "1147" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1148" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765643 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761856 ATOM PAIRS WERE FOUND FOR ATOM LIST 41825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29360 from a total of 761856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1148 -63.13014 0.57958 0.60572 INTE EXTERN> -28.72963 -34.40051 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1301" Parameter: A <- "-63.1301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7296" Parameter: B <- "-28.7296" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4005" Parameter: C <- "-34.4005" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1148 TOTAL ENERGY = -63.1301 RDTITL> * VAN DER WAALS = -28.7296 ELECTROSTATIC = -34.4005 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1148" Parameter: CONF_N -> "8002" Comparing "1148" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1149" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760074 ATOM PAIRS WERE FOUND FOR ATOM LIST 41710 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29566 from a total of 760074 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1149 -65.70463 2.57449 0.56832 INTE EXTERN> -33.30501 -32.39962 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7046" Parameter: A <- "-65.7046" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.305" Parameter: B <- "-33.305" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.3996" Parameter: C <- "-32.3996" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1149 TOTAL ENERGY = -65.7046 RDTITL> * VAN DER WAALS = -33.305 ELECTROSTATIC = -32.3996 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1149" Parameter: CONF_N -> "8002" Comparing "1149" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1150" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760074 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41568 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30110 from a total of 760601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1150 -61.19793 -4.50670 0.62396 INTE EXTERN> -28.37961 -32.81832 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.1979" Parameter: A <- "-61.1979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3796" Parameter: B <- "-28.3796" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.8183" Parameter: C <- "-32.8183" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1150 TOTAL ENERGY = -61.1979 RDTITL> * VAN DER WAALS = -28.3796 ELECTROSTATIC = -32.8183 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1150" Parameter: CONF_N -> "8002" Comparing "1150" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1151" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760820 ATOM PAIRS WERE FOUND FOR ATOM LIST 41672 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30008 from a total of 760820 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1151 -68.28042 7.08249 0.68240 INTE EXTERN> -28.23349 -40.04693 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2804" Parameter: A <- "-68.2804" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2335" Parameter: B <- "-28.2335" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0469" Parameter: C <- "-40.0469" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1151 TOTAL ENERGY = -68.2804 RDTITL> * VAN DER WAALS = -28.2335 ELECTROSTATIC = -40.0469 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1151" Parameter: CONF_N -> "8002" Comparing "1151" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1152" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760820 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764780 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30298 from a total of 764780 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1152 -65.92575 -2.35467 0.75388 INTE EXTERN> -23.17906 -42.74669 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9258" Parameter: A <- "-65.9258" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.1791" Parameter: B <- "-23.1791" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7467" Parameter: C <- "-42.7467" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1152 TOTAL ENERGY = -65.9258 RDTITL> * VAN DER WAALS = -23.1791 ELECTROSTATIC = -42.7467 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1152" Parameter: CONF_N -> "8002" Comparing "1152" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1153" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764780 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755706 ATOM PAIRS WERE FOUND FOR ATOM LIST 41487 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29977 from a total of 755706 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1153 -61.55240 -4.37335 0.78391 INTE EXTERN> -23.02870 -38.52371 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.5524" Parameter: A <- "-61.5524" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.0287" Parameter: B <- "-23.0287" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5237" Parameter: C <- "-38.5237" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1153 TOTAL ENERGY = -61.5524 RDTITL> * VAN DER WAALS = -23.0287 ELECTROSTATIC = -38.5237 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1153" Parameter: CONF_N -> "8002" Comparing "1153" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1154" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755706 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755400 ATOM PAIRS WERE FOUND FOR ATOM LIST 41460 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29536 from a total of 755400 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1154 -62.51884 0.96644 0.74142 INTE EXTERN> -24.87882 -37.64002 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5188" Parameter: A <- "-62.5188" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8788" Parameter: B <- "-24.8788" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.64" Parameter: C <- "-37.64" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1154 TOTAL ENERGY = -62.5188 RDTITL> * VAN DER WAALS = -24.8788 ELECTROSTATIC = -37.64 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1154" Parameter: CONF_N -> "8002" Comparing "1154" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1155" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755400 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762453 ATOM PAIRS WERE FOUND FOR ATOM LIST 41848 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29774 from a total of 762453 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1155 -68.74683 6.22799 0.61234 INTE EXTERN> -28.47952 -40.26732 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7468" Parameter: A <- "-68.7468" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4795" Parameter: B <- "-28.4795" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2673" Parameter: C <- "-40.2673" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1155 TOTAL ENERGY = -68.7468 RDTITL> * VAN DER WAALS = -28.4795 ELECTROSTATIC = -40.2673 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1155" Parameter: CONF_N -> "8002" Comparing "1155" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1156" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762453 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755604 ATOM PAIRS WERE FOUND FOR ATOM LIST 41518 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29292 from a total of 755604 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1156 -66.99584 -1.75100 0.59977 INTE EXTERN> -29.62281 -37.37303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9958" Parameter: A <- "-66.9958" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6228" Parameter: B <- "-29.6228" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.373" Parameter: C <- "-37.373" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1156 TOTAL ENERGY = -66.9958 RDTITL> * VAN DER WAALS = -29.6228 ELECTROSTATIC = -37.373 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1156" Parameter: CONF_N -> "8002" Comparing "1156" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1157" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755604 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759726 ATOM PAIRS WERE FOUND FOR ATOM LIST 41689 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29638 from a total of 759726 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1157 -62.63121 -4.36463 0.55407 INTE EXTERN> -29.43446 -33.19674 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.6312" Parameter: A <- "-62.6312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4345" Parameter: B <- "-29.4345" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1967" Parameter: C <- "-33.1967" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1157 TOTAL ENERGY = -62.6312 RDTITL> * VAN DER WAALS = -29.4345 ELECTROSTATIC = -33.1967 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1157" Parameter: CONF_N -> "8002" Comparing "1157" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1158" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759726 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756134 ATOM PAIRS WERE FOUND FOR ATOM LIST 41341 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29749 from a total of 756134 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1158 -62.05682 -0.57439 0.70659 INTE EXTERN> -24.69574 -37.36108 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.0568" Parameter: A <- "-62.0568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6957" Parameter: B <- "-24.6957" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3611" Parameter: C <- "-37.3611" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1158 TOTAL ENERGY = -62.0568 RDTITL> * VAN DER WAALS = -24.6957 ELECTROSTATIC = -37.3611 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1158" Parameter: CONF_N -> "8002" Comparing "1158" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1159" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756134 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758575 ATOM PAIRS WERE FOUND FOR ATOM LIST 41723 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29762 from a total of 758575 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1159 -59.18660 -2.87022 0.71407 INTE EXTERN> -21.56350 -37.62310 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.1866" Parameter: A <- "-59.1866" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.5635" Parameter: B <- "-21.5635" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6231" Parameter: C <- "-37.6231" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1159 TOTAL ENERGY = -59.1866 RDTITL> * VAN DER WAALS = -21.5635 ELECTROSTATIC = -37.6231 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1159" Parameter: CONF_N -> "8002" Comparing "1159" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1160" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758575 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756556 ATOM PAIRS WERE FOUND FOR ATOM LIST 41580 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29078 from a total of 756556 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1160 -65.57021 6.38361 0.62661 INTE EXTERN> -26.93235 -38.63787 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5702" Parameter: A <- "-65.5702" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9323" Parameter: B <- "-26.9323" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6379" Parameter: C <- "-38.6379" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1160 TOTAL ENERGY = -65.5702 RDTITL> * VAN DER WAALS = -26.9323 ELECTROSTATIC = -38.6379 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1160" Parameter: CONF_N -> "8002" Comparing "1160" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1161" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756556 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753939 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29549 from a total of 753939 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1161 -63.72357 -1.84664 0.62615 INTE EXTERN> -27.22126 -36.50231 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7236" Parameter: A <- "-63.7236" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2213" Parameter: B <- "-27.2213" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5023" Parameter: C <- "-36.5023" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1161 TOTAL ENERGY = -63.7236 RDTITL> * VAN DER WAALS = -27.2213 ELECTROSTATIC = -36.5023 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1161" Parameter: CONF_N -> "8002" Comparing "1161" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1162" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753939 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751874 ATOM PAIRS WERE FOUND FOR ATOM LIST 41396 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29217 from a total of 751874 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1162 -66.77223 3.04866 0.60086 INTE EXTERN> -26.83576 -39.93648 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7722" Parameter: A <- "-66.7722" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8358" Parameter: B <- "-26.8358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9365" Parameter: C <- "-39.9365" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1162 TOTAL ENERGY = -66.7722 RDTITL> * VAN DER WAALS = -26.8358 ELECTROSTATIC = -39.9365 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1162" Parameter: CONF_N -> "8002" Comparing "1162" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1163" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751874 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756620 ATOM PAIRS WERE FOUND FOR ATOM LIST 41508 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29217 from a total of 756620 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1163 -67.50593 0.73369 0.61059 INTE EXTERN> -29.25069 -38.25524 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5059" Parameter: A <- "-67.5059" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2507" Parameter: B <- "-29.2507" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2552" Parameter: C <- "-38.2552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1163 TOTAL ENERGY = -67.5059 RDTITL> * VAN DER WAALS = -29.2507 ELECTROSTATIC = -38.2552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1163" Parameter: CONF_N -> "8002" Comparing "1163" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1164" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756620 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754804 ATOM PAIRS WERE FOUND FOR ATOM LIST 41364 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29609 from a total of 754804 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1164 -65.70338 -1.80254 0.57000 INTE EXTERN> -29.86287 -35.84052 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7034" Parameter: A <- "-65.7034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8629" Parameter: B <- "-29.8629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8405" Parameter: C <- "-35.8405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1164 TOTAL ENERGY = -65.7034 RDTITL> * VAN DER WAALS = -29.8629 ELECTROSTATIC = -35.8405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1164" Parameter: CONF_N -> "8002" Comparing "1164" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1165" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754804 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758499 ATOM PAIRS WERE FOUND FOR ATOM LIST 41749 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29775 from a total of 758499 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1165 -62.54810 -3.15529 0.66608 INTE EXTERN> -26.82876 -35.71934 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5481" Parameter: A <- "-62.5481" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8288" Parameter: B <- "-26.8288" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7193" Parameter: C <- "-35.7193" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1165 TOTAL ENERGY = -62.5481 RDTITL> * VAN DER WAALS = -26.8288 ELECTROSTATIC = -35.7193 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1165" Parameter: CONF_N -> "8002" Comparing "1165" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1166" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758499 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761676 ATOM PAIRS WERE FOUND FOR ATOM LIST 41982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29693 from a total of 761676 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1166 -66.08255 3.53445 0.69349 INTE EXTERN> -23.22779 -42.85476 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0825" Parameter: A <- "-66.0825" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.2278" Parameter: B <- "-23.2278" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8548" Parameter: C <- "-42.8548" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1166 TOTAL ENERGY = -66.0825 RDTITL> * VAN DER WAALS = -23.2278 ELECTROSTATIC = -42.8548 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1166" Parameter: CONF_N -> "8002" Comparing "1166" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1167" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761676 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757398 ATOM PAIRS WERE FOUND FOR ATOM LIST 41680 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29347 from a total of 757398 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1167 -68.94147 2.85892 0.71680 INTE EXTERN> -25.38730 -43.55416 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9415" Parameter: A <- "-68.9415" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3873" Parameter: B <- "-25.3873" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5542" Parameter: C <- "-43.5542" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1167 TOTAL ENERGY = -68.9415 RDTITL> * VAN DER WAALS = -25.3873 ELECTROSTATIC = -43.5542 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1167" Parameter: CONF_N -> "8002" Comparing "1167" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1168" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757398 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762639 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29273 from a total of 762639 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1168 -61.87844 -7.06303 0.78549 INTE EXTERN> -23.98115 -37.89729 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.8784" Parameter: A <- "-61.8784" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9812" Parameter: B <- "-23.9812" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8973" Parameter: C <- "-37.8973" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1168 TOTAL ENERGY = -61.8784 RDTITL> * VAN DER WAALS = -23.9812 ELECTROSTATIC = -37.8973 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1168" Parameter: CONF_N -> "8002" Comparing "1168" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1169" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762639 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766619 ATOM PAIRS WERE FOUND FOR ATOM LIST 42249 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28968 from a total of 766619 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1169 -63.26915 1.39071 0.64165 INTE EXTERN> -26.59883 -36.67032 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.2692" Parameter: A <- "-63.2692" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5988" Parameter: B <- "-26.5988" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6703" Parameter: C <- "-36.6703" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1169 TOTAL ENERGY = -63.2692 RDTITL> * VAN DER WAALS = -26.5988 ELECTROSTATIC = -36.6703 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1169" Parameter: CONF_N -> "8002" Comparing "1169" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1170" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766619 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755906 ATOM PAIRS WERE FOUND FOR ATOM LIST 41570 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29296 from a total of 755906 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1170 -62.52435 -0.74480 0.71216 INTE EXTERN> -24.85708 -37.66727 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5244" Parameter: A <- "-62.5244" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8571" Parameter: B <- "-24.8571" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6673" Parameter: C <- "-37.6673" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1170 TOTAL ENERGY = -62.5244 RDTITL> * VAN DER WAALS = -24.8571 ELECTROSTATIC = -37.6673 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1170" Parameter: CONF_N -> "8002" Comparing "1170" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1171" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755906 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764839 ATOM PAIRS WERE FOUND FOR ATOM LIST 41962 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29622 from a total of 764839 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1171 -65.74675 3.22240 0.55710 INTE EXTERN> -30.94147 -34.80528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7467" Parameter: A <- "-65.7467" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9415" Parameter: B <- "-30.9415" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8053" Parameter: C <- "-34.8053" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1171 TOTAL ENERGY = -65.7467 RDTITL> * VAN DER WAALS = -30.9415 ELECTROSTATIC = -34.8053 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1171" Parameter: CONF_N -> "8002" Comparing "1171" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1172" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764839 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759817 ATOM PAIRS WERE FOUND FOR ATOM LIST 41859 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29731 from a total of 759817 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1172 -64.02304 -1.72371 0.59678 INTE EXTERN> -27.15524 -36.86780 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.023" Parameter: A <- "-64.023" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1552" Parameter: B <- "-27.1552" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8678" Parameter: C <- "-36.8678" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1172 TOTAL ENERGY = -64.023 RDTITL> * VAN DER WAALS = -27.1552 ELECTROSTATIC = -36.8678 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1172" Parameter: CONF_N -> "8002" Comparing "1172" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1173" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759817 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765848 ATOM PAIRS WERE FOUND FOR ATOM LIST 42015 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29898 from a total of 765848 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1173 -67.61057 3.58753 0.74590 INTE EXTERN> -23.88628 -43.72429 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6106" Parameter: A <- "-67.6106" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8863" Parameter: B <- "-23.8863" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7243" Parameter: C <- "-43.7243" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1173 TOTAL ENERGY = -67.6106 RDTITL> * VAN DER WAALS = -23.8863 ELECTROSTATIC = -43.7243 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1173" Parameter: CONF_N -> "8002" Comparing "1173" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1174" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765848 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761031 ATOM PAIRS WERE FOUND FOR ATOM LIST 41786 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30008 from a total of 761031 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1174 -66.04355 -1.56701 0.67823 INTE EXTERN> -27.01395 -39.02960 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0436" Parameter: A <- "-66.0436" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.014" Parameter: B <- "-27.014" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0296" Parameter: C <- "-39.0296" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1174 TOTAL ENERGY = -66.0436 RDTITL> * VAN DER WAALS = -27.014 ELECTROSTATIC = -39.0296 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1174" Parameter: CONF_N -> "8002" Comparing "1174" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1175" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761031 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762553 ATOM PAIRS WERE FOUND FOR ATOM LIST 41683 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29732 from a total of 762553 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1175 -65.91172 -0.13184 0.76722 INTE EXTERN> -22.60743 -43.30428 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9117" Parameter: A <- "-65.9117" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.6074" Parameter: B <- "-22.6074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3043" Parameter: C <- "-43.3043" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1175 TOTAL ENERGY = -65.9117 RDTITL> * VAN DER WAALS = -22.6074 ELECTROSTATIC = -43.3043 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1175" Parameter: CONF_N -> "8002" Comparing "1175" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1176" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762553 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764416 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29570 from a total of 764416 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1176 -62.75866 -3.15306 0.66573 INTE EXTERN> -27.31663 -35.44203 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7587" Parameter: A <- "-62.7587" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3166" Parameter: B <- "-27.3166" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.442" Parameter: C <- "-35.442" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1176 TOTAL ENERGY = -62.7587 RDTITL> * VAN DER WAALS = -27.3166 ELECTROSTATIC = -35.442 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1176" Parameter: CONF_N -> "8002" Comparing "1176" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1177" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764416 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760673 ATOM PAIRS WERE FOUND FOR ATOM LIST 41682 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29856 from a total of 760673 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1177 -62.37552 -0.38314 0.66321 INTE EXTERN> -27.60338 -34.77214 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3755" Parameter: A <- "-62.3755" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6034" Parameter: B <- "-27.6034" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7721" Parameter: C <- "-34.7721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1177 TOTAL ENERGY = -62.3755 RDTITL> * VAN DER WAALS = -27.6034 ELECTROSTATIC = -34.7721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1177" Parameter: CONF_N -> "8002" Comparing "1177" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1178" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760673 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756416 ATOM PAIRS WERE FOUND FOR ATOM LIST 41516 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30193 from a total of 756416 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1178 -68.14542 5.76990 0.70688 INTE EXTERN> -25.32292 -42.82250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1454" Parameter: A <- "-68.1454" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3229" Parameter: B <- "-25.3229" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8225" Parameter: C <- "-42.8225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1178 TOTAL ENERGY = -68.1454 RDTITL> * VAN DER WAALS = -25.3229 ELECTROSTATIC = -42.8225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1178" Parameter: CONF_N -> "8002" Comparing "1178" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1179" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756416 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757453 ATOM PAIRS WERE FOUND FOR ATOM LIST 41603 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29620 from a total of 757453 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1179 -62.81184 -5.33358 0.60811 INTE EXTERN> -30.39879 -32.41305 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.8118" Parameter: A <- "-62.8118" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3988" Parameter: B <- "-30.3988" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.4131" Parameter: C <- "-32.4131" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1179 TOTAL ENERGY = -62.8118 RDTITL> * VAN DER WAALS = -30.3988 ELECTROSTATIC = -32.4131 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1179" Parameter: CONF_N -> "8002" Comparing "1179" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1180" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757453 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756666 ATOM PAIRS WERE FOUND FOR ATOM LIST 41513 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29743 from a total of 756666 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1180 -71.24440 8.43255 0.68168 INTE EXTERN> -27.18560 -44.05880 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2444" Parameter: A <- "-71.2444" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1856" Parameter: B <- "-27.1856" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0588" Parameter: C <- "-44.0588" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1180 TOTAL ENERGY = -71.2444 RDTITL> * VAN DER WAALS = -27.1856 ELECTROSTATIC = -44.0588 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1180" Parameter: CONF_N -> "8002" Comparing "1180" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1181" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756666 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762811 ATOM PAIRS WERE FOUND FOR ATOM LIST 41941 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29681 from a total of 762811 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1181 -63.97702 -7.26737 0.69173 INTE EXTERN> -26.78756 -37.18946 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.977" Parameter: A <- "-63.977" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7876" Parameter: B <- "-26.7876" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1895" Parameter: C <- "-37.1895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1181 TOTAL ENERGY = -63.977 RDTITL> * VAN DER WAALS = -26.7876 ELECTROSTATIC = -37.1895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1181" Parameter: CONF_N -> "8002" Comparing "1181" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1182" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762811 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767096 ATOM PAIRS WERE FOUND FOR ATOM LIST 42012 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30147 from a total of 767096 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1182 -60.49461 -3.48241 0.56393 INTE EXTERN> -28.58756 -31.90705 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.4946" Parameter: A <- "-60.4946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5876" Parameter: B <- "-28.5876" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.9071" Parameter: C <- "-31.9071" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1182 TOTAL ENERGY = -60.4946 RDTITL> * VAN DER WAALS = -28.5876 ELECTROSTATIC = -31.9071 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1182" Parameter: CONF_N -> "8002" Comparing "1182" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1183" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767096 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762074 ATOM PAIRS WERE FOUND FOR ATOM LIST 42066 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30356 from a total of 762074 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1183 -55.62573 -4.86888 0.66638 INTE EXTERN> -27.01256 -28.61317 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.6257" Parameter: A <- "-55.6257" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0126" Parameter: B <- "-27.0126" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.6132" Parameter: C <- "-28.6132" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1183 TOTAL ENERGY = -55.6257 RDTITL> * VAN DER WAALS = -27.0126 ELECTROSTATIC = -28.6132 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1183" Parameter: CONF_N -> "8002" Comparing "1183" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1184" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762074 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761618 ATOM PAIRS WERE FOUND FOR ATOM LIST 41987 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30012 from a total of 761618 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1184 -64.22965 8.60392 0.55118 INTE EXTERN> -30.74451 -33.48515 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2297" Parameter: A <- "-64.2297" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7445" Parameter: B <- "-30.7445" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.4851" Parameter: C <- "-33.4851" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1184 TOTAL ENERGY = -64.2297 RDTITL> * VAN DER WAALS = -30.7445 ELECTROSTATIC = -33.4851 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1184" Parameter: CONF_N -> "8002" Comparing "1184" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1185" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761618 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763689 ATOM PAIRS WERE FOUND FOR ATOM LIST 41977 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30380 from a total of 763689 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1185 -70.02996 5.80030 0.62799 INTE EXTERN> -31.49807 -38.53189 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.03" Parameter: A <- "-70.03" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4981" Parameter: B <- "-31.4981" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5319" Parameter: C <- "-38.5319" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1185 TOTAL ENERGY = -70.03 RDTITL> * VAN DER WAALS = -31.4981 ELECTROSTATIC = -38.5319 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1185" Parameter: CONF_N -> "8002" Comparing "1185" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1186" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763689 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767172 ATOM PAIRS WERE FOUND FOR ATOM LIST 42064 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30620 from a total of 767172 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1186 -65.68035 -4.34960 0.62098 INTE EXTERN> -29.33050 -36.34985 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6804" Parameter: A <- "-65.6804" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3305" Parameter: B <- "-29.3305" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3499" Parameter: C <- "-36.3499" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1186 TOTAL ENERGY = -65.6804 RDTITL> * VAN DER WAALS = -29.3305 ELECTROSTATIC = -36.3499 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1186" Parameter: CONF_N -> "8002" Comparing "1186" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1187" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767172 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764602 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30224 from a total of 764602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1187 -72.18399 6.50364 0.55525 INTE EXTERN> -33.83144 -38.35255 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.184" Parameter: A <- "-72.184" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8314" Parameter: B <- "-33.8314" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3526" Parameter: C <- "-38.3526" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1187 TOTAL ENERGY = -72.184 RDTITL> * VAN DER WAALS = -33.8314 ELECTROSTATIC = -38.3526 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1187" Parameter: CONF_N -> "8002" Comparing "1187" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1188" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764198 ATOM PAIRS WERE FOUND FOR ATOM LIST 41983 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30472 from a total of 764198 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1188 -66.57059 -5.61340 0.60379 INTE EXTERN> -29.72012 -36.85047 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5706" Parameter: A <- "-66.5706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7201" Parameter: B <- "-29.7201" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8505" Parameter: C <- "-36.8505" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1188 TOTAL ENERGY = -66.5706 RDTITL> * VAN DER WAALS = -29.7201 ELECTROSTATIC = -36.8505 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1188" Parameter: CONF_N -> "8002" Comparing "1188" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1189" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764198 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768083 ATOM PAIRS WERE FOUND FOR ATOM LIST 42079 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30670 from a total of 768083 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1189 -60.49958 -6.07101 0.55539 INTE EXTERN> -29.03419 -31.46539 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.4996" Parameter: A <- "-60.4996" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0342" Parameter: B <- "-29.0342" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4654" Parameter: C <- "-31.4654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1189 TOTAL ENERGY = -60.4996 RDTITL> * VAN DER WAALS = -29.0342 ELECTROSTATIC = -31.4654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1189" Parameter: CONF_N -> "8002" Comparing "1189" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1190" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768083 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765129 ATOM PAIRS WERE FOUND FOR ATOM LIST 41999 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30185 from a total of 765129 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1190 -67.28953 6.78995 0.64618 INTE EXTERN> -29.01367 -38.27587 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2895" Parameter: A <- "-67.2895" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0137" Parameter: B <- "-29.0137" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2759" Parameter: C <- "-38.2759" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1190 TOTAL ENERGY = -67.2895 RDTITL> * VAN DER WAALS = -29.0137 ELECTROSTATIC = -38.2759 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1190" Parameter: CONF_N -> "8002" Comparing "1190" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1191" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765129 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770142 ATOM PAIRS WERE FOUND FOR ATOM LIST 42409 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30379 from a total of 770142 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1191 -60.59639 -6.69314 0.46800 INTE EXTERN> -34.12125 -26.47514 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.5964" Parameter: A <- "-60.5964" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1213" Parameter: B <- "-34.1213" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-26.4751" Parameter: C <- "-26.4751" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1191 TOTAL ENERGY = -60.5964 RDTITL> * VAN DER WAALS = -34.1213 ELECTROSTATIC = -26.4751 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1191" Parameter: CONF_N -> "8002" Comparing "1191" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1192" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770142 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764145 ATOM PAIRS WERE FOUND FOR ATOM LIST 42098 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29946 from a total of 764145 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1192 -64.14841 3.55202 0.72455 INTE EXTERN> -27.98254 -36.16587 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1484" Parameter: A <- "-64.1484" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9825" Parameter: B <- "-27.9825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1659" Parameter: C <- "-36.1659" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1192 TOTAL ENERGY = -64.1484 RDTITL> * VAN DER WAALS = -27.9825 ELECTROSTATIC = -36.1659 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1192" Parameter: CONF_N -> "8002" Comparing "1192" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1193" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764145 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764432 ATOM PAIRS WERE FOUND FOR ATOM LIST 42077 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30425 from a total of 764432 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1193 -58.35517 -5.79324 0.67309 INTE EXTERN> -26.86682 -31.48836 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.3552" Parameter: A <- "-58.3552" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8668" Parameter: B <- "-26.8668" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4884" Parameter: C <- "-31.4884" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1193 TOTAL ENERGY = -58.3552 RDTITL> * VAN DER WAALS = -26.8668 ELECTROSTATIC = -31.4884 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1193" Parameter: CONF_N -> "8002" Comparing "1193" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1194" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764432 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762253 ATOM PAIRS WERE FOUND FOR ATOM LIST 41672 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30251 from a total of 762253 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1194 -64.08411 5.72893 0.68740 INTE EXTERN> -27.23930 -36.84481 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0841" Parameter: A <- "-64.0841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2393" Parameter: B <- "-27.2393" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8448" Parameter: C <- "-36.8448" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1194 TOTAL ENERGY = -64.0841 RDTITL> * VAN DER WAALS = -27.2393 ELECTROSTATIC = -36.8448 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1194" Parameter: CONF_N -> "8002" Comparing "1194" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1195" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762253 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758623 ATOM PAIRS WERE FOUND FOR ATOM LIST 41671 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30105 from a total of 758623 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1195 -61.69667 -2.38744 0.62128 INTE EXTERN> -31.30233 -30.39434 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.6967" Parameter: A <- "-61.6967" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3023" Parameter: B <- "-31.3023" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.3943" Parameter: C <- "-30.3943" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1195 TOTAL ENERGY = -61.6967 RDTITL> * VAN DER WAALS = -31.3023 ELECTROSTATIC = -30.3943 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1195" Parameter: CONF_N -> "8002" Comparing "1195" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1196" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758623 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761965 ATOM PAIRS WERE FOUND FOR ATOM LIST 41996 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30423 from a total of 761965 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1196 -63.25157 1.55490 0.72817 INTE EXTERN> -24.16711 -39.08446 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.2516" Parameter: A <- "-63.2516" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1671" Parameter: B <- "-24.1671" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0845" Parameter: C <- "-39.0845" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1196 TOTAL ENERGY = -63.2516 RDTITL> * VAN DER WAALS = -24.1671 ELECTROSTATIC = -39.0845 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1196" Parameter: CONF_N -> "8002" Comparing "1196" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1197" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761965 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763029 ATOM PAIRS WERE FOUND FOR ATOM LIST 41917 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30314 from a total of 763029 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1197 -67.20889 3.95732 0.58880 INTE EXTERN> -29.88541 -37.32348 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2089" Parameter: A <- "-67.2089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8854" Parameter: B <- "-29.8854" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3235" Parameter: C <- "-37.3235" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1197 TOTAL ENERGY = -67.2089 RDTITL> * VAN DER WAALS = -29.8854 ELECTROSTATIC = -37.3235 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1197" Parameter: CONF_N -> "8002" Comparing "1197" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1198" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763029 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762544 ATOM PAIRS WERE FOUND FOR ATOM LIST 41882 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29534 from a total of 762544 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1198 -60.93661 -6.27227 0.63418 INTE EXTERN> -28.44388 -32.49273 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.9366" Parameter: A <- "-60.9366" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4439" Parameter: B <- "-28.4439" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.4927" Parameter: C <- "-32.4927" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1198 TOTAL ENERGY = -60.9366 RDTITL> * VAN DER WAALS = -28.4439 ELECTROSTATIC = -32.4927 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1198" Parameter: CONF_N -> "8002" Comparing "1198" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1199" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762544 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760733 ATOM PAIRS WERE FOUND FOR ATOM LIST 41834 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29687 from a total of 760733 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1199 -60.90643 -0.03018 0.74473 INTE EXTERN> -24.66856 -36.23787 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.9064" Parameter: A <- "-60.9064" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6686" Parameter: B <- "-24.6686" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2379" Parameter: C <- "-36.2379" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1199 TOTAL ENERGY = -60.9064 RDTITL> * VAN DER WAALS = -24.6686 ELECTROSTATIC = -36.2379 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1199" Parameter: CONF_N -> "8002" Comparing "1199" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1200" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760733 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764176 ATOM PAIRS WERE FOUND FOR ATOM LIST 41941 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30294 from a total of 764176 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1200 -58.56972 -2.33671 0.69333 INTE EXTERN> -26.13667 -32.43305 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.5697" Parameter: A <- "-58.5697" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1367" Parameter: B <- "-26.1367" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.4331" Parameter: C <- "-32.4331" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1200 TOTAL ENERGY = -58.5697 RDTITL> * VAN DER WAALS = -26.1367 ELECTROSTATIC = -32.4331 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1200" Parameter: CONF_N -> "8002" Comparing "1200" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1201" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764176 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759995 ATOM PAIRS WERE FOUND FOR ATOM LIST 41749 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29447 from a total of 759995 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1201 -72.93056 14.36084 0.61684 INTE EXTERN> -31.11008 -41.82048 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9306" Parameter: A <- "-72.9306" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1101" Parameter: B <- "-31.1101" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8205" Parameter: C <- "-41.8205" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1201 TOTAL ENERGY = -72.9306 RDTITL> * VAN DER WAALS = -31.1101 ELECTROSTATIC = -41.8205 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1201" Parameter: CONF_N -> "8002" Comparing "1201" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1202" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759995 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760998 ATOM PAIRS WERE FOUND FOR ATOM LIST 41578 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29417 from a total of 760998 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1202 -65.41415 -7.51641 0.71913 INTE EXTERN> -24.12516 -41.28899 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4141" Parameter: A <- "-65.4141" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1252" Parameter: B <- "-24.1252" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.289" Parameter: C <- "-41.289" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1202 TOTAL ENERGY = -65.4141 RDTITL> * VAN DER WAALS = -24.1252 ELECTROSTATIC = -41.289 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1202" Parameter: CONF_N -> "8002" Comparing "1202" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1203" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760998 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761298 ATOM PAIRS WERE FOUND FOR ATOM LIST 41801 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29175 from a total of 761298 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1203 -69.97313 4.55899 0.65785 INTE EXTERN> -29.37324 -40.59989 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9731" Parameter: A <- "-69.9731" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3732" Parameter: B <- "-29.3732" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5999" Parameter: C <- "-40.5999" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1203 TOTAL ENERGY = -69.9731 RDTITL> * VAN DER WAALS = -29.3732 ELECTROSTATIC = -40.5999 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1203" Parameter: CONF_N -> "8002" Comparing "1203" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1204" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761298 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761703 ATOM PAIRS WERE FOUND FOR ATOM LIST 41804 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29241 from a total of 761703 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1204 -67.13297 -2.84017 0.67881 INTE EXTERN> -27.18945 -39.94352 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.133" Parameter: A <- "-67.133" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1894" Parameter: B <- "-27.1894" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9435" Parameter: C <- "-39.9435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1204 TOTAL ENERGY = -67.133 RDTITL> * VAN DER WAALS = -27.1894 ELECTROSTATIC = -39.9435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1204" Parameter: CONF_N -> "8002" Comparing "1204" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1205" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761703 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767975 ATOM PAIRS WERE FOUND FOR ATOM LIST 42225 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29720 from a total of 767975 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1205 -65.60702 -1.52594 0.67248 INTE EXTERN> -27.10783 -38.49919 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.607" Parameter: A <- "-65.607" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1078" Parameter: B <- "-27.1078" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4992" Parameter: C <- "-38.4992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1205 TOTAL ENERGY = -65.607 RDTITL> * VAN DER WAALS = -27.1078 ELECTROSTATIC = -38.4992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1205" Parameter: CONF_N -> "8002" Comparing "1205" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1206" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767975 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763337 ATOM PAIRS WERE FOUND FOR ATOM LIST 41969 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30390 from a total of 763337 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1206 -65.20004 -0.40698 0.61906 INTE EXTERN> -28.28457 -36.91547 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2" Parameter: A <- "-65.2" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2846" Parameter: B <- "-28.2846" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9155" Parameter: C <- "-36.9155" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1206 TOTAL ENERGY = -65.2 RDTITL> * VAN DER WAALS = -28.2846 ELECTROSTATIC = -36.9155 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1206" Parameter: CONF_N -> "8002" Comparing "1206" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1207" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763337 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763773 ATOM PAIRS WERE FOUND FOR ATOM LIST 42039 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29914 from a total of 763773 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1207 -63.59786 -1.60218 0.64541 INTE EXTERN> -27.15218 -36.44568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5979" Parameter: A <- "-63.5979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1522" Parameter: B <- "-27.1522" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4457" Parameter: C <- "-36.4457" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1207 TOTAL ENERGY = -63.5979 RDTITL> * VAN DER WAALS = -27.1522 ELECTROSTATIC = -36.4457 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1207" Parameter: CONF_N -> "8002" Comparing "1207" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1208" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763773 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763070 ATOM PAIRS WERE FOUND FOR ATOM LIST 42003 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29697 from a total of 763070 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1208 -63.93836 0.34049 0.66242 INTE EXTERN> -28.88705 -35.05130 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.9384" Parameter: A <- "-63.9384" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8871" Parameter: B <- "-28.8871" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0513" Parameter: C <- "-35.0513" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1208 TOTAL ENERGY = -63.9384 RDTITL> * VAN DER WAALS = -28.8871 ELECTROSTATIC = -35.0513 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1208" Parameter: CONF_N -> "8002" Comparing "1208" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1209" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763070 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764810 ATOM PAIRS WERE FOUND FOR ATOM LIST 41957 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29903 from a total of 764810 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1209 -63.51523 -0.42313 0.81304 INTE EXTERN> -23.37095 -40.14427 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5152" Parameter: A <- "-63.5152" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.371" Parameter: B <- "-23.371" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1443" Parameter: C <- "-40.1443" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1209 TOTAL ENERGY = -63.5152 RDTITL> * VAN DER WAALS = -23.371 ELECTROSTATIC = -40.1443 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1209" Parameter: CONF_N -> "8002" Comparing "1209" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1210" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764810 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764775 ATOM PAIRS WERE FOUND FOR ATOM LIST 41978 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29227 from a total of 764775 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1210 -62.37521 -1.14001 0.61925 INTE EXTERN> -29.87269 -32.50252 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3752" Parameter: A <- "-62.3752" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8727" Parameter: B <- "-29.8727" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5025" Parameter: C <- "-32.5025" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1210 TOTAL ENERGY = -62.3752 RDTITL> * VAN DER WAALS = -29.8727 ELECTROSTATIC = -32.5025 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1210" Parameter: CONF_N -> "8002" Comparing "1210" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1211" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764775 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766365 ATOM PAIRS WERE FOUND FOR ATOM LIST 41981 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29516 from a total of 766365 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1211 -77.13051 14.75529 0.69343 INTE EXTERN> -31.31566 -45.81485 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1305" Parameter: A <- "-77.1305" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3157" Parameter: B <- "-31.3157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8148" Parameter: C <- "-45.8148" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1211 TOTAL ENERGY = -77.1305 RDTITL> * VAN DER WAALS = -31.3157 ELECTROSTATIC = -45.8148 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1211" Parameter: CONF_N -> "8002" Comparing "1211" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1212" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766365 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765569 ATOM PAIRS WERE FOUND FOR ATOM LIST 42119 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30242 from a total of 765569 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1212 -59.85253 -17.27797 0.62421 INTE EXTERN> -30.31204 -29.54049 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.8525" Parameter: A <- "-59.8525" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.312" Parameter: B <- "-30.312" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.5405" Parameter: C <- "-29.5405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1212 TOTAL ENERGY = -59.8525 RDTITL> * VAN DER WAALS = -30.312 ELECTROSTATIC = -29.5405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1212" Parameter: CONF_N -> "8002" Comparing "1212" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1213" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765569 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765664 ATOM PAIRS WERE FOUND FOR ATOM LIST 42025 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30442 from a total of 765664 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1213 -67.25456 7.40202 0.71718 INTE EXTERN> -26.51576 -40.73879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2546" Parameter: A <- "-67.2546" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5158" Parameter: B <- "-26.5158" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7388" Parameter: C <- "-40.7388" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1213 TOTAL ENERGY = -67.2546 RDTITL> * VAN DER WAALS = -26.5158 ELECTROSTATIC = -40.7388 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1213" Parameter: CONF_N -> "8002" Comparing "1213" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1214" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765664 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760336 ATOM PAIRS WERE FOUND FOR ATOM LIST 41686 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30110 from a total of 760336 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1214 -65.96219 -1.29236 0.56012 INTE EXTERN> -32.13214 -33.83005 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9622" Parameter: A <- "-65.9622" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1321" Parameter: B <- "-32.1321" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8301" Parameter: C <- "-33.8301" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1214 TOTAL ENERGY = -65.9622 RDTITL> * VAN DER WAALS = -32.1321 ELECTROSTATIC = -33.8301 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1214" Parameter: CONF_N -> "8002" Comparing "1214" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1215" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760336 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765191 ATOM PAIRS WERE FOUND FOR ATOM LIST 41975 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30295 from a total of 765191 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1215 -66.92609 0.96390 0.68426 INTE EXTERN> -29.60692 -37.31917 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9261" Parameter: A <- "-66.9261" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6069" Parameter: B <- "-29.6069" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3192" Parameter: C <- "-37.3192" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1215 TOTAL ENERGY = -66.9261 RDTITL> * VAN DER WAALS = -29.6069 ELECTROSTATIC = -37.3192 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1215" Parameter: CONF_N -> "8002" Comparing "1215" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1216" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765191 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762325 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29803 from a total of 762325 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1216 -66.83604 -0.09005 0.62415 INTE EXTERN> -32.26503 -34.57101 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.836" Parameter: A <- "-66.836" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.265" Parameter: B <- "-32.265" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.571" Parameter: C <- "-34.571" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1216 TOTAL ENERGY = -66.836 RDTITL> * VAN DER WAALS = -32.265 ELECTROSTATIC = -34.571 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1216" Parameter: CONF_N -> "8002" Comparing "1216" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1217" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762325 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763342 ATOM PAIRS WERE FOUND FOR ATOM LIST 41763 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29931 from a total of 763342 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1217 -65.80700 -1.02904 0.66554 INTE EXTERN> -28.59751 -37.20948 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.807" Parameter: A <- "-65.807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5975" Parameter: B <- "-28.5975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2095" Parameter: C <- "-37.2095" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1217 TOTAL ENERGY = -65.807 RDTITL> * VAN DER WAALS = -28.5975 ELECTROSTATIC = -37.2095 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1217" Parameter: CONF_N -> "8002" Comparing "1217" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1218" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763342 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769254 ATOM PAIRS WERE FOUND FOR ATOM LIST 42203 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30271 from a total of 769254 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1218 -68.99231 3.18531 0.67636 INTE EXTERN> -30.31990 -38.67241 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9923" Parameter: A <- "-68.9923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3199" Parameter: B <- "-30.3199" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6724" Parameter: C <- "-38.6724" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1218 TOTAL ENERGY = -68.9923 RDTITL> * VAN DER WAALS = -30.3199 ELECTROSTATIC = -38.6724 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1218" Parameter: CONF_N -> "8002" Comparing "1218" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1219" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769254 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765837 ATOM PAIRS WERE FOUND FOR ATOM LIST 42166 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30111 from a total of 765837 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1219 -66.07836 -2.91395 0.61897 INTE EXTERN> -31.31198 -34.76638 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0784" Parameter: A <- "-66.0784" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.312" Parameter: B <- "-31.312" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7664" Parameter: C <- "-34.7664" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1219 TOTAL ENERGY = -66.0784 RDTITL> * VAN DER WAALS = -31.312 ELECTROSTATIC = -34.7664 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1219" Parameter: CONF_N -> "8002" Comparing "1219" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1220" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765837 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767712 ATOM PAIRS WERE FOUND FOR ATOM LIST 42100 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29124 from a total of 767712 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1220 -64.19206 -1.88631 0.66817 INTE EXTERN> -29.22384 -34.96821 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1921" Parameter: A <- "-64.1921" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2238" Parameter: B <- "-29.2238" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9682" Parameter: C <- "-34.9682" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1220 TOTAL ENERGY = -64.1921 RDTITL> * VAN DER WAALS = -29.2238 ELECTROSTATIC = -34.9682 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1220" Parameter: CONF_N -> "8002" Comparing "1220" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1221" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767712 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767087 ATOM PAIRS WERE FOUND FOR ATOM LIST 42040 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30117 from a total of 767087 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1221 -68.39422 4.20217 0.84141 INTE EXTERN> -23.99775 -44.39648 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3942" Parameter: A <- "-68.3942" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9977" Parameter: B <- "-23.9977" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3965" Parameter: C <- "-44.3965" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1221 TOTAL ENERGY = -68.3942 RDTITL> * VAN DER WAALS = -23.9977 ELECTROSTATIC = -44.3965 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1221" Parameter: CONF_N -> "8002" Comparing "1221" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1222" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767087 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764221 ATOM PAIRS WERE FOUND FOR ATOM LIST 41986 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30325 from a total of 764221 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1222 -64.57407 -3.82016 0.64223 INTE EXTERN> -28.65511 -35.91896 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5741" Parameter: A <- "-64.5741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6551" Parameter: B <- "-28.6551" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.919" Parameter: C <- "-35.919" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1222 TOTAL ENERGY = -64.5741 RDTITL> * VAN DER WAALS = -28.6551 ELECTROSTATIC = -35.919 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1222" Parameter: CONF_N -> "8002" Comparing "1222" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1223" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764221 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763002 ATOM PAIRS WERE FOUND FOR ATOM LIST 41829 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30095 from a total of 763002 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1223 -70.33010 5.75604 0.57122 INTE EXTERN> -31.77800 -38.55211 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3301" Parameter: A <- "-70.3301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.778" Parameter: B <- "-31.778" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5521" Parameter: C <- "-38.5521" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1223 TOTAL ENERGY = -70.3301 RDTITL> * VAN DER WAALS = -31.778 ELECTROSTATIC = -38.5521 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1223" Parameter: CONF_N -> "8002" Comparing "1223" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1224" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763002 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757690 ATOM PAIRS WERE FOUND FOR ATOM LIST 41592 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29730 from a total of 757690 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1224 -62.17383 -8.15627 0.60649 INTE EXTERN> -29.86401 -32.30983 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.1738" Parameter: A <- "-62.1738" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.864" Parameter: B <- "-29.864" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.3098" Parameter: C <- "-32.3098" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1224 TOTAL ENERGY = -62.1738 RDTITL> * VAN DER WAALS = -29.864 ELECTROSTATIC = -32.3098 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1224" Parameter: CONF_N -> "8002" Comparing "1224" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1225" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757690 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762543 ATOM PAIRS WERE FOUND FOR ATOM LIST 42033 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30551 from a total of 762543 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1225 -63.33572 1.16188 0.56514 INTE EXTERN> -32.03368 -31.30204 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3357" Parameter: A <- "-63.3357" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0337" Parameter: B <- "-32.0337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.302" Parameter: C <- "-31.302" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1225 TOTAL ENERGY = -63.3357 RDTITL> * VAN DER WAALS = -32.0337 ELECTROSTATIC = -31.302 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1225" Parameter: CONF_N -> "8002" Comparing "1225" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1226" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762543 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766875 ATOM PAIRS WERE FOUND FOR ATOM LIST 42047 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30265 from a total of 766875 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1226 -71.77816 8.44245 0.58350 INTE EXTERN> -33.85977 -37.91840 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7782" Parameter: A <- "-71.7782" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8598" Parameter: B <- "-33.8598" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9184" Parameter: C <- "-37.9184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1226 TOTAL ENERGY = -71.7782 RDTITL> * VAN DER WAALS = -33.8598 ELECTROSTATIC = -37.9184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1226" Parameter: CONF_N -> "8002" Comparing "1226" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1227" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766875 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764104 ATOM PAIRS WERE FOUND FOR ATOM LIST 41760 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30323 from a total of 764104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1227 -69.36962 -2.40854 0.76033 INTE EXTERN> -27.36354 -42.00608 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3696" Parameter: A <- "-69.3696" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3635" Parameter: B <- "-27.3635" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0061" Parameter: C <- "-42.0061" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1227 TOTAL ENERGY = -69.3696 RDTITL> * VAN DER WAALS = -27.3635 ELECTROSTATIC = -42.0061 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1227" Parameter: CONF_N -> "8002" Comparing "1227" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1228" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762696 ATOM PAIRS WERE FOUND FOR ATOM LIST 41915 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30388 from a total of 762696 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1228 -65.41932 -3.95030 0.67336 INTE EXTERN> -28.30599 -37.11333 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4193" Parameter: A <- "-65.4193" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.306" Parameter: B <- "-28.306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1133" Parameter: C <- "-37.1133" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1228 TOTAL ENERGY = -65.4193 RDTITL> * VAN DER WAALS = -28.306 ELECTROSTATIC = -37.1133 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1228" Parameter: CONF_N -> "8002" Comparing "1228" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1229" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762696 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762263 ATOM PAIRS WERE FOUND FOR ATOM LIST 41859 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29999 from a total of 762263 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1229 -63.89749 -1.52183 0.55548 INTE EXTERN> -30.65761 -33.23988 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.8975" Parameter: A <- "-63.8975" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6576" Parameter: B <- "-30.6576" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2399" Parameter: C <- "-33.2399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1229 TOTAL ENERGY = -63.8975 RDTITL> * VAN DER WAALS = -30.6576 ELECTROSTATIC = -33.2399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1229" Parameter: CONF_N -> "8002" Comparing "1229" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1230" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762263 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762475 ATOM PAIRS WERE FOUND FOR ATOM LIST 41919 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30102 from a total of 762475 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1230 -70.62853 6.73104 0.63310 INTE EXTERN> -30.17335 -40.45518 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6285" Parameter: A <- "-70.6285" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1733" Parameter: B <- "-30.1733" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4552" Parameter: C <- "-40.4552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1230 TOTAL ENERGY = -70.6285 RDTITL> * VAN DER WAALS = -30.1733 ELECTROSTATIC = -40.4552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1230" Parameter: CONF_N -> "8002" Comparing "1230" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1231" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762475 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767513 ATOM PAIRS WERE FOUND FOR ATOM LIST 42097 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30081 from a total of 767513 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1231 -67.84699 -2.78154 0.64873 INTE EXTERN> -31.62054 -36.22645 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.847" Parameter: A <- "-67.847" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6205" Parameter: B <- "-31.6205" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2264" Parameter: C <- "-36.2264" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1231 TOTAL ENERGY = -67.847 RDTITL> * VAN DER WAALS = -31.6205 ELECTROSTATIC = -36.2264 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1231" Parameter: CONF_N -> "8002" Comparing "1231" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1232" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767513 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761291 ATOM PAIRS WERE FOUND FOR ATOM LIST 41785 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30357 from a total of 761291 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1232 -69.58566 1.73867 0.64394 INTE EXTERN> -29.21674 -40.36893 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5857" Parameter: A <- "-69.5857" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2167" Parameter: B <- "-29.2167" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3689" Parameter: C <- "-40.3689" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1232 TOTAL ENERGY = -69.5857 RDTITL> * VAN DER WAALS = -29.2167 ELECTROSTATIC = -40.3689 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1232" Parameter: CONF_N -> "8002" Comparing "1232" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1233" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761291 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763880 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30466 from a total of 763880 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1233 -63.76654 -5.81913 0.65950 INTE EXTERN> -27.23418 -36.53235 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7665" Parameter: A <- "-63.7665" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2342" Parameter: B <- "-27.2342" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5324" Parameter: C <- "-36.5324" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1233 TOTAL ENERGY = -63.7665 RDTITL> * VAN DER WAALS = -27.2342 ELECTROSTATIC = -36.5324 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1233" Parameter: CONF_N -> "8002" Comparing "1233" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1234" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763880 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769278 ATOM PAIRS WERE FOUND FOR ATOM LIST 42143 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30162 from a total of 769278 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1234 -63.79640 0.02986 0.63843 INTE EXTERN> -30.02892 -33.76747 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7964" Parameter: A <- "-63.7964" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0289" Parameter: B <- "-30.0289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7675" Parameter: C <- "-33.7675" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1234 TOTAL ENERGY = -63.7964 RDTITL> * VAN DER WAALS = -30.0289 ELECTROSTATIC = -33.7675 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1234" Parameter: CONF_N -> "8002" Comparing "1234" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1235" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769278 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762608 ATOM PAIRS WERE FOUND FOR ATOM LIST 41621 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30296 from a total of 762608 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1235 -66.48180 2.68540 0.58692 INTE EXTERN> -30.47298 -36.00882 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4818" Parameter: A <- "-66.4818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.473" Parameter: B <- "-30.473" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0088" Parameter: C <- "-36.0088" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1235 TOTAL ENERGY = -66.4818 RDTITL> * VAN DER WAALS = -30.473 ELECTROSTATIC = -36.0088 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1235" Parameter: CONF_N -> "8002" Comparing "1235" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1236" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762608 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768220 ATOM PAIRS WERE FOUND FOR ATOM LIST 41930 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30311 from a total of 768220 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1236 -67.18363 0.70183 0.61939 INTE EXTERN> -30.60165 -36.58198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1836" Parameter: A <- "-67.1836" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6016" Parameter: B <- "-30.6016" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.582" Parameter: C <- "-36.582" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1236 TOTAL ENERGY = -67.1836 RDTITL> * VAN DER WAALS = -30.6016 ELECTROSTATIC = -36.582 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1236" Parameter: CONF_N -> "8002" Comparing "1236" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1237" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768220 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770726 ATOM PAIRS WERE FOUND FOR ATOM LIST 42233 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30118 from a total of 770726 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1237 -71.65488 4.47126 0.61464 INTE EXTERN> -31.53491 -40.11997 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6549" Parameter: A <- "-71.6549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5349" Parameter: B <- "-31.5349" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.12" Parameter: C <- "-40.12" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1237 TOTAL ENERGY = -71.6549 RDTITL> * VAN DER WAALS = -31.5349 ELECTROSTATIC = -40.12 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1237" Parameter: CONF_N -> "8002" Comparing "1237" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1238" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770726 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765102 ATOM PAIRS WERE FOUND FOR ATOM LIST 41796 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29355 from a total of 765102 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1238 -71.61879 -0.03610 0.62617 INTE EXTERN> -31.27496 -40.34382 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6188" Parameter: A <- "-71.6188" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.275" Parameter: B <- "-31.275" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3438" Parameter: C <- "-40.3438" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1238 TOTAL ENERGY = -71.6188 RDTITL> * VAN DER WAALS = -31.275 ELECTROSTATIC = -40.3438 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1238" Parameter: CONF_N -> "8002" Comparing "1238" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1239" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765102 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760322 ATOM PAIRS WERE FOUND FOR ATOM LIST 41665 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29762 from a total of 760322 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1239 -63.55397 -8.06481 0.63794 INTE EXTERN> -28.97155 -34.58242 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.554" Parameter: A <- "-63.554" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9716" Parameter: B <- "-28.9716" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5824" Parameter: C <- "-34.5824" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1239 TOTAL ENERGY = -63.554 RDTITL> * VAN DER WAALS = -28.9716 ELECTROSTATIC = -34.5824 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1239" Parameter: CONF_N -> "8002" Comparing "1239" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1240" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760322 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763272 ATOM PAIRS WERE FOUND FOR ATOM LIST 41771 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30051 from a total of 763272 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1240 -67.80101 4.24704 0.66431 INTE EXTERN> -29.75743 -38.04358 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.801" Parameter: A <- "-67.801" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7574" Parameter: B <- "-29.7574" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0436" Parameter: C <- "-38.0436" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1240 TOTAL ENERGY = -67.801 RDTITL> * VAN DER WAALS = -29.7574 ELECTROSTATIC = -38.0436 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1240" Parameter: CONF_N -> "8002" Comparing "1240" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1241" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763272 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765266 ATOM PAIRS WERE FOUND FOR ATOM LIST 42015 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29769 from a total of 765266 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1241 -65.51977 -2.28124 0.59672 INTE EXTERN> -29.04499 -36.47479 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5198" Parameter: A <- "-65.5198" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.045" Parameter: B <- "-29.045" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4748" Parameter: C <- "-36.4748" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1241 TOTAL ENERGY = -65.5198 RDTITL> * VAN DER WAALS = -29.045 ELECTROSTATIC = -36.4748 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1241" Parameter: CONF_N -> "8002" Comparing "1241" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1242" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765266 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769128 ATOM PAIRS WERE FOUND FOR ATOM LIST 42089 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30372 from a total of 769128 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1242 -69.83272 4.31295 0.66424 INTE EXTERN> -29.30876 -40.52396 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8327" Parameter: A <- "-69.8327" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3088" Parameter: B <- "-29.3088" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.524" Parameter: C <- "-40.524" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1242 TOTAL ENERGY = -69.8327 RDTITL> * VAN DER WAALS = -29.3088 ELECTROSTATIC = -40.524 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1242" Parameter: CONF_N -> "8002" Comparing "1242" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1243" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769128 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760434 ATOM PAIRS WERE FOUND FOR ATOM LIST 41918 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29418 from a total of 760434 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1243 -65.86574 -3.96698 0.57727 INTE EXTERN> -32.14730 -33.71844 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8657" Parameter: A <- "-65.8657" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1473" Parameter: B <- "-32.1473" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7184" Parameter: C <- "-33.7184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1243 TOTAL ENERGY = -65.8657 RDTITL> * VAN DER WAALS = -32.1473 ELECTROSTATIC = -33.7184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1243" Parameter: CONF_N -> "8002" Comparing "1243" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1244" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760434 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761536 ATOM PAIRS WERE FOUND FOR ATOM LIST 41994 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29704 from a total of 761536 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1244 -68.55406 2.68832 0.62848 INTE EXTERN> -29.60111 -38.95295 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5541" Parameter: A <- "-68.5541" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6011" Parameter: B <- "-29.6011" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.953" Parameter: C <- "-38.953" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1244 TOTAL ENERGY = -68.5541 RDTITL> * VAN DER WAALS = -29.6011 ELECTROSTATIC = -38.953 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1244" Parameter: CONF_N -> "8002" Comparing "1244" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1245" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761536 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767806 ATOM PAIRS WERE FOUND FOR ATOM LIST 42190 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29846 from a total of 767806 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1245 -71.09952 2.54546 0.70967 INTE EXTERN> -27.24867 -43.85085 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0995" Parameter: A <- "-71.0995" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2487" Parameter: B <- "-27.2487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8508" Parameter: C <- "-43.8508" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1245 TOTAL ENERGY = -71.0995 RDTITL> * VAN DER WAALS = -27.2487 ELECTROSTATIC = -43.8508 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1245" Parameter: CONF_N -> "8002" Comparing "1245" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1246" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767806 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762777 ATOM PAIRS WERE FOUND FOR ATOM LIST 41974 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29617 from a total of 762777 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1246 -69.66824 -1.43128 0.58861 INTE EXTERN> -32.00216 -37.66608 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6682" Parameter: A <- "-69.6682" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0022" Parameter: B <- "-32.0022" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6661" Parameter: C <- "-37.6661" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1246 TOTAL ENERGY = -69.6682 RDTITL> * VAN DER WAALS = -32.0022 ELECTROSTATIC = -37.6661 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1246" Parameter: CONF_N -> "8002" Comparing "1246" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1247" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762777 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763289 ATOM PAIRS WERE FOUND FOR ATOM LIST 41856 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30075 from a total of 763289 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1247 -68.74068 -0.92757 0.71839 INTE EXTERN> -27.35966 -41.38102 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7407" Parameter: A <- "-68.7407" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3597" Parameter: B <- "-27.3597" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.381" Parameter: C <- "-41.381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1247 TOTAL ENERGY = -68.7407 RDTITL> * VAN DER WAALS = -27.3597 ELECTROSTATIC = -41.381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1247" Parameter: CONF_N -> "8002" Comparing "1247" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1248" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763289 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762991 ATOM PAIRS WERE FOUND FOR ATOM LIST 41673 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 762991 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1248 -68.53878 -0.20189 0.59227 INTE EXTERN> -31.93982 -36.59896 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5388" Parameter: A <- "-68.5388" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9398" Parameter: B <- "-31.9398" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.599" Parameter: C <- "-36.599" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1248 TOTAL ENERGY = -68.5388 RDTITL> * VAN DER WAALS = -31.9398 ELECTROSTATIC = -36.599 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1248" Parameter: CONF_N -> "8002" Comparing "1248" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1249" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762991 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766529 ATOM PAIRS WERE FOUND FOR ATOM LIST 41956 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30421 from a total of 766529 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1249 -60.25457 -8.28421 0.66116 INTE EXTERN> -30.46655 -29.78802 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.2546" Parameter: A <- "-60.2546" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4666" Parameter: B <- "-30.4666" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.788" Parameter: C <- "-29.788" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1249 TOTAL ENERGY = -60.2546 RDTITL> * VAN DER WAALS = -30.4666 ELECTROSTATIC = -29.788 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1249" Parameter: CONF_N -> "8002" Comparing "1249" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1250" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766529 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761457 ATOM PAIRS WERE FOUND FOR ATOM LIST 41971 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30252 from a total of 761457 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1250 -71.84206 11.58748 0.64965 INTE EXTERN> -30.71492 -41.12714 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8421" Parameter: A <- "-71.8421" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7149" Parameter: B <- "-30.7149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1271" Parameter: C <- "-41.1271" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1250 TOTAL ENERGY = -71.8421 RDTITL> * VAN DER WAALS = -30.7149 ELECTROSTATIC = -41.1271 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1250" Parameter: CONF_N -> "8002" Comparing "1250" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1251" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761457 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760937 ATOM PAIRS WERE FOUND FOR ATOM LIST 41934 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30217 from a total of 760937 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1251 -55.81904 -16.02301 0.50984 INTE EXTERN> -28.99757 -26.82148 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.819" Parameter: A <- "-55.819" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9976" Parameter: B <- "-28.9976" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-26.8215" Parameter: C <- "-26.8215" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1251 TOTAL ENERGY = -55.819 RDTITL> * VAN DER WAALS = -28.9976 ELECTROSTATIC = -26.8215 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1251" Parameter: CONF_N -> "8002" Comparing "1251" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1252" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760937 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771469 ATOM PAIRS WERE FOUND FOR ATOM LIST 42290 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30521 from a total of 771469 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1252 -62.97411 7.15507 0.66083 INTE EXTERN> -27.62473 -35.34939 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9741" Parameter: A <- "-62.9741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6247" Parameter: B <- "-27.6247" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3494" Parameter: C <- "-35.3494" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1252 TOTAL ENERGY = -62.9741 RDTITL> * VAN DER WAALS = -27.6247 ELECTROSTATIC = -35.3494 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1252" Parameter: CONF_N -> "8002" Comparing "1252" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1253" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771469 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766845 ATOM PAIRS WERE FOUND FOR ATOM LIST 42252 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29565 from a total of 766845 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1253 -63.74186 0.76775 0.68727 INTE EXTERN> -24.77920 -38.96266 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7419" Parameter: A <- "-63.7419" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7792" Parameter: B <- "-24.7792" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9627" Parameter: C <- "-38.9627" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1253 TOTAL ENERGY = -63.7419 RDTITL> * VAN DER WAALS = -24.7792 ELECTROSTATIC = -38.9627 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1253" Parameter: CONF_N -> "8002" Comparing "1253" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1254" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766845 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767466 ATOM PAIRS WERE FOUND FOR ATOM LIST 42038 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29836 from a total of 767466 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1254 -66.63100 2.88913 0.59563 INTE EXTERN> -31.22222 -35.40878 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.631" Parameter: A <- "-66.631" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2222" Parameter: B <- "-31.2222" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4088" Parameter: C <- "-35.4088" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1254 TOTAL ENERGY = -66.631 RDTITL> * VAN DER WAALS = -31.2222 ELECTROSTATIC = -35.4088 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1254" Parameter: CONF_N -> "8002" Comparing "1254" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1255" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767466 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770176 ATOM PAIRS WERE FOUND FOR ATOM LIST 42242 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30326 from a total of 770176 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1255 -67.70792 1.07692 0.56441 INTE EXTERN> -33.55231 -34.15561 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7079" Parameter: A <- "-67.7079" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5523" Parameter: B <- "-33.5523" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1556" Parameter: C <- "-34.1556" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1255 TOTAL ENERGY = -67.7079 RDTITL> * VAN DER WAALS = -33.5523 ELECTROSTATIC = -34.1556 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1255" Parameter: CONF_N -> "8002" Comparing "1255" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1256" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770176 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771463 ATOM PAIRS WERE FOUND FOR ATOM LIST 42205 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30152 from a total of 771463 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1256 -64.27118 -3.43674 0.76157 INTE EXTERN> -24.02823 -40.24295 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2712" Parameter: A <- "-64.2712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0282" Parameter: B <- "-24.0282" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.243" Parameter: C <- "-40.243" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1256 TOTAL ENERGY = -64.2712 RDTITL> * VAN DER WAALS = -24.0282 ELECTROSTATIC = -40.243 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1256" Parameter: CONF_N -> "8002" Comparing "1256" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1257" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771463 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769888 ATOM PAIRS WERE FOUND FOR ATOM LIST 42372 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30520 from a total of 769888 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1257 -63.96626 -0.30492 0.61336 INTE EXTERN> -28.88405 -35.08221 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.9663" Parameter: A <- "-63.9663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8841" Parameter: B <- "-28.8841" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0822" Parameter: C <- "-35.0822" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1257 TOTAL ENERGY = -63.9663 RDTITL> * VAN DER WAALS = -28.8841 ELECTROSTATIC = -35.0822 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1257" Parameter: CONF_N -> "8002" Comparing "1257" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1258" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769888 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762399 ATOM PAIRS WERE FOUND FOR ATOM LIST 41875 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29951 from a total of 762399 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1258 -68.05208 4.08582 0.60483 INTE EXTERN> -31.39908 -36.65300 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0521" Parameter: A <- "-68.0521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3991" Parameter: B <- "-31.3991" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.653" Parameter: C <- "-36.653" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1258 TOTAL ENERGY = -68.0521 RDTITL> * VAN DER WAALS = -31.3991 ELECTROSTATIC = -36.653 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1258" Parameter: CONF_N -> "8002" Comparing "1258" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1259" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762399 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765713 ATOM PAIRS WERE FOUND FOR ATOM LIST 41924 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29782 from a total of 765713 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1259 -66.91785 -1.13424 0.65582 INTE EXTERN> -28.16531 -38.75254 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9178" Parameter: A <- "-66.9178" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1653" Parameter: B <- "-28.1653" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7525" Parameter: C <- "-38.7525" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1259 TOTAL ENERGY = -66.9178 RDTITL> * VAN DER WAALS = -28.1653 ELECTROSTATIC = -38.7525 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1259" Parameter: CONF_N -> "8002" Comparing "1259" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1260" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765713 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763547 ATOM PAIRS WERE FOUND FOR ATOM LIST 41946 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30656 from a total of 763547 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1260 -69.86055 2.94270 0.68092 INTE EXTERN> -28.37139 -41.48916 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8605" Parameter: A <- "-69.8605" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3714" Parameter: B <- "-28.3714" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4892" Parameter: C <- "-41.4892" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1260 TOTAL ENERGY = -69.8605 RDTITL> * VAN DER WAALS = -28.3714 ELECTROSTATIC = -41.4892 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1260" Parameter: CONF_N -> "8002" Comparing "1260" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1261" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763547 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763242 ATOM PAIRS WERE FOUND FOR ATOM LIST 41994 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29761 from a total of 763242 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1261 -74.29431 4.43376 0.57432 INTE EXTERN> -32.89398 -41.40033 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2943" Parameter: A <- "-74.2943" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.894" Parameter: B <- "-32.894" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4003" Parameter: C <- "-41.4003" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1261 TOTAL ENERGY = -74.2943 RDTITL> * VAN DER WAALS = -32.894 ELECTROSTATIC = -41.4003 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1261" Parameter: CONF_N -> "8002" Comparing "1261" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1262" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763242 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767887 ATOM PAIRS WERE FOUND FOR ATOM LIST 42195 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29636 from a total of 767887 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1262 -74.83666 0.54235 0.61977 INTE EXTERN> -29.90092 -44.93574 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8367" Parameter: A <- "-74.8367" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9009" Parameter: B <- "-29.9009" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9357" Parameter: C <- "-44.9357" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1262 TOTAL ENERGY = -74.8367 RDTITL> * VAN DER WAALS = -29.9009 ELECTROSTATIC = -44.9357 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1262" Parameter: CONF_N -> "8002" Comparing "1262" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1263" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767887 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771148 ATOM PAIRS WERE FOUND FOR ATOM LIST 42382 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29836 from a total of 771148 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1263 -68.41441 -6.42225 0.56993 INTE EXTERN> -32.60238 -35.81203 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4144" Parameter: A <- "-68.4144" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6024" Parameter: B <- "-32.6024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.812" Parameter: C <- "-35.812" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1263 TOTAL ENERGY = -68.4144 RDTITL> * VAN DER WAALS = -32.6024 ELECTROSTATIC = -35.812 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1263" Parameter: CONF_N -> "8002" Comparing "1263" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1264" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771148 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 774079 ATOM PAIRS WERE FOUND FOR ATOM LIST 42421 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30379 from a total of 774079 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1264 -70.47086 2.05645 0.63921 INTE EXTERN> -28.30213 -42.16873 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4709" Parameter: A <- "-70.4709" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3021" Parameter: B <- "-28.3021" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1687" Parameter: C <- "-42.1687" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1264 TOTAL ENERGY = -70.4709 RDTITL> * VAN DER WAALS = -28.3021 ELECTROSTATIC = -42.1687 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1264" Parameter: CONF_N -> "8002" Comparing "1264" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1265" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 774079 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772873 ATOM PAIRS WERE FOUND FOR ATOM LIST 42419 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29667 from a total of 772873 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1265 -68.62670 -1.84416 0.56933 INTE EXTERN> -30.96056 -37.66614 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6267" Parameter: A <- "-68.6267" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9606" Parameter: B <- "-30.9606" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6661" Parameter: C <- "-37.6661" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1265 TOTAL ENERGY = -68.6267 RDTITL> * VAN DER WAALS = -30.9606 ELECTROSTATIC = -37.6661 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1265" Parameter: CONF_N -> "8002" Comparing "1265" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1266" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772873 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771902 ATOM PAIRS WERE FOUND FOR ATOM LIST 42385 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29790 from a total of 771902 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1266 -72.98291 4.35621 0.65640 INTE EXTERN> -30.69375 -42.28916 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9829" Parameter: A <- "-72.9829" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6937" Parameter: B <- "-30.6937" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2892" Parameter: C <- "-42.2892" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1266 TOTAL ENERGY = -72.9829 RDTITL> * VAN DER WAALS = -30.6937 ELECTROSTATIC = -42.2892 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1266" Parameter: CONF_N -> "8002" Comparing "1266" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1267" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771902 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 773679 ATOM PAIRS WERE FOUND FOR ATOM LIST 42533 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30340 from a total of 773679 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1267 -74.18465 1.20174 0.69004 INTE EXTERN> -30.02349 -44.16115 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1846" Parameter: A <- "-74.1846" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0235" Parameter: B <- "-30.0235" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1612" Parameter: C <- "-44.1612" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1267 TOTAL ENERGY = -74.1846 RDTITL> * VAN DER WAALS = -30.0235 ELECTROSTATIC = -44.1612 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1267" Parameter: CONF_N -> "8002" Comparing "1267" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1268" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 773679 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 778428 ATOM PAIRS WERE FOUND FOR ATOM LIST 42515 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30085 from a total of 778428 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1268 -67.82317 -6.36147 0.71844 INTE EXTERN> -28.28455 -39.53863 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8232" Parameter: A <- "-67.8232" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2845" Parameter: B <- "-28.2845" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5386" Parameter: C <- "-39.5386" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1268 TOTAL ENERGY = -67.8232 RDTITL> * VAN DER WAALS = -28.2845 ELECTROSTATIC = -39.5386 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1268" Parameter: CONF_N -> "8002" Comparing "1268" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1269" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 778428 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769572 ATOM PAIRS WERE FOUND FOR ATOM LIST 42185 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29902 from a total of 769572 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1269 -73.46697 5.64380 0.69791 INTE EXTERN> -29.12484 -44.34214 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.467" Parameter: A <- "-73.467" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1248" Parameter: B <- "-29.1248" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3421" Parameter: C <- "-44.3421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1269 TOTAL ENERGY = -73.467 RDTITL> * VAN DER WAALS = -29.1248 ELECTROSTATIC = -44.3421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1269" Parameter: CONF_N -> "8002" Comparing "1269" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1270" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769572 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771612 ATOM PAIRS WERE FOUND FOR ATOM LIST 42245 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30177 from a total of 771612 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1270 -70.73106 -2.73592 0.65804 INTE EXTERN> -27.81065 -42.92041 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7311" Parameter: A <- "-70.7311" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8107" Parameter: B <- "-27.8107" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9204" Parameter: C <- "-42.9204" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1270 TOTAL ENERGY = -70.7311 RDTITL> * VAN DER WAALS = -27.8107 ELECTROSTATIC = -42.9204 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1270" Parameter: CONF_N -> "8002" Comparing "1270" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1271" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771612 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769637 ATOM PAIRS WERE FOUND FOR ATOM LIST 42071 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29220 from a total of 769637 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1271 -68.01118 -2.71988 0.71997 INTE EXTERN> -26.04556 -41.96562 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0112" Parameter: A <- "-68.0112" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0456" Parameter: B <- "-26.0456" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9656" Parameter: C <- "-41.9656" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1271 TOTAL ENERGY = -68.0112 RDTITL> * VAN DER WAALS = -26.0456 ELECTROSTATIC = -41.9656 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1271" Parameter: CONF_N -> "8002" Comparing "1271" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1272" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769637 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769343 ATOM PAIRS WERE FOUND FOR ATOM LIST 41962 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30396 from a total of 769343 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1272 -66.40527 -1.60591 0.59858 INTE EXTERN> -28.94005 -37.46521 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4053" Parameter: A <- "-66.4053" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9401" Parameter: B <- "-28.9401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4652" Parameter: C <- "-37.4652" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1272 TOTAL ENERGY = -66.4053 RDTITL> * VAN DER WAALS = -28.9401 ELECTROSTATIC = -37.4652 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1272" Parameter: CONF_N -> "8002" Comparing "1272" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1273" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769343 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 775909 ATOM PAIRS WERE FOUND FOR ATOM LIST 42546 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29918 from a total of 775909 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1273 -75.07904 8.67377 0.59278 INTE EXTERN> -31.10495 -43.97409 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.079" Parameter: A <- "-75.079" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1049" Parameter: B <- "-31.1049" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9741" Parameter: C <- "-43.9741" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1273 TOTAL ENERGY = -75.079 RDTITL> * VAN DER WAALS = -31.1049 ELECTROSTATIC = -43.9741 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1273" Parameter: CONF_N -> "8002" Comparing "1273" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1274" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 775909 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767194 ATOM PAIRS WERE FOUND FOR ATOM LIST 42035 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30132 from a total of 767194 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1274 -66.27914 -8.79989 0.63328 INTE EXTERN> -28.56861 -37.71054 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2791" Parameter: A <- "-66.2791" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5686" Parameter: B <- "-28.5686" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7105" Parameter: C <- "-37.7105" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1274 TOTAL ENERGY = -66.2791 RDTITL> * VAN DER WAALS = -28.5686 ELECTROSTATIC = -37.7105 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1274" Parameter: CONF_N -> "8002" Comparing "1274" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1275" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767194 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767491 ATOM PAIRS WERE FOUND FOR ATOM LIST 41904 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30292 from a total of 767491 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1275 -64.49666 -1.78249 0.54931 INTE EXTERN> -30.14172 -34.35493 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.4967" Parameter: A <- "-64.4967" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1417" Parameter: B <- "-30.1417" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3549" Parameter: C <- "-34.3549" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1275 TOTAL ENERGY = -64.4967 RDTITL> * VAN DER WAALS = -30.1417 ELECTROSTATIC = -34.3549 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1275" Parameter: CONF_N -> "8002" Comparing "1275" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1276" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767491 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 774422 ATOM PAIRS WERE FOUND FOR ATOM LIST 42367 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29821 from a total of 774422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1276 -66.89394 2.39729 0.66276 INTE EXTERN> -25.98178 -40.91216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8939" Parameter: A <- "-66.8939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9818" Parameter: B <- "-25.9818" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9122" Parameter: C <- "-40.9122" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1276 TOTAL ENERGY = -66.8939 RDTITL> * VAN DER WAALS = -25.9818 ELECTROSTATIC = -40.9122 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1276" Parameter: CONF_N -> "8002" Comparing "1276" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1277" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 774422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769164 ATOM PAIRS WERE FOUND FOR ATOM LIST 42155 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29886 from a total of 769164 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1277 -54.90182 -11.99212 0.62597 INTE EXTERN> -26.68483 -28.21700 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-54.9018" Parameter: A <- "-54.9018" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6848" Parameter: B <- "-26.6848" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.217" Parameter: C <- "-28.217" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1277 TOTAL ENERGY = -54.9018 RDTITL> * VAN DER WAALS = -26.6848 ELECTROSTATIC = -28.217 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1277" Parameter: CONF_N -> "8002" Comparing "1277" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1278" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769164 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766497 ATOM PAIRS WERE FOUND FOR ATOM LIST 42062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30089 from a total of 766497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1278 -66.74244 11.84061 0.62569 INTE EXTERN> -28.57522 -38.16722 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7424" Parameter: A <- "-66.7424" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5752" Parameter: B <- "-28.5752" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1672" Parameter: C <- "-38.1672" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1278 TOTAL ENERGY = -66.7424 RDTITL> * VAN DER WAALS = -28.5752 ELECTROSTATIC = -38.1672 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1278" Parameter: CONF_N -> "8002" Comparing "1278" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1279" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769512 ATOM PAIRS WERE FOUND FOR ATOM LIST 42086 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29864 from a total of 769512 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1279 -65.60449 -1.13794 0.64401 INTE EXTERN> -28.26552 -37.33897 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6045" Parameter: A <- "-65.6045" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2655" Parameter: B <- "-28.2655" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.339" Parameter: C <- "-37.339" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1279 TOTAL ENERGY = -65.6045 RDTITL> * VAN DER WAALS = -28.2655 ELECTROSTATIC = -37.339 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1279" Parameter: CONF_N -> "8002" Comparing "1279" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1280" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769512 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765660 ATOM PAIRS WERE FOUND FOR ATOM LIST 42184 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29785 from a total of 765660 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1280 -64.74125 -0.86325 0.72028 INTE EXTERN> -26.26908 -38.47217 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7412" Parameter: A <- "-64.7412" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2691" Parameter: B <- "-26.2691" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4722" Parameter: C <- "-38.4722" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1280 TOTAL ENERGY = -64.7412 RDTITL> * VAN DER WAALS = -26.2691 ELECTROSTATIC = -38.4722 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1280" Parameter: CONF_N -> "8002" Comparing "1280" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1281" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765660 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769591 ATOM PAIRS WERE FOUND FOR ATOM LIST 42171 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30359 from a total of 769591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1281 -68.29097 3.54972 0.61265 INTE EXTERN> -29.66399 -38.62698 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.291" Parameter: A <- "-68.291" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.664" Parameter: B <- "-29.664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.627" Parameter: C <- "-38.627" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1281 TOTAL ENERGY = -68.291 RDTITL> * VAN DER WAALS = -29.664 ELECTROSTATIC = -38.627 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1281" Parameter: CONF_N -> "8002" Comparing "1281" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1282" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764834 ATOM PAIRS WERE FOUND FOR ATOM LIST 42047 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30355 from a total of 764834 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1282 -66.43180 -1.85917 0.86875 INTE EXTERN> -21.35096 -45.08084 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4318" Parameter: A <- "-66.4318" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.351" Parameter: B <- "-21.351" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0808" Parameter: C <- "-45.0808" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1282 TOTAL ENERGY = -66.4318 RDTITL> * VAN DER WAALS = -21.351 ELECTROSTATIC = -45.0808 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1282" Parameter: CONF_N -> "8002" Comparing "1282" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1283" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764834 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770946 ATOM PAIRS WERE FOUND FOR ATOM LIST 42219 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30311 from a total of 770946 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1283 -66.78668 0.35488 0.71133 INTE EXTERN> -26.19625 -40.59042 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7867" Parameter: A <- "-66.7867" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1963" Parameter: B <- "-26.1963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5904" Parameter: C <- "-40.5904" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1283 TOTAL ENERGY = -66.7867 RDTITL> * VAN DER WAALS = -26.1963 ELECTROSTATIC = -40.5904 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1283" Parameter: CONF_N -> "8002" Comparing "1283" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1284" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770946 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765252 ATOM PAIRS WERE FOUND FOR ATOM LIST 41877 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30554 from a total of 765252 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1284 -69.98693 3.20025 0.57037 INTE EXTERN> -30.29085 -39.69608 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9869" Parameter: A <- "-69.9869" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2909" Parameter: B <- "-30.2909" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6961" Parameter: C <- "-39.6961" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1284 TOTAL ENERGY = -69.9869 RDTITL> * VAN DER WAALS = -30.2909 ELECTROSTATIC = -39.6961 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1284" Parameter: CONF_N -> "8002" Comparing "1284" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1285" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765252 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769264 ATOM PAIRS WERE FOUND FOR ATOM LIST 42397 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30635 from a total of 769264 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1285 -66.58993 -3.39700 0.74317 INTE EXTERN> -25.08974 -41.50019 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5899" Parameter: A <- "-66.5899" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0897" Parameter: B <- "-25.0897" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5002" Parameter: C <- "-41.5002" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1285 TOTAL ENERGY = -66.5899 RDTITL> * VAN DER WAALS = -25.0897 ELECTROSTATIC = -41.5002 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1285" Parameter: CONF_N -> "8002" Comparing "1285" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1286" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769264 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 775005 ATOM PAIRS WERE FOUND FOR ATOM LIST 42520 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30581 from a total of 775005 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1286 -70.42150 3.83157 0.76092 INTE EXTERN> -23.97399 -46.44751 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4215" Parameter: A <- "-70.4215" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.974" Parameter: B <- "-23.974" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4475" Parameter: C <- "-46.4475" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1286 TOTAL ENERGY = -70.4215 RDTITL> * VAN DER WAALS = -23.974 ELECTROSTATIC = -46.4475 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1286" Parameter: CONF_N -> "8002" Comparing "1286" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1287" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 775005 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764870 ATOM PAIRS WERE FOUND FOR ATOM LIST 42036 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29702 from a total of 764870 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1287 -70.19392 -0.22758 0.64831 INTE EXTERN> -28.99147 -41.20246 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1939" Parameter: A <- "-70.1939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9915" Parameter: B <- "-28.9915" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2025" Parameter: C <- "-41.2025" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1287 TOTAL ENERGY = -70.1939 RDTITL> * VAN DER WAALS = -28.9915 ELECTROSTATIC = -41.2025 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1287" Parameter: CONF_N -> "8002" Comparing "1287" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1288" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764870 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761583 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29003 from a total of 761583 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1288 -71.48275 1.28883 0.63420 INTE EXTERN> -28.15024 -43.33250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4827" Parameter: A <- "-71.4827" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1502" Parameter: B <- "-28.1502" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3325" Parameter: C <- "-43.3325" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1288 TOTAL ENERGY = -71.4827 RDTITL> * VAN DER WAALS = -28.1502 ELECTROSTATIC = -43.3325 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1288" Parameter: CONF_N -> "8002" Comparing "1288" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1289" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761583 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763758 ATOM PAIRS WERE FOUND FOR ATOM LIST 41806 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29676 from a total of 763758 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1289 -68.63848 -2.84427 0.87176 INTE EXTERN> -20.56792 -48.07056 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6385" Parameter: A <- "-68.6385" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.5679" Parameter: B <- "-20.5679" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0706" Parameter: C <- "-48.0706" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1289 TOTAL ENERGY = -68.6385 RDTITL> * VAN DER WAALS = -20.5679 ELECTROSTATIC = -48.0706 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1289" Parameter: CONF_N -> "8002" Comparing "1289" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1290" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763758 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29100 from a total of 765110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1290 -67.05318 -1.58530 0.61010 INTE EXTERN> -31.94017 -35.11301 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0532" Parameter: A <- "-67.0532" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9402" Parameter: B <- "-31.9402" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.113" Parameter: C <- "-35.113" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1290 TOTAL ENERGY = -67.0532 RDTITL> * VAN DER WAALS = -31.9402 ELECTROSTATIC = -35.113 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1290" Parameter: CONF_N -> "8002" Comparing "1290" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1291" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763742 ATOM PAIRS WERE FOUND FOR ATOM LIST 42107 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29890 from a total of 763742 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1291 -71.01310 3.95992 0.62916 INTE EXTERN> -27.84861 -43.16449 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0131" Parameter: A <- "-71.0131" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8486" Parameter: B <- "-27.8486" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1645" Parameter: C <- "-43.1645" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1291 TOTAL ENERGY = -71.0131 RDTITL> * VAN DER WAALS = -27.8486 ELECTROSTATIC = -43.1645 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1291" Parameter: CONF_N -> "8002" Comparing "1291" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1292" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763742 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768282 ATOM PAIRS WERE FOUND FOR ATOM LIST 42021 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29534 from a total of 768282 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1292 -66.94103 -4.07206 0.81087 INTE EXTERN> -23.72754 -43.21349 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.941" Parameter: A <- "-66.941" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7275" Parameter: B <- "-23.7275" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2135" Parameter: C <- "-43.2135" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1292 TOTAL ENERGY = -66.941 RDTITL> * VAN DER WAALS = -23.7275 ELECTROSTATIC = -43.2135 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1292" Parameter: CONF_N -> "8002" Comparing "1292" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1293" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768282 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761828 ATOM PAIRS WERE FOUND FOR ATOM LIST 41674 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29768 from a total of 761828 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1293 -70.55650 3.61546 0.71861 INTE EXTERN> -28.37116 -42.18534 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5565" Parameter: A <- "-70.5565" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3712" Parameter: B <- "-28.3712" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1853" Parameter: C <- "-42.1853" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1293 TOTAL ENERGY = -70.5565 RDTITL> * VAN DER WAALS = -28.3712 ELECTROSTATIC = -42.1853 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1293" Parameter: CONF_N -> "8002" Comparing "1293" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1294" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761828 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769048 ATOM PAIRS WERE FOUND FOR ATOM LIST 42025 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29616 from a total of 769048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1294 -65.66571 -4.89079 0.66640 INTE EXTERN> -26.36473 -39.30099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6657" Parameter: A <- "-65.6657" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3647" Parameter: B <- "-26.3647" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.301" Parameter: C <- "-39.301" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1294 TOTAL ENERGY = -65.6657 RDTITL> * VAN DER WAALS = -26.3647 ELECTROSTATIC = -39.301 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1294" Parameter: CONF_N -> "8002" Comparing "1294" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1295" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765708 ATOM PAIRS WERE FOUND FOR ATOM LIST 41953 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29486 from a total of 765708 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1295 -64.97074 -0.69497 0.62448 INTE EXTERN> -29.97535 -34.99539 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9707" Parameter: A <- "-64.9707" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9753" Parameter: B <- "-29.9753" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9954" Parameter: C <- "-34.9954" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1295 TOTAL ENERGY = -64.9707 RDTITL> * VAN DER WAALS = -29.9753 ELECTROSTATIC = -34.9954 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1295" Parameter: CONF_N -> "8002" Comparing "1295" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1296" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765708 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771105 ATOM PAIRS WERE FOUND FOR ATOM LIST 42281 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29848 from a total of 771105 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1296 -65.64153 0.67079 0.67535 INTE EXTERN> -25.78067 -39.86086 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6415" Parameter: A <- "-65.6415" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7807" Parameter: B <- "-25.7807" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8609" Parameter: C <- "-39.8609" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1296 TOTAL ENERGY = -65.6415 RDTITL> * VAN DER WAALS = -25.7807 ELECTROSTATIC = -39.8609 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1296" Parameter: CONF_N -> "8002" Comparing "1296" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1297" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771105 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769721 ATOM PAIRS WERE FOUND FOR ATOM LIST 42053 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30060 from a total of 769721 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1297 -70.92155 5.28002 0.61042 INTE EXTERN> -30.62947 -40.29208 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9215" Parameter: A <- "-70.9215" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6295" Parameter: B <- "-30.6295" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2921" Parameter: C <- "-40.2921" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1297 TOTAL ENERGY = -70.9215 RDTITL> * VAN DER WAALS = -30.6295 ELECTROSTATIC = -40.2921 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1297" Parameter: CONF_N -> "8002" Comparing "1297" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1298" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769721 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771087 ATOM PAIRS WERE FOUND FOR ATOM LIST 42174 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30122 from a total of 771087 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1298 -69.67073 -1.25082 0.75337 INTE EXTERN> -23.65520 -46.01553 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6707" Parameter: A <- "-69.6707" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6552" Parameter: B <- "-23.6552" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0155" Parameter: C <- "-46.0155" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1298 TOTAL ENERGY = -69.6707 RDTITL> * VAN DER WAALS = -23.6552 ELECTROSTATIC = -46.0155 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1298" Parameter: CONF_N -> "8002" Comparing "1298" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1299" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771087 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767008 ATOM PAIRS WERE FOUND FOR ATOM LIST 42103 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29112 from a total of 767008 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1299 -66.99729 -2.67343 0.70882 INTE EXTERN> -26.82249 -40.17480 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9973" Parameter: A <- "-66.9973" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8225" Parameter: B <- "-26.8225" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1748" Parameter: C <- "-40.1748" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1299 TOTAL ENERGY = -66.9973 RDTITL> * VAN DER WAALS = -26.8225 ELECTROSTATIC = -40.1748 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1299" Parameter: CONF_N -> "8002" Comparing "1299" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1300" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767008 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766190 ATOM PAIRS WERE FOUND FOR ATOM LIST 42068 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30004 from a total of 766190 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1300 -70.44421 3.44692 0.69275 INTE EXTERN> -28.12165 -42.32255 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4442" Parameter: A <- "-70.4442" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1217" Parameter: B <- "-28.1217" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3226" Parameter: C <- "-42.3226" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1300 TOTAL ENERGY = -70.4442 RDTITL> * VAN DER WAALS = -28.1217 ELECTROSTATIC = -42.3226 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1300" Parameter: CONF_N -> "8002" Comparing "1300" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1301" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766190 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771392 ATOM PAIRS WERE FOUND FOR ATOM LIST 42396 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30169 from a total of 771392 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1301 -68.66502 -1.77919 0.78591 INTE EXTERN> -22.77127 -45.89375 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.665" Parameter: A <- "-68.665" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.7713" Parameter: B <- "-22.7713" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8938" Parameter: C <- "-45.8938" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1301 TOTAL ENERGY = -68.665 RDTITL> * VAN DER WAALS = -22.7713 ELECTROSTATIC = -45.8938 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1301" Parameter: CONF_N -> "8002" Comparing "1301" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1302" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771392 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770255 ATOM PAIRS WERE FOUND FOR ATOM LIST 42286 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29828 from a total of 770255 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1302 -68.27746 -0.38756 0.58718 INTE EXTERN> -31.60409 -36.67336 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2775" Parameter: A <- "-68.2775" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6041" Parameter: B <- "-31.6041" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6734" Parameter: C <- "-36.6734" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1302 TOTAL ENERGY = -68.2775 RDTITL> * VAN DER WAALS = -31.6041 ELECTROSTATIC = -36.6734 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1302" Parameter: CONF_N -> "8002" Comparing "1302" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1303" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770255 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769728 ATOM PAIRS WERE FOUND FOR ATOM LIST 42206 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30022 from a total of 769728 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1303 -58.34555 -9.93190 0.56897 INTE EXTERN> -30.55770 -27.78785 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.3456" Parameter: A <- "-58.3456" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5577" Parameter: B <- "-30.5577" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.7879" Parameter: C <- "-27.7879" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1303 TOTAL ENERGY = -58.3456 RDTITL> * VAN DER WAALS = -30.5577 ELECTROSTATIC = -27.7879 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1303" Parameter: CONF_N -> "8002" Comparing "1303" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1304" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769728 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761829 ATOM PAIRS WERE FOUND FOR ATOM LIST 41893 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29945 from a total of 761829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1304 -70.24374 11.89819 0.65022 INTE EXTERN> -28.60073 -41.64301 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2437" Parameter: A <- "-70.2437" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6007" Parameter: B <- "-28.6007" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.643" Parameter: C <- "-41.643" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1304 TOTAL ENERGY = -70.2437 RDTITL> * VAN DER WAALS = -28.6007 ELECTROSTATIC = -41.643 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1304" Parameter: CONF_N -> "8002" Comparing "1304" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1305" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763029 ATOM PAIRS WERE FOUND FOR ATOM LIST 41914 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29211 from a total of 763029 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1305 -65.65737 -4.58637 0.57469 INTE EXTERN> -30.22473 -35.43264 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6574" Parameter: A <- "-65.6574" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2247" Parameter: B <- "-30.2247" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4326" Parameter: C <- "-35.4326" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1305 TOTAL ENERGY = -65.6574 RDTITL> * VAN DER WAALS = -30.2247 ELECTROSTATIC = -35.4326 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1305" Parameter: CONF_N -> "8002" Comparing "1305" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1306" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763029 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752697 ATOM PAIRS WERE FOUND FOR ATOM LIST 41587 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29087 from a total of 752697 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1306 -70.14091 4.48354 0.65663 INTE EXTERN> -26.87491 -43.26600 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1409" Parameter: A <- "-70.1409" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8749" Parameter: B <- "-26.8749" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.266" Parameter: C <- "-43.266" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1306 TOTAL ENERGY = -70.1409 RDTITL> * VAN DER WAALS = -26.8749 ELECTROSTATIC = -43.266 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1306" Parameter: CONF_N -> "8002" Comparing "1306" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1307" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752697 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761437 ATOM PAIRS WERE FOUND FOR ATOM LIST 41844 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28931 from a total of 761437 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1307 -69.54695 -0.59396 0.63263 INTE EXTERN> -28.76592 -40.78102 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5469" Parameter: A <- "-69.5469" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7659" Parameter: B <- "-28.7659" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.781" Parameter: C <- "-40.781" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1307 TOTAL ENERGY = -69.5469 RDTITL> * VAN DER WAALS = -28.7659 ELECTROSTATIC = -40.781 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1307" Parameter: CONF_N -> "8002" Comparing "1307" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1308" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761437 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759707 ATOM PAIRS WERE FOUND FOR ATOM LIST 41896 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29602 from a total of 759707 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1308 -70.30334 0.75639 0.68727 INTE EXTERN> -27.64622 -42.65711 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3033" Parameter: A <- "-70.3033" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6462" Parameter: B <- "-27.6462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6571" Parameter: C <- "-42.6571" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1308 TOTAL ENERGY = -70.3033 RDTITL> * VAN DER WAALS = -27.6462 ELECTROSTATIC = -42.6571 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1308" Parameter: CONF_N -> "8002" Comparing "1308" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1309" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759707 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763538 ATOM PAIRS WERE FOUND FOR ATOM LIST 41959 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29252 from a total of 763538 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1309 -62.20577 -8.09757 0.79794 INTE EXTERN> -22.72010 -39.48567 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.2058" Parameter: A <- "-62.2058" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.7201" Parameter: B <- "-22.7201" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4857" Parameter: C <- "-39.4857" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1309 TOTAL ENERGY = -62.2058 RDTITL> * VAN DER WAALS = -22.7201 ELECTROSTATIC = -39.4857 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1309" Parameter: CONF_N -> "8002" Comparing "1309" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1310" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763538 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768955 ATOM PAIRS WERE FOUND FOR ATOM LIST 41970 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29605 from a total of 768955 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1310 -68.81868 6.61291 0.70280 INTE EXTERN> -27.64136 -41.17732 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8187" Parameter: A <- "-68.8187" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6414" Parameter: B <- "-27.6414" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1773" Parameter: C <- "-41.1773" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1310 TOTAL ENERGY = -68.8187 RDTITL> * VAN DER WAALS = -27.6414 ELECTROSTATIC = -41.1773 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1310" Parameter: CONF_N -> "8002" Comparing "1310" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1311" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768955 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768087 ATOM PAIRS WERE FOUND FOR ATOM LIST 42222 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29649 from a total of 768087 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1311 -64.02061 -4.79807 0.57451 INTE EXTERN> -29.74689 -34.27372 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0206" Parameter: A <- "-64.0206" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7469" Parameter: B <- "-29.7469" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2737" Parameter: C <- "-34.2737" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1311 TOTAL ENERGY = -64.0206 RDTITL> * VAN DER WAALS = -29.7469 ELECTROSTATIC = -34.2737 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1311" Parameter: CONF_N -> "8002" Comparing "1311" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1312" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768087 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762262 ATOM PAIRS WERE FOUND FOR ATOM LIST 41635 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29413 from a total of 762262 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1312 -70.91092 6.89032 0.62161 INTE EXTERN> -30.15458 -40.75634 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9109" Parameter: A <- "-70.9109" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1546" Parameter: B <- "-30.1546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7563" Parameter: C <- "-40.7563" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1312 TOTAL ENERGY = -70.9109 RDTITL> * VAN DER WAALS = -30.1546 ELECTROSTATIC = -40.7563 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1312" Parameter: CONF_N -> "8002" Comparing "1312" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1313" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762262 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762899 ATOM PAIRS WERE FOUND FOR ATOM LIST 41974 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30062 from a total of 762899 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1313 -65.63427 -5.27665 0.67226 INTE EXTERN> -28.19086 -37.44341 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6343" Parameter: A <- "-65.6343" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1909" Parameter: B <- "-28.1909" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4434" Parameter: C <- "-37.4434" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1313 TOTAL ENERGY = -65.6343 RDTITL> * VAN DER WAALS = -28.1909 ELECTROSTATIC = -37.4434 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1313" Parameter: CONF_N -> "8002" Comparing "1313" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1314" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762899 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767626 ATOM PAIRS WERE FOUND FOR ATOM LIST 42181 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30088 from a total of 767626 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1314 -66.03233 0.39805 0.69658 INTE EXTERN> -26.35738 -39.67494 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0323" Parameter: A <- "-66.0323" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3574" Parameter: B <- "-26.3574" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6749" Parameter: C <- "-39.6749" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1314 TOTAL ENERGY = -66.0323 RDTITL> * VAN DER WAALS = -26.3574 ELECTROSTATIC = -39.6749 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1314" Parameter: CONF_N -> "8002" Comparing "1314" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1315" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767626 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 774343 ATOM PAIRS WERE FOUND FOR ATOM LIST 42401 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29493 from a total of 774343 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1315 -61.57015 -4.46218 0.71261 INTE EXTERN> -25.23155 -36.33861 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.5702" Parameter: A <- "-61.5702" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2315" Parameter: B <- "-25.2315" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3386" Parameter: C <- "-36.3386" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1315 TOTAL ENERGY = -61.5702 RDTITL> * VAN DER WAALS = -25.2315 ELECTROSTATIC = -36.3386 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1315" Parameter: CONF_N -> "8002" Comparing "1315" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1316" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 774343 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766162 ATOM PAIRS WERE FOUND FOR ATOM LIST 41993 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29115 from a total of 766162 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1316 -66.26950 4.69935 0.67239 INTE EXTERN> -27.22557 -39.04393 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2695" Parameter: A <- "-66.2695" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2256" Parameter: B <- "-27.2256" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0439" Parameter: C <- "-39.0439" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1316 TOTAL ENERGY = -66.2695 RDTITL> * VAN DER WAALS = -27.2256 ELECTROSTATIC = -39.0439 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1316" Parameter: CONF_N -> "8002" Comparing "1316" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1317" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766162 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765886 ATOM PAIRS WERE FOUND FOR ATOM LIST 42175 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29434 from a total of 765886 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1317 -65.37580 -0.89370 0.69348 INTE EXTERN> -25.91375 -39.46204 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3758" Parameter: A <- "-65.3758" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9138" Parameter: B <- "-25.9138" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.462" Parameter: C <- "-39.462" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1317 TOTAL ENERGY = -65.3758 RDTITL> * VAN DER WAALS = -25.9138 ELECTROSTATIC = -39.462 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1317" Parameter: CONF_N -> "8002" Comparing "1317" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1318" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765886 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769407 ATOM PAIRS WERE FOUND FOR ATOM LIST 42180 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30246 from a total of 769407 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1318 -73.37382 7.99802 0.74664 INTE EXTERN> -28.07454 -45.29928 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3738" Parameter: A <- "-73.3738" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0745" Parameter: B <- "-28.0745" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2993" Parameter: C <- "-45.2993" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1318 TOTAL ENERGY = -73.3738 RDTITL> * VAN DER WAALS = -28.0745 ELECTROSTATIC = -45.2993 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1318" Parameter: CONF_N -> "8002" Comparing "1318" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1319" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769407 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763056 ATOM PAIRS WERE FOUND FOR ATOM LIST 41983 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29803 from a total of 763056 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1319 -71.91345 -1.46036 0.60060 INTE EXTERN> -32.30352 -39.60993 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9135" Parameter: A <- "-71.9135" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3035" Parameter: B <- "-32.3035" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6099" Parameter: C <- "-39.6099" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1319 TOTAL ENERGY = -71.9135 RDTITL> * VAN DER WAALS = -32.3035 ELECTROSTATIC = -39.6099 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1319" Parameter: CONF_N -> "8002" Comparing "1319" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1320" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763056 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761059 ATOM PAIRS WERE FOUND FOR ATOM LIST 41844 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28903 from a total of 761059 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1320 -66.55636 -5.35709 0.62381 INTE EXTERN> -28.08429 -38.47207 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5564" Parameter: A <- "-66.5564" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0843" Parameter: B <- "-28.0843" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4721" Parameter: C <- "-38.4721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1320 TOTAL ENERGY = -66.5564 RDTITL> * VAN DER WAALS = -28.0843 ELECTROSTATIC = -38.4721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1320" Parameter: CONF_N -> "8002" Comparing "1320" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1321" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761059 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765507 ATOM PAIRS WERE FOUND FOR ATOM LIST 41977 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30229 from a total of 765507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1321 -73.58795 7.03160 0.72636 INTE EXTERN> -27.58563 -46.00233 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.588" Parameter: A <- "-73.588" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5856" Parameter: B <- "-27.5856" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0023" Parameter: C <- "-46.0023" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1321 TOTAL ENERGY = -73.588 RDTITL> * VAN DER WAALS = -27.5856 ELECTROSTATIC = -46.0023 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1321" Parameter: CONF_N -> "8002" Comparing "1321" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1322" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764847 ATOM PAIRS WERE FOUND FOR ATOM LIST 41993 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29690 from a total of 764847 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1322 -66.82050 -6.76745 0.63458 INTE EXTERN> -27.42029 -39.40021 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8205" Parameter: A <- "-66.8205" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4203" Parameter: B <- "-27.4203" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4002" Parameter: C <- "-39.4002" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1322 TOTAL ENERGY = -66.8205 RDTITL> * VAN DER WAALS = -27.4203 ELECTROSTATIC = -39.4002 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1322" Parameter: CONF_N -> "8002" Comparing "1322" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1323" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764847 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763063 ATOM PAIRS WERE FOUND FOR ATOM LIST 41962 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29186 from a total of 763063 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1323 -61.40646 -5.41405 0.64077 INTE EXTERN> -29.19387 -32.21258 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.4065" Parameter: A <- "-61.4065" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1939" Parameter: B <- "-29.1939" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2126" Parameter: C <- "-32.2126" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1323 TOTAL ENERGY = -61.4065 RDTITL> * VAN DER WAALS = -29.1939 ELECTROSTATIC = -32.2126 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1323" Parameter: CONF_N -> "8002" Comparing "1323" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1324" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763063 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760096 ATOM PAIRS WERE FOUND FOR ATOM LIST 41720 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29024 from a total of 760096 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1324 -68.19902 6.79257 0.91064 INTE EXTERN> -23.28881 -44.91021 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.199" Parameter: A <- "-68.199" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.2888" Parameter: B <- "-23.2888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9102" Parameter: C <- "-44.9102" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1324 TOTAL ENERGY = -68.199 RDTITL> * VAN DER WAALS = -23.2888 ELECTROSTATIC = -44.9102 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1324" Parameter: CONF_N -> "8002" Comparing "1324" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1325" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760096 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758993 ATOM PAIRS WERE FOUND FOR ATOM LIST 41764 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28929 from a total of 758993 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1325 -72.39678 4.19776 0.70283 INTE EXTERN> -27.47285 -44.92393 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3968" Parameter: A <- "-72.3968" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4728" Parameter: B <- "-27.4728" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9239" Parameter: C <- "-44.9239" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1325 TOTAL ENERGY = -72.3968 RDTITL> * VAN DER WAALS = -27.4728 ELECTROSTATIC = -44.9239 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1325" Parameter: CONF_N -> "8002" Comparing "1325" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1326" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758993 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761348 ATOM PAIRS WERE FOUND FOR ATOM LIST 41889 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29073 from a total of 761348 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1326 -64.38729 -8.00949 0.67936 INTE EXTERN> -25.16560 -39.22170 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3873" Parameter: A <- "-64.3873" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1656" Parameter: B <- "-25.1656" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2217" Parameter: C <- "-39.2217" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1326 TOTAL ENERGY = -64.3873 RDTITL> * VAN DER WAALS = -25.1656 ELECTROSTATIC = -39.2217 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1326" Parameter: CONF_N -> "8002" Comparing "1326" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1327" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761348 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759864 ATOM PAIRS WERE FOUND FOR ATOM LIST 41722 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29196 from a total of 759864 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1327 -72.53360 8.14631 0.68460 INTE EXTERN> -27.99127 -44.54233 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5336" Parameter: A <- "-72.5336" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9913" Parameter: B <- "-27.9913" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5423" Parameter: C <- "-44.5423" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1327 TOTAL ENERGY = -72.5336 RDTITL> * VAN DER WAALS = -27.9913 ELECTROSTATIC = -44.5423 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1327" Parameter: CONF_N -> "8002" Comparing "1327" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1328" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759864 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758918 ATOM PAIRS WERE FOUND FOR ATOM LIST 41738 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29553 from a total of 758918 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1328 -76.06930 3.53570 0.72296 INTE EXTERN> -27.25690 -48.81240 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0693" Parameter: A <- "-76.0693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2569" Parameter: B <- "-27.2569" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8124" Parameter: C <- "-48.8124" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1328 TOTAL ENERGY = -76.0693 RDTITL> * VAN DER WAALS = -27.2569 ELECTROSTATIC = -48.8124 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1328" Parameter: CONF_N -> "8002" Comparing "1328" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1329" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758918 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753168 ATOM PAIRS WERE FOUND FOR ATOM LIST 41597 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29641 from a total of 753168 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1329 -63.53678 -12.53252 0.74161 INTE EXTERN> -25.61729 -37.91949 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5368" Parameter: A <- "-63.5368" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6173" Parameter: B <- "-25.6173" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9195" Parameter: C <- "-37.9195" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1329 TOTAL ENERGY = -63.5368 RDTITL> * VAN DER WAALS = -25.6173 ELECTROSTATIC = -37.9195 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1329" Parameter: CONF_N -> "8002" Comparing "1329" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1330" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753168 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761549 ATOM PAIRS WERE FOUND FOR ATOM LIST 41722 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29800 from a total of 761549 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1330 -68.47417 4.93740 0.63831 INTE EXTERN> -29.73428 -38.73989 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4742" Parameter: A <- "-68.4742" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7343" Parameter: B <- "-29.7343" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7399" Parameter: C <- "-38.7399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1330 TOTAL ENERGY = -68.4742 RDTITL> * VAN DER WAALS = -29.7343 ELECTROSTATIC = -38.7399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1330" Parameter: CONF_N -> "8002" Comparing "1330" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1331" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761549 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765393 ATOM PAIRS WERE FOUND FOR ATOM LIST 42189 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29825 from a total of 765393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1331 -59.95994 -8.51423 0.78028 INTE EXTERN> -23.06308 -36.89687 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.9599" Parameter: A <- "-59.9599" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.0631" Parameter: B <- "-23.0631" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8969" Parameter: C <- "-36.8969" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1331 TOTAL ENERGY = -59.9599 RDTITL> * VAN DER WAALS = -23.0631 ELECTROSTATIC = -36.8969 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1331" Parameter: CONF_N -> "8002" Comparing "1331" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1332" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762702 ATOM PAIRS WERE FOUND FOR ATOM LIST 41795 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29577 from a total of 762702 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1332 -69.93443 9.97449 0.58809 INTE EXTERN> -31.59169 -38.34274 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9344" Parameter: A <- "-69.9344" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5917" Parameter: B <- "-31.5917" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3427" Parameter: C <- "-38.3427" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1332 TOTAL ENERGY = -69.9344 RDTITL> * VAN DER WAALS = -31.5917 ELECTROSTATIC = -38.3427 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1332" Parameter: CONF_N -> "8002" Comparing "1332" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1333" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762702 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753362 ATOM PAIRS WERE FOUND FOR ATOM LIST 41460 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29343 from a total of 753362 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1333 -66.51495 -3.41948 0.74148 INTE EXTERN> -26.13110 -40.38384 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5149" Parameter: A <- "-66.5149" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1311" Parameter: B <- "-26.1311" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3838" Parameter: C <- "-40.3838" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1333 TOTAL ENERGY = -66.5149 RDTITL> * VAN DER WAALS = -26.1311 ELECTROSTATIC = -40.3838 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1333" Parameter: CONF_N -> "8002" Comparing "1333" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1334" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753362 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761805 ATOM PAIRS WERE FOUND FOR ATOM LIST 41655 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29165 from a total of 761805 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1334 -67.06698 0.55203 0.68553 INTE EXTERN> -27.54799 -39.51899 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.067" Parameter: A <- "-67.067" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.548" Parameter: B <- "-27.548" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.519" Parameter: C <- "-39.519" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1334 TOTAL ENERGY = -67.067 RDTITL> * VAN DER WAALS = -27.548 ELECTROSTATIC = -39.519 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1334" Parameter: CONF_N -> "8002" Comparing "1334" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1335" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761805 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758621 ATOM PAIRS WERE FOUND FOR ATOM LIST 41824 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29156 from a total of 758621 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1335 -72.95766 5.89068 0.72774 INTE EXTERN> -27.72760 -45.23005 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9577" Parameter: A <- "-72.9577" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7276" Parameter: B <- "-27.7276" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2301" Parameter: C <- "-45.2301" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1335 TOTAL ENERGY = -72.9577 RDTITL> * VAN DER WAALS = -27.7276 ELECTROSTATIC = -45.2301 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1335" Parameter: CONF_N -> "8002" Comparing "1335" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1336" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758621 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764354 ATOM PAIRS WERE FOUND FOR ATOM LIST 41974 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29582 from a total of 764354 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1336 -69.92329 -3.03436 0.54230 INTE EXTERN> -32.64063 -37.28266 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9233" Parameter: A <- "-69.9233" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6406" Parameter: B <- "-32.6406" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2827" Parameter: C <- "-37.2827" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1336 TOTAL ENERGY = -69.9233 RDTITL> * VAN DER WAALS = -32.6406 ELECTROSTATIC = -37.2827 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1336" Parameter: CONF_N -> "8002" Comparing "1336" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1337" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764354 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763442 ATOM PAIRS WERE FOUND FOR ATOM LIST 42185 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29239 from a total of 763442 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1337 -67.47903 -2.44426 0.75891 INTE EXTERN> -24.40477 -43.07426 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.479" Parameter: A <- "-67.479" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4048" Parameter: B <- "-24.4048" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0743" Parameter: C <- "-43.0743" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1337 TOTAL ENERGY = -67.479 RDTITL> * VAN DER WAALS = -24.4048 ELECTROSTATIC = -43.0743 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1337" Parameter: CONF_N -> "8002" Comparing "1337" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1338" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763442 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766165 ATOM PAIRS WERE FOUND FOR ATOM LIST 42067 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30287 from a total of 766165 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1338 -62.25693 -5.22210 0.67549 INTE EXTERN> -27.03133 -35.22560 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.2569" Parameter: A <- "-62.2569" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0313" Parameter: B <- "-27.0313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2256" Parameter: C <- "-35.2256" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1338 TOTAL ENERGY = -62.2569 RDTITL> * VAN DER WAALS = -27.0313 ELECTROSTATIC = -35.2256 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1338" Parameter: CONF_N -> "8002" Comparing "1338" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1339" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766165 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767352 ATOM PAIRS WERE FOUND FOR ATOM LIST 42322 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29847 from a total of 767352 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1339 -62.42554 0.16862 0.67924 INTE EXTERN> -27.72128 -34.70426 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.4255" Parameter: A <- "-62.4255" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7213" Parameter: B <- "-27.7213" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7043" Parameter: C <- "-34.7043" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1339 TOTAL ENERGY = -62.4255 RDTITL> * VAN DER WAALS = -27.7213 ELECTROSTATIC = -34.7043 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1339" Parameter: CONF_N -> "8002" Comparing "1339" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1340" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767352 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767155 ATOM PAIRS WERE FOUND FOR ATOM LIST 42228 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30282 from a total of 767155 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1340 -69.18031 6.75477 0.72488 INTE EXTERN> -25.07985 -44.10047 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1803" Parameter: A <- "-69.1803" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0798" Parameter: B <- "-25.0798" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1005" Parameter: C <- "-44.1005" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1340 TOTAL ENERGY = -69.1803 RDTITL> * VAN DER WAALS = -25.0798 ELECTROSTATIC = -44.1005 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1340" Parameter: CONF_N -> "8002" Comparing "1340" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1341" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767155 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762428 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29546 from a total of 762428 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1341 -67.34978 -1.83054 0.64050 INTE EXTERN> -29.10662 -38.24315 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3498" Parameter: A <- "-67.3498" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1066" Parameter: B <- "-29.1066" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2432" Parameter: C <- "-38.2432" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1341 TOTAL ENERGY = -67.3498 RDTITL> * VAN DER WAALS = -29.1066 ELECTROSTATIC = -38.2432 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1341" Parameter: CONF_N -> "8002" Comparing "1341" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1342" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762428 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766292 ATOM PAIRS WERE FOUND FOR ATOM LIST 42068 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29376 from a total of 766292 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1342 -70.72482 3.37504 0.70188 INTE EXTERN> -26.41242 -44.31239 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7248" Parameter: A <- "-70.7248" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4124" Parameter: B <- "-26.4124" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3124" Parameter: C <- "-44.3124" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1342 TOTAL ENERGY = -70.7248 RDTITL> * VAN DER WAALS = -26.4124 ELECTROSTATIC = -44.3124 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1342" Parameter: CONF_N -> "8002" Comparing "1342" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1343" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766292 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764141 ATOM PAIRS WERE FOUND FOR ATOM LIST 42022 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29430 from a total of 764141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1343 -70.29615 -0.42867 0.74640 INTE EXTERN> -24.76548 -45.53067 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2962" Parameter: A <- "-70.2962" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7655" Parameter: B <- "-24.7655" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5307" Parameter: C <- "-45.5307" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1343 TOTAL ENERGY = -70.2962 RDTITL> * VAN DER WAALS = -24.7655 ELECTROSTATIC = -45.5307 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1343" Parameter: CONF_N -> "8002" Comparing "1343" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1344" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763407 ATOM PAIRS WERE FOUND FOR ATOM LIST 41935 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29396 from a total of 763407 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1344 -68.69473 -1.60143 0.67358 INTE EXTERN> -27.93381 -40.76092 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6947" Parameter: A <- "-68.6947" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9338" Parameter: B <- "-27.9338" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7609" Parameter: C <- "-40.7609" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1344 TOTAL ENERGY = -68.6947 RDTITL> * VAN DER WAALS = -27.9338 ELECTROSTATIC = -40.7609 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1344" Parameter: CONF_N -> "8002" Comparing "1344" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1345" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763407 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766559 ATOM PAIRS WERE FOUND FOR ATOM LIST 41921 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28663 from a total of 766559 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1345 -58.85567 -9.83905 0.65798 INTE EXTERN> -27.27577 -31.57990 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.8557" Parameter: A <- "-58.8557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2758" Parameter: B <- "-27.2758" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.5799" Parameter: C <- "-31.5799" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1345 TOTAL ENERGY = -58.8557 RDTITL> * VAN DER WAALS = -27.2758 ELECTROSTATIC = -31.5799 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1345" Parameter: CONF_N -> "8002" Comparing "1345" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1346" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766559 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761173 ATOM PAIRS WERE FOUND FOR ATOM LIST 41786 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29491 from a total of 761173 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1346 -69.91402 11.05835 0.70533 INTE EXTERN> -26.24175 -43.67227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.914" Parameter: A <- "-69.914" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2417" Parameter: B <- "-26.2417" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6723" Parameter: C <- "-43.6723" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1346 TOTAL ENERGY = -69.914 RDTITL> * VAN DER WAALS = -26.2417 ELECTROSTATIC = -43.6723 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1346" Parameter: CONF_N -> "8002" Comparing "1346" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1347" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761173 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758454 ATOM PAIRS WERE FOUND FOR ATOM LIST 41495 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28808 from a total of 758454 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1347 -69.59636 -0.31767 0.62168 INTE EXTERN> -29.77420 -39.82216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5964" Parameter: A <- "-69.5964" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7742" Parameter: B <- "-29.7742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8222" Parameter: C <- "-39.8222" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1347 TOTAL ENERGY = -69.5964 RDTITL> * VAN DER WAALS = -29.7742 ELECTROSTATIC = -39.8222 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1347" Parameter: CONF_N -> "8002" Comparing "1347" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1348" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758454 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754317 ATOM PAIRS WERE FOUND FOR ATOM LIST 41562 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29066 from a total of 754317 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1348 -61.61498 -7.98137 0.60415 INTE EXTERN> -29.90236 -31.71262 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.615" Parameter: A <- "-61.615" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9024" Parameter: B <- "-29.9024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.7126" Parameter: C <- "-31.7126" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1348 TOTAL ENERGY = -61.615 RDTITL> * VAN DER WAALS = -29.9024 ELECTROSTATIC = -31.7126 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1348" Parameter: CONF_N -> "8002" Comparing "1348" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1349" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754317 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758890 ATOM PAIRS WERE FOUND FOR ATOM LIST 41639 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28916 from a total of 758890 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1349 -69.09191 7.47693 0.68498 INTE EXTERN> -28.98594 -40.10597 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0919" Parameter: A <- "-69.0919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9859" Parameter: B <- "-28.9859" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.106" Parameter: C <- "-40.106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1349 TOTAL ENERGY = -69.0919 RDTITL> * VAN DER WAALS = -28.9859 ELECTROSTATIC = -40.106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1349" Parameter: CONF_N -> "8002" Comparing "1349" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1350" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758890 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758292 ATOM PAIRS WERE FOUND FOR ATOM LIST 41499 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29435 from a total of 758292 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1350 -65.75763 -3.33428 0.67144 INTE EXTERN> -25.76660 -39.99103 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7576" Parameter: A <- "-65.7576" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7666" Parameter: B <- "-25.7666" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.991" Parameter: C <- "-39.991" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1350 TOTAL ENERGY = -65.7576 RDTITL> * VAN DER WAALS = -25.7666 ELECTROSTATIC = -39.991 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1350" Parameter: CONF_N -> "8002" Comparing "1350" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1351" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758292 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761686 ATOM PAIRS WERE FOUND FOR ATOM LIST 41891 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29060 from a total of 761686 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1351 -66.10230 0.34467 0.83401 INTE EXTERN> -23.39659 -42.70571 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1023" Parameter: A <- "-66.1023" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.3966" Parameter: B <- "-23.3966" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7057" Parameter: C <- "-42.7057" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1351 TOTAL ENERGY = -66.1023 RDTITL> * VAN DER WAALS = -23.3966 ELECTROSTATIC = -42.7057 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1351" Parameter: CONF_N -> "8002" Comparing "1351" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1352" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761686 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763733 ATOM PAIRS WERE FOUND FOR ATOM LIST 41966 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29217 from a total of 763733 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1352 -68.66633 2.56403 0.65588 INTE EXTERN> -30.98126 -37.68508 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6663" Parameter: A <- "-68.6663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9813" Parameter: B <- "-30.9813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6851" Parameter: C <- "-37.6851" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1352 TOTAL ENERGY = -68.6663 RDTITL> * VAN DER WAALS = -30.9813 ELECTROSTATIC = -37.6851 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1352" Parameter: CONF_N -> "8002" Comparing "1352" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1353" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763733 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761622 ATOM PAIRS WERE FOUND FOR ATOM LIST 41891 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28763 from a total of 761622 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1353 -64.96690 -3.69943 0.61783 INTE EXTERN> -28.57530 -36.39160 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9669" Parameter: A <- "-64.9669" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5753" Parameter: B <- "-28.5753" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3916" Parameter: C <- "-36.3916" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1353 TOTAL ENERGY = -64.9669 RDTITL> * VAN DER WAALS = -28.5753 ELECTROSTATIC = -36.3916 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1353" Parameter: CONF_N -> "8002" Comparing "1353" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1354" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761622 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761468 ATOM PAIRS WERE FOUND FOR ATOM LIST 41817 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29150 from a total of 761468 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1354 -69.07726 4.11036 0.74406 INTE EXTERN> -26.67471 -42.40254 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0773" Parameter: A <- "-69.0773" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6747" Parameter: B <- "-26.6747" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4025" Parameter: C <- "-42.4025" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1354 TOTAL ENERGY = -69.0773 RDTITL> * VAN DER WAALS = -26.6747 ELECTROSTATIC = -42.4025 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1354" Parameter: CONF_N -> "8002" Comparing "1354" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1355" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761468 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762521 ATOM PAIRS WERE FOUND FOR ATOM LIST 42001 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29775 from a total of 762521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1355 -68.48192 -0.59534 0.78671 INTE EXTERN> -24.16593 -44.31599 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4819" Parameter: A <- "-68.4819" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1659" Parameter: B <- "-24.1659" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.316" Parameter: C <- "-44.316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1355 TOTAL ENERGY = -68.4819 RDTITL> * VAN DER WAALS = -24.1659 ELECTROSTATIC = -44.316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1355" Parameter: CONF_N -> "8002" Comparing "1355" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1356" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772479 ATOM PAIRS WERE FOUND FOR ATOM LIST 42504 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28929 from a total of 772479 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1356 -69.94720 1.46528 0.62638 INTE EXTERN> -29.55830 -40.38890 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9472" Parameter: A <- "-69.9472" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5583" Parameter: B <- "-29.5583" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3889" Parameter: C <- "-40.3889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1356 TOTAL ENERGY = -69.9472 RDTITL> * VAN DER WAALS = -29.5583 ELECTROSTATIC = -40.3889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1356" Parameter: CONF_N -> "8002" Comparing "1356" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1357" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772479 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764303 ATOM PAIRS WERE FOUND FOR ATOM LIST 41965 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29166 from a total of 764303 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1357 -62.99595 -6.95126 0.64008 INTE EXTERN> -27.43500 -35.56095 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9959" Parameter: A <- "-62.9959" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.435" Parameter: B <- "-27.435" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5609" Parameter: C <- "-35.5609" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1357 TOTAL ENERGY = -62.9959 RDTITL> * VAN DER WAALS = -27.435 ELECTROSTATIC = -35.5609 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1357" Parameter: CONF_N -> "8002" Comparing "1357" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1358" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764303 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763078 ATOM PAIRS WERE FOUND FOR ATOM LIST 41902 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29127 from a total of 763078 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1358 -74.28289 11.28694 0.72225 INTE EXTERN> -24.26449 -50.01840 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2829" Parameter: A <- "-74.2829" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2645" Parameter: B <- "-24.2645" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0184" Parameter: C <- "-50.0184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1358 TOTAL ENERGY = -74.2829 RDTITL> * VAN DER WAALS = -24.2645 ELECTROSTATIC = -50.0184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1358" Parameter: CONF_N -> "8002" Comparing "1358" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1359" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763078 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767788 ATOM PAIRS WERE FOUND FOR ATOM LIST 42357 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29571 from a total of 767788 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1359 -70.45487 -3.82801 0.62308 INTE EXTERN> -30.42259 -40.03229 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4549" Parameter: A <- "-70.4549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4226" Parameter: B <- "-30.4226" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0323" Parameter: C <- "-40.0323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1359 TOTAL ENERGY = -70.4549 RDTITL> * VAN DER WAALS = -30.4226 ELECTROSTATIC = -40.0323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1359" Parameter: CONF_N -> "8002" Comparing "1359" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1360" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767788 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764574 ATOM PAIRS WERE FOUND FOR ATOM LIST 41960 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28728 from a total of 764574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1360 -69.22195 -1.23293 0.57565 INTE EXTERN> -31.54910 -37.67285 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2219" Parameter: A <- "-69.2219" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5491" Parameter: B <- "-31.5491" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6728" Parameter: C <- "-37.6728" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1360 TOTAL ENERGY = -69.2219 RDTITL> * VAN DER WAALS = -31.5491 ELECTROSTATIC = -37.6728 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1360" Parameter: CONF_N -> "8002" Comparing "1360" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1361" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762330 ATOM PAIRS WERE FOUND FOR ATOM LIST 41847 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29053 from a total of 762330 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1361 -62.54313 -6.67882 0.87879 INTE EXTERN> -23.01719 -39.52593 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5431" Parameter: A <- "-62.5431" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.0172" Parameter: B <- "-23.0172" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5259" Parameter: C <- "-39.5259" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1361 TOTAL ENERGY = -62.5431 RDTITL> * VAN DER WAALS = -23.0172 ELECTROSTATIC = -39.5259 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1361" Parameter: CONF_N -> "8002" Comparing "1361" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1362" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762330 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763960 ATOM PAIRS WERE FOUND FOR ATOM LIST 42106 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29116 from a total of 763960 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1362 -66.94241 4.39928 0.73237 INTE EXTERN> -24.23991 -42.70250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9424" Parameter: A <- "-66.9424" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2399" Parameter: B <- "-24.2399" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7025" Parameter: C <- "-42.7025" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1362 TOTAL ENERGY = -66.9424 RDTITL> * VAN DER WAALS = -24.2399 ELECTROSTATIC = -42.7025 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1362" Parameter: CONF_N -> "8002" Comparing "1362" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1363" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763960 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768747 ATOM PAIRS WERE FOUND FOR ATOM LIST 42047 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29142 from a total of 768747 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1363 -69.58836 2.64595 0.63921 INTE EXTERN> -28.74928 -40.83909 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5884" Parameter: A <- "-69.5884" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7493" Parameter: B <- "-28.7493" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8391" Parameter: C <- "-40.8391" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1363 TOTAL ENERGY = -69.5884 RDTITL> * VAN DER WAALS = -28.7493 ELECTROSTATIC = -40.8391 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1363" Parameter: CONF_N -> "8002" Comparing "1363" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1364" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768747 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765773 ATOM PAIRS WERE FOUND FOR ATOM LIST 41873 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29235 from a total of 765773 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1364 -68.33466 -1.25370 0.70109 INTE EXTERN> -28.05960 -40.27505 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3347" Parameter: A <- "-68.3347" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0596" Parameter: B <- "-28.0596" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2751" Parameter: C <- "-40.2751" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1364 TOTAL ENERGY = -68.3347 RDTITL> * VAN DER WAALS = -28.0596 ELECTROSTATIC = -40.2751 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1364" Parameter: CONF_N -> "8002" Comparing "1364" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1365" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765773 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765897 ATOM PAIRS WERE FOUND FOR ATOM LIST 42270 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29435 from a total of 765897 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1365 -69.25561 0.92095 0.73352 INTE EXTERN> -22.81079 -46.44482 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2556" Parameter: A <- "-69.2556" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.8108" Parameter: B <- "-22.8108" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4448" Parameter: C <- "-46.4448" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1365 TOTAL ENERGY = -69.2556 RDTITL> * VAN DER WAALS = -22.8108 ELECTROSTATIC = -46.4448 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1365" Parameter: CONF_N -> "8002" Comparing "1365" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1366" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765897 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772703 ATOM PAIRS WERE FOUND FOR ATOM LIST 42406 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29265 from a total of 772703 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1366 -66.70944 -2.54617 0.74632 INTE EXTERN> -23.05002 -43.65942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7094" Parameter: A <- "-66.7094" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.05" Parameter: B <- "-23.05" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6594" Parameter: C <- "-43.6594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1366 TOTAL ENERGY = -66.7094 RDTITL> * VAN DER WAALS = -23.05 ELECTROSTATIC = -43.6594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1366" Parameter: CONF_N -> "8002" Comparing "1366" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1367" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772703 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761879 ATOM PAIRS WERE FOUND FOR ATOM LIST 41834 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29642 from a total of 761879 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1367 -72.63890 5.92947 0.55971 INTE EXTERN> -32.23939 -40.39951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6389" Parameter: A <- "-72.6389" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2394" Parameter: B <- "-32.2394" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3995" Parameter: C <- "-40.3995" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1367 TOTAL ENERGY = -72.6389 RDTITL> * VAN DER WAALS = -32.2394 ELECTROSTATIC = -40.3995 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1367" Parameter: CONF_N -> "8002" Comparing "1367" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1368" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761879 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763700 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29487 from a total of 763700 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1368 -65.24130 -7.39760 0.68823 INTE EXTERN> -26.71671 -38.52459 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2413" Parameter: A <- "-65.2413" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7167" Parameter: B <- "-26.7167" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5246" Parameter: C <- "-38.5246" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1368 TOTAL ENERGY = -65.2413 RDTITL> * VAN DER WAALS = -26.7167 ELECTROSTATIC = -38.5246 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1368" Parameter: CONF_N -> "8002" Comparing "1368" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1369" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763700 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760774 ATOM PAIRS WERE FOUND FOR ATOM LIST 41885 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28894 from a total of 760774 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1369 -64.50852 -0.73278 0.69689 INTE EXTERN> -23.37756 -41.13097 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5085" Parameter: A <- "-64.5085" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.3776" Parameter: B <- "-23.3776" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.131" Parameter: C <- "-41.131" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1369 TOTAL ENERGY = -64.5085 RDTITL> * VAN DER WAALS = -23.3776 ELECTROSTATIC = -41.131 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1369" Parameter: CONF_N -> "8002" Comparing "1369" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1370" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760774 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764048 ATOM PAIRS WERE FOUND FOR ATOM LIST 41891 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29481 from a total of 764048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1370 -72.19933 7.69080 0.70461 INTE EXTERN> -28.78453 -43.41479 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1993" Parameter: A <- "-72.1993" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7845" Parameter: B <- "-28.7845" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4148" Parameter: C <- "-43.4148" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1370 TOTAL ENERGY = -72.1993 RDTITL> * VAN DER WAALS = -28.7845 ELECTROSTATIC = -43.4148 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1370" Parameter: CONF_N -> "8002" Comparing "1370" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1371" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763263 ATOM PAIRS WERE FOUND FOR ATOM LIST 41954 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29092 from a total of 763263 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1371 -68.77315 -3.42618 0.69087 INTE EXTERN> -26.33713 -42.43601 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7731" Parameter: A <- "-68.7731" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3371" Parameter: B <- "-26.3371" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.436" Parameter: C <- "-42.436" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1371 TOTAL ENERGY = -68.7731 RDTITL> * VAN DER WAALS = -26.3371 ELECTROSTATIC = -42.436 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1371" Parameter: CONF_N -> "8002" Comparing "1371" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1372" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763263 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761900 ATOM PAIRS WERE FOUND FOR ATOM LIST 41999 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28496 from a total of 761900 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1372 -62.34825 -6.42489 0.60006 INTE EXTERN> -27.22213 -35.12612 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3483" Parameter: A <- "-62.3483" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2221" Parameter: B <- "-27.2221" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1261" Parameter: C <- "-35.1261" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1372 TOTAL ENERGY = -62.3483 RDTITL> * VAN DER WAALS = -27.2221 ELECTROSTATIC = -35.1261 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1372" Parameter: CONF_N -> "8002" Comparing "1372" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1373" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761900 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764048 ATOM PAIRS WERE FOUND FOR ATOM LIST 41899 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29523 from a total of 764048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1373 -67.45655 5.10830 0.73745 INTE EXTERN> -23.58227 -43.87428 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4565" Parameter: A <- "-67.4565" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.5823" Parameter: B <- "-23.5823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8743" Parameter: C <- "-43.8743" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1373 TOTAL ENERGY = -67.4565 RDTITL> * VAN DER WAALS = -23.5823 ELECTROSTATIC = -43.8743 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1373" Parameter: CONF_N -> "8002" Comparing "1373" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1374" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762000 ATOM PAIRS WERE FOUND FOR ATOM LIST 41766 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29491 from a total of 762000 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1374 -69.71343 2.25688 0.62808 INTE EXTERN> -27.04781 -42.66562 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7134" Parameter: A <- "-69.7134" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0478" Parameter: B <- "-27.0478" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6656" Parameter: C <- "-42.6656" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1374 TOTAL ENERGY = -69.7134 RDTITL> * VAN DER WAALS = -27.0478 ELECTROSTATIC = -42.6656 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1374" Parameter: CONF_N -> "8002" Comparing "1374" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1375" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762000 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759443 ATOM PAIRS WERE FOUND FOR ATOM LIST 41927 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29099 from a total of 759443 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1375 -61.82410 -7.88932 0.57609 INTE EXTERN> -27.25135 -34.57276 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.8241" Parameter: A <- "-61.8241" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2513" Parameter: B <- "-27.2513" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5728" Parameter: C <- "-34.5728" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1375 TOTAL ENERGY = -61.8241 RDTITL> * VAN DER WAALS = -27.2513 ELECTROSTATIC = -34.5728 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1375" Parameter: CONF_N -> "8002" Comparing "1375" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1376" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759443 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758104 ATOM PAIRS WERE FOUND FOR ATOM LIST 41923 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29502 from a total of 758104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1376 -64.03090 2.20679 0.59957 INTE EXTERN> -28.37712 -35.65378 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0309" Parameter: A <- "-64.0309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3771" Parameter: B <- "-28.3771" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6538" Parameter: C <- "-35.6538" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1376 TOTAL ENERGY = -64.0309 RDTITL> * VAN DER WAALS = -28.3771 ELECTROSTATIC = -35.6538 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1376" Parameter: CONF_N -> "8002" Comparing "1376" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1377" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762148 ATOM PAIRS WERE FOUND FOR ATOM LIST 41802 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29229 from a total of 762148 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1377 -68.97600 4.94510 0.69614 INTE EXTERN> -26.42959 -42.54641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.976" Parameter: A <- "-68.976" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4296" Parameter: B <- "-26.4296" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5464" Parameter: C <- "-42.5464" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1377 TOTAL ENERGY = -68.976 RDTITL> * VAN DER WAALS = -26.4296 ELECTROSTATIC = -42.5464 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1377" Parameter: CONF_N -> "8002" Comparing "1377" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1378" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762148 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760403 ATOM PAIRS WERE FOUND FOR ATOM LIST 41840 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29354 from a total of 760403 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1378 -64.44100 -4.53500 0.76044 INTE EXTERN> -22.72305 -41.71796 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.441" Parameter: A <- "-64.441" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.723" Parameter: B <- "-22.723" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.718" Parameter: C <- "-41.718" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1378 TOTAL ENERGY = -64.441 RDTITL> * VAN DER WAALS = -22.723 ELECTROSTATIC = -41.718 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1378" Parameter: CONF_N -> "8002" Comparing "1378" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1379" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760403 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41734 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28945 from a total of 757526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1379 -64.05670 -0.38431 0.61989 INTE EXTERN> -26.60054 -37.45616 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0567" Parameter: A <- "-64.0567" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6005" Parameter: B <- "-26.6005" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4562" Parameter: C <- "-37.4562" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1379 TOTAL ENERGY = -64.0567 RDTITL> * VAN DER WAALS = -26.6005 ELECTROSTATIC = -37.4562 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1379" Parameter: CONF_N -> "8002" Comparing "1379" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1380" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758878 ATOM PAIRS WERE FOUND FOR ATOM LIST 41655 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29999 from a total of 758878 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1380 -61.67592 -2.38078 0.62366 INTE EXTERN> -26.43208 -35.24384 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.6759" Parameter: A <- "-61.6759" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4321" Parameter: B <- "-26.4321" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2438" Parameter: C <- "-35.2438" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1380 TOTAL ENERGY = -61.6759 RDTITL> * VAN DER WAALS = -26.4321 ELECTROSTATIC = -35.2438 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1380" Parameter: CONF_N -> "8002" Comparing "1380" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1381" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758878 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765066 ATOM PAIRS WERE FOUND FOR ATOM LIST 42238 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29896 from a total of 765066 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1381 -64.81814 3.14223 0.71092 INTE EXTERN> -22.55915 -42.25899 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8181" Parameter: A <- "-64.8181" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.5591" Parameter: B <- "-22.5591" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.259" Parameter: C <- "-42.259" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1381 TOTAL ENERGY = -64.8181 RDTITL> * VAN DER WAALS = -22.5591 ELECTROSTATIC = -42.259 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1381" Parameter: CONF_N -> "8002" Comparing "1381" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1382" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765066 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763044 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29386 from a total of 763044 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1382 -55.50183 -9.31631 0.62522 INTE EXTERN> -27.92051 -27.58132 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.5018" Parameter: A <- "-55.5018" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9205" Parameter: B <- "-27.9205" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.5813" Parameter: C <- "-27.5813" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1382 TOTAL ENERGY = -55.5018 RDTITL> * VAN DER WAALS = -27.9205 ELECTROSTATIC = -27.5813 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1382" Parameter: CONF_N -> "8002" Comparing "1382" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1383" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763044 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764315 ATOM PAIRS WERE FOUND FOR ATOM LIST 42119 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29685 from a total of 764315 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1383 -63.75878 8.25695 0.76806 INTE EXTERN> -24.65899 -39.09979 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7588" Parameter: A <- "-63.7588" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.659" Parameter: B <- "-24.659" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0998" Parameter: C <- "-39.0998" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1383 TOTAL ENERGY = -63.7588 RDTITL> * VAN DER WAALS = -24.659 ELECTROSTATIC = -39.0998 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1383" Parameter: CONF_N -> "8002" Comparing "1383" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1384" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764315 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761378 ATOM PAIRS WERE FOUND FOR ATOM LIST 41814 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29395 from a total of 761378 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1384 -62.36720 -1.39158 0.69438 INTE EXTERN> -27.01911 -35.34809 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3672" Parameter: A <- "-62.3672" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0191" Parameter: B <- "-27.0191" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3481" Parameter: C <- "-35.3481" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1384 TOTAL ENERGY = -62.3672 RDTITL> * VAN DER WAALS = -27.0191 ELECTROSTATIC = -35.3481 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1384" Parameter: CONF_N -> "8002" Comparing "1384" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1385" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761378 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755733 ATOM PAIRS WERE FOUND FOR ATOM LIST 41461 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29616 from a total of 755733 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1385 -62.77341 0.40621 0.57009 INTE EXTERN> -27.22298 -35.55043 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7734" Parameter: A <- "-62.7734" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.223" Parameter: B <- "-27.223" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5504" Parameter: C <- "-35.5504" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1385 TOTAL ENERGY = -62.7734 RDTITL> * VAN DER WAALS = -27.223 ELECTROSTATIC = -35.5504 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1385" Parameter: CONF_N -> "8002" Comparing "1385" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1386" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755733 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760327 ATOM PAIRS WERE FOUND FOR ATOM LIST 41585 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29358 from a total of 760327 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1386 -65.58386 2.81044 0.72442 INTE EXTERN> -26.47527 -39.10858 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5839" Parameter: A <- "-65.5839" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4753" Parameter: B <- "-26.4753" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1086" Parameter: C <- "-39.1086" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1386 TOTAL ENERGY = -65.5839 RDTITL> * VAN DER WAALS = -26.4753 ELECTROSTATIC = -39.1086 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1386" Parameter: CONF_N -> "8002" Comparing "1386" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1387" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760327 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763160 ATOM PAIRS WERE FOUND FOR ATOM LIST 42007 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29647 from a total of 763160 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1387 -68.04744 2.46358 0.65808 INTE EXTERN> -28.77074 -39.27670 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0474" Parameter: A <- "-68.0474" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7707" Parameter: B <- "-28.7707" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2767" Parameter: C <- "-39.2767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1387 TOTAL ENERGY = -68.0474 RDTITL> * VAN DER WAALS = -28.7707 ELECTROSTATIC = -39.2767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1387" Parameter: CONF_N -> "8002" Comparing "1387" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1388" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763160 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767134 ATOM PAIRS WERE FOUND FOR ATOM LIST 42229 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30008 from a total of 767134 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1388 -66.70412 -1.34332 0.66414 INTE EXTERN> -28.75052 -37.95360 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7041" Parameter: A <- "-66.7041" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7505" Parameter: B <- "-28.7505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9536" Parameter: C <- "-37.9536" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1388 TOTAL ENERGY = -66.7041 RDTITL> * VAN DER WAALS = -28.7505 ELECTROSTATIC = -37.9536 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1388" Parameter: CONF_N -> "8002" Comparing "1388" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1389" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767134 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759051 ATOM PAIRS WERE FOUND FOR ATOM LIST 41830 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28686 from a total of 759051 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1389 -68.69135 1.98723 0.67950 INTE EXTERN> -26.18954 -42.50181 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6913" Parameter: A <- "-68.6913" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1895" Parameter: B <- "-26.1895" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5018" Parameter: C <- "-42.5018" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1389 TOTAL ENERGY = -68.6913 RDTITL> * VAN DER WAALS = -26.1895 ELECTROSTATIC = -42.5018 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1389" Parameter: CONF_N -> "8002" Comparing "1389" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1390" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759051 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761044 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29261 from a total of 761044 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1390 -71.35787 2.66653 0.67380 INTE EXTERN> -30.34607 -41.01180 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3579" Parameter: A <- "-71.3579" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3461" Parameter: B <- "-30.3461" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0118" Parameter: C <- "-41.0118" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1390 TOTAL ENERGY = -71.3579 RDTITL> * VAN DER WAALS = -30.3461 ELECTROSTATIC = -41.0118 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1390" Parameter: CONF_N -> "8002" Comparing "1390" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1391" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761044 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764341 ATOM PAIRS WERE FOUND FOR ATOM LIST 41867 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29654 from a total of 764341 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1391 -67.83538 -3.52250 0.55297 INTE EXTERN> -30.39343 -37.44195 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8354" Parameter: A <- "-67.8354" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3934" Parameter: B <- "-30.3934" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4419" Parameter: C <- "-37.4419" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1391 TOTAL ENERGY = -67.8354 RDTITL> * VAN DER WAALS = -30.3934 ELECTROSTATIC = -37.4419 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1391" Parameter: CONF_N -> "8002" Comparing "1391" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1392" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764341 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763517 ATOM PAIRS WERE FOUND FOR ATOM LIST 42170 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29130 from a total of 763517 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1392 -65.46993 -2.36545 0.85416 INTE EXTERN> -24.01305 -41.45688 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4699" Parameter: A <- "-65.4699" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.013" Parameter: B <- "-24.013" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4569" Parameter: C <- "-41.4569" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1392 TOTAL ENERGY = -65.4699 RDTITL> * VAN DER WAALS = -24.013 ELECTROSTATIC = -41.4569 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1392" Parameter: CONF_N -> "8002" Comparing "1392" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1393" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763517 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763405 ATOM PAIRS WERE FOUND FOR ATOM LIST 42109 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29766 from a total of 763405 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1393 -80.83679 15.36686 0.69541 INTE EXTERN> -29.85072 -50.98607 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.8368" Parameter: A <- "-80.8368" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8507" Parameter: B <- "-29.8507" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9861" Parameter: C <- "-50.9861" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1393 TOTAL ENERGY = -80.8368 RDTITL> * VAN DER WAALS = -29.8507 ELECTROSTATIC = -50.9861 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1393" Parameter: CONF_N -> "8002" Comparing "1393" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1394" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763405 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763679 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30038 from a total of 763679 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1394 -69.19255 -11.64424 0.88595 INTE EXTERN> -22.96783 -46.22472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1925" Parameter: A <- "-69.1925" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.9678" Parameter: B <- "-22.9678" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2247" Parameter: C <- "-46.2247" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1394 TOTAL ENERGY = -69.1925 RDTITL> * VAN DER WAALS = -22.9678 ELECTROSTATIC = -46.2247 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1394" Parameter: CONF_N -> "8002" Comparing "1394" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1395" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763679 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761751 ATOM PAIRS WERE FOUND FOR ATOM LIST 41804 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29516 from a total of 761751 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1395 -72.33212 3.13957 0.67539 INTE EXTERN> -29.47854 -42.85358 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3321" Parameter: A <- "-72.3321" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4785" Parameter: B <- "-29.4785" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8536" Parameter: C <- "-42.8536" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1395 TOTAL ENERGY = -72.3321 RDTITL> * VAN DER WAALS = -29.4785 ELECTROSTATIC = -42.8536 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1395" Parameter: CONF_N -> "8002" Comparing "1395" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1396" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761751 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764551 ATOM PAIRS WERE FOUND FOR ATOM LIST 42103 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29478 from a total of 764551 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1396 -64.35337 -7.97875 0.63382 INTE EXTERN> -28.63225 -35.72112 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3534" Parameter: A <- "-64.3534" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6322" Parameter: B <- "-28.6322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7211" Parameter: C <- "-35.7211" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1396 TOTAL ENERGY = -64.3534 RDTITL> * VAN DER WAALS = -28.6322 ELECTROSTATIC = -35.7211 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1396" Parameter: CONF_N -> "8002" Comparing "1396" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1397" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764551 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763646 ATOM PAIRS WERE FOUND FOR ATOM LIST 42027 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29937 from a total of 763646 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1397 -81.87206 17.51869 0.72934 INTE EXTERN> -26.87283 -54.99923 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8721" Parameter: A <- "-81.8721" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8728" Parameter: B <- "-26.8728" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.9992" Parameter: C <- "-54.9992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1397 TOTAL ENERGY = -81.8721 RDTITL> * VAN DER WAALS = -26.8728 ELECTROSTATIC = -54.9992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1397" Parameter: CONF_N -> "8002" Comparing "1397" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1398" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763646 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767451 ATOM PAIRS WERE FOUND FOR ATOM LIST 41974 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29870 from a total of 767451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1398 -73.64269 -8.22937 0.65910 INTE EXTERN> -29.19896 -44.44373 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6427" Parameter: A <- "-73.6427" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.199" Parameter: B <- "-29.199" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4437" Parameter: C <- "-44.4437" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1398 TOTAL ENERGY = -73.6427 RDTITL> * VAN DER WAALS = -29.199 ELECTROSTATIC = -44.4437 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1398" Parameter: CONF_N -> "8002" Comparing "1398" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1399" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762438 ATOM PAIRS WERE FOUND FOR ATOM LIST 41975 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30071 from a total of 762438 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1399 -77.87784 4.23515 0.72164 INTE EXTERN> -25.71244 -52.16540 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8778" Parameter: A <- "-77.8778" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7124" Parameter: B <- "-25.7124" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1654" Parameter: C <- "-52.1654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1399 TOTAL ENERGY = -77.8778 RDTITL> * VAN DER WAALS = -25.7124 ELECTROSTATIC = -52.1654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1399" Parameter: CONF_N -> "8002" Comparing "1399" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1400" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762438 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761247 ATOM PAIRS WERE FOUND FOR ATOM LIST 41841 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29725 from a total of 761247 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1400 -72.89313 -4.98470 0.70524 INTE EXTERN> -26.56724 -46.32590 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8931" Parameter: A <- "-72.8931" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5672" Parameter: B <- "-26.5672" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3259" Parameter: C <- "-46.3259" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1400 TOTAL ENERGY = -72.8931 RDTITL> * VAN DER WAALS = -26.5672 ELECTROSTATIC = -46.3259 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1400" Parameter: CONF_N -> "8002" Comparing "1400" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1401" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761247 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756631 ATOM PAIRS WERE FOUND FOR ATOM LIST 41615 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29502 from a total of 756631 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1401 -74.06124 1.16811 0.79487 INTE EXTERN> -25.53231 -48.52893 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0612" Parameter: A <- "-74.0612" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5323" Parameter: B <- "-25.5323" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5289" Parameter: C <- "-48.5289" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1401 TOTAL ENERGY = -74.0612 RDTITL> * VAN DER WAALS = -25.5323 ELECTROSTATIC = -48.5289 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1401" Parameter: CONF_N -> "8002" Comparing "1401" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1402" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756631 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753188 ATOM PAIRS WERE FOUND FOR ATOM LIST 41451 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28922 from a total of 753188 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1402 -71.19661 -2.86464 0.73573 INTE EXTERN> -25.08249 -46.11411 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1966" Parameter: A <- "-71.1966" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0825" Parameter: B <- "-25.0825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1141" Parameter: C <- "-46.1141" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1402 TOTAL ENERGY = -71.1966 RDTITL> * VAN DER WAALS = -25.0825 ELECTROSTATIC = -46.1141 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1402" Parameter: CONF_N -> "8002" Comparing "1402" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1403" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753188 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764986 ATOM PAIRS WERE FOUND FOR ATOM LIST 42092 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30098 from a total of 764986 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1403 -73.89799 2.70138 0.74068 INTE EXTERN> -26.39725 -47.50074 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.898" Parameter: A <- "-73.898" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3973" Parameter: B <- "-26.3973" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5007" Parameter: C <- "-47.5007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1403 TOTAL ENERGY = -73.898 RDTITL> * VAN DER WAALS = -26.3973 ELECTROSTATIC = -47.5007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1403" Parameter: CONF_N -> "8002" Comparing "1403" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1404" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764986 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760856 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29523 from a total of 760856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1404 -74.88955 0.99156 0.61324 INTE EXTERN> -30.19468 -44.69486 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8895" Parameter: A <- "-74.8895" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1947" Parameter: B <- "-30.1947" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6949" Parameter: C <- "-44.6949" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1404 TOTAL ENERGY = -74.8895 RDTITL> * VAN DER WAALS = -30.1947 ELECTROSTATIC = -44.6949 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1404" Parameter: CONF_N -> "8002" Comparing "1404" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1405" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760270 ATOM PAIRS WERE FOUND FOR ATOM LIST 41951 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29279 from a total of 760270 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1405 -66.75406 -8.13549 0.53681 INTE EXTERN> -30.15083 -36.60323 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7541" Parameter: A <- "-66.7541" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1508" Parameter: B <- "-30.1508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6032" Parameter: C <- "-36.6032" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1405 TOTAL ENERGY = -66.7541 RDTITL> * VAN DER WAALS = -30.1508 ELECTROSTATIC = -36.6032 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1405" Parameter: CONF_N -> "8002" Comparing "1405" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1406" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760270 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759859 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29600 from a total of 759859 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1406 -76.53971 9.78565 0.78093 INTE EXTERN> -25.44365 -51.09605 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5397" Parameter: A <- "-76.5397" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4437" Parameter: B <- "-25.4437" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0961" Parameter: C <- "-51.0961" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1406 TOTAL ENERGY = -76.5397 RDTITL> * VAN DER WAALS = -25.4437 ELECTROSTATIC = -51.0961 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1406" Parameter: CONF_N -> "8002" Comparing "1406" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1407" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759859 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761927 ATOM PAIRS WERE FOUND FOR ATOM LIST 41832 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30031 from a total of 761927 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1407 -67.15948 -9.38022 0.68308 INTE EXTERN> -24.51769 -42.64179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1595" Parameter: A <- "-67.1595" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5177" Parameter: B <- "-24.5177" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6418" Parameter: C <- "-42.6418" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1407 TOTAL ENERGY = -67.1595 RDTITL> * VAN DER WAALS = -24.5177 ELECTROSTATIC = -42.6418 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1407" Parameter: CONF_N -> "8002" Comparing "1407" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1408" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761927 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758507 ATOM PAIRS WERE FOUND FOR ATOM LIST 41922 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29830 from a total of 758507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1408 -75.37408 8.21459 0.70627 INTE EXTERN> -27.34414 -48.02994 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3741" Parameter: A <- "-75.3741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3441" Parameter: B <- "-27.3441" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0299" Parameter: C <- "-48.0299" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1408 TOTAL ENERGY = -75.3741 RDTITL> * VAN DER WAALS = -27.3441 ELECTROSTATIC = -48.0299 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1408" Parameter: CONF_N -> "8002" Comparing "1408" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1409" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759760 ATOM PAIRS WERE FOUND FOR ATOM LIST 41992 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29235 from a total of 759760 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1409 -71.76125 -3.61283 0.67665 INTE EXTERN> -28.30168 -43.45956 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7612" Parameter: A <- "-71.7612" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3017" Parameter: B <- "-28.3017" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4596" Parameter: C <- "-43.4596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1409 TOTAL ENERGY = -71.7612 RDTITL> * VAN DER WAALS = -28.3017 ELECTROSTATIC = -43.4596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1409" Parameter: CONF_N -> "8002" Comparing "1409" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1410" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759760 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758697 ATOM PAIRS WERE FOUND FOR ATOM LIST 41753 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29636 from a total of 758697 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1410 -76.79325 5.03200 0.67235 INTE EXTERN> -27.76420 -49.02905 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7932" Parameter: A <- "-76.7932" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7642" Parameter: B <- "-27.7642" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.029" Parameter: C <- "-49.029" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1410 TOTAL ENERGY = -76.7932 RDTITL> * VAN DER WAALS = -27.7642 ELECTROSTATIC = -49.029 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1410" Parameter: CONF_N -> "8002" Comparing "1410" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1411" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758697 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767447 ATOM PAIRS WERE FOUND FOR ATOM LIST 42225 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30222 from a total of 767447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1411 -73.71620 -3.07705 0.78253 INTE EXTERN> -27.86844 -45.84776 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7162" Parameter: A <- "-73.7162" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8684" Parameter: B <- "-27.8684" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8478" Parameter: C <- "-45.8478" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1411 TOTAL ENERGY = -73.7162 RDTITL> * VAN DER WAALS = -27.8684 ELECTROSTATIC = -45.8478 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1411" Parameter: CONF_N -> "8002" Comparing "1411" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1412" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759688 ATOM PAIRS WERE FOUND FOR ATOM LIST 42131 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29401 from a total of 759688 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1412 -71.74483 -1.97137 0.76230 INTE EXTERN> -22.64799 -49.09684 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7448" Parameter: A <- "-71.7448" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.648" Parameter: B <- "-22.648" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0968" Parameter: C <- "-49.0968" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1412 TOTAL ENERGY = -71.7448 RDTITL> * VAN DER WAALS = -22.648 ELECTROSTATIC = -49.0968 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1412" Parameter: CONF_N -> "8002" Comparing "1412" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1413" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759688 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760623 ATOM PAIRS WERE FOUND FOR ATOM LIST 41987 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29899 from a total of 760623 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1413 -77.90440 6.15957 0.69950 INTE EXTERN> -28.23873 -49.66567 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9044" Parameter: A <- "-77.9044" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2387" Parameter: B <- "-28.2387" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6657" Parameter: C <- "-49.6657" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1413 TOTAL ENERGY = -77.9044 RDTITL> * VAN DER WAALS = -28.2387 ELECTROSTATIC = -49.6657 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1413" Parameter: CONF_N -> "8002" Comparing "1413" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1414" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760623 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765762 ATOM PAIRS WERE FOUND FOR ATOM LIST 42083 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30261 from a total of 765762 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1414 -74.27587 -3.62853 0.69291 INTE EXTERN> -28.81796 -45.45791 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2759" Parameter: A <- "-74.2759" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.818" Parameter: B <- "-28.818" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4579" Parameter: C <- "-45.4579" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1414 TOTAL ENERGY = -74.2759 RDTITL> * VAN DER WAALS = -28.818 ELECTROSTATIC = -45.4579 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1414" Parameter: CONF_N -> "8002" Comparing "1414" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1415" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765762 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768458 ATOM PAIRS WERE FOUND FOR ATOM LIST 42196 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29984 from a total of 768458 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1415 -68.69188 -5.58400 0.66143 INTE EXTERN> -29.23977 -39.45210 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6919" Parameter: A <- "-68.6919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2398" Parameter: B <- "-29.2398" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4521" Parameter: C <- "-39.4521" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1415 TOTAL ENERGY = -68.6919 RDTITL> * VAN DER WAALS = -29.2398 ELECTROSTATIC = -39.4521 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1415" Parameter: CONF_N -> "8002" Comparing "1415" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1416" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768458 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757288 ATOM PAIRS WERE FOUND FOR ATOM LIST 41888 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29847 from a total of 757288 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1416 -74.11265 5.42077 0.68581 INTE EXTERN> -30.32727 -43.78538 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1126" Parameter: A <- "-74.1126" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3273" Parameter: B <- "-30.3273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7854" Parameter: C <- "-43.7854" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1416 TOTAL ENERGY = -74.1126 RDTITL> * VAN DER WAALS = -30.3273 ELECTROSTATIC = -43.7854 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1416" Parameter: CONF_N -> "8002" Comparing "1416" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1417" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757288 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763624 ATOM PAIRS WERE FOUND FOR ATOM LIST 41897 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30288 from a total of 763624 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1417 -74.87132 0.75867 0.76491 INTE EXTERN> -26.46307 -48.40825 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8713" Parameter: A <- "-74.8713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4631" Parameter: B <- "-26.4631" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4082" Parameter: C <- "-48.4082" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1417 TOTAL ENERGY = -74.8713 RDTITL> * VAN DER WAALS = -26.4631 ELECTROSTATIC = -48.4082 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1417" Parameter: CONF_N -> "8002" Comparing "1417" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1418" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763624 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765881 ATOM PAIRS WERE FOUND FOR ATOM LIST 42193 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29922 from a total of 765881 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1418 -72.61176 -2.25957 0.68094 INTE EXTERN> -27.60829 -45.00347 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6118" Parameter: A <- "-72.6118" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6083" Parameter: B <- "-27.6083" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0035" Parameter: C <- "-45.0035" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1418 TOTAL ENERGY = -72.6118 RDTITL> * VAN DER WAALS = -27.6083 ELECTROSTATIC = -45.0035 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1418" Parameter: CONF_N -> "8002" Comparing "1418" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1419" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765881 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760460 ATOM PAIRS WERE FOUND FOR ATOM LIST 41898 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29977 from a total of 760460 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1419 -70.97618 -1.63558 0.60384 INTE EXTERN> -31.70716 -39.26902 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9762" Parameter: A <- "-70.9762" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7072" Parameter: B <- "-31.7072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.269" Parameter: C <- "-39.269" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1419 TOTAL ENERGY = -70.9762 RDTITL> * VAN DER WAALS = -31.7072 ELECTROSTATIC = -39.269 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1419" Parameter: CONF_N -> "8002" Comparing "1419" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1420" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760460 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763969 ATOM PAIRS WERE FOUND FOR ATOM LIST 42059 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30384 from a total of 763969 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1420 -69.39943 -1.57675 0.66918 INTE EXTERN> -26.89718 -42.50225 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3994" Parameter: A <- "-69.3994" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8972" Parameter: B <- "-26.8972" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5022" Parameter: C <- "-42.5022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1420 TOTAL ENERGY = -69.3994 RDTITL> * VAN DER WAALS = -26.8972 ELECTROSTATIC = -42.5022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1420" Parameter: CONF_N -> "8002" Comparing "1420" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1421" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763969 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763683 ATOM PAIRS WERE FOUND FOR ATOM LIST 42157 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29829 from a total of 763683 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1421 -67.81724 -1.58219 0.62496 INTE EXTERN> -29.16879 -38.64845 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8172" Parameter: A <- "-67.8172" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1688" Parameter: B <- "-29.1688" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6485" Parameter: C <- "-38.6485" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1421 TOTAL ENERGY = -67.8172 RDTITL> * VAN DER WAALS = -29.1688 ELECTROSTATIC = -38.6485 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1421" Parameter: CONF_N -> "8002" Comparing "1421" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1422" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763683 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758911 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30050 from a total of 758911 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1422 -74.71776 6.90052 0.66867 INTE EXTERN> -29.14303 -45.57473 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7178" Parameter: A <- "-74.7178" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.143" Parameter: B <- "-29.143" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5747" Parameter: C <- "-45.5747" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1422 TOTAL ENERGY = -74.7178 RDTITL> * VAN DER WAALS = -29.143 ELECTROSTATIC = -45.5747 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1422" Parameter: CONF_N -> "8002" Comparing "1422" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1423" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758911 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760204 ATOM PAIRS WERE FOUND FOR ATOM LIST 41741 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30234 from a total of 760204 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1423 -67.69248 -7.02528 0.59890 INTE EXTERN> -29.53674 -38.15573 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6925" Parameter: A <- "-67.6925" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5367" Parameter: B <- "-29.5367" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1557" Parameter: C <- "-38.1557" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1423 TOTAL ENERGY = -67.6925 RDTITL> * VAN DER WAALS = -29.5367 ELECTROSTATIC = -38.1557 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1423" Parameter: CONF_N -> "8002" Comparing "1423" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1424" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760204 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762604 ATOM PAIRS WERE FOUND FOR ATOM LIST 41958 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29695 from a total of 762604 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1424 -62.19694 -5.49554 0.59418 INTE EXTERN> -28.32890 -33.86803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.1969" Parameter: A <- "-62.1969" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3289" Parameter: B <- "-28.3289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.868" Parameter: C <- "-33.868" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1424 TOTAL ENERGY = -62.1969 RDTITL> * VAN DER WAALS = -28.3289 ELECTROSTATIC = -33.868 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1424" Parameter: CONF_N -> "8002" Comparing "1424" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1425" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762604 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758788 ATOM PAIRS WERE FOUND FOR ATOM LIST 41966 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29126 from a total of 758788 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1425 -61.52502 -0.67192 0.58362 INTE EXTERN> -27.70076 -33.82426 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.525" Parameter: A <- "-61.525" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7008" Parameter: B <- "-27.7008" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8243" Parameter: C <- "-33.8243" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1425 TOTAL ENERGY = -61.525 RDTITL> * VAN DER WAALS = -27.7008 ELECTROSTATIC = -33.8243 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1425" Parameter: CONF_N -> "8002" Comparing "1425" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1426" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758788 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761198 ATOM PAIRS WERE FOUND FOR ATOM LIST 42033 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29856 from a total of 761198 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1426 -63.04913 1.52411 0.54773 INTE EXTERN> -29.34423 -33.70491 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.0491" Parameter: A <- "-63.0491" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3442" Parameter: B <- "-29.3442" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7049" Parameter: C <- "-33.7049" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1426 TOTAL ENERGY = -63.0491 RDTITL> * VAN DER WAALS = -29.3442 ELECTROSTATIC = -33.7049 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1426" Parameter: CONF_N -> "8002" Comparing "1426" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1427" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761198 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760458 ATOM PAIRS WERE FOUND FOR ATOM LIST 41951 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29736 from a total of 760458 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1427 -67.26460 4.21546 0.67456 INTE EXTERN> -26.25734 -41.00725 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2646" Parameter: A <- "-67.2646" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2573" Parameter: B <- "-26.2573" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0073" Parameter: C <- "-41.0073" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1427 TOTAL ENERGY = -67.2646 RDTITL> * VAN DER WAALS = -26.2573 ELECTROSTATIC = -41.0073 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1427" Parameter: CONF_N -> "8002" Comparing "1427" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1428" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760458 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757039 ATOM PAIRS WERE FOUND FOR ATOM LIST 41564 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29582 from a total of 757039 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1428 -65.72336 -1.54124 0.54088 INTE EXTERN> -31.54989 -34.17347 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7234" Parameter: A <- "-65.7234" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5499" Parameter: B <- "-31.5499" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1735" Parameter: C <- "-34.1735" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1428 TOTAL ENERGY = -65.7234 RDTITL> * VAN DER WAALS = -31.5499 ELECTROSTATIC = -34.1735 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1428" Parameter: CONF_N -> "8002" Comparing "1428" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1429" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757039 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757613 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29574 from a total of 757613 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1429 -74.13971 8.41635 0.67180 INTE EXTERN> -27.04919 -47.09051 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1397" Parameter: A <- "-74.1397" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0492" Parameter: B <- "-27.0492" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0905" Parameter: C <- "-47.0905" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1429 TOTAL ENERGY = -74.1397 RDTITL> * VAN DER WAALS = -27.0492 ELECTROSTATIC = -47.0905 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1429" Parameter: CONF_N -> "8002" Comparing "1429" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1430" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757613 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757276 ATOM PAIRS WERE FOUND FOR ATOM LIST 41483 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29111 from a total of 757276 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1430 -77.01793 2.87822 0.72301 INTE EXTERN> -27.58458 -49.43334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0179" Parameter: A <- "-77.0179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5846" Parameter: B <- "-27.5846" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4333" Parameter: C <- "-49.4333" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1430 TOTAL ENERGY = -77.0179 RDTITL> * VAN DER WAALS = -27.5846 ELECTROSTATIC = -49.4333 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1430" Parameter: CONF_N -> "8002" Comparing "1430" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1431" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757276 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759268 ATOM PAIRS WERE FOUND FOR ATOM LIST 41722 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29702 from a total of 759268 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1431 -72.01850 -4.99942 0.79390 INTE EXTERN> -25.17635 -46.84215 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0185" Parameter: A <- "-72.0185" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1764" Parameter: B <- "-25.1764" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8421" Parameter: C <- "-46.8421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1431 TOTAL ENERGY = -72.0185 RDTITL> * VAN DER WAALS = -25.1764 ELECTROSTATIC = -46.8421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1431" Parameter: CONF_N -> "8002" Comparing "1431" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1432" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759268 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762638 ATOM PAIRS WERE FOUND FOR ATOM LIST 42028 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29614 from a total of 762638 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1432 -74.11827 2.09977 0.73006 INTE EXTERN> -28.05333 -46.06494 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1183" Parameter: A <- "-74.1183" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0533" Parameter: B <- "-28.0533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0649" Parameter: C <- "-46.0649" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1432 TOTAL ENERGY = -74.1183 RDTITL> * VAN DER WAALS = -28.0533 ELECTROSTATIC = -46.0649 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1432" Parameter: CONF_N -> "8002" Comparing "1432" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1433" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762638 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760287 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29485 from a total of 760287 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1433 -70.93513 -3.18315 0.76213 INTE EXTERN> -26.27750 -44.65762 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9351" Parameter: A <- "-70.9351" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2775" Parameter: B <- "-26.2775" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6576" Parameter: C <- "-44.6576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1433 TOTAL ENERGY = -70.9351 RDTITL> * VAN DER WAALS = -26.2775 ELECTROSTATIC = -44.6576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1433" Parameter: CONF_N -> "8002" Comparing "1433" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1434" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760287 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758498 ATOM PAIRS WERE FOUND FOR ATOM LIST 41806 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29708 from a total of 758498 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1434 -70.99362 0.05849 0.78193 INTE EXTERN> -25.85339 -45.14023 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9936" Parameter: A <- "-70.9936" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8534" Parameter: B <- "-25.8534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1402" Parameter: C <- "-45.1402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1434 TOTAL ENERGY = -70.9936 RDTITL> * VAN DER WAALS = -25.8534 ELECTROSTATIC = -45.1402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1434" Parameter: CONF_N -> "8002" Comparing "1434" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1435" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758498 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754140 ATOM PAIRS WERE FOUND FOR ATOM LIST 41388 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29476 from a total of 754140 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1435 -70.52526 -0.46836 0.66322 INTE EXTERN> -26.13740 -44.38786 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5253" Parameter: A <- "-70.5253" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1374" Parameter: B <- "-26.1374" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3879" Parameter: C <- "-44.3879" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1435 TOTAL ENERGY = -70.5253 RDTITL> * VAN DER WAALS = -26.1374 ELECTROSTATIC = -44.3879 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1435" Parameter: CONF_N -> "8002" Comparing "1435" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1436" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754140 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755621 ATOM PAIRS WERE FOUND FOR ATOM LIST 41540 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28994 from a total of 755621 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1436 -69.13308 -1.39218 0.54741 INTE EXTERN> -29.61637 -39.51671 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1331" Parameter: A <- "-69.1331" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6164" Parameter: B <- "-29.6164" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5167" Parameter: C <- "-39.5167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1436 TOTAL ENERGY = -69.1331 RDTITL> * VAN DER WAALS = -29.6164 ELECTROSTATIC = -39.5167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1436" Parameter: CONF_N -> "8002" Comparing "1436" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1437" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755621 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759641 ATOM PAIRS WERE FOUND FOR ATOM LIST 41693 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29363 from a total of 759641 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1437 -69.97546 0.84238 0.60045 INTE EXTERN> -28.93616 -41.03930 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9755" Parameter: A <- "-69.9755" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9362" Parameter: B <- "-28.9362" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0393" Parameter: C <- "-41.0393" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1437 TOTAL ENERGY = -69.9755 RDTITL> * VAN DER WAALS = -28.9362 ELECTROSTATIC = -41.0393 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1437" Parameter: CONF_N -> "8002" Comparing "1437" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1438" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759641 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762154 ATOM PAIRS WERE FOUND FOR ATOM LIST 41934 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29641 from a total of 762154 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1438 -65.80798 -4.16748 0.68477 INTE EXTERN> -26.12151 -39.68648 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.808" Parameter: A <- "-65.808" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1215" Parameter: B <- "-26.1215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6865" Parameter: C <- "-39.6865" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1438 TOTAL ENERGY = -65.808 RDTITL> * VAN DER WAALS = -26.1215 ELECTROSTATIC = -39.6865 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1438" Parameter: CONF_N -> "8002" Comparing "1438" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1439" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762154 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760369 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29079 from a total of 760369 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1439 -68.24429 2.43631 0.52161 INTE EXTERN> -31.25489 -36.98941 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2443" Parameter: A <- "-68.2443" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2549" Parameter: B <- "-31.2549" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9894" Parameter: C <- "-36.9894" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1439 TOTAL ENERGY = -68.2443 RDTITL> * VAN DER WAALS = -31.2549 ELECTROSTATIC = -36.9894 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1439" Parameter: CONF_N -> "8002" Comparing "1439" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1440" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760369 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761594 ATOM PAIRS WERE FOUND FOR ATOM LIST 41796 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29894 from a total of 761594 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1440 -66.48546 -1.75884 0.66502 INTE EXTERN> -25.35767 -41.12778 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4855" Parameter: A <- "-66.4855" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3577" Parameter: B <- "-25.3577" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1278" Parameter: C <- "-41.1278" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1440 TOTAL ENERGY = -66.4855 RDTITL> * VAN DER WAALS = -25.3577 ELECTROSTATIC = -41.1278 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1440" Parameter: CONF_N -> "8002" Comparing "1440" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1441" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761594 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758877 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29495 from a total of 758877 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1441 -70.21199 3.72654 0.71196 INTE EXTERN> -24.98777 -45.22423 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.212" Parameter: A <- "-70.212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9878" Parameter: B <- "-24.9878" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2242" Parameter: C <- "-45.2242" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1441 TOTAL ENERGY = -70.212 RDTITL> * VAN DER WAALS = -24.9878 ELECTROSTATIC = -45.2242 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1441" Parameter: CONF_N -> "8002" Comparing "1441" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1442" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758877 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757036 ATOM PAIRS WERE FOUND FOR ATOM LIST 41725 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29224 from a total of 757036 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1442 -65.40978 -4.80221 0.63107 INTE EXTERN> -26.48605 -38.92373 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4098" Parameter: A <- "-65.4098" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.486" Parameter: B <- "-26.486" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9237" Parameter: C <- "-38.9237" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1442 TOTAL ENERGY = -65.4098 RDTITL> * VAN DER WAALS = -26.486 ELECTROSTATIC = -38.9237 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1442" Parameter: CONF_N -> "8002" Comparing "1442" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1443" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757036 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759619 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29364 from a total of 759619 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1443 -73.88375 8.47397 0.70395 INTE EXTERN> -28.13375 -45.75000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8838" Parameter: A <- "-73.8838" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1338" Parameter: B <- "-28.1338" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.75" Parameter: C <- "-45.75" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1443 TOTAL ENERGY = -73.8838 RDTITL> * VAN DER WAALS = -28.1338 ELECTROSTATIC = -45.75 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1443" Parameter: CONF_N -> "8002" Comparing "1443" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1444" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759619 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753824 ATOM PAIRS WERE FOUND FOR ATOM LIST 41423 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29246 from a total of 753824 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1444 -73.66004 -0.22371 0.58750 INTE EXTERN> -32.63150 -41.02855 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.66" Parameter: A <- "-73.66" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6315" Parameter: B <- "-32.6315" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0285" Parameter: C <- "-41.0285" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1444 TOTAL ENERGY = -73.66 RDTITL> * VAN DER WAALS = -32.6315 ELECTROSTATIC = -41.0285 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1444" Parameter: CONF_N -> "8002" Comparing "1444" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1445" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753824 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753057 ATOM PAIRS WERE FOUND FOR ATOM LIST 41238 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29092 from a total of 753057 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1445 -71.82499 -1.83505 0.60406 INTE EXTERN> -31.33608 -40.48891 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.825" Parameter: A <- "-71.825" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3361" Parameter: B <- "-31.3361" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4889" Parameter: C <- "-40.4889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1445 TOTAL ENERGY = -71.825 RDTITL> * VAN DER WAALS = -31.3361 ELECTROSTATIC = -40.4889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1445" Parameter: CONF_N -> "8002" Comparing "1445" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1446" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753057 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761614 ATOM PAIRS WERE FOUND FOR ATOM LIST 41644 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29587 from a total of 761614 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1446 -72.89842 1.07343 0.65770 INTE EXTERN> -26.88171 -46.01671 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8984" Parameter: A <- "-72.8984" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8817" Parameter: B <- "-26.8817" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0167" Parameter: C <- "-46.0167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1446 TOTAL ENERGY = -72.8984 RDTITL> * VAN DER WAALS = -26.8817 ELECTROSTATIC = -46.0167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1446" Parameter: CONF_N -> "8002" Comparing "1446" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1447" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761614 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751617 ATOM PAIRS WERE FOUND FOR ATOM LIST 41252 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29076 from a total of 751617 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1447 -65.91296 -6.98546 0.66655 INTE EXTERN> -25.26950 -40.64347 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.913" Parameter: A <- "-65.913" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2695" Parameter: B <- "-25.2695" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6435" Parameter: C <- "-40.6435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1447 TOTAL ENERGY = -65.913 RDTITL> * VAN DER WAALS = -25.2695 ELECTROSTATIC = -40.6435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1447" Parameter: CONF_N -> "8002" Comparing "1447" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1448" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751617 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758162 ATOM PAIRS WERE FOUND FOR ATOM LIST 41916 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29299 from a total of 758162 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1448 -76.56284 10.64988 0.68875 INTE EXTERN> -29.09774 -47.46510 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5628" Parameter: A <- "-76.5628" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0977" Parameter: B <- "-29.0977" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4651" Parameter: C <- "-47.4651" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1448 TOTAL ENERGY = -76.5628 RDTITL> * VAN DER WAALS = -29.0977 ELECTROSTATIC = -47.4651 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1448" Parameter: CONF_N -> "8002" Comparing "1448" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1449" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758162 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757934 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29273 from a total of 757934 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1449 -70.65036 -5.91248 0.72021 INTE EXTERN> -26.87682 -43.77354 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6504" Parameter: A <- "-70.6504" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8768" Parameter: B <- "-26.8768" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7735" Parameter: C <- "-43.7735" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1449 TOTAL ENERGY = -70.6504 RDTITL> * VAN DER WAALS = -26.8768 ELECTROSTATIC = -43.7735 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1449" Parameter: CONF_N -> "8002" Comparing "1449" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1450" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757934 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759514 ATOM PAIRS WERE FOUND FOR ATOM LIST 41720 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29677 from a total of 759514 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1450 -76.08706 5.43670 0.69868 INTE EXTERN> -30.13730 -45.94976 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0871" Parameter: A <- "-76.0871" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1373" Parameter: B <- "-30.1373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9498" Parameter: C <- "-45.9498" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1450 TOTAL ENERGY = -76.0871 RDTITL> * VAN DER WAALS = -30.1373 ELECTROSTATIC = -45.9498 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1450" Parameter: CONF_N -> "8002" Comparing "1450" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1451" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759514 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752605 ATOM PAIRS WERE FOUND FOR ATOM LIST 41202 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28821 from a total of 752605 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1451 -70.71029 -5.37677 0.68152 INTE EXTERN> -26.11098 -44.59931 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7103" Parameter: A <- "-70.7103" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.111" Parameter: B <- "-26.111" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5993" Parameter: C <- "-44.5993" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1451 TOTAL ENERGY = -70.7103 RDTITL> * VAN DER WAALS = -26.111 ELECTROSTATIC = -44.5993 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1451" Parameter: CONF_N -> "8002" Comparing "1451" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1452" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752605 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756628 ATOM PAIRS WERE FOUND FOR ATOM LIST 41500 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29086 from a total of 756628 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1452 -62.14452 -8.56577 0.63180 INTE EXTERN> -27.89870 -34.24582 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.1445" Parameter: A <- "-62.1445" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8987" Parameter: B <- "-27.8987" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2458" Parameter: C <- "-34.2458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1452 TOTAL ENERGY = -62.1445 RDTITL> * VAN DER WAALS = -27.8987 ELECTROSTATIC = -34.2458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1452" Parameter: CONF_N -> "8002" Comparing "1452" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1453" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756628 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761890 ATOM PAIRS WERE FOUND FOR ATOM LIST 41747 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29252 from a total of 761890 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1453 -72.37412 10.22961 0.64842 INTE EXTERN> -29.44651 -42.92761 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3741" Parameter: A <- "-72.3741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4465" Parameter: B <- "-29.4465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9276" Parameter: C <- "-42.9276" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1453 TOTAL ENERGY = -72.3741 RDTITL> * VAN DER WAALS = -29.4465 ELECTROSTATIC = -42.9276 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1453" Parameter: CONF_N -> "8002" Comparing "1453" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1454" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761890 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756888 ATOM PAIRS WERE FOUND FOR ATOM LIST 41718 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29250 from a total of 756888 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1454 -72.79413 0.42000 0.58645 INTE EXTERN> -30.99469 -41.79944 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7941" Parameter: A <- "-72.7941" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9947" Parameter: B <- "-30.9947" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7994" Parameter: C <- "-41.7994" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1454 TOTAL ENERGY = -72.7941 RDTITL> * VAN DER WAALS = -30.9947 ELECTROSTATIC = -41.7994 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1454" Parameter: CONF_N -> "8002" Comparing "1454" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1455" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756888 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758412 ATOM PAIRS WERE FOUND FOR ATOM LIST 41725 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29890 from a total of 758412 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1455 -70.58252 -2.21161 0.63259 INTE EXTERN> -29.44012 -41.14239 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5825" Parameter: A <- "-70.5825" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4401" Parameter: B <- "-29.4401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1424" Parameter: C <- "-41.1424" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1455 TOTAL ENERGY = -70.5825 RDTITL> * VAN DER WAALS = -29.4401 ELECTROSTATIC = -41.1424 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1455" Parameter: CONF_N -> "8002" Comparing "1455" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1456" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758412 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754592 ATOM PAIRS WERE FOUND FOR ATOM LIST 41409 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29136 from a total of 754592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1456 -68.91904 -1.66348 0.67334 INTE EXTERN> -28.69026 -40.22877 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.919" Parameter: A <- "-68.919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6903" Parameter: B <- "-28.6903" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2288" Parameter: C <- "-40.2288" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1456 TOTAL ENERGY = -68.919 RDTITL> * VAN DER WAALS = -28.6903 ELECTROSTATIC = -40.2288 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1456" Parameter: CONF_N -> "8002" Comparing "1456" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1457" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755188 ATOM PAIRS WERE FOUND FOR ATOM LIST 41408 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29478 from a total of 755188 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1457 -70.81921 1.90017 0.63291 INTE EXTERN> -28.94264 -41.87657 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8192" Parameter: A <- "-70.8192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9426" Parameter: B <- "-28.9426" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8766" Parameter: C <- "-41.8766" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1457 TOTAL ENERGY = -70.8192 RDTITL> * VAN DER WAALS = -28.9426 ELECTROSTATIC = -41.8766 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1457" Parameter: CONF_N -> "8002" Comparing "1457" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1458" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755188 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755748 ATOM PAIRS WERE FOUND FOR ATOM LIST 41378 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29066 from a total of 755748 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1458 -73.32723 2.50802 0.65482 INTE EXTERN> -30.32272 -43.00451 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3272" Parameter: A <- "-73.3272" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3227" Parameter: B <- "-30.3227" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0045" Parameter: C <- "-43.0045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1458 TOTAL ENERGY = -73.3272 RDTITL> * VAN DER WAALS = -30.3227 ELECTROSTATIC = -43.0045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1458" Parameter: CONF_N -> "8002" Comparing "1458" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1459" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755748 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754808 ATOM PAIRS WERE FOUND FOR ATOM LIST 41561 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29557 from a total of 754808 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1459 -64.77676 -8.55047 0.68732 INTE EXTERN> -25.64362 -39.13314 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7768" Parameter: A <- "-64.7768" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6436" Parameter: B <- "-25.6436" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1331" Parameter: C <- "-39.1331" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1459 TOTAL ENERGY = -64.7768 RDTITL> * VAN DER WAALS = -25.6436 ELECTROSTATIC = -39.1331 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1459" Parameter: CONF_N -> "8002" Comparing "1459" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1460" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754808 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753327 ATOM PAIRS WERE FOUND FOR ATOM LIST 41465 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29637 from a total of 753327 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1460 -69.90653 5.12977 0.65220 INTE EXTERN> -29.78245 -40.12408 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9065" Parameter: A <- "-69.9065" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7825" Parameter: B <- "-29.7825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1241" Parameter: C <- "-40.1241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1460 TOTAL ENERGY = -69.9065 RDTITL> * VAN DER WAALS = -29.7825 ELECTROSTATIC = -40.1241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1460" Parameter: CONF_N -> "8002" Comparing "1460" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1461" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753327 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755826 ATOM PAIRS WERE FOUND FOR ATOM LIST 41475 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29424 from a total of 755826 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1461 -73.73719 3.83065 0.70278 INTE EXTERN> -28.23411 -45.50308 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7372" Parameter: A <- "-73.7372" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2341" Parameter: B <- "-28.2341" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5031" Parameter: C <- "-45.5031" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1461 TOTAL ENERGY = -73.7372 RDTITL> * VAN DER WAALS = -28.2341 ELECTROSTATIC = -45.5031 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1461" Parameter: CONF_N -> "8002" Comparing "1461" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1462" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755826 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759531 ATOM PAIRS WERE FOUND FOR ATOM LIST 41679 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29645 from a total of 759531 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1462 -68.31450 -5.42268 0.67219 INTE EXTERN> -26.75309 -41.56141 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3145" Parameter: A <- "-68.3145" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7531" Parameter: B <- "-26.7531" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5614" Parameter: C <- "-41.5614" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1462 TOTAL ENERGY = -68.3145 RDTITL> * VAN DER WAALS = -26.7531 ELECTROSTATIC = -41.5614 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1462" Parameter: CONF_N -> "8002" Comparing "1462" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1463" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759531 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758449 ATOM PAIRS WERE FOUND FOR ATOM LIST 41649 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30222 from a total of 758449 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1463 -65.37345 -2.94105 0.76678 INTE EXTERN> -23.71198 -41.66147 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3735" Parameter: A <- "-65.3735" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.712" Parameter: B <- "-23.712" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6615" Parameter: C <- "-41.6615" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1463 TOTAL ENERGY = -65.3735 RDTITL> * VAN DER WAALS = -23.712 ELECTROSTATIC = -41.6615 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1463" Parameter: CONF_N -> "8002" Comparing "1463" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1464" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758449 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759182 ATOM PAIRS WERE FOUND FOR ATOM LIST 41715 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29188 from a total of 759182 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1464 -74.16874 8.79529 0.64244 INTE EXTERN> -30.66177 -43.50697 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1687" Parameter: A <- "-74.1687" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6618" Parameter: B <- "-30.6618" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.507" Parameter: C <- "-43.507" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1464 TOTAL ENERGY = -74.1687 RDTITL> * VAN DER WAALS = -30.6618 ELECTROSTATIC = -43.507 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1464" Parameter: CONF_N -> "8002" Comparing "1464" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1465" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759182 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761079 ATOM PAIRS WERE FOUND FOR ATOM LIST 42050 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29349 from a total of 761079 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1465 -67.96132 -6.20742 0.70623 INTE EXTERN> -27.33189 -40.62942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9613" Parameter: A <- "-67.9613" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3319" Parameter: B <- "-27.3319" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6294" Parameter: C <- "-40.6294" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1465 TOTAL ENERGY = -67.9613 RDTITL> * VAN DER WAALS = -27.3319 ELECTROSTATIC = -40.6294 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1465" Parameter: CONF_N -> "8002" Comparing "1465" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1466" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761079 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761856 ATOM PAIRS WERE FOUND FOR ATOM LIST 41856 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29372 from a total of 761856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1466 -68.62500 0.66368 0.59684 INTE EXTERN> -31.24810 -37.37689 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.625" Parameter: A <- "-68.625" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2481" Parameter: B <- "-31.2481" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3769" Parameter: C <- "-37.3769" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1466 TOTAL ENERGY = -68.625 RDTITL> * VAN DER WAALS = -31.2481 ELECTROSTATIC = -37.3769 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1466" Parameter: CONF_N -> "8002" Comparing "1466" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1467" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759634 ATOM PAIRS WERE FOUND FOR ATOM LIST 41982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29322 from a total of 759634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1467 -59.45678 -9.16822 0.58028 INTE EXTERN> -30.11283 -29.34394 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.4568" Parameter: A <- "-59.4568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1128" Parameter: B <- "-30.1128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.3439" Parameter: C <- "-29.3439" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1467 TOTAL ENERGY = -59.4568 RDTITL> * VAN DER WAALS = -30.1128 ELECTROSTATIC = -29.3439 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1467" Parameter: CONF_N -> "8002" Comparing "1467" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1468" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765720 ATOM PAIRS WERE FOUND FOR ATOM LIST 42120 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29731 from a total of 765720 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1468 -58.15543 -1.30134 0.56613 INTE EXTERN> -29.56574 -28.58969 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.1554" Parameter: A <- "-58.1554" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5657" Parameter: B <- "-29.5657" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.5897" Parameter: C <- "-28.5897" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1468 TOTAL ENERGY = -58.1554 RDTITL> * VAN DER WAALS = -29.5657 ELECTROSTATIC = -28.5897 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1468" Parameter: CONF_N -> "8002" Comparing "1468" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1469" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765720 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766473 ATOM PAIRS WERE FOUND FOR ATOM LIST 42064 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28984 from a total of 766473 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1469 -65.34158 7.18615 0.58117 INTE EXTERN> -31.35177 -33.98982 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3416" Parameter: A <- "-65.3416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3518" Parameter: B <- "-31.3518" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9898" Parameter: C <- "-33.9898" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1469 TOTAL ENERGY = -65.3416 RDTITL> * VAN DER WAALS = -31.3518 ELECTROSTATIC = -33.9898 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1469" Parameter: CONF_N -> "8002" Comparing "1469" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1470" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766473 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759278 ATOM PAIRS WERE FOUND FOR ATOM LIST 41841 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29353 from a total of 759278 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1470 -66.99415 1.65257 0.64915 INTE EXTERN> -26.65011 -40.34405 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9942" Parameter: A <- "-66.9942" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6501" Parameter: B <- "-26.6501" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.344" Parameter: C <- "-40.344" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1470 TOTAL ENERGY = -66.9942 RDTITL> * VAN DER WAALS = -26.6501 ELECTROSTATIC = -40.344 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1470" Parameter: CONF_N -> "8002" Comparing "1470" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1471" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759278 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761313 ATOM PAIRS WERE FOUND FOR ATOM LIST 41888 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28756 from a total of 761313 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1471 -61.98341 -5.01074 0.74034 INTE EXTERN> -23.00412 -38.97929 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.9834" Parameter: A <- "-61.9834" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.0041" Parameter: B <- "-23.0041" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9793" Parameter: C <- "-38.9793" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1471 TOTAL ENERGY = -61.9834 RDTITL> * VAN DER WAALS = -23.0041 ELECTROSTATIC = -38.9793 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1471" Parameter: CONF_N -> "8002" Comparing "1471" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1472" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761313 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754942 ATOM PAIRS WERE FOUND FOR ATOM LIST 41584 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28842 from a total of 754942 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1472 -64.56186 2.57845 0.80911 INTE EXTERN> -24.83291 -39.72895 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5619" Parameter: A <- "-64.5619" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8329" Parameter: B <- "-24.8329" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.729" Parameter: C <- "-39.729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1472 TOTAL ENERGY = -64.5619 RDTITL> * VAN DER WAALS = -24.8329 ELECTROSTATIC = -39.729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1472" Parameter: CONF_N -> "8002" Comparing "1472" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1473" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754942 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756670 ATOM PAIRS WERE FOUND FOR ATOM LIST 41549 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28869 from a total of 756670 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1473 -74.75392 10.19206 0.63189 INTE EXTERN> -30.69314 -44.06078 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7539" Parameter: A <- "-74.7539" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6931" Parameter: B <- "-30.6931" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0608" Parameter: C <- "-44.0608" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1473 TOTAL ENERGY = -74.7539 RDTITL> * VAN DER WAALS = -30.6931 ELECTROSTATIC = -44.0608 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1473" Parameter: CONF_N -> "8002" Comparing "1473" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1474" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756670 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753764 ATOM PAIRS WERE FOUND FOR ATOM LIST 41548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28775 from a total of 753764 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1474 -75.43560 0.68168 0.72989 INTE EXTERN> -24.96228 -50.47332 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4356" Parameter: A <- "-75.4356" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9623" Parameter: B <- "-24.9623" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4733" Parameter: C <- "-50.4733" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1474 TOTAL ENERGY = -75.4356 RDTITL> * VAN DER WAALS = -24.9623 ELECTROSTATIC = -50.4733 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1474" Parameter: CONF_N -> "8002" Comparing "1474" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1475" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753764 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754897 ATOM PAIRS WERE FOUND FOR ATOM LIST 41627 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28739 from a total of 754897 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1475 -69.21665 -6.21895 0.56561 INTE EXTERN> -28.37218 -40.84447 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2166" Parameter: A <- "-69.2166" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3722" Parameter: B <- "-28.3722" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8445" Parameter: C <- "-40.8445" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1475 TOTAL ENERGY = -69.2166 RDTITL> * VAN DER WAALS = -28.3722 ELECTROSTATIC = -40.8445 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1475" Parameter: CONF_N -> "8002" Comparing "1475" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1476" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754897 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754999 ATOM PAIRS WERE FOUND FOR ATOM LIST 41457 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28779 from a total of 754999 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1476 -67.56543 -1.65122 0.58709 INTE EXTERN> -28.44764 -39.11779 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5654" Parameter: A <- "-67.5654" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4476" Parameter: B <- "-28.4476" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1178" Parameter: C <- "-39.1178" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1476 TOTAL ENERGY = -67.5654 RDTITL> * VAN DER WAALS = -28.4476 ELECTROSTATIC = -39.1178 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1476" Parameter: CONF_N -> "8002" Comparing "1476" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1477" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754999 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758904 ATOM PAIRS WERE FOUND FOR ATOM LIST 41728 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28917 from a total of 758904 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1477 -68.83347 1.26804 0.67103 INTE EXTERN> -27.01895 -41.81453 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8335" Parameter: A <- "-68.8335" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0189" Parameter: B <- "-27.0189" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8145" Parameter: C <- "-41.8145" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1477 TOTAL ENERGY = -68.8335 RDTITL> * VAN DER WAALS = -27.0189 ELECTROSTATIC = -41.8145 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1477" Parameter: CONF_N -> "8002" Comparing "1477" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1478" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758904 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757536 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28937 from a total of 757536 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1478 -67.88967 -0.94380 0.58366 INTE EXTERN> -29.56453 -38.32515 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8897" Parameter: A <- "-67.8897" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5645" Parameter: B <- "-29.5645" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3251" Parameter: C <- "-38.3251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1478 TOTAL ENERGY = -67.8897 RDTITL> * VAN DER WAALS = -29.5645 ELECTROSTATIC = -38.3251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1478" Parameter: CONF_N -> "8002" Comparing "1478" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1479" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757536 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751974 ATOM PAIRS WERE FOUND FOR ATOM LIST 41812 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29130 from a total of 751974 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1479 -68.83525 0.94558 0.68556 INTE EXTERN> -26.83425 -42.00100 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8353" Parameter: A <- "-68.8353" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8343" Parameter: B <- "-26.8343" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.001" Parameter: C <- "-42.001" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1479 TOTAL ENERGY = -68.8353 RDTITL> * VAN DER WAALS = -26.8343 ELECTROSTATIC = -42.001 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1479" Parameter: CONF_N -> "8002" Comparing "1479" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1480" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751974 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41744 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28669 from a total of 757794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1480 -66.25572 -2.57953 0.58764 INTE EXTERN> -31.17342 -35.08229 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2557" Parameter: A <- "-66.2557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1734" Parameter: B <- "-31.1734" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0823" Parameter: C <- "-35.0823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1480 TOTAL ENERGY = -66.2557 RDTITL> * VAN DER WAALS = -31.1734 ELECTROSTATIC = -35.0823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1480" Parameter: CONF_N -> "8002" Comparing "1480" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1481" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760775 ATOM PAIRS WERE FOUND FOR ATOM LIST 41880 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29335 from a total of 760775 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1481 -62.47025 -3.78547 0.57267 INTE EXTERN> -26.63838 -35.83187 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.4703" Parameter: A <- "-62.4703" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6384" Parameter: B <- "-26.6384" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8319" Parameter: C <- "-35.8319" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1481 TOTAL ENERGY = -62.4703 RDTITL> * VAN DER WAALS = -26.6384 ELECTROSTATIC = -35.8319 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1481" Parameter: CONF_N -> "8002" Comparing "1481" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1482" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760775 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759289 ATOM PAIRS WERE FOUND FOR ATOM LIST 41790 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29224 from a total of 759289 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1482 -60.15176 -2.31850 0.63960 INTE EXTERN> -23.87967 -36.27208 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.1518" Parameter: A <- "-60.1518" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8797" Parameter: B <- "-23.8797" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2721" Parameter: C <- "-36.2721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1482 TOTAL ENERGY = -60.1518 RDTITL> * VAN DER WAALS = -23.8797 ELECTROSTATIC = -36.2721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1482" Parameter: CONF_N -> "8002" Comparing "1482" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1483" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759289 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761575 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28750 from a total of 761575 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1483 -68.00507 7.85332 0.61966 INTE EXTERN> -28.14472 -39.86036 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0051" Parameter: A <- "-68.0051" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1447" Parameter: B <- "-28.1447" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8604" Parameter: C <- "-39.8604" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1483 TOTAL ENERGY = -68.0051 RDTITL> * VAN DER WAALS = -28.1447 ELECTROSTATIC = -39.8604 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1483" Parameter: CONF_N -> "8002" Comparing "1483" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1484" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761575 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759114 ATOM PAIRS WERE FOUND FOR ATOM LIST 41922 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28923 from a total of 759114 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1484 -64.96648 -3.03859 0.65080 INTE EXTERN> -25.48868 -39.47780 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9665" Parameter: A <- "-64.9665" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4887" Parameter: B <- "-25.4887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4778" Parameter: C <- "-39.4778" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1484 TOTAL ENERGY = -64.9665 RDTITL> * VAN DER WAALS = -25.4887 ELECTROSTATIC = -39.4778 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1484" Parameter: CONF_N -> "8002" Comparing "1484" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1485" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759114 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751945 ATOM PAIRS WERE FOUND FOR ATOM LIST 41458 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28811 from a total of 751945 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1485 -69.40620 4.43972 0.61317 INTE EXTERN> -27.52831 -41.87789 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4062" Parameter: A <- "-69.4062" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5283" Parameter: B <- "-27.5283" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8779" Parameter: C <- "-41.8779" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1485 TOTAL ENERGY = -69.4062 RDTITL> * VAN DER WAALS = -27.5283 ELECTROSTATIC = -41.8779 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1485" Parameter: CONF_N -> "8002" Comparing "1485" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1486" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751945 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756380 ATOM PAIRS WERE FOUND FOR ATOM LIST 41624 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28974 from a total of 756380 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1486 -57.96310 -11.44310 0.49455 INTE EXTERN> -29.90436 -28.05874 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.9631" Parameter: A <- "-57.9631" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9044" Parameter: B <- "-29.9044" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.0587" Parameter: C <- "-28.0587" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1486 TOTAL ENERGY = -57.9631 RDTITL> * VAN DER WAALS = -29.9044 ELECTROSTATIC = -28.0587 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1486" Parameter: CONF_N -> "8002" Comparing "1486" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1487" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756380 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758756 ATOM PAIRS WERE FOUND FOR ATOM LIST 41757 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29330 from a total of 758756 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1487 -66.88007 8.91697 0.56303 INTE EXTERN> -30.62327 -36.25679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8801" Parameter: A <- "-66.8801" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6233" Parameter: B <- "-30.6233" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2568" Parameter: C <- "-36.2568" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1487 TOTAL ENERGY = -66.8801 RDTITL> * VAN DER WAALS = -30.6233 ELECTROSTATIC = -36.2568 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1487" Parameter: CONF_N -> "8002" Comparing "1487" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1488" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758756 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764412 ATOM PAIRS WERE FOUND FOR ATOM LIST 42195 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29590 from a total of 764412 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1488 -63.09444 -3.78563 0.79869 INTE EXTERN> -23.48848 -39.60596 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.0944" Parameter: A <- "-63.0944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4885" Parameter: B <- "-23.4885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.606" Parameter: C <- "-39.606" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1488 TOTAL ENERGY = -63.0944 RDTITL> * VAN DER WAALS = -23.4885 ELECTROSTATIC = -39.606 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1488" Parameter: CONF_N -> "8002" Comparing "1488" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1489" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764412 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757939 ATOM PAIRS WERE FOUND FOR ATOM LIST 41685 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29944 from a total of 757939 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1489 -61.01453 -2.07991 0.62462 INTE EXTERN> -25.81729 -35.19724 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.0145" Parameter: A <- "-61.0145" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8173" Parameter: B <- "-25.8173" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1972" Parameter: C <- "-35.1972" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1489 TOTAL ENERGY = -61.0145 RDTITL> * VAN DER WAALS = -25.8173 ELECTROSTATIC = -35.1972 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1489" Parameter: CONF_N -> "8002" Comparing "1489" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1490" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757939 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753656 ATOM PAIRS WERE FOUND FOR ATOM LIST 41612 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29267 from a total of 753656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1490 -63.42320 2.40868 0.61528 INTE EXTERN> -27.80745 -35.61575 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4232" Parameter: A <- "-63.4232" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8075" Parameter: B <- "-27.8075" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6158" Parameter: C <- "-35.6158" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1490 TOTAL ENERGY = -63.4232 RDTITL> * VAN DER WAALS = -27.8075 ELECTROSTATIC = -35.6158 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1490" Parameter: CONF_N -> "8002" Comparing "1490" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1491" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753830 ATOM PAIRS WERE FOUND FOR ATOM LIST 41280 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29028 from a total of 753830 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1491 -65.43061 2.00740 0.74750 INTE EXTERN> -23.96979 -41.46081 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4306" Parameter: A <- "-65.4306" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9698" Parameter: B <- "-23.9698" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4608" Parameter: C <- "-41.4608" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1491 TOTAL ENERGY = -65.4306 RDTITL> * VAN DER WAALS = -23.9698 ELECTROSTATIC = -41.4608 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1491" Parameter: CONF_N -> "8002" Comparing "1491" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1492" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753830 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753915 ATOM PAIRS WERE FOUND FOR ATOM LIST 41384 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29031 from a total of 753915 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1492 -64.28944 -1.14116 0.88919 INTE EXTERN> -18.85192 -45.43752 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2894" Parameter: A <- "-64.2894" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-18.8519" Parameter: B <- "-18.8519" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4375" Parameter: C <- "-45.4375" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1492 TOTAL ENERGY = -64.2894 RDTITL> * VAN DER WAALS = -18.8519 ELECTROSTATIC = -45.4375 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1492" Parameter: CONF_N -> "8002" Comparing "1492" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1493" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753915 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755200 ATOM PAIRS WERE FOUND FOR ATOM LIST 41644 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29200 from a total of 755200 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1493 -64.62886 0.33942 0.59753 INTE EXTERN> -29.64274 -34.98613 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6289" Parameter: A <- "-64.6289" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6427" Parameter: B <- "-29.6427" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9861" Parameter: C <- "-34.9861" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1493 TOTAL ENERGY = -64.6289 RDTITL> * VAN DER WAALS = -29.6427 ELECTROSTATIC = -34.9861 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1493" Parameter: CONF_N -> "8002" Comparing "1493" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1494" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755200 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751429 ATOM PAIRS WERE FOUND FOR ATOM LIST 41452 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29226 from a total of 751429 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1494 -62.81097 -1.81790 0.66215 INTE EXTERN> -24.71964 -38.09132 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.811" Parameter: A <- "-62.811" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7196" Parameter: B <- "-24.7196" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0913" Parameter: C <- "-38.0913" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1494 TOTAL ENERGY = -62.811 RDTITL> * VAN DER WAALS = -24.7196 ELECTROSTATIC = -38.0913 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1494" Parameter: CONF_N -> "8002" Comparing "1494" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1495" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751429 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754001 ATOM PAIRS WERE FOUND FOR ATOM LIST 41510 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29188 from a total of 754001 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1495 -69.65667 6.84571 0.69649 INTE EXTERN> -28.64264 -41.01403 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6567" Parameter: A <- "-69.6567" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6426" Parameter: B <- "-28.6426" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.014" Parameter: C <- "-41.014" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1495 TOTAL ENERGY = -69.6567 RDTITL> * VAN DER WAALS = -28.6426 ELECTROSTATIC = -41.014 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1495" Parameter: CONF_N -> "8002" Comparing "1495" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1496" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754001 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750330 ATOM PAIRS WERE FOUND FOR ATOM LIST 41432 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29543 from a total of 750330 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1496 -70.00277 0.34610 0.60071 INTE EXTERN> -28.78722 -41.21555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0028" Parameter: A <- "-70.0028" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7872" Parameter: B <- "-28.7872" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2156" Parameter: C <- "-41.2156" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1496 TOTAL ENERGY = -70.0028 RDTITL> * VAN DER WAALS = -28.7872 ELECTROSTATIC = -41.2156 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1496" Parameter: CONF_N -> "8002" Comparing "1496" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1497" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750330 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752915 ATOM PAIRS WERE FOUND FOR ATOM LIST 41592 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29056 from a total of 752915 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1497 -67.59571 -2.40706 0.71717 INTE EXTERN> -25.91855 -41.67716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5957" Parameter: A <- "-67.5957" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9186" Parameter: B <- "-25.9186" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6772" Parameter: C <- "-41.6772" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1497 TOTAL ENERGY = -67.5957 RDTITL> * VAN DER WAALS = -25.9186 ELECTROSTATIC = -41.6772 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1497" Parameter: CONF_N -> "8002" Comparing "1497" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1498" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752915 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758153 ATOM PAIRS WERE FOUND FOR ATOM LIST 41534 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29576 from a total of 758153 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1498 -64.78243 -2.81329 0.65192 INTE EXTERN> -27.32441 -37.45801 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7824" Parameter: A <- "-64.7824" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3244" Parameter: B <- "-27.3244" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.458" Parameter: C <- "-37.458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1498 TOTAL ENERGY = -64.7824 RDTITL> * VAN DER WAALS = -27.3244 ELECTROSTATIC = -37.458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1498" Parameter: CONF_N -> "8002" Comparing "1498" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1499" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758153 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748672 ATOM PAIRS WERE FOUND FOR ATOM LIST 41145 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29113 from a total of 748672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1499 -59.10849 -5.67393 0.56341 INTE EXTERN> -29.98056 -29.12793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.1085" Parameter: A <- "-59.1085" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9806" Parameter: B <- "-29.9806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.1279" Parameter: C <- "-29.1279" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1499 TOTAL ENERGY = -59.1085 RDTITL> * VAN DER WAALS = -29.9806 ELECTROSTATIC = -29.1279 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1499" Parameter: CONF_N -> "8002" Comparing "1499" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1500" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752907 ATOM PAIRS WERE FOUND FOR ATOM LIST 41437 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30074 from a total of 752907 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1500 -68.63140 9.52291 0.78715 INTE EXTERN> -22.05062 -46.58078 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6314" Parameter: A <- "-68.6314" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.0506" Parameter: B <- "-22.0506" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5808" Parameter: C <- "-46.5808" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1500 TOTAL ENERGY = -68.6314 RDTITL> * VAN DER WAALS = -22.0506 ELECTROSTATIC = -46.5808 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1500" Parameter: CONF_N -> "8002" Comparing "1500" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1501" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752907 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41458 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29362 from a total of 752794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1501 -66.76564 -1.86576 0.58981 INTE EXTERN> -30.89745 -35.86819 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7656" Parameter: A <- "-66.7656" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8974" Parameter: B <- "-30.8974" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8682" Parameter: C <- "-35.8682" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1501 TOTAL ENERGY = -66.7656 RDTITL> * VAN DER WAALS = -30.8974 ELECTROSTATIC = -35.8682 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1501" Parameter: CONF_N -> "8002" Comparing "1501" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1502" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41952 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29947 from a total of 759422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1502 -69.47420 2.70856 0.68324 INTE EXTERN> -27.02375 -42.45045 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4742" Parameter: A <- "-69.4742" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0237" Parameter: B <- "-27.0237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4505" Parameter: C <- "-42.4505" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1502 TOTAL ENERGY = -69.4742 RDTITL> * VAN DER WAALS = -27.0237 ELECTROSTATIC = -42.4505 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1502" Parameter: CONF_N -> "8002" Comparing "1502" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1503" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759449 ATOM PAIRS WERE FOUND FOR ATOM LIST 41639 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29932 from a total of 759449 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1503 -69.36577 -0.10843 0.66244 INTE EXTERN> -29.51045 -39.85532 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3658" Parameter: A <- "-69.3658" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5104" Parameter: B <- "-29.5104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8553" Parameter: C <- "-39.8553" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1503 TOTAL ENERGY = -69.3658 RDTITL> * VAN DER WAALS = -29.5104 ELECTROSTATIC = -39.8553 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1503" Parameter: CONF_N -> "8002" Comparing "1503" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1504" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759449 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757220 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30111 from a total of 757220 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1504 -72.05075 2.68498 0.75246 INTE EXTERN> -23.05084 -48.99991 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0508" Parameter: A <- "-72.0508" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.0508" Parameter: B <- "-23.0508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9999" Parameter: C <- "-48.9999" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1504 TOTAL ENERGY = -72.0508 RDTITL> * VAN DER WAALS = -23.0508 ELECTROSTATIC = -48.9999 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1504" Parameter: CONF_N -> "8002" Comparing "1504" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1505" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757220 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757768 ATOM PAIRS WERE FOUND FOR ATOM LIST 41747 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29696 from a total of 757768 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1505 -74.93961 2.88886 0.64705 INTE EXTERN> -32.31362 -42.62600 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9396" Parameter: A <- "-74.9396" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3136" Parameter: B <- "-32.3136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.626" Parameter: C <- "-42.626" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1505 TOTAL ENERGY = -74.9396 RDTITL> * VAN DER WAALS = -32.3136 ELECTROSTATIC = -42.626 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1505" Parameter: CONF_N -> "8002" Comparing "1505" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1506" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757768 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762061 ATOM PAIRS WERE FOUND FOR ATOM LIST 41881 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30065 from a total of 762061 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1506 -69.37231 -5.56731 0.65551 INTE EXTERN> -28.82956 -40.54275 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3723" Parameter: A <- "-69.3723" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8296" Parameter: B <- "-28.8296" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5427" Parameter: C <- "-40.5427" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1506 TOTAL ENERGY = -69.3723 RDTITL> * VAN DER WAALS = -28.8296 ELECTROSTATIC = -40.5427 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1506" Parameter: CONF_N -> "8002" Comparing "1506" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1507" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762061 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759905 ATOM PAIRS WERE FOUND FOR ATOM LIST 41835 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30210 from a total of 759905 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1507 -69.72416 0.35186 0.61017 INTE EXTERN> -29.00893 -40.71523 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7242" Parameter: A <- "-69.7242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0089" Parameter: B <- "-29.0089" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7152" Parameter: C <- "-40.7152" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1507 TOTAL ENERGY = -69.7242 RDTITL> * VAN DER WAALS = -29.0089 ELECTROSTATIC = -40.7152 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1507" Parameter: CONF_N -> "8002" Comparing "1507" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1508" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759905 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760880 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29996 from a total of 760880 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1508 -70.50373 0.77956 0.66800 INTE EXTERN> -29.41682 -41.08691 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5037" Parameter: A <- "-70.5037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4168" Parameter: B <- "-29.4168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0869" Parameter: C <- "-41.0869" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1508 TOTAL ENERGY = -70.5037 RDTITL> * VAN DER WAALS = -29.4168 ELECTROSTATIC = -41.0869 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1508" Parameter: CONF_N -> "8002" Comparing "1508" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1509" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760880 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762143 ATOM PAIRS WERE FOUND FOR ATOM LIST 42112 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30516 from a total of 762143 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1509 -68.18015 -2.32357 0.75585 INTE EXTERN> -24.81519 -43.36497 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1802" Parameter: A <- "-68.1802" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8152" Parameter: B <- "-24.8152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.365" Parameter: C <- "-43.365" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1509 TOTAL ENERGY = -68.1802 RDTITL> * VAN DER WAALS = -24.8152 ELECTROSTATIC = -43.365 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1509" Parameter: CONF_N -> "8002" Comparing "1509" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1510" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762143 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760675 ATOM PAIRS WERE FOUND FOR ATOM LIST 41861 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30341 from a total of 760675 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1510 -67.82473 -0.35542 0.58868 INTE EXTERN> -30.62340 -37.20133 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8247" Parameter: A <- "-67.8247" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6234" Parameter: B <- "-30.6234" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2013" Parameter: C <- "-37.2013" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1510 TOTAL ENERGY = -67.8247 RDTITL> * VAN DER WAALS = -30.6234 ELECTROSTATIC = -37.2013 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1510" Parameter: CONF_N -> "8002" Comparing "1510" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1511" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760675 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761257 ATOM PAIRS WERE FOUND FOR ATOM LIST 41781 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30000 from a total of 761257 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1511 -69.96255 2.13782 0.56799 INTE EXTERN> -32.83566 -37.12689 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9625" Parameter: A <- "-69.9625" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8357" Parameter: B <- "-32.8357" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1269" Parameter: C <- "-37.1269" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1511 TOTAL ENERGY = -69.9625 RDTITL> * VAN DER WAALS = -32.8357 ELECTROSTATIC = -37.1269 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1511" Parameter: CONF_N -> "8002" Comparing "1511" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1512" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761257 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764171 ATOM PAIRS WERE FOUND FOR ATOM LIST 42035 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30030 from a total of 764171 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1512 -69.40716 -0.55539 0.64447 INTE EXTERN> -29.91539 -39.49177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4072" Parameter: A <- "-69.4072" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9154" Parameter: B <- "-29.9154" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4918" Parameter: C <- "-39.4918" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1512 TOTAL ENERGY = -69.4072 RDTITL> * VAN DER WAALS = -29.9154 ELECTROSTATIC = -39.4918 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1512" Parameter: CONF_N -> "8002" Comparing "1512" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1513" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764171 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762239 ATOM PAIRS WERE FOUND FOR ATOM LIST 42152 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30190 from a total of 762239 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1513 -71.92556 2.51840 0.53689 INTE EXTERN> -33.78063 -38.14493 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9256" Parameter: A <- "-71.9256" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7806" Parameter: B <- "-33.7806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1449" Parameter: C <- "-38.1449" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1513 TOTAL ENERGY = -71.9256 RDTITL> * VAN DER WAALS = -33.7806 ELECTROSTATIC = -38.1449 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1513" Parameter: CONF_N -> "8002" Comparing "1513" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1514" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762239 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767193 ATOM PAIRS WERE FOUND FOR ATOM LIST 42332 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30268 from a total of 767193 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1514 -74.40341 2.47785 0.61064 INTE EXTERN> -30.93423 -43.46918 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4034" Parameter: A <- "-74.4034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9342" Parameter: B <- "-30.9342" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4692" Parameter: C <- "-43.4692" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1514 TOTAL ENERGY = -74.4034 RDTITL> * VAN DER WAALS = -30.9342 ELECTROSTATIC = -43.4692 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1514" Parameter: CONF_N -> "8002" Comparing "1514" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1515" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767193 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761259 ATOM PAIRS WERE FOUND FOR ATOM LIST 42002 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30411 from a total of 761259 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1515 -67.79758 -6.60582 0.53407 INTE EXTERN> -33.32319 -34.47439 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7976" Parameter: A <- "-67.7976" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3232" Parameter: B <- "-33.3232" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4744" Parameter: C <- "-34.4744" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1515 TOTAL ENERGY = -67.7976 RDTITL> * VAN DER WAALS = -33.3232 ELECTROSTATIC = -34.4744 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1515" Parameter: CONF_N -> "8002" Comparing "1515" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1516" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761259 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767412 ATOM PAIRS WERE FOUND FOR ATOM LIST 42420 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30246 from a total of 767412 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1516 -67.53997 -0.25762 0.61164 INTE EXTERN> -28.59753 -38.94244 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.54" Parameter: A <- "-67.54" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5975" Parameter: B <- "-28.5975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9424" Parameter: C <- "-38.9424" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1516 TOTAL ENERGY = -67.54 RDTITL> * VAN DER WAALS = -28.5975 ELECTROSTATIC = -38.9424 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1516" Parameter: CONF_N -> "8002" Comparing "1516" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1517" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767412 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766867 ATOM PAIRS WERE FOUND FOR ATOM LIST 42302 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30422 from a total of 766867 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1517 -75.47685 7.93688 0.59572 INTE EXTERN> -31.92089 -43.55596 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4769" Parameter: A <- "-75.4769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9209" Parameter: B <- "-31.9209" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.556" Parameter: C <- "-43.556" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1517 TOTAL ENERGY = -75.4769 RDTITL> * VAN DER WAALS = -31.9209 ELECTROSTATIC = -43.556 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1517" Parameter: CONF_N -> "8002" Comparing "1517" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1518" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766867 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763530 ATOM PAIRS WERE FOUND FOR ATOM LIST 42045 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30038 from a total of 763530 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1518 -72.38050 -3.09635 0.67178 INTE EXTERN> -26.37416 -46.00634 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3805" Parameter: A <- "-72.3805" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3742" Parameter: B <- "-26.3742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0063" Parameter: C <- "-46.0063" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1518 TOTAL ENERGY = -72.3805 RDTITL> * VAN DER WAALS = -26.3742 ELECTROSTATIC = -46.0063 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1518" Parameter: CONF_N -> "8002" Comparing "1518" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1519" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763530 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763733 ATOM PAIRS WERE FOUND FOR ATOM LIST 42043 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29840 from a total of 763733 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1519 -71.87293 -0.50757 0.60053 INTE EXTERN> -32.32612 -39.54681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8729" Parameter: A <- "-71.8729" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3261" Parameter: B <- "-32.3261" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5468" Parameter: C <- "-39.5468" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1519 TOTAL ENERGY = -71.8729 RDTITL> * VAN DER WAALS = -32.3261 ELECTROSTATIC = -39.5468 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1519" Parameter: CONF_N -> "8002" Comparing "1519" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1520" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763733 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762639 ATOM PAIRS WERE FOUND FOR ATOM LIST 42040 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29602 from a total of 762639 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1520 -67.06675 -4.80618 0.55522 INTE EXTERN> -31.87859 -35.18816 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0668" Parameter: A <- "-67.0668" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8786" Parameter: B <- "-31.8786" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1882" Parameter: C <- "-35.1882" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1520 TOTAL ENERGY = -67.0668 RDTITL> * VAN DER WAALS = -31.8786 ELECTROSTATIC = -35.1882 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1520" Parameter: CONF_N -> "8002" Comparing "1520" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1521" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762639 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761998 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29937 from a total of 761998 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1521 -69.99824 2.93149 0.55137 INTE EXTERN> -31.43743 -38.56081 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9982" Parameter: A <- "-69.9982" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4374" Parameter: B <- "-31.4374" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5608" Parameter: C <- "-38.5608" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1521 TOTAL ENERGY = -69.9982 RDTITL> * VAN DER WAALS = -31.4374 ELECTROSTATIC = -38.5608 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1521" Parameter: CONF_N -> "8002" Comparing "1521" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1522" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761998 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759393 ATOM PAIRS WERE FOUND FOR ATOM LIST 41840 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29455 from a total of 759393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1522 -66.29643 -3.70182 0.75925 INTE EXTERN> -24.40331 -41.89312 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2964" Parameter: A <- "-66.2964" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4033" Parameter: B <- "-24.4033" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8931" Parameter: C <- "-41.8931" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1522 TOTAL ENERGY = -66.2964 RDTITL> * VAN DER WAALS = -24.4033 ELECTROSTATIC = -41.8931 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1522" Parameter: CONF_N -> "8002" Comparing "1522" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1523" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760130 ATOM PAIRS WERE FOUND FOR ATOM LIST 41658 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29475 from a total of 760130 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1523 -66.69264 0.39622 0.61051 INTE EXTERN> -29.54087 -37.15177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6926" Parameter: A <- "-66.6926" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5409" Parameter: B <- "-29.5409" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1518" Parameter: C <- "-37.1518" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1523 TOTAL ENERGY = -66.6926 RDTITL> * VAN DER WAALS = -29.5409 ELECTROSTATIC = -37.1518 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1523" Parameter: CONF_N -> "8002" Comparing "1523" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1524" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760130 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761250 ATOM PAIRS WERE FOUND FOR ATOM LIST 41772 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29672 from a total of 761250 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1524 -70.88463 4.19199 0.64156 INTE EXTERN> -27.04965 -43.83498 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8846" Parameter: A <- "-70.8846" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0496" Parameter: B <- "-27.0496" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.835" Parameter: C <- "-43.835" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1524 TOTAL ENERGY = -70.8846 RDTITL> * VAN DER WAALS = -27.0496 ELECTROSTATIC = -43.835 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1524" Parameter: CONF_N -> "8002" Comparing "1524" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1525" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761250 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759547 ATOM PAIRS WERE FOUND FOR ATOM LIST 41636 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29483 from a total of 759547 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1525 -66.43000 -4.45463 0.55929 INTE EXTERN> -30.50929 -35.92072 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.43" Parameter: A <- "-66.43" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5093" Parameter: B <- "-30.5093" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9207" Parameter: C <- "-35.9207" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1525 TOTAL ENERGY = -66.43 RDTITL> * VAN DER WAALS = -30.5093 ELECTROSTATIC = -35.9207 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1525" Parameter: CONF_N -> "8002" Comparing "1525" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1526" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759547 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760048 ATOM PAIRS WERE FOUND FOR ATOM LIST 41872 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29954 from a total of 760048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1526 -64.37778 -2.05222 0.56134 INTE EXTERN> -29.18377 -35.19401 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3778" Parameter: A <- "-64.3778" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1838" Parameter: B <- "-29.1838" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.194" Parameter: C <- "-35.194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1526 TOTAL ENERGY = -64.3778 RDTITL> * VAN DER WAALS = -29.1838 ELECTROSTATIC = -35.194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1526" Parameter: CONF_N -> "8002" Comparing "1526" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1527" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754610 ATOM PAIRS WERE FOUND FOR ATOM LIST 41530 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29377 from a total of 754610 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1527 -67.59522 3.21744 0.56572 INTE EXTERN> -29.50931 -38.08591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5952" Parameter: A <- "-67.5952" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5093" Parameter: B <- "-29.5093" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0859" Parameter: C <- "-38.0859" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1527 TOTAL ENERGY = -67.5952 RDTITL> * VAN DER WAALS = -29.5093 ELECTROSTATIC = -38.0859 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1527" Parameter: CONF_N -> "8002" Comparing "1527" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1528" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754610 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755134 ATOM PAIRS WERE FOUND FOR ATOM LIST 41572 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29544 from a total of 755134 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1528 -65.34088 -2.25433 0.51433 INTE EXTERN> -32.25584 -33.08505 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3409" Parameter: A <- "-65.3409" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2558" Parameter: B <- "-32.2558" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.085" Parameter: C <- "-33.085" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1528 TOTAL ENERGY = -65.3409 RDTITL> * VAN DER WAALS = -32.2558 ELECTROSTATIC = -33.085 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1528" Parameter: CONF_N -> "8002" Comparing "1528" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1529" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755134 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760782 ATOM PAIRS WERE FOUND FOR ATOM LIST 41760 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29769 from a total of 760782 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1529 -64.89556 -0.44533 0.72083 INTE EXTERN> -24.85731 -40.03824 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8956" Parameter: A <- "-64.8956" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8573" Parameter: B <- "-24.8573" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0382" Parameter: C <- "-40.0382" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1529 TOTAL ENERGY = -64.8956 RDTITL> * VAN DER WAALS = -24.8573 ELECTROSTATIC = -40.0382 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1529" Parameter: CONF_N -> "8002" Comparing "1529" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1530" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760782 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765725 ATOM PAIRS WERE FOUND FOR ATOM LIST 42163 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30371 from a total of 765725 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1530 -64.23394 -0.66162 0.77413 INTE EXTERN> -22.07111 -42.16282 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2339" Parameter: A <- "-64.2339" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.0711" Parameter: B <- "-22.0711" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1628" Parameter: C <- "-42.1628" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1530 TOTAL ENERGY = -64.2339 RDTITL> * VAN DER WAALS = -22.0711 ELECTROSTATIC = -42.1628 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1530" Parameter: CONF_N -> "8002" Comparing "1530" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1531" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765725 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759425 ATOM PAIRS WERE FOUND FOR ATOM LIST 41991 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30081 from a total of 759425 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1531 -74.25545 10.02152 0.71298 INTE EXTERN> -26.30699 -47.94846 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2555" Parameter: A <- "-74.2555" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.307" Parameter: B <- "-26.307" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9485" Parameter: C <- "-47.9485" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1531 TOTAL ENERGY = -74.2555 RDTITL> * VAN DER WAALS = -26.307 ELECTROSTATIC = -47.9485 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1531" Parameter: CONF_N -> "8002" Comparing "1531" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1532" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759425 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756291 ATOM PAIRS WERE FOUND FOR ATOM LIST 41592 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29563 from a total of 756291 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1532 -69.78127 -4.47418 0.65373 INTE EXTERN> -27.96407 -41.81721 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7813" Parameter: A <- "-69.7813" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9641" Parameter: B <- "-27.9641" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8172" Parameter: C <- "-41.8172" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1532 TOTAL ENERGY = -69.7813 RDTITL> * VAN DER WAALS = -27.9641 ELECTROSTATIC = -41.8172 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1532" Parameter: CONF_N -> "8002" Comparing "1532" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1533" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756291 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763151 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29864 from a total of 763151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1533 -58.75546 -11.02581 0.52585 INTE EXTERN> -32.74724 -26.00822 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.7555" Parameter: A <- "-58.7555" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7472" Parameter: B <- "-32.7472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-26.0082" Parameter: C <- "-26.0082" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1533 TOTAL ENERGY = -58.7555 RDTITL> * VAN DER WAALS = -32.7472 ELECTROSTATIC = -26.0082 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1533" Parameter: CONF_N -> "8002" Comparing "1533" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1534" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761818 ATOM PAIRS WERE FOUND FOR ATOM LIST 41980 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29894 from a total of 761818 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1534 -66.06771 7.31225 0.61807 INTE EXTERN> -29.51129 -36.55643 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0677" Parameter: A <- "-66.0677" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5113" Parameter: B <- "-29.5113" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5564" Parameter: C <- "-36.5564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1534 TOTAL ENERGY = -66.0677 RDTITL> * VAN DER WAALS = -29.5113 ELECTROSTATIC = -36.5564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1534" Parameter: CONF_N -> "8002" Comparing "1534" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1535" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761818 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754497 ATOM PAIRS WERE FOUND FOR ATOM LIST 41600 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30042 from a total of 754497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1535 -64.99989 -1.06782 0.65597 INTE EXTERN> -27.85654 -37.14335 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9999" Parameter: A <- "-64.9999" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8565" Parameter: B <- "-27.8565" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1434" Parameter: C <- "-37.1434" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1535 TOTAL ENERGY = -64.9999 RDTITL> * VAN DER WAALS = -27.8565 ELECTROSTATIC = -37.1434 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1535" Parameter: CONF_N -> "8002" Comparing "1535" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1536" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758276 ATOM PAIRS WERE FOUND FOR ATOM LIST 41655 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29860 from a total of 758276 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1536 -70.84461 5.84473 0.62200 INTE EXTERN> -29.13524 -41.70937 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8446" Parameter: A <- "-70.8446" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1352" Parameter: B <- "-29.1352" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7094" Parameter: C <- "-41.7094" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1536 TOTAL ENERGY = -70.8446 RDTITL> * VAN DER WAALS = -29.1352 ELECTROSTATIC = -41.7094 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1536" Parameter: CONF_N -> "8002" Comparing "1536" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1537" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758276 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753065 ATOM PAIRS WERE FOUND FOR ATOM LIST 41430 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 753065 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1537 -70.86565 0.02104 0.61999 INTE EXTERN> -30.19365 -40.67201 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8657" Parameter: A <- "-70.8657" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1936" Parameter: B <- "-30.1936" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.672" Parameter: C <- "-40.672" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1537 TOTAL ENERGY = -70.8657 RDTITL> * VAN DER WAALS = -30.1936 ELECTROSTATIC = -40.672 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1537" Parameter: CONF_N -> "8002" Comparing "1537" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1538" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753065 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756803 ATOM PAIRS WERE FOUND FOR ATOM LIST 41757 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28982 from a total of 756803 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1538 -70.15083 -0.71482 0.66138 INTE EXTERN> -26.28084 -43.87000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1508" Parameter: A <- "-70.1508" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2808" Parameter: B <- "-26.2808" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.87" Parameter: C <- "-43.87" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1538 TOTAL ENERGY = -70.1508 RDTITL> * VAN DER WAALS = -26.2808 ELECTROSTATIC = -43.87 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1538" Parameter: CONF_N -> "8002" Comparing "1538" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1539" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756803 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758434 ATOM PAIRS WERE FOUND FOR ATOM LIST 41778 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29148 from a total of 758434 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1539 -74.47978 4.32895 0.76681 INTE EXTERN> -23.40607 -51.07371 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4798" Parameter: A <- "-74.4798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4061" Parameter: B <- "-23.4061" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0737" Parameter: C <- "-51.0737" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1539 TOTAL ENERGY = -74.4798 RDTITL> * VAN DER WAALS = -23.4061 ELECTROSTATIC = -51.0737 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1539" Parameter: CONF_N -> "8002" Comparing "1539" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1540" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758434 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760659 ATOM PAIRS WERE FOUND FOR ATOM LIST 41711 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29882 from a total of 760659 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1540 -77.91215 3.43237 0.66831 INTE EXTERN> -28.65336 -49.25879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9121" Parameter: A <- "-77.9121" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6534" Parameter: B <- "-28.6534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2588" Parameter: C <- "-49.2588" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1540 TOTAL ENERGY = -77.9121 RDTITL> * VAN DER WAALS = -28.6534 ELECTROSTATIC = -49.2588 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1540" Parameter: CONF_N -> "8002" Comparing "1540" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1541" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760659 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759994 ATOM PAIRS WERE FOUND FOR ATOM LIST 41759 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29315 from a total of 759994 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1541 -69.92720 -7.98495 0.65110 INTE EXTERN> -28.81212 -41.11508 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9272" Parameter: A <- "-69.9272" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8121" Parameter: B <- "-28.8121" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1151" Parameter: C <- "-41.1151" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1541 TOTAL ENERGY = -69.9272 RDTITL> * VAN DER WAALS = -28.8121 ELECTROSTATIC = -41.1151 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1541" Parameter: CONF_N -> "8002" Comparing "1541" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1542" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759994 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757685 ATOM PAIRS WERE FOUND FOR ATOM LIST 41806 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29474 from a total of 757685 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1542 -76.83684 6.90964 0.61518 INTE EXTERN> -31.34378 -45.49305 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8368" Parameter: A <- "-76.8368" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3438" Parameter: B <- "-31.3438" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4931" Parameter: C <- "-45.4931" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1542 TOTAL ENERGY = -76.8368 RDTITL> * VAN DER WAALS = -31.3438 ELECTROSTATIC = -45.4931 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1542" Parameter: CONF_N -> "8002" Comparing "1542" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1543" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757685 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760429 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30319 from a total of 760429 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1543 -70.13352 -6.70331 0.66261 INTE EXTERN> -26.54894 -43.58458 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1335" Parameter: A <- "-70.1335" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5489" Parameter: B <- "-26.5489" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5846" Parameter: C <- "-43.5846" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1543 TOTAL ENERGY = -70.1335 RDTITL> * VAN DER WAALS = -26.5489 ELECTROSTATIC = -43.5846 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1543" Parameter: CONF_N -> "8002" Comparing "1543" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1544" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760429 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760242 ATOM PAIRS WERE FOUND FOR ATOM LIST 41928 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30026 from a total of 760242 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1544 -70.52628 0.39276 0.60444 INTE EXTERN> -31.15228 -39.37400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5263" Parameter: A <- "-70.5263" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1523" Parameter: B <- "-31.1523" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.374" Parameter: C <- "-39.374" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1544 TOTAL ENERGY = -70.5263 RDTITL> * VAN DER WAALS = -31.1523 ELECTROSTATIC = -39.374 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1544" Parameter: CONF_N -> "8002" Comparing "1544" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1545" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760242 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755681 ATOM PAIRS WERE FOUND FOR ATOM LIST 41542 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29285 from a total of 755681 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1545 -76.30395 5.77767 0.73960 INTE EXTERN> -26.32369 -49.98026 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3039" Parameter: A <- "-76.3039" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3237" Parameter: B <- "-26.3237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9803" Parameter: C <- "-49.9803" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1545 TOTAL ENERGY = -76.3039 RDTITL> * VAN DER WAALS = -26.3237 ELECTROSTATIC = -49.9803 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1545" Parameter: CONF_N -> "8002" Comparing "1545" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1546" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755681 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760263 ATOM PAIRS WERE FOUND FOR ATOM LIST 41578 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29975 from a total of 760263 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1546 -79.36765 3.06371 0.76534 INTE EXTERN> -27.76497 -51.60268 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.3677" Parameter: A <- "-79.3677" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.765" Parameter: B <- "-27.765" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6027" Parameter: C <- "-51.6027" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1546 TOTAL ENERGY = -79.3677 RDTITL> * VAN DER WAALS = -27.765 ELECTROSTATIC = -51.6027 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1546" Parameter: CONF_N -> "8002" Comparing "1546" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1547" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760263 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757862 ATOM PAIRS WERE FOUND FOR ATOM LIST 41666 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29600 from a total of 757862 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1547 -71.84766 -7.51999 0.78377 INTE EXTERN> -24.71360 -47.13407 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8477" Parameter: A <- "-71.8477" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7136" Parameter: B <- "-24.7136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1341" Parameter: C <- "-47.1341" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1547 TOTAL ENERGY = -71.8477 RDTITL> * VAN DER WAALS = -24.7136 ELECTROSTATIC = -47.1341 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1547" Parameter: CONF_N -> "8002" Comparing "1547" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1548" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757862 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758419 ATOM PAIRS WERE FOUND FOR ATOM LIST 41693 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30727 from a total of 758419 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1548 -75.46706 3.61939 0.65615 INTE EXTERN> -28.83867 -46.62839 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4671" Parameter: A <- "-75.4671" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8387" Parameter: B <- "-28.8387" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6284" Parameter: C <- "-46.6284" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1548 TOTAL ENERGY = -75.4671 RDTITL> * VAN DER WAALS = -28.8387 ELECTROSTATIC = -46.6284 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1548" Parameter: CONF_N -> "8002" Comparing "1548" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1549" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758419 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763560 ATOM PAIRS WERE FOUND FOR ATOM LIST 41826 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29733 from a total of 763560 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1549 -71.38121 -4.08585 0.71981 INTE EXTERN> -27.40440 -43.97681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3812" Parameter: A <- "-71.3812" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4044" Parameter: B <- "-27.4044" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9768" Parameter: C <- "-43.9768" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1549 TOTAL ENERGY = -71.3812 RDTITL> * VAN DER WAALS = -27.4044 ELECTROSTATIC = -43.9768 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1549" Parameter: CONF_N -> "8002" Comparing "1549" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1550" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763560 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758231 ATOM PAIRS WERE FOUND FOR ATOM LIST 41523 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29620 from a total of 758231 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1550 -78.46177 7.08056 0.68758 INTE EXTERN> -28.53755 -49.92421 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4618" Parameter: A <- "-78.4618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5376" Parameter: B <- "-28.5376" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9242" Parameter: C <- "-49.9242" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1550 TOTAL ENERGY = -78.4618 RDTITL> * VAN DER WAALS = -28.5376 ELECTROSTATIC = -49.9242 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1550" Parameter: CONF_N -> "8002" Comparing "1550" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1551" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758231 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762911 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30253 from a total of 762911 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1551 -76.29372 -2.16805 0.68841 INTE EXTERN> -29.36566 -46.92806 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2937" Parameter: A <- "-76.2937" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3657" Parameter: B <- "-29.3657" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9281" Parameter: C <- "-46.9281" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1551 TOTAL ENERGY = -76.2937 RDTITL> * VAN DER WAALS = -29.3657 ELECTROSTATIC = -46.9281 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1551" Parameter: CONF_N -> "8002" Comparing "1551" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1552" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762911 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762272 ATOM PAIRS WERE FOUND FOR ATOM LIST 41940 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29822 from a total of 762272 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1552 -68.29227 -8.00145 0.61577 INTE EXTERN> -28.32507 -39.96721 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2923" Parameter: A <- "-68.2923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3251" Parameter: B <- "-28.3251" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9672" Parameter: C <- "-39.9672" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1552 TOTAL ENERGY = -68.2923 RDTITL> * VAN DER WAALS = -28.3251 ELECTROSTATIC = -39.9672 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1552" Parameter: CONF_N -> "8002" Comparing "1552" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1553" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762272 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760106 ATOM PAIRS WERE FOUND FOR ATOM LIST 41695 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29351 from a total of 760106 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1553 -75.64585 7.35358 0.58672 INTE EXTERN> -31.28468 -44.36118 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6459" Parameter: A <- "-75.6459" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2847" Parameter: B <- "-31.2847" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3612" Parameter: C <- "-44.3612" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1553 TOTAL ENERGY = -75.6459 RDTITL> * VAN DER WAALS = -31.2847 ELECTROSTATIC = -44.3612 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1553" Parameter: CONF_N -> "8002" Comparing "1553" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1554" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760106 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761959 ATOM PAIRS WERE FOUND FOR ATOM LIST 41736 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30142 from a total of 761959 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1554 -71.01049 -4.63536 0.80069 INTE EXTERN> -26.36547 -44.64502 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0105" Parameter: A <- "-71.0105" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3655" Parameter: B <- "-26.3655" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.645" Parameter: C <- "-44.645" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1554 TOTAL ENERGY = -71.0105 RDTITL> * VAN DER WAALS = -26.3655 ELECTROSTATIC = -44.645 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1554" Parameter: CONF_N -> "8002" Comparing "1554" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1555" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761959 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764634 ATOM PAIRS WERE FOUND FOR ATOM LIST 41997 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29854 from a total of 764634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1555 -74.14973 3.13924 0.69138 INTE EXTERN> -27.42755 -46.72218 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1497" Parameter: A <- "-74.1497" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4275" Parameter: B <- "-27.4275" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7222" Parameter: C <- "-46.7222" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1555 TOTAL ENERGY = -74.1497 RDTITL> * VAN DER WAALS = -27.4275 ELECTROSTATIC = -46.7222 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1555" Parameter: CONF_N -> "8002" Comparing "1555" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1556" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758313 ATOM PAIRS WERE FOUND FOR ATOM LIST 41842 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29976 from a total of 758313 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1556 -73.70569 -0.44404 0.62634 INTE EXTERN> -30.83229 -42.87340 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7057" Parameter: A <- "-73.7057" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8323" Parameter: B <- "-30.8323" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8734" Parameter: C <- "-42.8734" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1556 TOTAL ENERGY = -73.7057 RDTITL> * VAN DER WAALS = -30.8323 ELECTROSTATIC = -42.8734 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1556" Parameter: CONF_N -> "8002" Comparing "1556" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1557" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758313 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767170 ATOM PAIRS WERE FOUND FOR ATOM LIST 42171 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29964 from a total of 767170 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1557 -69.86623 -3.83946 0.59821 INTE EXTERN> -32.03973 -37.82650 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8662" Parameter: A <- "-69.8662" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0397" Parameter: B <- "-32.0397" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8265" Parameter: C <- "-37.8265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1557 TOTAL ENERGY = -69.8662 RDTITL> * VAN DER WAALS = -32.0397 ELECTROSTATIC = -37.8265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1557" Parameter: CONF_N -> "8002" Comparing "1557" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1558" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767170 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761649 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29781 from a total of 761649 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1558 -71.71606 1.84983 0.64668 INTE EXTERN> -30.43559 -41.28047 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7161" Parameter: A <- "-71.7161" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4356" Parameter: B <- "-30.4356" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2805" Parameter: C <- "-41.2805" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1558 TOTAL ENERGY = -71.7161 RDTITL> * VAN DER WAALS = -30.4356 ELECTROSTATIC = -41.2805 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1558" Parameter: CONF_N -> "8002" Comparing "1558" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1559" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761649 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763393 ATOM PAIRS WERE FOUND FOR ATOM LIST 41763 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30381 from a total of 763393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1559 -73.46928 1.75322 0.64489 INTE EXTERN> -29.54013 -43.92914 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4693" Parameter: A <- "-73.4693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5401" Parameter: B <- "-29.5401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9291" Parameter: C <- "-43.9291" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1559 TOTAL ENERGY = -73.4693 RDTITL> * VAN DER WAALS = -29.5401 ELECTROSTATIC = -43.9291 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1559" Parameter: CONF_N -> "8002" Comparing "1559" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1560" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761402 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29807 from a total of 761402 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1560 -71.15180 -2.31747 0.59966 INTE EXTERN> -31.31974 -39.83206 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1518" Parameter: A <- "-71.1518" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3197" Parameter: B <- "-31.3197" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8321" Parameter: C <- "-39.8321" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1560 TOTAL ENERGY = -71.1518 RDTITL> * VAN DER WAALS = -31.3197 ELECTROSTATIC = -39.8321 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1560" Parameter: CONF_N -> "8002" Comparing "1560" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1561" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761402 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763809 ATOM PAIRS WERE FOUND FOR ATOM LIST 41863 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29959 from a total of 763809 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1561 -65.22623 -5.92557 0.81424 INTE EXTERN> -22.27403 -42.95220 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2262" Parameter: A <- "-65.2262" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.274" Parameter: B <- "-22.274" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9522" Parameter: C <- "-42.9522" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1561 TOTAL ENERGY = -65.2262 RDTITL> * VAN DER WAALS = -22.274 ELECTROSTATIC = -42.9522 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1561" Parameter: CONF_N -> "8002" Comparing "1561" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1562" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763809 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41881 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29231 from a total of 762422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1562 -71.52607 6.29984 0.68664 INTE EXTERN> -30.81842 -40.70765 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5261" Parameter: A <- "-71.5261" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8184" Parameter: B <- "-30.8184" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7076" Parameter: C <- "-40.7076" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1562 TOTAL ENERGY = -71.5261 RDTITL> * VAN DER WAALS = -30.8184 ELECTROSTATIC = -40.7076 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1562" Parameter: CONF_N -> "8002" Comparing "1562" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1563" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763851 ATOM PAIRS WERE FOUND FOR ATOM LIST 41997 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30114 from a total of 763851 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1563 -72.63858 1.11251 0.56120 INTE EXTERN> -30.90537 -41.73321 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6386" Parameter: A <- "-72.6386" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9054" Parameter: B <- "-30.9054" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7332" Parameter: C <- "-41.7332" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1563 TOTAL ENERGY = -72.6386 RDTITL> * VAN DER WAALS = -30.9054 ELECTROSTATIC = -41.7332 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1563" Parameter: CONF_N -> "8002" Comparing "1563" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1564" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763851 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762626 ATOM PAIRS WERE FOUND FOR ATOM LIST 41762 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30058 from a total of 762626 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1564 -73.07170 0.43312 0.63338 INTE EXTERN> -32.56955 -40.50215 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0717" Parameter: A <- "-73.0717" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5695" Parameter: B <- "-32.5695" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5021" Parameter: C <- "-40.5021" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1564 TOTAL ENERGY = -73.0717 RDTITL> * VAN DER WAALS = -32.5695 ELECTROSTATIC = -40.5021 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1564" Parameter: CONF_N -> "8002" Comparing "1564" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1565" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762626 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756264 ATOM PAIRS WERE FOUND FOR ATOM LIST 41627 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29319 from a total of 756264 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1565 -75.76585 2.69415 0.71612 INTE EXTERN> -27.12818 -48.63767 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7659" Parameter: A <- "-75.7659" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1282" Parameter: B <- "-27.1282" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6377" Parameter: C <- "-48.6377" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1565 TOTAL ENERGY = -75.7659 RDTITL> * VAN DER WAALS = -27.1282 ELECTROSTATIC = -48.6377 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1565" Parameter: CONF_N -> "8002" Comparing "1565" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1566" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756264 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754683 ATOM PAIRS WERE FOUND FOR ATOM LIST 41493 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29869 from a total of 754683 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1566 -66.01183 -9.75402 0.60338 INTE EXTERN> -29.35430 -36.65753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0118" Parameter: A <- "-66.0118" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3543" Parameter: B <- "-29.3543" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6575" Parameter: C <- "-36.6575" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1566 TOTAL ENERGY = -66.0118 RDTITL> * VAN DER WAALS = -29.3543 ELECTROSTATIC = -36.6575 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1566" Parameter: CONF_N -> "8002" Comparing "1566" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1567" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754683 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754106 ATOM PAIRS WERE FOUND FOR ATOM LIST 41430 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29316 from a total of 754106 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1567 -68.00127 1.98943 0.60835 INTE EXTERN> -30.97833 -37.02293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0013" Parameter: A <- "-68.0013" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9783" Parameter: B <- "-30.9783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0229" Parameter: C <- "-37.0229" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1567 TOTAL ENERGY = -68.0013 RDTITL> * VAN DER WAALS = -30.9783 ELECTROSTATIC = -37.0229 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1567" Parameter: CONF_N -> "8002" Comparing "1567" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1568" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754106 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761478 ATOM PAIRS WERE FOUND FOR ATOM LIST 41815 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30333 from a total of 761478 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1568 -68.01138 0.01011 0.64249 INTE EXTERN> -28.92172 -39.08965 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0114" Parameter: A <- "-68.0114" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9217" Parameter: B <- "-28.9217" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0897" Parameter: C <- "-39.0897" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1568 TOTAL ENERGY = -68.0114 RDTITL> * VAN DER WAALS = -28.9217 ELECTROSTATIC = -39.0897 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1568" Parameter: CONF_N -> "8002" Comparing "1568" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1569" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761478 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763649 ATOM PAIRS WERE FOUND FOR ATOM LIST 42103 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29907 from a total of 763649 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1569 -76.14376 8.13239 0.61106 INTE EXTERN> -34.64929 -41.49447 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1438" Parameter: A <- "-76.1438" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6493" Parameter: B <- "-34.6493" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4945" Parameter: C <- "-41.4945" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1569 TOTAL ENERGY = -76.1438 RDTITL> * VAN DER WAALS = -34.6493 ELECTROSTATIC = -41.4945 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1569" Parameter: CONF_N -> "8002" Comparing "1569" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1570" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763649 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764618 ATOM PAIRS WERE FOUND FOR ATOM LIST 41973 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30027 from a total of 764618 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1570 -68.14157 -8.00220 0.56031 INTE EXTERN> -33.39024 -34.75133 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1416" Parameter: A <- "-68.1416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3902" Parameter: B <- "-33.3902" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7513" Parameter: C <- "-34.7513" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1570 TOTAL ENERGY = -68.1416 RDTITL> * VAN DER WAALS = -33.3902 ELECTROSTATIC = -34.7513 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1570" Parameter: CONF_N -> "8002" Comparing "1570" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1571" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764618 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762441 ATOM PAIRS WERE FOUND FOR ATOM LIST 41883 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30446 from a total of 762441 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1571 -64.19464 -3.94693 0.63995 INTE EXTERN> -27.42882 -36.76582 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1946" Parameter: A <- "-64.1946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4288" Parameter: B <- "-27.4288" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7658" Parameter: C <- "-36.7658" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1571 TOTAL ENERGY = -64.1946 RDTITL> * VAN DER WAALS = -27.4288 ELECTROSTATIC = -36.7658 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1571" Parameter: CONF_N -> "8002" Comparing "1571" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1572" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762441 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760942 ATOM PAIRS WERE FOUND FOR ATOM LIST 42161 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30327 from a total of 760942 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1572 -67.83421 3.63957 0.65080 INTE EXTERN> -30.50204 -37.33216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8342" Parameter: A <- "-67.8342" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.502" Parameter: B <- "-30.502" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3322" Parameter: C <- "-37.3322" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1572 TOTAL ENERGY = -67.8342 RDTITL> * VAN DER WAALS = -30.502 ELECTROSTATIC = -37.3322 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1572" Parameter: CONF_N -> "8002" Comparing "1572" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1573" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760942 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753752 ATOM PAIRS WERE FOUND FOR ATOM LIST 41424 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29526 from a total of 753752 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1573 -72.74349 4.90928 0.66860 INTE EXTERN> -28.89795 -43.84554 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7435" Parameter: A <- "-72.7435" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8979" Parameter: B <- "-28.8979" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8455" Parameter: C <- "-43.8455" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1573 TOTAL ENERGY = -72.7435 RDTITL> * VAN DER WAALS = -28.8979 ELECTROSTATIC = -43.8455 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1573" Parameter: CONF_N -> "8002" Comparing "1573" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1574" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753752 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762941 ATOM PAIRS WERE FOUND FOR ATOM LIST 41929 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29689 from a total of 762941 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1574 -69.30067 -3.44282 0.62808 INTE EXTERN> -29.28225 -40.01841 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3007" Parameter: A <- "-69.3007" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2823" Parameter: B <- "-29.2823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0184" Parameter: C <- "-40.0184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1574 TOTAL ENERGY = -69.3007 RDTITL> * VAN DER WAALS = -29.2823 ELECTROSTATIC = -40.0184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1574" Parameter: CONF_N -> "8002" Comparing "1574" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1575" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762941 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762907 ATOM PAIRS WERE FOUND FOR ATOM LIST 41923 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30189 from a total of 762907 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1575 -62.88637 -6.41430 0.56017 INTE EXTERN> -31.49070 -31.39567 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.8864" Parameter: A <- "-62.8864" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4907" Parameter: B <- "-31.4907" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.3957" Parameter: C <- "-31.3957" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1575 TOTAL ENERGY = -62.8864 RDTITL> * VAN DER WAALS = -31.4907 ELECTROSTATIC = -31.3957 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1575" Parameter: CONF_N -> "8002" Comparing "1575" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1576" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762907 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759720 ATOM PAIRS WERE FOUND FOR ATOM LIST 41773 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30059 from a total of 759720 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1576 -71.26054 8.37416 0.65900 INTE EXTERN> -30.23165 -41.02889 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2605" Parameter: A <- "-71.2605" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2316" Parameter: B <- "-30.2316" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0289" Parameter: C <- "-41.0289" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1576 TOTAL ENERGY = -71.2605 RDTITL> * VAN DER WAALS = -30.2316 ELECTROSTATIC = -41.0289 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1576" Parameter: CONF_N -> "8002" Comparing "1576" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1577" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759720 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767435 ATOM PAIRS WERE FOUND FOR ATOM LIST 42155 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30808 from a total of 767435 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1577 -70.25484 -1.00570 0.60625 INTE EXTERN> -30.61394 -39.64089 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2548" Parameter: A <- "-70.2548" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6139" Parameter: B <- "-30.6139" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6409" Parameter: C <- "-39.6409" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1577 TOTAL ENERGY = -70.2548 RDTITL> * VAN DER WAALS = -30.6139 ELECTROSTATIC = -39.6409 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1577" Parameter: CONF_N -> "8002" Comparing "1577" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1578" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767435 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769350 ATOM PAIRS WERE FOUND FOR ATOM LIST 42065 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30129 from a total of 769350 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1578 -68.55944 -1.69540 0.64096 INTE EXTERN> -28.34973 -40.20970 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5594" Parameter: A <- "-68.5594" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3497" Parameter: B <- "-28.3497" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2097" Parameter: C <- "-40.2097" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1578 TOTAL ENERGY = -68.5594 RDTITL> * VAN DER WAALS = -28.3497 ELECTROSTATIC = -40.2097 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1578" Parameter: CONF_N -> "8002" Comparing "1578" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1579" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769350 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762918 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30538 from a total of 762918 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1579 -62.58594 -5.97350 0.60182 INTE EXTERN> -29.00837 -33.57757 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5859" Parameter: A <- "-62.5859" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0084" Parameter: B <- "-29.0084" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.5776" Parameter: C <- "-33.5776" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1579 TOTAL ENERGY = -62.5859 RDTITL> * VAN DER WAALS = -29.0084 ELECTROSTATIC = -33.5776 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1579" Parameter: CONF_N -> "8002" Comparing "1579" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1580" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762918 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760497 ATOM PAIRS WERE FOUND FOR ATOM LIST 41769 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30063 from a total of 760497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1580 -63.32895 0.74302 0.71912 INTE EXTERN> -28.32800 -35.00096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.329" Parameter: A <- "-63.329" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.328" Parameter: B <- "-28.328" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.001" Parameter: C <- "-35.001" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1580 TOTAL ENERGY = -63.329 RDTITL> * VAN DER WAALS = -28.328 ELECTROSTATIC = -35.001 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1580" Parameter: CONF_N -> "8002" Comparing "1580" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1581" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760222 ATOM PAIRS WERE FOUND FOR ATOM LIST 41833 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30702 from a total of 760222 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1581 -66.96632 3.63737 0.64210 INTE EXTERN> -29.33237 -37.63395 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9663" Parameter: A <- "-66.9663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3324" Parameter: B <- "-29.3324" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.634" Parameter: C <- "-37.634" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1581 TOTAL ENERGY = -66.9663 RDTITL> * VAN DER WAALS = -29.3324 ELECTROSTATIC = -37.634 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1581" Parameter: CONF_N -> "8002" Comparing "1581" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1582" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760222 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763195 ATOM PAIRS WERE FOUND FOR ATOM LIST 42004 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30789 from a total of 763195 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1582 -61.19291 -5.77341 0.59894 INTE EXTERN> -28.89923 -32.29369 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.1929" Parameter: A <- "-61.1929" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8992" Parameter: B <- "-28.8992" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2937" Parameter: C <- "-32.2937" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1582 TOTAL ENERGY = -61.1929 RDTITL> * VAN DER WAALS = -28.8992 ELECTROSTATIC = -32.2937 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1582" Parameter: CONF_N -> "8002" Comparing "1582" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1583" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763195 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758165 ATOM PAIRS WERE FOUND FOR ATOM LIST 41904 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30277 from a total of 758165 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1583 -66.85765 5.66473 0.67632 INTE EXTERN> -28.01573 -38.84191 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8576" Parameter: A <- "-66.8576" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0157" Parameter: B <- "-28.0157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8419" Parameter: C <- "-38.8419" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1583 TOTAL ENERGY = -66.8576 RDTITL> * VAN DER WAALS = -28.0157 ELECTROSTATIC = -38.8419 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1583" Parameter: CONF_N -> "8002" Comparing "1583" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1584" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758165 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761860 ATOM PAIRS WERE FOUND FOR ATOM LIST 42012 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30651 from a total of 761860 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1584 -70.26002 3.40237 0.55224 INTE EXTERN> -34.16235 -36.09767 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.26" Parameter: A <- "-70.26" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1624" Parameter: B <- "-34.1624" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0977" Parameter: C <- "-36.0977" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1584 TOTAL ENERGY = -70.26 RDTITL> * VAN DER WAALS = -34.1624 ELECTROSTATIC = -36.0977 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1584" Parameter: CONF_N -> "8002" Comparing "1584" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1585" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761860 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762952 ATOM PAIRS WERE FOUND FOR ATOM LIST 41930 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30451 from a total of 762952 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1585 -59.83497 -10.42506 0.55855 INTE EXTERN> -31.73609 -28.09888 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.835" Parameter: A <- "-59.835" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7361" Parameter: B <- "-31.7361" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.0989" Parameter: C <- "-28.0989" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1585 TOTAL ENERGY = -59.835 RDTITL> * VAN DER WAALS = -31.7361 ELECTROSTATIC = -28.0989 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1585" Parameter: CONF_N -> "8002" Comparing "1585" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1586" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762952 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756019 ATOM PAIRS WERE FOUND FOR ATOM LIST 41727 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30296 from a total of 756019 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1586 -61.87608 2.04111 0.62714 INTE EXTERN> -29.54100 -32.33508 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.8761" Parameter: A <- "-61.8761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.541" Parameter: B <- "-29.541" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.3351" Parameter: C <- "-32.3351" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1586 TOTAL ENERGY = -61.8761 RDTITL> * VAN DER WAALS = -29.541 ELECTROSTATIC = -32.3351 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1586" Parameter: CONF_N -> "8002" Comparing "1586" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1587" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756019 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757303 ATOM PAIRS WERE FOUND FOR ATOM LIST 41690 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30296 from a total of 757303 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1587 -67.67928 5.80320 0.74763 INTE EXTERN> -25.77809 -41.90119 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6793" Parameter: A <- "-67.6793" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7781" Parameter: B <- "-25.7781" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9012" Parameter: C <- "-41.9012" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1587 TOTAL ENERGY = -67.6793 RDTITL> * VAN DER WAALS = -25.7781 ELECTROSTATIC = -41.9012 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1587" Parameter: CONF_N -> "8002" Comparing "1587" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1588" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757303 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764672 ATOM PAIRS WERE FOUND FOR ATOM LIST 41991 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30501 from a total of 764672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1588 -63.10146 -4.57782 0.67123 INTE EXTERN> -29.48852 -33.61295 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1015" Parameter: A <- "-63.1015" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4885" Parameter: B <- "-29.4885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6129" Parameter: C <- "-33.6129" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1588 TOTAL ENERGY = -63.1015 RDTITL> * VAN DER WAALS = -29.4885 ELECTROSTATIC = -33.6129 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1588" Parameter: CONF_N -> "8002" Comparing "1588" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1589" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763647 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30115 from a total of 763647 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1589 -64.56204 1.46057 0.68387 INTE EXTERN> -26.27294 -38.28910 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.562" Parameter: A <- "-64.562" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2729" Parameter: B <- "-26.2729" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2891" Parameter: C <- "-38.2891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1589 TOTAL ENERGY = -64.562 RDTITL> * VAN DER WAALS = -26.2729 ELECTROSTATIC = -38.2891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1589" Parameter: CONF_N -> "8002" Comparing "1589" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1590" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763647 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759445 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29853 from a total of 759445 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1590 -72.67964 8.11760 0.55965 INTE EXTERN> -30.53306 -42.14658 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6796" Parameter: A <- "-72.6796" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5331" Parameter: B <- "-30.5331" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1466" Parameter: C <- "-42.1466" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1590 TOTAL ENERGY = -72.6796 RDTITL> * VAN DER WAALS = -30.5331 ELECTROSTATIC = -42.1466 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1590" Parameter: CONF_N -> "8002" Comparing "1590" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1591" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759445 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762388 ATOM PAIRS WERE FOUND FOR ATOM LIST 41913 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30425 from a total of 762388 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1591 -67.47850 -5.20114 0.65339 INTE EXTERN> -29.94889 -37.52961 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4785" Parameter: A <- "-67.4785" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9489" Parameter: B <- "-29.9489" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5296" Parameter: C <- "-37.5296" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1591 TOTAL ENERGY = -67.4785 RDTITL> * VAN DER WAALS = -29.9489 ELECTROSTATIC = -37.5296 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1591" Parameter: CONF_N -> "8002" Comparing "1591" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1592" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762388 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41756 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29736 from a total of 760009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1592 -74.06454 6.58604 0.69250 INTE EXTERN> -26.39269 -47.67185 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0645" Parameter: A <- "-74.0645" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3927" Parameter: B <- "-26.3927" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6718" Parameter: C <- "-47.6718" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1592 TOTAL ENERGY = -74.0645 RDTITL> * VAN DER WAALS = -26.3927 ELECTROSTATIC = -47.6718 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1592" Parameter: CONF_N -> "8002" Comparing "1592" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1593" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758104 ATOM PAIRS WERE FOUND FOR ATOM LIST 41655 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29913 from a total of 758104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1593 -73.03353 -1.03101 0.65214 INTE EXTERN> -28.56576 -44.46777 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0335" Parameter: A <- "-73.0335" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5658" Parameter: B <- "-28.5658" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4678" Parameter: C <- "-44.4678" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1593 TOTAL ENERGY = -73.0335 RDTITL> * VAN DER WAALS = -28.5658 ELECTROSTATIC = -44.4678 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1593" Parameter: CONF_N -> "8002" Comparing "1593" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1594" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762790 ATOM PAIRS WERE FOUND FOR ATOM LIST 41828 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30286 from a total of 762790 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1594 -79.13874 6.10521 0.66983 INTE EXTERN> -28.09962 -51.03912 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1387" Parameter: A <- "-79.1387" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0996" Parameter: B <- "-28.0996" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0391" Parameter: C <- "-51.0391" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1594 TOTAL ENERGY = -79.1387 RDTITL> * VAN DER WAALS = -28.0996 ELECTROSTATIC = -51.0391 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1594" Parameter: CONF_N -> "8002" Comparing "1594" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1595" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762790 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762002 ATOM PAIRS WERE FOUND FOR ATOM LIST 41792 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29941 from a total of 762002 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1595 -75.68680 -3.45194 0.54977 INTE EXTERN> -34.57012 -41.11668 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6868" Parameter: A <- "-75.6868" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.5701" Parameter: B <- "-34.5701" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1167" Parameter: C <- "-41.1167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1595 TOTAL ENERGY = -75.6868 RDTITL> * VAN DER WAALS = -34.5701 ELECTROSTATIC = -41.1167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1595" Parameter: CONF_N -> "8002" Comparing "1595" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1596" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762002 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763591 ATOM PAIRS WERE FOUND FOR ATOM LIST 41888 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30310 from a total of 763591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1596 -66.37942 -9.30738 0.62387 INTE EXTERN> -27.85006 -38.52936 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3794" Parameter: A <- "-66.3794" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8501" Parameter: B <- "-27.8501" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5294" Parameter: C <- "-38.5294" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1596 TOTAL ENERGY = -66.3794 RDTITL> * VAN DER WAALS = -27.8501 ELECTROSTATIC = -38.5294 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1596" Parameter: CONF_N -> "8002" Comparing "1596" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1597" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753847 ATOM PAIRS WERE FOUND FOR ATOM LIST 41435 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29659 from a total of 753847 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1597 -67.14657 0.76715 0.56592 INTE EXTERN> -32.14206 -35.00451 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1466" Parameter: A <- "-67.1466" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1421" Parameter: B <- "-32.1421" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0045" Parameter: C <- "-35.0045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1597 TOTAL ENERGY = -67.1466 RDTITL> * VAN DER WAALS = -32.1421 ELECTROSTATIC = -35.0045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1597" Parameter: CONF_N -> "8002" Comparing "1597" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1598" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753847 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761106 ATOM PAIRS WERE FOUND FOR ATOM LIST 41648 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29717 from a total of 761106 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1598 -63.19468 -3.95189 0.57209 INTE EXTERN> -28.85585 -34.33882 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1947" Parameter: A <- "-63.1947" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8559" Parameter: B <- "-28.8559" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3388" Parameter: C <- "-34.3388" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1598 TOTAL ENERGY = -63.1947 RDTITL> * VAN DER WAALS = -28.8559 ELECTROSTATIC = -34.3388 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1598" Parameter: CONF_N -> "8002" Comparing "1598" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1599" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761106 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763144 ATOM PAIRS WERE FOUND FOR ATOM LIST 41861 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30048 from a total of 763144 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1599 -66.56777 3.37310 0.58873 INTE EXTERN> -28.32324 -38.24454 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5678" Parameter: A <- "-66.5678" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3232" Parameter: B <- "-28.3232" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2445" Parameter: C <- "-38.2445" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1599 TOTAL ENERGY = -66.5678 RDTITL> * VAN DER WAALS = -28.3232 ELECTROSTATIC = -38.2445 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1599" Parameter: CONF_N -> "8002" Comparing "1599" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1600" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763144 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766447 ATOM PAIRS WERE FOUND FOR ATOM LIST 42057 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29776 from a total of 766447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1600 -67.82087 1.25310 0.65063 INTE EXTERN> -26.54499 -41.27588 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8209" Parameter: A <- "-67.8209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.545" Parameter: B <- "-26.545" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2759" Parameter: C <- "-41.2759" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1600 TOTAL ENERGY = -67.8209 RDTITL> * VAN DER WAALS = -26.545 ELECTROSTATIC = -41.2759 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1600" Parameter: CONF_N -> "8002" Comparing "1600" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1601" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763598 ATOM PAIRS WERE FOUND FOR ATOM LIST 41830 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30491 from a total of 763598 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1601 -69.36079 1.53992 0.63143 INTE EXTERN> -29.19626 -40.16453 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3608" Parameter: A <- "-69.3608" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1963" Parameter: B <- "-29.1963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1645" Parameter: C <- "-40.1645" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1601 TOTAL ENERGY = -69.3608 RDTITL> * VAN DER WAALS = -29.1963 ELECTROSTATIC = -40.1645 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1601" Parameter: CONF_N -> "8002" Comparing "1601" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1602" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763598 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761485 ATOM PAIRS WERE FOUND FOR ATOM LIST 41811 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29783 from a total of 761485 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1602 -66.46087 -2.89992 0.63550 INTE EXTERN> -28.49824 -37.96263 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4609" Parameter: A <- "-66.4609" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4982" Parameter: B <- "-28.4982" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9626" Parameter: C <- "-37.9626" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1602 TOTAL ENERGY = -66.4609 RDTITL> * VAN DER WAALS = -28.4982 ELECTROSTATIC = -37.9626 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1602" Parameter: CONF_N -> "8002" Comparing "1602" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1603" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761485 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760983 ATOM PAIRS WERE FOUND FOR ATOM LIST 41721 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29869 from a total of 760983 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1603 -66.47790 0.01703 0.52478 INTE EXTERN> -30.97419 -35.50371 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4779" Parameter: A <- "-66.4779" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9742" Parameter: B <- "-30.9742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5037" Parameter: C <- "-35.5037" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1603 TOTAL ENERGY = -66.4779 RDTITL> * VAN DER WAALS = -30.9742 ELECTROSTATIC = -35.5037 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1603" Parameter: CONF_N -> "8002" Comparing "1603" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1604" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760983 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752227 ATOM PAIRS WERE FOUND FOR ATOM LIST 41363 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29197 from a total of 752227 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1604 -61.52839 -4.94951 0.61572 INTE EXTERN> -27.31386 -34.21453 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.5284" Parameter: A <- "-61.5284" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3139" Parameter: B <- "-27.3139" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2145" Parameter: C <- "-34.2145" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1604 TOTAL ENERGY = -61.5284 RDTITL> * VAN DER WAALS = -27.3139 ELECTROSTATIC = -34.2145 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1604" Parameter: CONF_N -> "8002" Comparing "1604" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1605" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752227 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758383 ATOM PAIRS WERE FOUND FOR ATOM LIST 41436 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29383 from a total of 758383 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1605 -61.61008 0.08169 0.57632 INTE EXTERN> -26.43769 -35.17239 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.6101" Parameter: A <- "-61.6101" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4377" Parameter: B <- "-26.4377" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1724" Parameter: C <- "-35.1724" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1605 TOTAL ENERGY = -61.6101 RDTITL> * VAN DER WAALS = -26.4377 ELECTROSTATIC = -35.1724 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1605" Parameter: CONF_N -> "8002" Comparing "1605" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1606" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758383 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761449 ATOM PAIRS WERE FOUND FOR ATOM LIST 41651 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29944 from a total of 761449 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1606 -63.47218 1.86210 0.59679 INTE EXTERN> -28.26103 -35.21115 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4722" Parameter: A <- "-63.4722" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.261" Parameter: B <- "-28.261" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2111" Parameter: C <- "-35.2111" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1606 TOTAL ENERGY = -63.4722 RDTITL> * VAN DER WAALS = -28.261 ELECTROSTATIC = -35.2111 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1606" Parameter: CONF_N -> "8002" Comparing "1606" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1607" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761449 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759931 ATOM PAIRS WERE FOUND FOR ATOM LIST 42003 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29359 from a total of 759931 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1607 -64.68233 1.21014 0.59655 INTE EXTERN> -28.27450 -36.40783 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6823" Parameter: A <- "-64.6823" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2745" Parameter: B <- "-28.2745" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4078" Parameter: C <- "-36.4078" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1607 TOTAL ENERGY = -64.6823 RDTITL> * VAN DER WAALS = -28.2745 ELECTROSTATIC = -36.4078 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1607" Parameter: CONF_N -> "8002" Comparing "1607" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1608" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759931 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756656 ATOM PAIRS WERE FOUND FOR ATOM LIST 41416 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29793 from a total of 756656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1608 -67.88776 3.20543 0.59019 INTE EXTERN> -29.29841 -38.58934 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8878" Parameter: A <- "-67.8878" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2984" Parameter: B <- "-29.2984" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5893" Parameter: C <- "-38.5893" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1608 TOTAL ENERGY = -67.8878 RDTITL> * VAN DER WAALS = -29.2984 ELECTROSTATIC = -38.5893 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1608" Parameter: CONF_N -> "8002" Comparing "1608" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1609" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749517 ATOM PAIRS WERE FOUND FOR ATOM LIST 41134 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29386 from a total of 749517 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1609 -63.69337 -4.19438 0.58659 INTE EXTERN> -28.05209 -35.64128 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6934" Parameter: A <- "-63.6934" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0521" Parameter: B <- "-28.0521" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6413" Parameter: C <- "-35.6413" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1609 TOTAL ENERGY = -63.6934 RDTITL> * VAN DER WAALS = -28.0521 ELECTROSTATIC = -35.6413 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1609" Parameter: CONF_N -> "8002" Comparing "1609" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1610" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749517 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757797 ATOM PAIRS WERE FOUND FOR ATOM LIST 41657 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29517 from a total of 757797 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1610 -68.19116 4.49779 0.59240 INTE EXTERN> -29.40608 -38.78508 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1912" Parameter: A <- "-68.1912" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4061" Parameter: B <- "-29.4061" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7851" Parameter: C <- "-38.7851" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1610 TOTAL ENERGY = -68.1912 RDTITL> * VAN DER WAALS = -29.4061 ELECTROSTATIC = -38.7851 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1610" Parameter: CONF_N -> "8002" Comparing "1610" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1611" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757797 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761534 ATOM PAIRS WERE FOUND FOR ATOM LIST 41942 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30113 from a total of 761534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1611 -72.27853 4.08736 0.62594 INTE EXTERN> -30.01263 -42.26590 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2785" Parameter: A <- "-72.2785" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0126" Parameter: B <- "-30.0126" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2659" Parameter: C <- "-42.2659" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1611 TOTAL ENERGY = -72.2785 RDTITL> * VAN DER WAALS = -30.0126 ELECTROSTATIC = -42.2659 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1611" Parameter: CONF_N -> "8002" Comparing "1611" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1612" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763002 ATOM PAIRS WERE FOUND FOR ATOM LIST 41920 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29874 from a total of 763002 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1612 -60.54767 -11.73086 0.58334 INTE EXTERN> -28.34585 -32.20182 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.5477" Parameter: A <- "-60.5477" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3458" Parameter: B <- "-28.3458" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2018" Parameter: C <- "-32.2018" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1612 TOTAL ENERGY = -60.5477 RDTITL> * VAN DER WAALS = -28.3458 ELECTROSTATIC = -32.2018 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1612" Parameter: CONF_N -> "8002" Comparing "1612" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1613" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763002 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769387 ATOM PAIRS WERE FOUND FOR ATOM LIST 42295 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30107 from a total of 769387 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1613 -64.79072 4.24305 0.62471 INTE EXTERN> -32.51954 -32.27118 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7907" Parameter: A <- "-64.7907" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5195" Parameter: B <- "-32.5195" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2712" Parameter: C <- "-32.2712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1613 TOTAL ENERGY = -64.7907 RDTITL> * VAN DER WAALS = -32.5195 ELECTROSTATIC = -32.2712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1613" Parameter: CONF_N -> "8002" Comparing "1613" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1614" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769387 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762629 ATOM PAIRS WERE FOUND FOR ATOM LIST 41887 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30069 from a total of 762629 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1614 -63.08795 -1.70277 0.61738 INTE EXTERN> -30.92508 -32.16287 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.0879" Parameter: A <- "-63.0879" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9251" Parameter: B <- "-30.9251" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.1629" Parameter: C <- "-32.1629" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1614 TOTAL ENERGY = -63.0879 RDTITL> * VAN DER WAALS = -30.9251 ELECTROSTATIC = -32.1629 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1614" Parameter: CONF_N -> "8002" Comparing "1614" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1615" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762629 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762484 ATOM PAIRS WERE FOUND FOR ATOM LIST 42064 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29842 from a total of 762484 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1615 -68.31798 5.23003 0.58942 INTE EXTERN> -30.49098 -37.82700 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.318" Parameter: A <- "-68.318" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.491" Parameter: B <- "-30.491" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.827" Parameter: C <- "-37.827" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1615 TOTAL ENERGY = -68.318 RDTITL> * VAN DER WAALS = -30.491 ELECTROSTATIC = -37.827 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1615" Parameter: CONF_N -> "8002" Comparing "1615" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1616" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762484 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754308 ATOM PAIRS WERE FOUND FOR ATOM LIST 41579 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29261 from a total of 754308 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1616 -71.03623 2.71825 0.67403 INTE EXTERN> -28.78303 -42.25319 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0362" Parameter: A <- "-71.0362" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.783" Parameter: B <- "-28.783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2532" Parameter: C <- "-42.2532" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1616 TOTAL ENERGY = -71.0362 RDTITL> * VAN DER WAALS = -28.783 ELECTROSTATIC = -42.2532 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1616" Parameter: CONF_N -> "8002" Comparing "1616" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1617" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754308 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757196 ATOM PAIRS WERE FOUND FOR ATOM LIST 41623 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29403 from a total of 757196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1617 -71.47534 0.43911 0.62321 INTE EXTERN> -29.66704 -41.80830 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4753" Parameter: A <- "-71.4753" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.667" Parameter: B <- "-29.667" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8083" Parameter: C <- "-41.8083" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1617 TOTAL ENERGY = -71.4753 RDTITL> * VAN DER WAALS = -29.667 ELECTROSTATIC = -41.8083 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1617" Parameter: CONF_N -> "8002" Comparing "1617" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1618" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761634 ATOM PAIRS WERE FOUND FOR ATOM LIST 41920 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29838 from a total of 761634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1618 -66.65203 -4.82331 0.48375 INTE EXTERN> -32.22054 -34.43150 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.652" Parameter: A <- "-66.652" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2205" Parameter: B <- "-32.2205" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4315" Parameter: C <- "-34.4315" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1618 TOTAL ENERGY = -66.652 RDTITL> * VAN DER WAALS = -32.2205 ELECTROSTATIC = -34.4315 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1618" Parameter: CONF_N -> "8002" Comparing "1618" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1619" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759756 ATOM PAIRS WERE FOUND FOR ATOM LIST 41982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29447 from a total of 759756 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1619 -66.01571 -0.63633 0.64870 INTE EXTERN> -27.09928 -38.91642 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0157" Parameter: A <- "-66.0157" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0993" Parameter: B <- "-27.0993" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9164" Parameter: C <- "-38.9164" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1619 TOTAL ENERGY = -66.0157 RDTITL> * VAN DER WAALS = -27.0993 ELECTROSTATIC = -38.9164 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1619" Parameter: CONF_N -> "8002" Comparing "1619" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1620" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759756 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757370 ATOM PAIRS WERE FOUND FOR ATOM LIST 41587 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29573 from a total of 757370 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1620 -63.68954 -2.32617 0.55763 INTE EXTERN> -28.32510 -35.36444 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6895" Parameter: A <- "-63.6895" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3251" Parameter: B <- "-28.3251" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3644" Parameter: C <- "-35.3644" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1620 TOTAL ENERGY = -63.6895 RDTITL> * VAN DER WAALS = -28.3251 ELECTROSTATIC = -35.3644 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1620" Parameter: CONF_N -> "8002" Comparing "1620" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1621" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757370 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758988 ATOM PAIRS WERE FOUND FOR ATOM LIST 41734 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30068 from a total of 758988 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1621 -70.95659 7.26705 0.57641 INTE EXTERN> -29.94272 -41.01387 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9566" Parameter: A <- "-70.9566" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9427" Parameter: B <- "-29.9427" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0139" Parameter: C <- "-41.0139" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1621 TOTAL ENERGY = -70.9566 RDTITL> * VAN DER WAALS = -29.9427 ELECTROSTATIC = -41.0139 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1621" Parameter: CONF_N -> "8002" Comparing "1621" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1622" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758988 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762764 ATOM PAIRS WERE FOUND FOR ATOM LIST 41827 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29975 from a total of 762764 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1622 -66.63011 -4.32648 0.60096 INTE EXTERN> -30.34105 -36.28906 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6301" Parameter: A <- "-66.6301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.341" Parameter: B <- "-30.341" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2891" Parameter: C <- "-36.2891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1622 TOTAL ENERGY = -66.6301 RDTITL> * VAN DER WAALS = -30.341 ELECTROSTATIC = -36.2891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1622" Parameter: CONF_N -> "8002" Comparing "1622" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1623" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762764 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759925 ATOM PAIRS WERE FOUND FOR ATOM LIST 41659 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29923 from a total of 759925 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1623 -71.97322 5.34312 0.64744 INTE EXTERN> -28.87407 -43.09915 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9732" Parameter: A <- "-71.9732" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8741" Parameter: B <- "-28.8741" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0992" Parameter: C <- "-43.0992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1623 TOTAL ENERGY = -71.9732 RDTITL> * VAN DER WAALS = -28.8741 ELECTROSTATIC = -43.0992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1623" Parameter: CONF_N -> "8002" Comparing "1623" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1624" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759925 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759446 ATOM PAIRS WERE FOUND FOR ATOM LIST 41795 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29178 from a total of 759446 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1624 -71.80167 -0.17156 0.61292 INTE EXTERN> -28.91432 -42.88735 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8017" Parameter: A <- "-71.8017" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9143" Parameter: B <- "-28.9143" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8873" Parameter: C <- "-42.8873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1624 TOTAL ENERGY = -71.8017 RDTITL> * VAN DER WAALS = -28.9143 ELECTROSTATIC = -42.8873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1624" Parameter: CONF_N -> "8002" Comparing "1624" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1625" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759446 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759194 ATOM PAIRS WERE FOUND FOR ATOM LIST 41762 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28848 from a total of 759194 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1625 -72.44859 0.64693 0.54759 INTE EXTERN> -31.92434 -40.52425 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4486" Parameter: A <- "-72.4486" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9243" Parameter: B <- "-31.9243" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5243" Parameter: C <- "-40.5243" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1625 TOTAL ENERGY = -72.4486 RDTITL> * VAN DER WAALS = -31.9243 ELECTROSTATIC = -40.5243 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1625" Parameter: CONF_N -> "8002" Comparing "1625" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1626" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759194 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756097 ATOM PAIRS WERE FOUND FOR ATOM LIST 41509 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28918 from a total of 756097 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1626 -67.83750 -4.61110 0.45177 INTE EXTERN> -34.66031 -33.17718 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8375" Parameter: A <- "-67.8375" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6603" Parameter: B <- "-34.6603" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1772" Parameter: C <- "-33.1772" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1626 TOTAL ENERGY = -67.8375 RDTITL> * VAN DER WAALS = -34.6603 ELECTROSTATIC = -33.1772 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1626" Parameter: CONF_N -> "8002" Comparing "1626" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1627" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756097 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757725 ATOM PAIRS WERE FOUND FOR ATOM LIST 41639 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28957 from a total of 757725 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1627 -68.56991 0.73241 0.66833 INTE EXTERN> -30.93467 -37.63523 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5699" Parameter: A <- "-68.5699" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9347" Parameter: B <- "-30.9347" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6352" Parameter: C <- "-37.6352" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1627 TOTAL ENERGY = -68.5699 RDTITL> * VAN DER WAALS = -30.9347 ELECTROSTATIC = -37.6352 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1627" Parameter: CONF_N -> "8002" Comparing "1627" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1628" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757725 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756034 ATOM PAIRS WERE FOUND FOR ATOM LIST 41670 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29427 from a total of 756034 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1628 -70.46558 1.89567 0.56619 INTE EXTERN> -31.07147 -39.39410 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4656" Parameter: A <- "-70.4656" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0715" Parameter: B <- "-31.0715" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3941" Parameter: C <- "-39.3941" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1628 TOTAL ENERGY = -70.4656 RDTITL> * VAN DER WAALS = -31.0715 ELECTROSTATIC = -39.3941 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1628" Parameter: CONF_N -> "8002" Comparing "1628" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1629" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756034 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763262 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28613 from a total of 763262 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1629 -67.00298 -3.46260 0.64238 INTE EXTERN> -29.24550 -37.75748 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.003" Parameter: A <- "-67.003" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2455" Parameter: B <- "-29.2455" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7575" Parameter: C <- "-37.7575" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1629 TOTAL ENERGY = -67.003 RDTITL> * VAN DER WAALS = -29.2455 ELECTROSTATIC = -37.7575 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1629" Parameter: CONF_N -> "8002" Comparing "1629" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1630" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763262 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756658 ATOM PAIRS WERE FOUND FOR ATOM LIST 41595 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29456 from a total of 756658 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1630 -71.01908 4.01610 0.55840 INTE EXTERN> -32.17064 -38.84844 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0191" Parameter: A <- "-71.0191" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1706" Parameter: B <- "-32.1706" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8484" Parameter: C <- "-38.8484" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1630 TOTAL ENERGY = -71.0191 RDTITL> * VAN DER WAALS = -32.1706 ELECTROSTATIC = -38.8484 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1630" Parameter: CONF_N -> "8002" Comparing "1630" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1631" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756658 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759030 ATOM PAIRS WERE FOUND FOR ATOM LIST 41724 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29643 from a total of 759030 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1631 -70.01079 -1.00829 0.59224 INTE EXTERN> -29.60033 -40.41045 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0108" Parameter: A <- "-70.0108" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6003" Parameter: B <- "-29.6003" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4105" Parameter: C <- "-40.4105" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1631 TOTAL ENERGY = -70.0108 RDTITL> * VAN DER WAALS = -29.6003 ELECTROSTATIC = -40.4105 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1631" Parameter: CONF_N -> "8002" Comparing "1631" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1632" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759030 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768837 ATOM PAIRS WERE FOUND FOR ATOM LIST 41995 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30015 from a total of 768837 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1632 -79.66207 9.65128 0.69306 INTE EXTERN> -31.78987 -47.87219 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6621" Parameter: A <- "-79.6621" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7899" Parameter: B <- "-31.7899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8722" Parameter: C <- "-47.8722" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1632 TOTAL ENERGY = -79.6621 RDTITL> * VAN DER WAALS = -31.7899 ELECTROSTATIC = -47.8722 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1632" Parameter: CONF_N -> "8002" Comparing "1632" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1633" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768837 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765515 ATOM PAIRS WERE FOUND FOR ATOM LIST 42005 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30181 from a total of 765515 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1633 -76.56458 -3.09749 0.62130 INTE EXTERN> -34.01867 -42.54591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5646" Parameter: A <- "-76.5646" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0187" Parameter: B <- "-34.0187" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5459" Parameter: C <- "-42.5459" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1633 TOTAL ENERGY = -76.5646 RDTITL> * VAN DER WAALS = -34.0187 ELECTROSTATIC = -42.5459 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1633" Parameter: CONF_N -> "8002" Comparing "1633" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1634" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765515 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41729 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29335 from a total of 756794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1634 -67.84136 -8.72321 0.66891 INTE EXTERN> -27.93801 -39.90336 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8414" Parameter: A <- "-67.8414" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.938" Parameter: B <- "-27.938" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9034" Parameter: C <- "-39.9034" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1634 TOTAL ENERGY = -67.8414 RDTITL> * VAN DER WAALS = -27.938 ELECTROSTATIC = -39.9034 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1634" Parameter: CONF_N -> "8002" Comparing "1634" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1635" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762304 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29714 from a total of 762304 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1635 -75.98592 8.14455 0.73708 INTE EXTERN> -27.83749 -48.14842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9859" Parameter: A <- "-75.9859" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8375" Parameter: B <- "-27.8375" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1484" Parameter: C <- "-48.1484" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1635 TOTAL ENERGY = -75.9859 RDTITL> * VAN DER WAALS = -27.8375 ELECTROSTATIC = -48.1484 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1635" Parameter: CONF_N -> "8002" Comparing "1635" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1636" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762304 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754302 ATOM PAIRS WERE FOUND FOR ATOM LIST 41475 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28874 from a total of 754302 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1636 -72.81189 -3.17403 0.50009 INTE EXTERN> -36.82843 -35.98346 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8119" Parameter: A <- "-72.8119" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.8284" Parameter: B <- "-36.8284" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9835" Parameter: C <- "-35.9835" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1636 TOTAL ENERGY = -72.8119 RDTITL> * VAN DER WAALS = -36.8284 ELECTROSTATIC = -35.9835 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1636" Parameter: CONF_N -> "8002" Comparing "1636" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1637" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754302 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750140 ATOM PAIRS WERE FOUND FOR ATOM LIST 41257 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29064 from a total of 750140 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1637 -69.79239 -3.01950 0.62625 INTE EXTERN> -31.29493 -38.49745 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7924" Parameter: A <- "-69.7924" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2949" Parameter: B <- "-31.2949" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4975" Parameter: C <- "-38.4975" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1637 TOTAL ENERGY = -69.7924 RDTITL> * VAN DER WAALS = -31.2949 ELECTROSTATIC = -38.4975 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1637" Parameter: CONF_N -> "8002" Comparing "1637" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1638" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750140 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757834 ATOM PAIRS WERE FOUND FOR ATOM LIST 41676 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28010 from a total of 757834 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1638 -67.18831 -2.60408 0.64830 INTE EXTERN> -26.88869 -40.29961 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1883" Parameter: A <- "-67.1883" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8887" Parameter: B <- "-26.8887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2996" Parameter: C <- "-40.2996" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1638 TOTAL ENERGY = -67.1883 RDTITL> * VAN DER WAALS = -26.8887 ELECTROSTATIC = -40.2996 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1638" Parameter: CONF_N -> "8002" Comparing "1638" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1639" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757834 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760585 ATOM PAIRS WERE FOUND FOR ATOM LIST 41564 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29377 from a total of 760585 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1639 -72.44193 5.25363 0.70150 INTE EXTERN> -27.96979 -44.47214 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4419" Parameter: A <- "-72.4419" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9698" Parameter: B <- "-27.9698" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4721" Parameter: C <- "-44.4721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1639 TOTAL ENERGY = -72.4419 RDTITL> * VAN DER WAALS = -27.9698 ELECTROSTATIC = -44.4721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1639" Parameter: CONF_N -> "8002" Comparing "1639" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1640" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760585 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754425 ATOM PAIRS WERE FOUND FOR ATOM LIST 41412 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28780 from a total of 754425 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1640 -76.66270 4.22077 0.62520 INTE EXTERN> -32.56000 -44.10270 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6627" Parameter: A <- "-76.6627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.56" Parameter: B <- "-32.56" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1027" Parameter: C <- "-44.1027" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1640 TOTAL ENERGY = -76.6627 RDTITL> * VAN DER WAALS = -32.56 ELECTROSTATIC = -44.1027 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1640" Parameter: CONF_N -> "8002" Comparing "1640" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1641" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754425 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757061 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29393 from a total of 757061 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1641 -71.41776 -5.24494 0.61745 INTE EXTERN> -27.33821 -44.07955 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4178" Parameter: A <- "-71.4178" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3382" Parameter: B <- "-27.3382" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0796" Parameter: C <- "-44.0796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1641 TOTAL ENERGY = -71.4178 RDTITL> * VAN DER WAALS = -27.3382 ELECTROSTATIC = -44.0796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1641" Parameter: CONF_N -> "8002" Comparing "1641" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1642" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757061 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758028 ATOM PAIRS WERE FOUND FOR ATOM LIST 41570 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28802 from a total of 758028 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1642 -70.34758 -1.07018 0.56116 INTE EXTERN> -32.47812 -37.86946 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3476" Parameter: A <- "-70.3476" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4781" Parameter: B <- "-32.4781" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8695" Parameter: C <- "-37.8695" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1642 TOTAL ENERGY = -70.3476 RDTITL> * VAN DER WAALS = -32.4781 ELECTROSTATIC = -37.8695 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1642" Parameter: CONF_N -> "8002" Comparing "1642" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1643" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758028 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753957 ATOM PAIRS WERE FOUND FOR ATOM LIST 41118 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28667 from a total of 753957 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1643 -68.30952 -2.03806 0.59792 INTE EXTERN> -27.20510 -41.10442 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3095" Parameter: A <- "-68.3095" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2051" Parameter: B <- "-27.2051" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1044" Parameter: C <- "-41.1044" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1643 TOTAL ENERGY = -68.3095 RDTITL> * VAN DER WAALS = -27.2051 ELECTROSTATIC = -41.1044 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1643" Parameter: CONF_N -> "8002" Comparing "1643" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1644" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753957 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756202 ATOM PAIRS WERE FOUND FOR ATOM LIST 41484 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29221 from a total of 756202 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1644 -65.62400 -2.68552 0.61143 INTE EXTERN> -30.93786 -34.68614 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.624" Parameter: A <- "-65.624" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9379" Parameter: B <- "-30.9379" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.6861" Parameter: C <- "-34.6861" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1644 TOTAL ENERGY = -65.624 RDTITL> * VAN DER WAALS = -30.9379 ELECTROSTATIC = -34.6861 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1644" Parameter: CONF_N -> "8002" Comparing "1644" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1645" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756202 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765351 ATOM PAIRS WERE FOUND FOR ATOM LIST 41823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29732 from a total of 765351 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1645 -70.18991 4.56591 0.60327 INTE EXTERN> -30.69877 -39.49114 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1899" Parameter: A <- "-70.1899" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6988" Parameter: B <- "-30.6988" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4911" Parameter: C <- "-39.4911" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1645 TOTAL ENERGY = -70.1899 RDTITL> * VAN DER WAALS = -30.6988 ELECTROSTATIC = -39.4911 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1645" Parameter: CONF_N -> "8002" Comparing "1645" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1646" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765351 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763381 ATOM PAIRS WERE FOUND FOR ATOM LIST 41783 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29164 from a total of 763381 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1646 -68.31913 -1.87078 0.57386 INTE EXTERN> -30.83683 -37.48230 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3191" Parameter: A <- "-68.3191" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8368" Parameter: B <- "-30.8368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4823" Parameter: C <- "-37.4823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1646 TOTAL ENERGY = -68.3191 RDTITL> * VAN DER WAALS = -30.8368 ELECTROSTATIC = -37.4823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1646" Parameter: CONF_N -> "8002" Comparing "1646" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1647" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763381 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766740 ATOM PAIRS WERE FOUND FOR ATOM LIST 41930 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29517 from a total of 766740 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1647 -71.23190 2.91277 0.57522 INTE EXTERN> -33.25536 -37.97653 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2319" Parameter: A <- "-71.2319" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2554" Parameter: B <- "-33.2554" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9765" Parameter: C <- "-37.9765" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1647 TOTAL ENERGY = -71.2319 RDTITL> * VAN DER WAALS = -33.2554 ELECTROSTATIC = -37.9765 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1647" Parameter: CONF_N -> "8002" Comparing "1647" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1648" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766740 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762178 ATOM PAIRS WERE FOUND FOR ATOM LIST 41767 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29555 from a total of 762178 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1648 -76.40651 5.17462 0.68945 INTE EXTERN> -30.66485 -45.74167 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4065" Parameter: A <- "-76.4065" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6648" Parameter: B <- "-30.6648" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7417" Parameter: C <- "-45.7417" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1648 TOTAL ENERGY = -76.4065 RDTITL> * VAN DER WAALS = -30.6648 ELECTROSTATIC = -45.7417 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1648" Parameter: CONF_N -> "8002" Comparing "1648" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1649" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762178 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761696 ATOM PAIRS WERE FOUND FOR ATOM LIST 41710 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28816 from a total of 761696 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1649 -77.84771 1.44119 0.53756 INTE EXTERN> -37.10820 -40.73950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8477" Parameter: A <- "-77.8477" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-37.1082" Parameter: B <- "-37.1082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7395" Parameter: C <- "-40.7395" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1649 TOTAL ENERGY = -77.8477 RDTITL> * VAN DER WAALS = -37.1082 ELECTROSTATIC = -40.7395 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1649" Parameter: CONF_N -> "8002" Comparing "1649" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1650" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761696 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767649 ATOM PAIRS WERE FOUND FOR ATOM LIST 42030 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29726 from a total of 767649 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1650 -75.11030 -2.73741 0.56039 INTE EXTERN> -33.21492 -41.89538 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1103" Parameter: A <- "-75.1103" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2149" Parameter: B <- "-33.2149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8954" Parameter: C <- "-41.8954" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1650 TOTAL ENERGY = -75.1103 RDTITL> * VAN DER WAALS = -33.2149 ELECTROSTATIC = -41.8954 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1650" Parameter: CONF_N -> "8002" Comparing "1650" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1651" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767649 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759164 ATOM PAIRS WERE FOUND FOR ATOM LIST 41525 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28852 from a total of 759164 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1651 -76.10734 0.99704 0.67019 INTE EXTERN> -30.65389 -45.45345 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1073" Parameter: A <- "-76.1073" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6539" Parameter: B <- "-30.6539" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4535" Parameter: C <- "-45.4535" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1651 TOTAL ENERGY = -76.1073 RDTITL> * VAN DER WAALS = -30.6539 ELECTROSTATIC = -45.4535 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1651" Parameter: CONF_N -> "8002" Comparing "1651" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1652" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759164 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759968 ATOM PAIRS WERE FOUND FOR ATOM LIST 41558 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29052 from a total of 759968 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1652 -77.42801 1.32067 0.64066 INTE EXTERN> -31.19901 -46.22900 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.428" Parameter: A <- "-77.428" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.199" Parameter: B <- "-31.199" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.229" Parameter: C <- "-46.229" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1652 TOTAL ENERGY = -77.428 RDTITL> * VAN DER WAALS = -31.199 ELECTROSTATIC = -46.229 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1652" Parameter: CONF_N -> "8002" Comparing "1652" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1653" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759968 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763583 ATOM PAIRS WERE FOUND FOR ATOM LIST 41982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29640 from a total of 763583 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1653 -76.97644 -0.45157 0.58627 INTE EXTERN> -32.72860 -44.24784 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9764" Parameter: A <- "-76.9764" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7286" Parameter: B <- "-32.7286" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2478" Parameter: C <- "-44.2478" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1653 TOTAL ENERGY = -76.9764 RDTITL> * VAN DER WAALS = -32.7286 ELECTROSTATIC = -44.2478 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1653" Parameter: CONF_N -> "8002" Comparing "1653" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1654" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763583 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764941 ATOM PAIRS WERE FOUND FOR ATOM LIST 41912 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29873 from a total of 764941 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1654 -77.77968 0.80324 0.68461 INTE EXTERN> -30.28044 -47.49924 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7797" Parameter: A <- "-77.7797" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2804" Parameter: B <- "-30.2804" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4992" Parameter: C <- "-47.4992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1654 TOTAL ENERGY = -77.7797 RDTITL> * VAN DER WAALS = -30.2804 ELECTROSTATIC = -47.4992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1654" Parameter: CONF_N -> "8002" Comparing "1654" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1655" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764941 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761643 ATOM PAIRS WERE FOUND FOR ATOM LIST 41959 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29419 from a total of 761643 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1655 -72.94197 -4.83771 0.77586 INTE EXTERN> -27.02445 -45.91753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.942" Parameter: A <- "-72.942" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0244" Parameter: B <- "-27.0244" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9175" Parameter: C <- "-45.9175" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1655 TOTAL ENERGY = -72.942 RDTITL> * VAN DER WAALS = -27.0244 ELECTROSTATIC = -45.9175 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1655" Parameter: CONF_N -> "8002" Comparing "1655" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1656" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761643 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757463 ATOM PAIRS WERE FOUND FOR ATOM LIST 41813 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29285 from a total of 757463 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1656 -69.03636 -3.90562 0.72456 INTE EXTERN> -27.84568 -41.19067 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0364" Parameter: A <- "-69.0364" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8457" Parameter: B <- "-27.8457" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1907" Parameter: C <- "-41.1907" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1656 TOTAL ENERGY = -69.0364 RDTITL> * VAN DER WAALS = -27.8457 ELECTROSTATIC = -41.1907 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1656" Parameter: CONF_N -> "8002" Comparing "1656" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1657" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757463 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761264 ATOM PAIRS WERE FOUND FOR ATOM LIST 41886 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28841 from a total of 761264 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1657 -70.87140 1.83505 0.59430 INTE EXTERN> -30.16221 -40.70919 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8714" Parameter: A <- "-70.8714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1622" Parameter: B <- "-30.1622" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7092" Parameter: C <- "-40.7092" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1657 TOTAL ENERGY = -70.8714 RDTITL> * VAN DER WAALS = -30.1622 ELECTROSTATIC = -40.7092 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1657" Parameter: CONF_N -> "8002" Comparing "1657" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1658" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761264 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764087 ATOM PAIRS WERE FOUND FOR ATOM LIST 41851 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28638 from a total of 764087 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1658 -79.76241 8.89101 0.68968 INTE EXTERN> -29.86339 -49.89902 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7624" Parameter: A <- "-79.7624" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8634" Parameter: B <- "-29.8634" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.899" Parameter: C <- "-49.899" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1658 TOTAL ENERGY = -79.7624 RDTITL> * VAN DER WAALS = -29.8634 ELECTROSTATIC = -49.899 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1658" Parameter: CONF_N -> "8002" Comparing "1658" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1659" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764087 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763949 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29476 from a total of 763949 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1659 -78.31470 -1.44771 0.74919 INTE EXTERN> -28.94177 -49.37293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3147" Parameter: A <- "-78.3147" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9418" Parameter: B <- "-28.9418" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3729" Parameter: C <- "-49.3729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1659 TOTAL ENERGY = -78.3147 RDTITL> * VAN DER WAALS = -28.9418 ELECTROSTATIC = -49.3729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1659" Parameter: CONF_N -> "8002" Comparing "1659" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1660" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763949 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761299 ATOM PAIRS WERE FOUND FOR ATOM LIST 41695 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29392 from a total of 761299 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1660 -78.55111 0.23640 0.66867 INTE EXTERN> -32.06340 -46.48771 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5511" Parameter: A <- "-78.5511" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0634" Parameter: B <- "-32.0634" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4877" Parameter: C <- "-46.4877" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1660 TOTAL ENERGY = -78.5511 RDTITL> * VAN DER WAALS = -32.0634 ELECTROSTATIC = -46.4877 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1660" Parameter: CONF_N -> "8002" Comparing "1660" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1661" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761299 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756237 ATOM PAIRS WERE FOUND FOR ATOM LIST 41635 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29420 from a total of 756237 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1661 -77.19540 -1.35570 0.69865 INTE EXTERN> -30.93061 -46.26479 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1954" Parameter: A <- "-77.1954" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9306" Parameter: B <- "-30.9306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2648" Parameter: C <- "-46.2648" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1661 TOTAL ENERGY = -77.1954 RDTITL> * VAN DER WAALS = -30.9306 ELECTROSTATIC = -46.2648 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1661" Parameter: CONF_N -> "8002" Comparing "1661" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1662" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756237 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762258 ATOM PAIRS WERE FOUND FOR ATOM LIST 41786 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29183 from a total of 762258 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1662 -69.45448 -7.74093 0.67801 INTE EXTERN> -30.12332 -39.33116 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4545" Parameter: A <- "-69.4545" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1233" Parameter: B <- "-30.1233" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3312" Parameter: C <- "-39.3312" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1662 TOTAL ENERGY = -69.4545 RDTITL> * VAN DER WAALS = -30.1233 ELECTROSTATIC = -39.3312 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1662" Parameter: CONF_N -> "8002" Comparing "1662" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1663" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762258 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763062 ATOM PAIRS WERE FOUND FOR ATOM LIST 41887 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29429 from a total of 763062 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1663 -74.22455 4.77007 0.64588 INTE EXTERN> -32.75487 -41.46968 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2245" Parameter: A <- "-74.2245" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7549" Parameter: B <- "-32.7549" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4697" Parameter: C <- "-41.4697" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1663 TOTAL ENERGY = -74.2245 RDTITL> * VAN DER WAALS = -32.7549 ELECTROSTATIC = -41.4697 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1663" Parameter: CONF_N -> "8002" Comparing "1663" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1664" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763062 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762198 ATOM PAIRS WERE FOUND FOR ATOM LIST 41925 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29010 from a total of 762198 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1664 -71.01651 -3.20804 0.60680 INTE EXTERN> -32.55356 -38.46295 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0165" Parameter: A <- "-71.0165" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5536" Parameter: B <- "-32.5536" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.463" Parameter: C <- "-38.463" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1664 TOTAL ENERGY = -71.0165 RDTITL> * VAN DER WAALS = -32.5536 ELECTROSTATIC = -38.463 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1664" Parameter: CONF_N -> "8002" Comparing "1664" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1665" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762198 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762158 ATOM PAIRS WERE FOUND FOR ATOM LIST 41966 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29859 from a total of 762158 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1665 -77.92814 6.91163 0.60232 INTE EXTERN> -34.66525 -43.26289 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9281" Parameter: A <- "-77.9281" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6653" Parameter: B <- "-34.6653" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2629" Parameter: C <- "-43.2629" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1665 TOTAL ENERGY = -77.9281 RDTITL> * VAN DER WAALS = -34.6653 ELECTROSTATIC = -43.2629 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1665" Parameter: CONF_N -> "8002" Comparing "1665" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1666" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762158 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759022 ATOM PAIRS WERE FOUND FOR ATOM LIST 41616 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29221 from a total of 759022 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1666 -74.35375 -3.57439 0.71507 INTE EXTERN> -28.85001 -45.50374 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3537" Parameter: A <- "-74.3537" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.85" Parameter: B <- "-28.85" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5037" Parameter: C <- "-45.5037" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1666 TOTAL ENERGY = -74.3537 RDTITL> * VAN DER WAALS = -28.85 ELECTROSTATIC = -45.5037 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1666" Parameter: CONF_N -> "8002" Comparing "1666" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1667" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759022 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759255 ATOM PAIRS WERE FOUND FOR ATOM LIST 41718 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29386 from a total of 759255 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1667 -78.00683 3.65308 0.70476 INTE EXTERN> -29.62645 -48.38038 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0068" Parameter: A <- "-78.0068" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6265" Parameter: B <- "-29.6265" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3804" Parameter: C <- "-48.3804" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1667 TOTAL ENERGY = -78.0068 RDTITL> * VAN DER WAALS = -29.6265 ELECTROSTATIC = -48.3804 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1667" Parameter: CONF_N -> "8002" Comparing "1667" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1668" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759255 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762244 ATOM PAIRS WERE FOUND FOR ATOM LIST 41960 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29249 from a total of 762244 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1668 -75.56524 -2.44159 0.75214 INTE EXTERN> -27.22126 -48.34397 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5652" Parameter: A <- "-75.5652" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2213" Parameter: B <- "-27.2213" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.344" Parameter: C <- "-48.344" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1668 TOTAL ENERGY = -75.5652 RDTITL> * VAN DER WAALS = -27.2213 ELECTROSTATIC = -48.344 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1668" Parameter: CONF_N -> "8002" Comparing "1668" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1669" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762244 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758085 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29109 from a total of 758085 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1669 -80.60013 5.03490 0.68423 INTE EXTERN> -30.18233 -50.41780 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6001" Parameter: A <- "-80.6001" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1823" Parameter: B <- "-30.1823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4178" Parameter: C <- "-50.4178" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1669 TOTAL ENERGY = -80.6001 RDTITL> * VAN DER WAALS = -30.1823 ELECTROSTATIC = -50.4178 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1669" Parameter: CONF_N -> "8002" Comparing "1669" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1670" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758085 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764978 ATOM PAIRS WERE FOUND FOR ATOM LIST 42074 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29746 from a total of 764978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1670 -74.94892 -5.65121 0.65750 INTE EXTERN> -28.61065 -46.33827 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9489" Parameter: A <- "-74.9489" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6107" Parameter: B <- "-28.6107" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3383" Parameter: C <- "-46.3383" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1670 TOTAL ENERGY = -74.9489 RDTITL> * VAN DER WAALS = -28.6107 ELECTROSTATIC = -46.3383 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1670" Parameter: CONF_N -> "8002" Comparing "1670" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1671" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763755 ATOM PAIRS WERE FOUND FOR ATOM LIST 41948 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29537 from a total of 763755 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1671 -71.24114 -3.70778 0.66275 INTE EXTERN> -29.45454 -41.78660 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2411" Parameter: A <- "-71.2411" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4545" Parameter: B <- "-29.4545" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7866" Parameter: C <- "-41.7866" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1671 TOTAL ENERGY = -71.2411 RDTITL> * VAN DER WAALS = -29.4545 ELECTROSTATIC = -41.7866 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1671" Parameter: CONF_N -> "8002" Comparing "1671" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1672" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763755 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761445 ATOM PAIRS WERE FOUND FOR ATOM LIST 42039 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29281 from a total of 761445 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1672 -79.86760 8.62646 0.72118 INTE EXTERN> -29.58098 -50.28662 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8676" Parameter: A <- "-79.8676" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.581" Parameter: B <- "-29.581" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2866" Parameter: C <- "-50.2866" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1672 TOTAL ENERGY = -79.8676 RDTITL> * VAN DER WAALS = -29.581 ELECTROSTATIC = -50.2866 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1672" Parameter: CONF_N -> "8002" Comparing "1672" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1673" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761445 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761375 ATOM PAIRS WERE FOUND FOR ATOM LIST 42053 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29406 from a total of 761375 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1673 -70.70892 -9.15868 0.62816 INTE EXTERN> -31.75111 -38.95781 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7089" Parameter: A <- "-70.7089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7511" Parameter: B <- "-31.7511" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9578" Parameter: C <- "-38.9578" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1673 TOTAL ENERGY = -70.7089 RDTITL> * VAN DER WAALS = -31.7511 ELECTROSTATIC = -38.9578 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1673" Parameter: CONF_N -> "8002" Comparing "1673" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1674" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761375 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760672 ATOM PAIRS WERE FOUND FOR ATOM LIST 41799 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29604 from a total of 760672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1674 -76.73311 6.02418 0.65560 INTE EXTERN> -32.60617 -44.12694 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7331" Parameter: A <- "-76.7331" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6062" Parameter: B <- "-32.6062" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1269" Parameter: C <- "-44.1269" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1674 TOTAL ENERGY = -76.7331 RDTITL> * VAN DER WAALS = -32.6062 ELECTROSTATIC = -44.1269 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1674" Parameter: CONF_N -> "8002" Comparing "1674" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1675" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760352 ATOM PAIRS WERE FOUND FOR ATOM LIST 41879 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29501 from a total of 760352 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1675 -67.94571 -8.78740 0.54943 INTE EXTERN> -36.27817 -31.66754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9457" Parameter: A <- "-67.9457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.2782" Parameter: B <- "-36.2782" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.6675" Parameter: C <- "-31.6675" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1675 TOTAL ENERGY = -67.9457 RDTITL> * VAN DER WAALS = -36.2782 ELECTROSTATIC = -31.6675 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1675" Parameter: CONF_N -> "8002" Comparing "1675" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1676" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760352 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764766 ATOM PAIRS WERE FOUND FOR ATOM LIST 42008 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29727 from a total of 764766 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1676 -70.58506 2.63935 0.63167 INTE EXTERN> -35.17909 -35.40597 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5851" Parameter: A <- "-70.5851" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.1791" Parameter: B <- "-35.1791" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.406" Parameter: C <- "-35.406" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1676 TOTAL ENERGY = -70.5851 RDTITL> * VAN DER WAALS = -35.1791 ELECTROSTATIC = -35.406 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1676" Parameter: CONF_N -> "8002" Comparing "1676" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1677" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764766 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763173 ATOM PAIRS WERE FOUND FOR ATOM LIST 41881 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29921 from a total of 763173 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1677 -80.97398 10.38892 0.71220 INTE EXTERN> -29.76770 -51.20628 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.974" Parameter: A <- "-80.974" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7677" Parameter: B <- "-29.7677" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2063" Parameter: C <- "-51.2063" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1677 TOTAL ENERGY = -80.974 RDTITL> * VAN DER WAALS = -29.7677 ELECTROSTATIC = -51.2063 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1677" Parameter: CONF_N -> "8002" Comparing "1677" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1678" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763173 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763371 ATOM PAIRS WERE FOUND FOR ATOM LIST 41969 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29866 from a total of 763371 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1678 -85.13846 4.16449 0.60070 INTE EXTERN> -34.31206 -50.82641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.1385" Parameter: A <- "-85.1385" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3121" Parameter: B <- "-34.3121" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8264" Parameter: C <- "-50.8264" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1678 TOTAL ENERGY = -85.1385 RDTITL> * VAN DER WAALS = -34.3121 ELECTROSTATIC = -50.8264 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1678" Parameter: CONF_N -> "8002" Comparing "1678" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1679" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763371 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756998 ATOM PAIRS WERE FOUND FOR ATOM LIST 41485 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29040 from a total of 756998 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1679 -79.78503 -5.35343 0.68649 INTE EXTERN> -31.53700 -48.24803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.785" Parameter: A <- "-79.785" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.537" Parameter: B <- "-31.537" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.248" Parameter: C <- "-48.248" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1679 TOTAL ENERGY = -79.785 RDTITL> * VAN DER WAALS = -31.537 ELECTROSTATIC = -48.248 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1679" Parameter: CONF_N -> "8002" Comparing "1679" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1680" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756998 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765619 ATOM PAIRS WERE FOUND FOR ATOM LIST 42131 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29674 from a total of 765619 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1680 -85.29880 5.51377 0.72213 INTE EXTERN> -31.30617 -53.99262 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.2988" Parameter: A <- "-85.2988" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3062" Parameter: B <- "-31.3062" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.9926" Parameter: C <- "-53.9926" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1680 TOTAL ENERGY = -85.2988 RDTITL> * VAN DER WAALS = -31.3062 ELECTROSTATIC = -53.9926 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1680" Parameter: CONF_N -> "8002" Comparing "1680" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1681" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765619 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764232 ATOM PAIRS WERE FOUND FOR ATOM LIST 41810 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29702 from a total of 764232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1681 -79.06675 -6.23204 0.71337 INTE EXTERN> -28.69049 -50.37626 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0668" Parameter: A <- "-79.0668" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6905" Parameter: B <- "-28.6905" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3763" Parameter: C <- "-50.3763" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1681 TOTAL ENERGY = -79.0668 RDTITL> * VAN DER WAALS = -28.6905 ELECTROSTATIC = -50.3763 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1681" Parameter: CONF_N -> "8002" Comparing "1681" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1682" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762348 ATOM PAIRS WERE FOUND FOR ATOM LIST 41944 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29614 from a total of 762348 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1682 -77.66635 -1.40040 0.69983 INTE EXTERN> -30.08258 -47.58377 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6664" Parameter: A <- "-77.6664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0826" Parameter: B <- "-30.0826" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5838" Parameter: C <- "-47.5838" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1682 TOTAL ENERGY = -77.6664 RDTITL> * VAN DER WAALS = -30.0826 ELECTROSTATIC = -47.5838 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1682" Parameter: CONF_N -> "8002" Comparing "1682" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1683" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762348 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759183 ATOM PAIRS WERE FOUND FOR ATOM LIST 41814 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29733 from a total of 759183 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1683 -77.16954 -0.49681 0.65823 INTE EXTERN> -30.69479 -46.47475 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1695" Parameter: A <- "-77.1695" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6948" Parameter: B <- "-30.6948" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4748" Parameter: C <- "-46.4748" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1683 TOTAL ENERGY = -77.1695 RDTITL> * VAN DER WAALS = -30.6948 ELECTROSTATIC = -46.4748 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1683" Parameter: CONF_N -> "8002" Comparing "1683" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1684" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759183 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761407 ATOM PAIRS WERE FOUND FOR ATOM LIST 41813 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30040 from a total of 761407 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1684 -77.81861 0.64907 0.60319 INTE EXTERN> -32.37800 -45.44061 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8186" Parameter: A <- "-77.8186" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.378" Parameter: B <- "-32.378" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4406" Parameter: C <- "-45.4406" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1684 TOTAL ENERGY = -77.8186 RDTITL> * VAN DER WAALS = -32.378 ELECTROSTATIC = -45.4406 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1684" Parameter: CONF_N -> "8002" Comparing "1684" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1685" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761407 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762778 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29388 from a total of 762778 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1685 -74.11778 -3.70083 0.63507 INTE EXTERN> -33.53145 -40.58633 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1178" Parameter: A <- "-74.1178" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5314" Parameter: B <- "-33.5314" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5863" Parameter: C <- "-40.5863" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1685 TOTAL ENERGY = -74.1178 RDTITL> * VAN DER WAALS = -33.5314 ELECTROSTATIC = -40.5863 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1685" Parameter: CONF_N -> "8002" Comparing "1685" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1686" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762778 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764327 ATOM PAIRS WERE FOUND FOR ATOM LIST 41960 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29695 from a total of 764327 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1686 -74.86549 0.74771 0.59929 INTE EXTERN> -33.89957 -40.96591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8655" Parameter: A <- "-74.8655" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8996" Parameter: B <- "-33.8996" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9659" Parameter: C <- "-40.9659" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1686 TOTAL ENERGY = -74.8655 RDTITL> * VAN DER WAALS = -33.8996 ELECTROSTATIC = -40.9659 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1686" Parameter: CONF_N -> "8002" Comparing "1686" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1687" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764327 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765450 ATOM PAIRS WERE FOUND FOR ATOM LIST 42029 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29630 from a total of 765450 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1687 -79.78602 4.92053 0.68264 INTE EXTERN> -31.91457 -47.87145 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.786" Parameter: A <- "-79.786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9146" Parameter: B <- "-31.9146" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8714" Parameter: C <- "-47.8714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1687 TOTAL ENERGY = -79.786 RDTITL> * VAN DER WAALS = -31.9146 ELECTROSTATIC = -47.8714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1687" Parameter: CONF_N -> "8002" Comparing "1687" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1688" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765450 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762662 ATOM PAIRS WERE FOUND FOR ATOM LIST 41976 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29199 from a total of 762662 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1688 -73.54840 -6.23763 0.79381 INTE EXTERN> -25.21711 -48.33128 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5484" Parameter: A <- "-73.5484" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2171" Parameter: B <- "-25.2171" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3313" Parameter: C <- "-48.3313" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1688 TOTAL ENERGY = -73.5484 RDTITL> * VAN DER WAALS = -25.2171 ELECTROSTATIC = -48.3313 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1688" Parameter: CONF_N -> "8002" Comparing "1688" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1689" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762662 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758209 ATOM PAIRS WERE FOUND FOR ATOM LIST 41689 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29356 from a total of 758209 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1689 -70.85583 -2.69256 0.67334 INTE EXTERN> -31.69632 -39.15951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8558" Parameter: A <- "-70.8558" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6963" Parameter: B <- "-31.6963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1595" Parameter: C <- "-39.1595" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1689 TOTAL ENERGY = -70.8558 RDTITL> * VAN DER WAALS = -31.6963 ELECTROSTATIC = -39.1595 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1689" Parameter: CONF_N -> "8002" Comparing "1689" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1690" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758209 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760684 ATOM PAIRS WERE FOUND FOR ATOM LIST 41784 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30018 from a total of 760684 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1690 -68.34338 -2.51246 0.66108 INTE EXTERN> -29.23959 -39.10379 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3434" Parameter: A <- "-68.3434" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2396" Parameter: B <- "-29.2396" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1038" Parameter: C <- "-39.1038" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1690 TOTAL ENERGY = -68.3434 RDTITL> * VAN DER WAALS = -29.2396 ELECTROSTATIC = -39.1038 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1690" Parameter: CONF_N -> "8002" Comparing "1690" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1691" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760684 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763892 ATOM PAIRS WERE FOUND FOR ATOM LIST 41704 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29309 from a total of 763892 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1691 -68.30573 -0.03765 0.57821 INTE EXTERN> -32.56568 -35.74005 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3057" Parameter: A <- "-68.3057" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5657" Parameter: B <- "-32.5657" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7401" Parameter: C <- "-35.7401" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1691 TOTAL ENERGY = -68.3057 RDTITL> * VAN DER WAALS = -32.5657 ELECTROSTATIC = -35.7401 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1691" Parameter: CONF_N -> "8002" Comparing "1691" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1692" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763892 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763539 ATOM PAIRS WERE FOUND FOR ATOM LIST 41763 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29417 from a total of 763539 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1692 -67.16657 -1.13916 0.69876 INTE EXTERN> -30.70842 -36.45815 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1666" Parameter: A <- "-67.1666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7084" Parameter: B <- "-30.7084" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4581" Parameter: C <- "-36.4581" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1692 TOTAL ENERGY = -67.1666 RDTITL> * VAN DER WAALS = -30.7084 ELECTROSTATIC = -36.4581 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1692" Parameter: CONF_N -> "8002" Comparing "1692" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1693" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763539 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762826 ATOM PAIRS WERE FOUND FOR ATOM LIST 41723 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29321 from a total of 762826 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1693 -65.96843 -1.19814 0.59700 INTE EXTERN> -34.16443 -31.80400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9684" Parameter: A <- "-65.9684" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1644" Parameter: B <- "-34.1644" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.804" Parameter: C <- "-31.804" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1693 TOTAL ENERGY = -65.9684 RDTITL> * VAN DER WAALS = -34.1644 ELECTROSTATIC = -31.804 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1693" Parameter: CONF_N -> "8002" Comparing "1693" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1694" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762826 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755613 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28942 from a total of 755613 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1694 -70.43709 4.46866 0.59157 INTE EXTERN> -31.38177 -39.05532 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4371" Parameter: A <- "-70.4371" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3818" Parameter: B <- "-31.3818" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0553" Parameter: C <- "-39.0553" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1694 TOTAL ENERGY = -70.4371 RDTITL> * VAN DER WAALS = -31.3818 ELECTROSTATIC = -39.0553 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1694" Parameter: CONF_N -> "8002" Comparing "1694" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1695" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755613 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764602 ATOM PAIRS WERE FOUND FOR ATOM LIST 41942 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29321 from a total of 764602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1695 -81.61444 11.17734 0.66887 INTE EXTERN> -30.87544 -50.73900 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6144" Parameter: A <- "-81.6144" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8754" Parameter: B <- "-30.8754" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.739" Parameter: C <- "-50.739" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1695 TOTAL ENERGY = -81.6144 RDTITL> * VAN DER WAALS = -30.8754 ELECTROSTATIC = -50.739 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1695" Parameter: CONF_N -> "8002" Comparing "1695" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1696" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760251 ATOM PAIRS WERE FOUND FOR ATOM LIST 41713 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29247 from a total of 760251 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1696 -79.84788 -1.76656 0.71218 INTE EXTERN> -31.08086 -48.76702 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8479" Parameter: A <- "-79.8479" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0809" Parameter: B <- "-31.0809" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.767" Parameter: C <- "-48.767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1696 TOTAL ENERGY = -79.8479 RDTITL> * VAN DER WAALS = -31.0809 ELECTROSTATIC = -48.767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1696" Parameter: CONF_N -> "8002" Comparing "1696" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1697" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760251 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763744 ATOM PAIRS WERE FOUND FOR ATOM LIST 41925 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29679 from a total of 763744 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1697 -70.51336 -9.33452 0.75127 INTE EXTERN> -27.63544 -42.87792 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5134" Parameter: A <- "-70.5134" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6354" Parameter: B <- "-27.6354" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8779" Parameter: C <- "-42.8779" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1697 TOTAL ENERGY = -70.5134 RDTITL> * VAN DER WAALS = -27.6354 ELECTROSTATIC = -42.8779 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1697" Parameter: CONF_N -> "8002" Comparing "1697" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1698" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763744 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765444 ATOM PAIRS WERE FOUND FOR ATOM LIST 42004 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30028 from a total of 765444 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1698 -76.54592 6.03256 0.74462 INTE EXTERN> -28.58035 -47.96556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5459" Parameter: A <- "-76.5459" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5804" Parameter: B <- "-28.5804" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9656" Parameter: C <- "-47.9656" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1698 TOTAL ENERGY = -76.5459 RDTITL> * VAN DER WAALS = -28.5804 ELECTROSTATIC = -47.9656 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1698" Parameter: CONF_N -> "8002" Comparing "1698" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1699" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765444 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764802 ATOM PAIRS WERE FOUND FOR ATOM LIST 42120 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29742 from a total of 764802 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1699 -77.47915 0.93323 0.63124 INTE EXTERN> -29.93676 -47.54239 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4792" Parameter: A <- "-77.4792" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9368" Parameter: B <- "-29.9368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5424" Parameter: C <- "-47.5424" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1699 TOTAL ENERGY = -77.4792 RDTITL> * VAN DER WAALS = -29.9368 ELECTROSTATIC = -47.5424 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1699" Parameter: CONF_N -> "8002" Comparing "1699" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1700" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764802 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762188 ATOM PAIRS WERE FOUND FOR ATOM LIST 41840 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29672 from a total of 762188 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1700 -70.24721 -7.23194 0.60124 INTE EXTERN> -32.74032 -37.50689 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2472" Parameter: A <- "-70.2472" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7403" Parameter: B <- "-32.7403" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5069" Parameter: C <- "-37.5069" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1700 TOTAL ENERGY = -70.2472 RDTITL> * VAN DER WAALS = -32.7403 ELECTROSTATIC = -37.5069 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1700" Parameter: CONF_N -> "8002" Comparing "1700" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1701" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762188 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766395 ATOM PAIRS WERE FOUND FOR ATOM LIST 41880 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29054 from a total of 766395 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1701 -67.87134 -2.37587 0.65303 INTE EXTERN> -27.50467 -40.36667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8713" Parameter: A <- "-67.8713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5047" Parameter: B <- "-27.5047" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3667" Parameter: C <- "-40.3667" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1701 TOTAL ENERGY = -67.8713 RDTITL> * VAN DER WAALS = -27.5047 ELECTROSTATIC = -40.3667 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1701" Parameter: CONF_N -> "8002" Comparing "1701" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1702" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766395 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761424 ATOM PAIRS WERE FOUND FOR ATOM LIST 41890 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29517 from a total of 761424 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1702 -73.76786 5.89652 0.52849 INTE EXTERN> -32.78754 -40.98032 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7679" Parameter: A <- "-73.7679" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7875" Parameter: B <- "-32.7875" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9803" Parameter: C <- "-40.9803" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1702 TOTAL ENERGY = -73.7679 RDTITL> * VAN DER WAALS = -32.7875 ELECTROSTATIC = -40.9803 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1702" Parameter: CONF_N -> "8002" Comparing "1702" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1703" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761424 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758842 ATOM PAIRS WERE FOUND FOR ATOM LIST 41810 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29799 from a total of 758842 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1703 -77.78032 4.01246 0.66373 INTE EXTERN> -30.21825 -47.56207 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7803" Parameter: A <- "-77.7803" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2182" Parameter: B <- "-30.2182" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5621" Parameter: C <- "-47.5621" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1703 TOTAL ENERGY = -77.7803 RDTITL> * VAN DER WAALS = -30.2182 ELECTROSTATIC = -47.5621 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1703" Parameter: CONF_N -> "8002" Comparing "1703" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1704" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758842 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759791 ATOM PAIRS WERE FOUND FOR ATOM LIST 41733 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30267 from a total of 759791 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1704 -72.53557 -5.24475 0.67874 INTE EXTERN> -29.20753 -43.32804 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5356" Parameter: A <- "-72.5356" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2075" Parameter: B <- "-29.2075" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.328" Parameter: C <- "-43.328" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1704 TOTAL ENERGY = -72.5356 RDTITL> * VAN DER WAALS = -29.2075 ELECTROSTATIC = -43.328 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1704" Parameter: CONF_N -> "8002" Comparing "1704" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1705" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759791 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761181 ATOM PAIRS WERE FOUND FOR ATOM LIST 41716 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29920 from a total of 761181 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1705 -79.14424 6.60867 0.66429 INTE EXTERN> -29.60226 -49.54198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1442" Parameter: A <- "-79.1442" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6023" Parameter: B <- "-29.6023" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.542" Parameter: C <- "-49.542" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1705 TOTAL ENERGY = -79.1442 RDTITL> * VAN DER WAALS = -29.6023 ELECTROSTATIC = -49.542 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1705" Parameter: CONF_N -> "8002" Comparing "1705" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1706" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761181 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757744 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30062 from a total of 757744 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1706 -79.96033 0.81609 0.67844 INTE EXTERN> -29.71519 -50.24514 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9603" Parameter: A <- "-79.9603" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7152" Parameter: B <- "-29.7152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2451" Parameter: C <- "-50.2451" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1706 TOTAL ENERGY = -79.9603 RDTITL> * VAN DER WAALS = -29.7152 ELECTROSTATIC = -50.2451 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1706" Parameter: CONF_N -> "8002" Comparing "1706" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1707" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757744 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757809 ATOM PAIRS WERE FOUND FOR ATOM LIST 41576 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29625 from a total of 757809 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1707 -68.84405 -11.11627 0.59881 INTE EXTERN> -31.85340 -36.99065 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8441" Parameter: A <- "-68.8441" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8534" Parameter: B <- "-31.8534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9906" Parameter: C <- "-36.9906" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1707 TOTAL ENERGY = -68.8441 RDTITL> * VAN DER WAALS = -31.8534 ELECTROSTATIC = -36.9906 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1707" Parameter: CONF_N -> "8002" Comparing "1707" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1708" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757809 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758055 ATOM PAIRS WERE FOUND FOR ATOM LIST 41818 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29856 from a total of 758055 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1708 -72.49045 3.64640 0.67048 INTE EXTERN> -30.03040 -42.46005 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4905" Parameter: A <- "-72.4905" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0304" Parameter: B <- "-30.0304" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4601" Parameter: C <- "-42.4601" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1708 TOTAL ENERGY = -72.4905 RDTITL> * VAN DER WAALS = -30.0304 ELECTROSTATIC = -42.4601 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1708" Parameter: CONF_N -> "8002" Comparing "1708" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1709" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758055 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758642 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 758642 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1709 -70.89157 -1.59888 0.65760 INTE EXTERN> -27.21438 -43.67719 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8916" Parameter: A <- "-70.8916" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2144" Parameter: B <- "-27.2144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6772" Parameter: C <- "-43.6772" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1709 TOTAL ENERGY = -70.8916 RDTITL> * VAN DER WAALS = -27.2144 ELECTROSTATIC = -43.6772 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1709" Parameter: CONF_N -> "8002" Comparing "1709" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1710" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758642 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755879 ATOM PAIRS WERE FOUND FOR ATOM LIST 41539 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29403 from a total of 755879 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1710 -70.10893 -0.78264 0.76931 INTE EXTERN> -25.13040 -44.97853 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1089" Parameter: A <- "-70.1089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1304" Parameter: B <- "-25.1304" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9785" Parameter: C <- "-44.9785" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1710 TOTAL ENERGY = -70.1089 RDTITL> * VAN DER WAALS = -25.1304 ELECTROSTATIC = -44.9785 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1710" Parameter: CONF_N -> "8002" Comparing "1710" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1711" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755879 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755543 ATOM PAIRS WERE FOUND FOR ATOM LIST 41531 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29390 from a total of 755543 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1711 -78.03180 7.92287 0.75056 INTE EXTERN> -29.02556 -49.00624 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0318" Parameter: A <- "-78.0318" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0256" Parameter: B <- "-29.0256" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0062" Parameter: C <- "-49.0062" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1711 TOTAL ENERGY = -78.0318 RDTITL> * VAN DER WAALS = -29.0256 ELECTROSTATIC = -49.0062 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1711" Parameter: CONF_N -> "8002" Comparing "1711" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1712" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755543 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765295 ATOM PAIRS WERE FOUND FOR ATOM LIST 42059 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29689 from a total of 765295 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1712 -78.91322 0.88143 0.65918 INTE EXTERN> -30.68811 -48.22511 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9132" Parameter: A <- "-78.9132" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6881" Parameter: B <- "-30.6881" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2251" Parameter: C <- "-48.2251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1712 TOTAL ENERGY = -78.9132 RDTITL> * VAN DER WAALS = -30.6881 ELECTROSTATIC = -48.2251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1712" Parameter: CONF_N -> "8002" Comparing "1712" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1713" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765295 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760238 ATOM PAIRS WERE FOUND FOR ATOM LIST 41693 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29450 from a total of 760238 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1713 -77.12751 -1.78571 0.68861 INTE EXTERN> -29.20236 -47.92514 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1275" Parameter: A <- "-77.1275" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2024" Parameter: B <- "-29.2024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9251" Parameter: C <- "-47.9251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1713 TOTAL ENERGY = -77.1275 RDTITL> * VAN DER WAALS = -29.2024 ELECTROSTATIC = -47.9251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1713" Parameter: CONF_N -> "8002" Comparing "1713" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1714" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760238 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757481 ATOM PAIRS WERE FOUND FOR ATOM LIST 41641 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29268 from a total of 757481 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1714 -79.43156 2.30405 0.63260 INTE EXTERN> -32.32318 -47.10838 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4316" Parameter: A <- "-79.4316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3232" Parameter: B <- "-32.3232" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1084" Parameter: C <- "-47.1084" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1714 TOTAL ENERGY = -79.4316 RDTITL> * VAN DER WAALS = -32.3232 ELECTROSTATIC = -47.1084 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1714" Parameter: CONF_N -> "8002" Comparing "1714" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1715" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757481 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763320 ATOM PAIRS WERE FOUND FOR ATOM LIST 42048 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29727 from a total of 763320 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1715 -81.46481 2.03325 0.68124 INTE EXTERN> -31.67986 -49.78495 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4648" Parameter: A <- "-81.4648" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6799" Parameter: B <- "-31.6799" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7849" Parameter: C <- "-49.7849" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1715 TOTAL ENERGY = -81.4648 RDTITL> * VAN DER WAALS = -31.6799 ELECTROSTATIC = -49.7849 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1715" Parameter: CONF_N -> "8002" Comparing "1715" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1716" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763320 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758975 ATOM PAIRS WERE FOUND FOR ATOM LIST 41717 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28570 from a total of 758975 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1716 -74.25378 -7.21103 0.79301 INTE EXTERN> -24.93919 -49.31459 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2538" Parameter: A <- "-74.2538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9392" Parameter: B <- "-24.9392" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3146" Parameter: C <- "-49.3146" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1716 TOTAL ENERGY = -74.2538 RDTITL> * VAN DER WAALS = -24.9392 ELECTROSTATIC = -49.3146 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1716" Parameter: CONF_N -> "8002" Comparing "1716" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1717" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758975 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763155 ATOM PAIRS WERE FOUND FOR ATOM LIST 41939 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29482 from a total of 763155 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1717 -78.81387 4.56009 0.73900 INTE EXTERN> -29.70045 -49.11342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8139" Parameter: A <- "-78.8139" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7004" Parameter: B <- "-29.7004" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1134" Parameter: C <- "-49.1134" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1717 TOTAL ENERGY = -78.8139 RDTITL> * VAN DER WAALS = -29.7004 ELECTROSTATIC = -49.1134 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1717" Parameter: CONF_N -> "8002" Comparing "1717" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1718" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763155 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768743 ATOM PAIRS WERE FOUND FOR ATOM LIST 42237 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29335 from a total of 768743 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1718 -72.77899 -6.03488 0.68841 INTE EXTERN> -29.42148 -43.35751 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.779" Parameter: A <- "-72.779" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4215" Parameter: B <- "-29.4215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3575" Parameter: C <- "-43.3575" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1718 TOTAL ENERGY = -72.779 RDTITL> * VAN DER WAALS = -29.4215 ELECTROSTATIC = -43.3575 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1718" Parameter: CONF_N -> "8002" Comparing "1718" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1719" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768743 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763277 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29265 from a total of 763277 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1719 -75.57683 2.79783 0.62803 INTE EXTERN> -31.15806 -44.41877 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5768" Parameter: A <- "-75.5768" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1581" Parameter: B <- "-31.1581" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4188" Parameter: C <- "-44.4188" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1719 TOTAL ENERGY = -75.5768 RDTITL> * VAN DER WAALS = -31.1581 ELECTROSTATIC = -44.4188 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1719" Parameter: CONF_N -> "8002" Comparing "1719" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1720" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763277 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764323 ATOM PAIRS WERE FOUND FOR ATOM LIST 41974 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28635 from a total of 764323 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1720 -74.61202 -0.96481 0.67009 INTE EXTERN> -28.41862 -46.19340 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.612" Parameter: A <- "-74.612" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4186" Parameter: B <- "-28.4186" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1934" Parameter: C <- "-46.1934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1720 TOTAL ENERGY = -74.612 RDTITL> * VAN DER WAALS = -28.4186 ELECTROSTATIC = -46.1934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1720" Parameter: CONF_N -> "8002" Comparing "1720" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1721" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764323 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766860 ATOM PAIRS WERE FOUND FOR ATOM LIST 42024 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28667 from a total of 766860 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1721 -78.01976 3.40774 0.68357 INTE EXTERN> -30.89074 -47.12902 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0198" Parameter: A <- "-78.0198" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8907" Parameter: B <- "-30.8907" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.129" Parameter: C <- "-47.129" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1721 TOTAL ENERGY = -78.0198 RDTITL> * VAN DER WAALS = -30.8907 ELECTROSTATIC = -47.129 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1721" Parameter: CONF_N -> "8002" Comparing "1721" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1722" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766860 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763089 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28778 from a total of 763089 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1722 -71.27772 -6.74204 0.63897 INTE EXTERN> -31.16111 -40.11661 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2777" Parameter: A <- "-71.2777" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1611" Parameter: B <- "-31.1611" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1166" Parameter: C <- "-40.1166" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1722 TOTAL ENERGY = -71.2777 RDTITL> * VAN DER WAALS = -31.1611 ELECTROSTATIC = -40.1166 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1722" Parameter: CONF_N -> "8002" Comparing "1722" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1723" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763089 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764535 ATOM PAIRS WERE FOUND FOR ATOM LIST 41706 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28972 from a total of 764535 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1723 -72.95548 1.67776 0.65528 INTE EXTERN> -30.33527 -42.62021 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9555" Parameter: A <- "-72.9555" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3353" Parameter: B <- "-30.3353" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6202" Parameter: C <- "-42.6202" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1723 TOTAL ENERGY = -72.9555 RDTITL> * VAN DER WAALS = -30.3353 ELECTROSTATIC = -42.6202 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1723" Parameter: CONF_N -> "8002" Comparing "1723" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1724" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764535 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762587 ATOM PAIRS WERE FOUND FOR ATOM LIST 41705 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29264 from a total of 762587 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1724 -73.91932 0.96383 0.50149 INTE EXTERN> -33.39931 -40.52000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9193" Parameter: A <- "-73.9193" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3993" Parameter: B <- "-33.3993" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.52" Parameter: C <- "-40.52" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1724 TOTAL ENERGY = -73.9193 RDTITL> * VAN DER WAALS = -33.3993 ELECTROSTATIC = -40.52 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1724" Parameter: CONF_N -> "8002" Comparing "1724" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1725" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762587 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758912 ATOM PAIRS WERE FOUND FOR ATOM LIST 41580 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28965 from a total of 758912 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1725 -72.93845 -0.98086 0.60723 INTE EXTERN> -29.69565 -43.24280 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9385" Parameter: A <- "-72.9385" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6957" Parameter: B <- "-29.6957" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2428" Parameter: C <- "-43.2428" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1725 TOTAL ENERGY = -72.9385 RDTITL> * VAN DER WAALS = -29.6957 ELECTROSTATIC = -43.2428 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1725" Parameter: CONF_N -> "8002" Comparing "1725" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1726" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758912 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760753 ATOM PAIRS WERE FOUND FOR ATOM LIST 41659 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29124 from a total of 760753 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1726 -77.58885 4.65039 0.55676 INTE EXTERN> -34.55811 -43.03074 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5888" Parameter: A <- "-77.5888" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.5581" Parameter: B <- "-34.5581" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0307" Parameter: C <- "-43.0307" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1726 TOTAL ENERGY = -77.5888 RDTITL> * VAN DER WAALS = -34.5581 ELECTROSTATIC = -43.0307 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1726" Parameter: CONF_N -> "8002" Comparing "1726" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1727" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760753 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764151 ATOM PAIRS WERE FOUND FOR ATOM LIST 41859 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29143 from a total of 764151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1727 -78.29415 0.70531 0.58460 INTE EXTERN> -34.21786 -44.07629 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2942" Parameter: A <- "-78.2942" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.2179" Parameter: B <- "-34.2179" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0763" Parameter: C <- "-44.0763" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1727 TOTAL ENERGY = -78.2942 RDTITL> * VAN DER WAALS = -34.2179 ELECTROSTATIC = -44.0763 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1727" Parameter: CONF_N -> "8002" Comparing "1727" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1728" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760917 ATOM PAIRS WERE FOUND FOR ATOM LIST 41819 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28683 from a total of 760917 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1728 -65.41056 -12.88359 0.58445 INTE EXTERN> -31.89700 -33.51356 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4106" Parameter: A <- "-65.4106" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.897" Parameter: B <- "-31.897" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.5136" Parameter: C <- "-33.5136" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1728 TOTAL ENERGY = -65.4106 RDTITL> * VAN DER WAALS = -31.897 ELECTROSTATIC = -33.5136 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1728" Parameter: CONF_N -> "8002" Comparing "1728" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1729" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760917 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759106 ATOM PAIRS WERE FOUND FOR ATOM LIST 41865 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28789 from a total of 759106 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1729 -71.23265 5.82209 0.60429 INTE EXTERN> -28.33163 -42.90102 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2327" Parameter: A <- "-71.2327" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3316" Parameter: B <- "-28.3316" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.901" Parameter: C <- "-42.901" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1729 TOTAL ENERGY = -71.2327 RDTITL> * VAN DER WAALS = -28.3316 ELECTROSTATIC = -42.901 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1729" Parameter: CONF_N -> "8002" Comparing "1729" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1730" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759106 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760358 ATOM PAIRS WERE FOUND FOR ATOM LIST 41829 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28753 from a total of 760358 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1730 -71.63889 0.40623 0.66429 INTE EXTERN> -29.77332 -41.86557 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6389" Parameter: A <- "-71.6389" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7733" Parameter: B <- "-29.7733" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8656" Parameter: C <- "-41.8656" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1730 TOTAL ENERGY = -71.6389 RDTITL> * VAN DER WAALS = -29.7733 ELECTROSTATIC = -41.8656 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1730" Parameter: CONF_N -> "8002" Comparing "1730" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1731" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760358 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764179 ATOM PAIRS WERE FOUND FOR ATOM LIST 41819 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29825 from a total of 764179 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1731 -64.62846 -7.01042 0.40548 INTE EXTERN> -34.36058 -30.26788 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6285" Parameter: A <- "-64.6285" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3606" Parameter: B <- "-34.3606" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.2679" Parameter: C <- "-30.2679" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1731 TOTAL ENERGY = -64.6285 RDTITL> * VAN DER WAALS = -34.3606 ELECTROSTATIC = -30.2679 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1731" Parameter: CONF_N -> "8002" Comparing "1731" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1732" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764179 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759525 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28959 from a total of 759525 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1732 -66.59068 1.96222 0.64574 INTE EXTERN> -28.66181 -37.92888 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5907" Parameter: A <- "-66.5907" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6618" Parameter: B <- "-28.6618" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9289" Parameter: C <- "-37.9289" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1732 TOTAL ENERGY = -66.5907 RDTITL> * VAN DER WAALS = -28.6618 ELECTROSTATIC = -37.9289 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1732" Parameter: CONF_N -> "8002" Comparing "1732" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1733" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759525 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759796 ATOM PAIRS WERE FOUND FOR ATOM LIST 41630 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29501 from a total of 759796 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1733 -68.32482 1.73414 0.55433 INTE EXTERN> -31.98960 -36.33522 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3248" Parameter: A <- "-68.3248" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9896" Parameter: B <- "-31.9896" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3352" Parameter: C <- "-36.3352" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1733 TOTAL ENERGY = -68.3248 RDTITL> * VAN DER WAALS = -31.9896 ELECTROSTATIC = -36.3352 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1733" Parameter: CONF_N -> "8002" Comparing "1733" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1734" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759796 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755703 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29674 from a total of 755703 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1734 -74.51923 6.19441 0.66561 INTE EXTERN> -28.29536 -46.22387 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5192" Parameter: A <- "-74.5192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2954" Parameter: B <- "-28.2954" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2239" Parameter: C <- "-46.2239" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1734 TOTAL ENERGY = -74.5192 RDTITL> * VAN DER WAALS = -28.2954 ELECTROSTATIC = -46.2239 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1734" Parameter: CONF_N -> "8002" Comparing "1734" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1735" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755703 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761190 ATOM PAIRS WERE FOUND FOR ATOM LIST 41835 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29503 from a total of 761190 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1735 -60.03523 -14.48400 0.47205 INTE EXTERN> -32.59317 -27.44206 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.0352" Parameter: A <- "-60.0352" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5932" Parameter: B <- "-32.5932" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.4421" Parameter: C <- "-27.4421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1735 TOTAL ENERGY = -60.0352 RDTITL> * VAN DER WAALS = -32.5932 ELECTROSTATIC = -27.4421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1735" Parameter: CONF_N -> "8002" Comparing "1735" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1736" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761190 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755614 ATOM PAIRS WERE FOUND FOR ATOM LIST 41600 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29754 from a total of 755614 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1736 -67.95408 7.91885 0.67282 INTE EXTERN> -28.61018 -39.34390 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9541" Parameter: A <- "-67.9541" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6102" Parameter: B <- "-28.6102" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3439" Parameter: C <- "-39.3439" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1736 TOTAL ENERGY = -67.9541 RDTITL> * VAN DER WAALS = -28.6102 ELECTROSTATIC = -39.3439 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1736" Parameter: CONF_N -> "8002" Comparing "1736" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1737" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755614 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759870 ATOM PAIRS WERE FOUND FOR ATOM LIST 41761 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29535 from a total of 759870 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1737 -70.68846 2.73438 0.67715 INTE EXTERN> -28.90841 -41.78005 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6885" Parameter: A <- "-70.6885" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9084" Parameter: B <- "-28.9084" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7801" Parameter: C <- "-41.7801" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1737 TOTAL ENERGY = -70.6885 RDTITL> * VAN DER WAALS = -28.9084 ELECTROSTATIC = -41.7801 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1737" Parameter: CONF_N -> "8002" Comparing "1737" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1738" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759870 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759610 ATOM PAIRS WERE FOUND FOR ATOM LIST 41524 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29570 from a total of 759610 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1738 -73.84310 3.15465 0.67147 INTE EXTERN> -27.18052 -46.66258 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8431" Parameter: A <- "-73.8431" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1805" Parameter: B <- "-27.1805" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6626" Parameter: C <- "-46.6626" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1738 TOTAL ENERGY = -73.8431 RDTITL> * VAN DER WAALS = -27.1805 ELECTROSTATIC = -46.6626 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1738" Parameter: CONF_N -> "8002" Comparing "1738" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1739" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759610 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763220 ATOM PAIRS WERE FOUND FOR ATOM LIST 41754 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29760 from a total of 763220 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1739 -65.53449 -8.30861 0.58878 INTE EXTERN> -30.41908 -35.11541 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5345" Parameter: A <- "-65.5345" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4191" Parameter: B <- "-30.4191" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1154" Parameter: C <- "-35.1154" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1739 TOTAL ENERGY = -65.5345 RDTITL> * VAN DER WAALS = -30.4191 ELECTROSTATIC = -35.1154 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1739" Parameter: CONF_N -> "8002" Comparing "1739" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1740" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763220 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758490 ATOM PAIRS WERE FOUND FOR ATOM LIST 41825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29998 from a total of 758490 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1740 -63.19250 -2.34199 0.57324 INTE EXTERN> -27.78364 -35.40886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1925" Parameter: A <- "-63.1925" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7836" Parameter: B <- "-27.7836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4089" Parameter: C <- "-35.4089" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1740 TOTAL ENERGY = -63.1925 RDTITL> * VAN DER WAALS = -27.7836 ELECTROSTATIC = -35.4089 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1740" Parameter: CONF_N -> "8002" Comparing "1740" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1741" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758490 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767331 ATOM PAIRS WERE FOUND FOR ATOM LIST 41997 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29774 from a total of 767331 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1741 -62.92314 -0.26936 0.63816 INTE EXTERN> -29.57061 -33.35253 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9231" Parameter: A <- "-62.9231" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5706" Parameter: B <- "-29.5706" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.3525" Parameter: C <- "-33.3525" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1741 TOTAL ENERGY = -62.9231 RDTITL> * VAN DER WAALS = -29.5706 ELECTROSTATIC = -33.3525 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1741" Parameter: CONF_N -> "8002" Comparing "1741" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1742" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767331 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765174 ATOM PAIRS WERE FOUND FOR ATOM LIST 41995 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30624 from a total of 765174 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1742 -67.40081 4.47767 0.58852 INTE EXTERN> -29.58094 -37.81987 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4008" Parameter: A <- "-67.4008" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5809" Parameter: B <- "-29.5809" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8199" Parameter: C <- "-37.8199" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1742 TOTAL ENERGY = -67.4008 RDTITL> * VAN DER WAALS = -29.5809 ELECTROSTATIC = -37.8199 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1742" Parameter: CONF_N -> "8002" Comparing "1742" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1743" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765174 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764418 ATOM PAIRS WERE FOUND FOR ATOM LIST 41991 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29763 from a total of 764418 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1743 -65.32462 -2.07619 0.68394 INTE EXTERN> -28.79803 -36.52659 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3246" Parameter: A <- "-65.3246" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.798" Parameter: B <- "-28.798" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5266" Parameter: C <- "-36.5266" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1743 TOTAL ENERGY = -65.3246 RDTITL> * VAN DER WAALS = -28.798 ELECTROSTATIC = -36.5266 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1743" Parameter: CONF_N -> "8002" Comparing "1743" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1744" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764418 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765903 ATOM PAIRS WERE FOUND FOR ATOM LIST 41873 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29276 from a total of 765903 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1744 -60.73954 -4.58508 0.62200 INTE EXTERN> -29.83827 -30.90127 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.7395" Parameter: A <- "-60.7395" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8383" Parameter: B <- "-29.8383" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.9013" Parameter: C <- "-30.9013" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1744 TOTAL ENERGY = -60.7395 RDTITL> * VAN DER WAALS = -29.8383 ELECTROSTATIC = -30.9013 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1744" Parameter: CONF_N -> "8002" Comparing "1744" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1745" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765903 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767371 ATOM PAIRS WERE FOUND FOR ATOM LIST 42161 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29375 from a total of 767371 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1745 -60.01733 -0.72221 0.54901 INTE EXTERN> -30.25480 -29.76253 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.0173" Parameter: A <- "-60.0173" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2548" Parameter: B <- "-30.2548" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.7625" Parameter: C <- "-29.7625" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1745 TOTAL ENERGY = -60.0173 RDTITL> * VAN DER WAALS = -30.2548 ELECTROSTATIC = -29.7625 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1745" Parameter: CONF_N -> "8002" Comparing "1745" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1746" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767371 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764196 ATOM PAIRS WERE FOUND FOR ATOM LIST 41853 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29675 from a total of 764196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1746 -63.56408 3.54675 0.55461 INTE EXTERN> -29.50608 -34.05800 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5641" Parameter: A <- "-63.5641" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5061" Parameter: B <- "-29.5061" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.058" Parameter: C <- "-34.058" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1746 TOTAL ENERGY = -63.5641 RDTITL> * VAN DER WAALS = -29.5061 ELECTROSTATIC = -34.058 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1746" Parameter: CONF_N -> "8002" Comparing "1746" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1747" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760590 ATOM PAIRS WERE FOUND FOR ATOM LIST 41889 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29057 from a total of 760590 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1747 -60.43779 -3.12629 0.54527 INTE EXTERN> -30.02007 -30.41772 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.4378" Parameter: A <- "-60.4378" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0201" Parameter: B <- "-30.0201" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.4177" Parameter: C <- "-30.4177" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1747 TOTAL ENERGY = -60.4378 RDTITL> * VAN DER WAALS = -30.0201 ELECTROSTATIC = -30.4177 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1747" Parameter: CONF_N -> "8002" Comparing "1747" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1748" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760590 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767995 ATOM PAIRS WERE FOUND FOR ATOM LIST 42165 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30174 from a total of 767995 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1748 -66.51846 6.08067 0.63994 INTE EXTERN> -27.71930 -38.79916 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5185" Parameter: A <- "-66.5185" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7193" Parameter: B <- "-27.7193" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7992" Parameter: C <- "-38.7992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1748 TOTAL ENERGY = -66.5185 RDTITL> * VAN DER WAALS = -27.7193 ELECTROSTATIC = -38.7992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1748" Parameter: CONF_N -> "8002" Comparing "1748" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1749" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767995 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763402 ATOM PAIRS WERE FOUND FOR ATOM LIST 41982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29491 from a total of 763402 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1749 -59.17400 -7.34446 0.50576 INTE EXTERN> -31.66809 -27.50591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.174" Parameter: A <- "-59.174" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6681" Parameter: B <- "-31.6681" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.5059" Parameter: C <- "-27.5059" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1749 TOTAL ENERGY = -59.174 RDTITL> * VAN DER WAALS = -31.6681 ELECTROSTATIC = -27.5059 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1749" Parameter: CONF_N -> "8002" Comparing "1749" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1750" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763402 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762204 ATOM PAIRS WERE FOUND FOR ATOM LIST 41887 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29605 from a total of 762204 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1750 -62.70978 3.53578 0.57414 INTE EXTERN> -30.51954 -32.19024 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7098" Parameter: A <- "-62.7098" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5195" Parameter: B <- "-30.5195" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.1902" Parameter: C <- "-32.1902" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1750 TOTAL ENERGY = -62.7098 RDTITL> * VAN DER WAALS = -30.5195 ELECTROSTATIC = -32.1902 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1750" Parameter: CONF_N -> "8002" Comparing "1750" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1751" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762204 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751025 ATOM PAIRS WERE FOUND FOR ATOM LIST 41429 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29078 from a total of 751025 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1751 -61.95378 -0.75601 0.51679 INTE EXTERN> -29.42230 -32.53148 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.9538" Parameter: A <- "-61.9538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4223" Parameter: B <- "-29.4223" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5315" Parameter: C <- "-32.5315" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1751 TOTAL ENERGY = -61.9538 RDTITL> * VAN DER WAALS = -29.4223 ELECTROSTATIC = -32.5315 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1751" Parameter: CONF_N -> "8002" Comparing "1751" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1752" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751025 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759752 ATOM PAIRS WERE FOUND FOR ATOM LIST 41825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29001 from a total of 759752 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1752 -63.11837 1.16459 0.56572 INTE EXTERN> -28.07486 -35.04351 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1184" Parameter: A <- "-63.1184" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0749" Parameter: B <- "-28.0749" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0435" Parameter: C <- "-35.0435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1752 TOTAL ENERGY = -63.1184 RDTITL> * VAN DER WAALS = -28.0749 ELECTROSTATIC = -35.0435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1752" Parameter: CONF_N -> "8002" Comparing "1752" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1753" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759752 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763661 ATOM PAIRS WERE FOUND FOR ATOM LIST 41852 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29983 from a total of 763661 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1753 -66.06345 2.94508 0.60661 INTE EXTERN> -27.37624 -38.68720 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0634" Parameter: A <- "-66.0634" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3762" Parameter: B <- "-27.3762" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6872" Parameter: C <- "-38.6872" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1753 TOTAL ENERGY = -66.0634 RDTITL> * VAN DER WAALS = -27.3762 ELECTROSTATIC = -38.6872 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1753" Parameter: CONF_N -> "8002" Comparing "1753" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1754" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763661 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761508 ATOM PAIRS WERE FOUND FOR ATOM LIST 41984 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29493 from a total of 761508 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1754 -66.92658 0.86314 0.56563 INTE EXTERN> -29.94866 -36.97793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9266" Parameter: A <- "-66.9266" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9487" Parameter: B <- "-29.9487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9779" Parameter: C <- "-36.9779" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1754 TOTAL ENERGY = -66.9266 RDTITL> * VAN DER WAALS = -29.9487 ELECTROSTATIC = -36.9779 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1754" Parameter: CONF_N -> "8002" Comparing "1754" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1755" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761508 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758977 ATOM PAIRS WERE FOUND FOR ATOM LIST 41715 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29736 from a total of 758977 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1755 -63.10823 -3.81835 0.58563 INTE EXTERN> -29.67207 -33.43617 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1082" Parameter: A <- "-63.1082" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6721" Parameter: B <- "-29.6721" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.4362" Parameter: C <- "-33.4362" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1755 TOTAL ENERGY = -63.1082 RDTITL> * VAN DER WAALS = -29.6721 ELECTROSTATIC = -33.4362 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1755" Parameter: CONF_N -> "8002" Comparing "1755" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1756" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758977 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753851 ATOM PAIRS WERE FOUND FOR ATOM LIST 41589 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29451 from a total of 753851 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1756 -61.44090 -1.66734 0.70391 INTE EXTERN> -24.21733 -37.22357 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.4409" Parameter: A <- "-61.4409" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2173" Parameter: B <- "-24.2173" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2236" Parameter: C <- "-37.2236" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1756 TOTAL ENERGY = -61.4409 RDTITL> * VAN DER WAALS = -24.2173 ELECTROSTATIC = -37.2236 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1756" Parameter: CONF_N -> "8002" Comparing "1756" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1757" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753851 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752908 ATOM PAIRS WERE FOUND FOR ATOM LIST 41546 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29257 from a total of 752908 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1757 -57.46706 -3.97384 0.57792 INTE EXTERN> -27.87189 -29.59517 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.4671" Parameter: A <- "-57.4671" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8719" Parameter: B <- "-27.8719" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.5952" Parameter: C <- "-29.5952" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1757 TOTAL ENERGY = -57.4671 RDTITL> * VAN DER WAALS = -27.8719 ELECTROSTATIC = -29.5952 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1757" Parameter: CONF_N -> "8002" Comparing "1757" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1758" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752908 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759482 ATOM PAIRS WERE FOUND FOR ATOM LIST 41715 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29628 from a total of 759482 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1758 -70.74534 13.27828 0.63248 INTE EXTERN> -30.46032 -40.28502 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7453" Parameter: A <- "-70.7453" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4603" Parameter: B <- "-30.4603" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.285" Parameter: C <- "-40.285" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1758 TOTAL ENERGY = -70.7453 RDTITL> * VAN DER WAALS = -30.4603 ELECTROSTATIC = -40.285 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1758" Parameter: CONF_N -> "8002" Comparing "1758" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1759" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759482 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759760 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30119 from a total of 759760 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1759 -61.42417 -9.32117 0.58605 INTE EXTERN> -27.57119 -33.85298 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.4242" Parameter: A <- "-61.4242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5712" Parameter: B <- "-27.5712" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.853" Parameter: C <- "-33.853" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1759 TOTAL ENERGY = -61.4242 RDTITL> * VAN DER WAALS = -27.5712 ELECTROSTATIC = -33.853 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1759" Parameter: CONF_N -> "8002" Comparing "1759" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1760" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759760 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758039 ATOM PAIRS WERE FOUND FOR ATOM LIST 41691 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29498 from a total of 758039 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1760 -57.33489 -4.08928 0.51474 INTE EXTERN> -30.45871 -26.87619 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.3349" Parameter: A <- "-57.3349" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4587" Parameter: B <- "-30.4587" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-26.8762" Parameter: C <- "-26.8762" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1760 TOTAL ENERGY = -57.3349 RDTITL> * VAN DER WAALS = -30.4587 ELECTROSTATIC = -26.8762 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1760" Parameter: CONF_N -> "8002" Comparing "1760" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1761" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758039 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758223 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29366 from a total of 758223 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1761 -69.11565 11.78076 0.53023 INTE EXTERN> -32.45514 -36.66052 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1157" Parameter: A <- "-69.1157" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4551" Parameter: B <- "-32.4551" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6605" Parameter: C <- "-36.6605" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1761 TOTAL ENERGY = -69.1157 RDTITL> * VAN DER WAALS = -32.4551 ELECTROSTATIC = -36.6605 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1761" Parameter: CONF_N -> "8002" Comparing "1761" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1762" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758223 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761349 ATOM PAIRS WERE FOUND FOR ATOM LIST 41959 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29917 from a total of 761349 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1762 -69.40547 0.28981 0.66097 INTE EXTERN> -28.83582 -40.56965 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4055" Parameter: A <- "-69.4055" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8358" Parameter: B <- "-28.8358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5696" Parameter: C <- "-40.5696" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1762 TOTAL ENERGY = -69.4055 RDTITL> * VAN DER WAALS = -28.8358 ELECTROSTATIC = -40.5696 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1762" Parameter: CONF_N -> "8002" Comparing "1762" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1763" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761349 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758294 ATOM PAIRS WERE FOUND FOR ATOM LIST 41623 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30200 from a total of 758294 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1763 -70.22208 0.81662 0.54368 INTE EXTERN> -32.26247 -37.95961 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2221" Parameter: A <- "-70.2221" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2625" Parameter: B <- "-32.2625" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9596" Parameter: C <- "-37.9596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1763 TOTAL ENERGY = -70.2221 RDTITL> * VAN DER WAALS = -32.2625 ELECTROSTATIC = -37.9596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1763" Parameter: CONF_N -> "8002" Comparing "1763" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1764" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758294 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757217 ATOM PAIRS WERE FOUND FOR ATOM LIST 41567 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29627 from a total of 757217 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1764 -58.54072 -11.68136 0.52382 INTE EXTERN> -29.30898 -29.23174 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.5407" Parameter: A <- "-58.5407" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.309" Parameter: B <- "-29.309" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.2317" Parameter: C <- "-29.2317" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1764 TOTAL ENERGY = -58.5407 RDTITL> * VAN DER WAALS = -29.309 ELECTROSTATIC = -29.2317 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1764" Parameter: CONF_N -> "8002" Comparing "1764" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1765" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757217 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751200 ATOM PAIRS WERE FOUND FOR ATOM LIST 41407 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29164 from a total of 751200 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1765 -70.59614 12.05542 0.59761 INTE EXTERN> -28.28003 -42.31612 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5961" Parameter: A <- "-70.5961" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.28" Parameter: B <- "-28.28" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3161" Parameter: C <- "-42.3161" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1765 TOTAL ENERGY = -70.5961 RDTITL> * VAN DER WAALS = -28.28 ELECTROSTATIC = -42.3161 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1765" Parameter: CONF_N -> "8002" Comparing "1765" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1766" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751200 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759926 ATOM PAIRS WERE FOUND FOR ATOM LIST 41993 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30064 from a total of 759926 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1766 -67.95578 -2.64036 0.56155 INTE EXTERN> -33.17964 -34.77613 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9558" Parameter: A <- "-67.9558" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1796" Parameter: B <- "-33.1796" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7761" Parameter: C <- "-34.7761" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1766 TOTAL ENERGY = -67.9558 RDTITL> * VAN DER WAALS = -33.1796 ELECTROSTATIC = -34.7761 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1766" Parameter: CONF_N -> "8002" Comparing "1766" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1767" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759926 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758188 ATOM PAIRS WERE FOUND FOR ATOM LIST 41775 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29928 from a total of 758188 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1767 -71.38360 3.42782 0.59877 INTE EXTERN> -30.78770 -40.59590 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3836" Parameter: A <- "-71.3836" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7877" Parameter: B <- "-30.7877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5959" Parameter: C <- "-40.5959" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1767 TOTAL ENERGY = -71.3836 RDTITL> * VAN DER WAALS = -30.7877 ELECTROSTATIC = -40.5959 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1767" Parameter: CONF_N -> "8002" Comparing "1767" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1768" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758188 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761406 ATOM PAIRS WERE FOUND FOR ATOM LIST 41960 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 761406 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1768 -70.27026 -1.11334 0.51323 INTE EXTERN> -33.81106 -36.45920 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2703" Parameter: A <- "-70.2703" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8111" Parameter: B <- "-33.8111" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4592" Parameter: C <- "-36.4592" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1768 TOTAL ENERGY = -70.2703 RDTITL> * VAN DER WAALS = -33.8111 ELECTROSTATIC = -36.4592 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1768" Parameter: CONF_N -> "8002" Comparing "1768" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1769" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761406 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762973 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30349 from a total of 762973 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1769 -65.33292 -4.93734 0.58613 INTE EXTERN> -29.92653 -35.40639 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3329" Parameter: A <- "-65.3329" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9265" Parameter: B <- "-29.9265" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4064" Parameter: C <- "-35.4064" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1769 TOTAL ENERGY = -65.3329 RDTITL> * VAN DER WAALS = -29.9265 ELECTROSTATIC = -35.4064 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1769" Parameter: CONF_N -> "8002" Comparing "1769" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1770" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762973 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759609 ATOM PAIRS WERE FOUND FOR ATOM LIST 41636 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30066 from a total of 759609 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1770 -64.90792 -0.42500 0.53407 INTE EXTERN> -33.26986 -31.63806 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9079" Parameter: A <- "-64.9079" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2699" Parameter: B <- "-33.2699" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.6381" Parameter: C <- "-31.6381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1770 TOTAL ENERGY = -64.9079 RDTITL> * VAN DER WAALS = -33.2699 ELECTROSTATIC = -31.6381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1770" Parameter: CONF_N -> "8002" Comparing "1770" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1771" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759609 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756789 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30234 from a total of 756789 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1771 -68.70825 3.80033 0.61852 INTE EXTERN> -29.76142 -38.94683 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7083" Parameter: A <- "-68.7083" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7614" Parameter: B <- "-29.7614" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9468" Parameter: C <- "-38.9468" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1771 TOTAL ENERGY = -68.7083 RDTITL> * VAN DER WAALS = -29.7614 ELECTROSTATIC = -38.9468 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1771" Parameter: CONF_N -> "8002" Comparing "1771" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1772" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756789 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761974 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30330 from a total of 761974 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1772 -67.60934 -1.09891 0.51575 INTE EXTERN> -32.98316 -34.62618 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6093" Parameter: A <- "-67.6093" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9832" Parameter: B <- "-32.9832" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.6262" Parameter: C <- "-34.6262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1772 TOTAL ENERGY = -67.6093 RDTITL> * VAN DER WAALS = -32.9832 ELECTROSTATIC = -34.6262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1772" Parameter: CONF_N -> "8002" Comparing "1772" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1773" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761974 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758835 ATOM PAIRS WERE FOUND FOR ATOM LIST 41733 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29715 from a total of 758835 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1773 -65.75185 -1.85749 0.62317 INTE EXTERN> -30.00262 -35.74924 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7519" Parameter: A <- "-65.7519" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0026" Parameter: B <- "-30.0026" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7492" Parameter: C <- "-35.7492" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1773 TOTAL ENERGY = -65.7519 RDTITL> * VAN DER WAALS = -30.0026 ELECTROSTATIC = -35.7492 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1773" Parameter: CONF_N -> "8002" Comparing "1773" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1774" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758835 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762334 ATOM PAIRS WERE FOUND FOR ATOM LIST 41891 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30387 from a total of 762334 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1774 -66.97329 1.22144 0.66832 INTE EXTERN> -27.90133 -39.07196 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9733" Parameter: A <- "-66.9733" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9013" Parameter: B <- "-27.9013" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.072" Parameter: C <- "-39.072" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1774 TOTAL ENERGY = -66.9733 RDTITL> * VAN DER WAALS = -27.9013 ELECTROSTATIC = -39.072 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1774" Parameter: CONF_N -> "8002" Comparing "1774" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1775" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762334 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756953 ATOM PAIRS WERE FOUND FOR ATOM LIST 41694 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29985 from a total of 756953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1775 -68.92716 1.95387 0.59415 INTE EXTERN> -31.71311 -37.21405 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9272" Parameter: A <- "-68.9272" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7131" Parameter: B <- "-31.7131" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2141" Parameter: C <- "-37.2141" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1775 TOTAL ENERGY = -68.9272 RDTITL> * VAN DER WAALS = -31.7131 ELECTROSTATIC = -37.2141 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1775" Parameter: CONF_N -> "8002" Comparing "1775" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1776" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756617 ATOM PAIRS WERE FOUND FOR ATOM LIST 41704 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29969 from a total of 756617 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1776 -71.76889 2.84172 0.59770 INTE EXTERN> -30.88710 -40.88178 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7689" Parameter: A <- "-71.7689" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8871" Parameter: B <- "-30.8871" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8818" Parameter: C <- "-40.8818" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1776 TOTAL ENERGY = -71.7689 RDTITL> * VAN DER WAALS = -30.8871 ELECTROSTATIC = -40.8818 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1776" Parameter: CONF_N -> "8002" Comparing "1776" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1777" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756617 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758356 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30220 from a total of 758356 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1777 -55.51959 -16.24929 0.60325 INTE EXTERN> -25.42893 -30.09067 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.5196" Parameter: A <- "-55.5196" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4289" Parameter: B <- "-25.4289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.0907" Parameter: C <- "-30.0907" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1777 TOTAL ENERGY = -55.5196 RDTITL> * VAN DER WAALS = -25.4289 ELECTROSTATIC = -30.0907 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1777" Parameter: CONF_N -> "8002" Comparing "1777" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1778" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758356 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766463 ATOM PAIRS WERE FOUND FOR ATOM LIST 41973 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30020 from a total of 766463 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1778 -66.60458 11.08498 0.66364 INTE EXTERN> -29.40434 -37.20024 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6046" Parameter: A <- "-66.6046" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4043" Parameter: B <- "-29.4043" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2002" Parameter: C <- "-37.2002" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1778 TOTAL ENERGY = -66.6046 RDTITL> * VAN DER WAALS = -29.4043 ELECTROSTATIC = -37.2002 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1778" Parameter: CONF_N -> "8002" Comparing "1778" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1779" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766463 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762329 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29893 from a total of 762329 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1779 -73.37510 6.77053 0.61659 INTE EXTERN> -32.69126 -40.68384 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3751" Parameter: A <- "-73.3751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6913" Parameter: B <- "-32.6913" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6838" Parameter: C <- "-40.6838" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1779 TOTAL ENERGY = -73.3751 RDTITL> * VAN DER WAALS = -32.6913 ELECTROSTATIC = -40.6838 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1779" Parameter: CONF_N -> "8002" Comparing "1779" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1780" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762329 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759658 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29839 from a total of 759658 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1780 -64.54946 -8.82564 0.56327 INTE EXTERN> -30.25327 -34.29619 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5495" Parameter: A <- "-64.5495" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2533" Parameter: B <- "-30.2533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2962" Parameter: C <- "-34.2962" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1780 TOTAL ENERGY = -64.5495 RDTITL> * VAN DER WAALS = -30.2533 ELECTROSTATIC = -34.2962 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1780" Parameter: CONF_N -> "8002" Comparing "1780" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1781" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759658 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760940 ATOM PAIRS WERE FOUND FOR ATOM LIST 41853 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29875 from a total of 760940 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1781 -68.70335 4.15389 0.64367 INTE EXTERN> -26.81842 -41.88493 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7034" Parameter: A <- "-68.7034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8184" Parameter: B <- "-26.8184" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8849" Parameter: C <- "-41.8849" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1781 TOTAL ENERGY = -68.7034 RDTITL> * VAN DER WAALS = -26.8184 ELECTROSTATIC = -41.8849 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1781" Parameter: CONF_N -> "8002" Comparing "1781" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1782" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760940 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769989 ATOM PAIRS WERE FOUND FOR ATOM LIST 42411 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30131 from a total of 769989 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1782 -69.14016 0.43680 0.60762 INTE EXTERN> -30.82378 -38.31638 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1402" Parameter: A <- "-69.1402" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8238" Parameter: B <- "-30.8238" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3164" Parameter: C <- "-38.3164" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1782 TOTAL ENERGY = -69.1402 RDTITL> * VAN DER WAALS = -30.8238 ELECTROSTATIC = -38.3164 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1782" Parameter: CONF_N -> "8002" Comparing "1782" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1783" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769989 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760381 ATOM PAIRS WERE FOUND FOR ATOM LIST 42130 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29800 from a total of 760381 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1783 -64.07695 -5.06321 0.68791 INTE EXTERN> -25.90274 -38.17421 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0769" Parameter: A <- "-64.0769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9027" Parameter: B <- "-25.9027" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1742" Parameter: C <- "-38.1742" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1783 TOTAL ENERGY = -64.0769 RDTITL> * VAN DER WAALS = -25.9027 ELECTROSTATIC = -38.1742 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1783" Parameter: CONF_N -> "8002" Comparing "1783" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1784" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760381 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763307 ATOM PAIRS WERE FOUND FOR ATOM LIST 41994 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29654 from a total of 763307 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1784 -67.24631 3.16936 0.73229 INTE EXTERN> -25.03604 -42.21027 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2463" Parameter: A <- "-67.2463" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.036" Parameter: B <- "-25.036" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2103" Parameter: C <- "-42.2103" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1784 TOTAL ENERGY = -67.2463 RDTITL> * VAN DER WAALS = -25.036 ELECTROSTATIC = -42.2103 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1784" Parameter: CONF_N -> "8002" Comparing "1784" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1785" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763307 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762848 ATOM PAIRS WERE FOUND FOR ATOM LIST 42016 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30128 from a total of 762848 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1785 -67.40921 0.16291 0.53948 INTE EXTERN> -34.02449 -33.38472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4092" Parameter: A <- "-67.4092" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0245" Parameter: B <- "-34.0245" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.3847" Parameter: C <- "-33.3847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1785 TOTAL ENERGY = -67.4092 RDTITL> * VAN DER WAALS = -34.0245 ELECTROSTATIC = -33.3847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1785" Parameter: CONF_N -> "8002" Comparing "1785" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1786" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762848 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762446 ATOM PAIRS WERE FOUND FOR ATOM LIST 42094 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30613 from a total of 762446 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1786 -66.58323 -0.82598 0.69613 INTE EXTERN> -26.52222 -40.06100 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5832" Parameter: A <- "-66.5832" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5222" Parameter: B <- "-26.5222" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.061" Parameter: C <- "-40.061" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1786 TOTAL ENERGY = -66.5832 RDTITL> * VAN DER WAALS = -26.5222 ELECTROSTATIC = -40.061 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1786" Parameter: CONF_N -> "8002" Comparing "1786" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1787" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762446 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761268 ATOM PAIRS WERE FOUND FOR ATOM LIST 41949 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29845 from a total of 761268 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1787 -67.78626 1.20304 0.58699 INTE EXTERN> -32.42808 -35.35818 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7863" Parameter: A <- "-67.7863" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4281" Parameter: B <- "-32.4281" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3582" Parameter: C <- "-35.3582" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1787 TOTAL ENERGY = -67.7863 RDTITL> * VAN DER WAALS = -32.4281 ELECTROSTATIC = -35.3582 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1787" Parameter: CONF_N -> "8002" Comparing "1787" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1788" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761268 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769014 ATOM PAIRS WERE FOUND FOR ATOM LIST 42421 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30794 from a total of 769014 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1788 -77.31654 9.53028 0.66772 INTE EXTERN> -30.57223 -46.74431 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3165" Parameter: A <- "-77.3165" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5722" Parameter: B <- "-30.5722" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7443" Parameter: C <- "-46.7443" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1788 TOTAL ENERGY = -77.3165 RDTITL> * VAN DER WAALS = -30.5722 ELECTROSTATIC = -46.7443 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1788" Parameter: CONF_N -> "8002" Comparing "1788" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1789" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769014 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759518 ATOM PAIRS WERE FOUND FOR ATOM LIST 41991 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30246 from a total of 759518 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1789 -69.99410 -7.32244 0.61563 INTE EXTERN> -29.99880 -39.99530 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9941" Parameter: A <- "-69.9941" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9988" Parameter: B <- "-29.9988" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9953" Parameter: C <- "-39.9953" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1789 TOTAL ENERGY = -69.9941 RDTITL> * VAN DER WAALS = -29.9988 ELECTROSTATIC = -39.9953 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1789" Parameter: CONF_N -> "8002" Comparing "1789" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1790" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759518 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758527 ATOM PAIRS WERE FOUND FOR ATOM LIST 41887 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30182 from a total of 758527 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1790 -76.12996 6.13586 0.60519 INTE EXTERN> -32.76006 -43.36990 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.13" Parameter: A <- "-76.13" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7601" Parameter: B <- "-32.7601" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3699" Parameter: C <- "-43.3699" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1790 TOTAL ENERGY = -76.13 RDTITL> * VAN DER WAALS = -32.7601 ELECTROSTATIC = -43.3699 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1790" Parameter: CONF_N -> "8002" Comparing "1790" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1791" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758527 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755415 ATOM PAIRS WERE FOUND FOR ATOM LIST 41646 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29932 from a total of 755415 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1791 -66.92308 -9.20688 0.66842 INTE EXTERN> -29.42082 -37.50227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9231" Parameter: A <- "-66.9231" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4208" Parameter: B <- "-29.4208" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5023" Parameter: C <- "-37.5023" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1791 TOTAL ENERGY = -66.9231 RDTITL> * VAN DER WAALS = -29.4208 ELECTROSTATIC = -37.5023 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1791" Parameter: CONF_N -> "8002" Comparing "1791" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1792" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755415 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760759 ATOM PAIRS WERE FOUND FOR ATOM LIST 41907 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29739 from a total of 760759 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1792 -74.06780 7.14472 0.61337 INTE EXTERN> -32.95571 -41.11209 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0678" Parameter: A <- "-74.0678" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9557" Parameter: B <- "-32.9557" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1121" Parameter: C <- "-41.1121" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1792 TOTAL ENERGY = -74.0678 RDTITL> * VAN DER WAALS = -32.9557 ELECTROSTATIC = -41.1121 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1792" Parameter: CONF_N -> "8002" Comparing "1792" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1793" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760759 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758049 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29848 from a total of 758049 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1793 -63.57614 -10.49166 0.60326 INTE EXTERN> -31.52101 -32.05513 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5761" Parameter: A <- "-63.5761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.521" Parameter: B <- "-31.521" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.0551" Parameter: C <- "-32.0551" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1793 TOTAL ENERGY = -63.5761 RDTITL> * VAN DER WAALS = -31.521 ELECTROSTATIC = -32.0551 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1793" Parameter: CONF_N -> "8002" Comparing "1793" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1794" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758049 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753955 ATOM PAIRS WERE FOUND FOR ATOM LIST 41815 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29191 from a total of 753955 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1794 -71.88494 8.30880 0.54795 INTE EXTERN> -34.44199 -37.44295 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8849" Parameter: A <- "-71.8849" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.442" Parameter: B <- "-34.442" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.443" Parameter: C <- "-37.443" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1794 TOTAL ENERGY = -71.8849 RDTITL> * VAN DER WAALS = -34.442 ELECTROSTATIC = -37.443 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1794" Parameter: CONF_N -> "8002" Comparing "1794" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1795" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753955 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753189 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29757 from a total of 753189 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1795 -67.83291 -4.05203 0.57023 INTE EXTERN> -31.80079 -36.03212 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8329" Parameter: A <- "-67.8329" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8008" Parameter: B <- "-31.8008" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0321" Parameter: C <- "-36.0321" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1795 TOTAL ENERGY = -67.8329 RDTITL> * VAN DER WAALS = -31.8008 ELECTROSTATIC = -36.0321 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1795" Parameter: CONF_N -> "8002" Comparing "1795" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1796" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753189 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765797 ATOM PAIRS WERE FOUND FOR ATOM LIST 42134 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29225 from a total of 765797 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1796 -72.81821 4.98530 0.59931 INTE EXTERN> -33.35127 -39.46694 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8182" Parameter: A <- "-72.8182" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3513" Parameter: B <- "-33.3513" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4669" Parameter: C <- "-39.4669" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1796 TOTAL ENERGY = -72.8182 RDTITL> * VAN DER WAALS = -33.3513 ELECTROSTATIC = -39.4669 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1796" Parameter: CONF_N -> "8002" Comparing "1796" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1797" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765797 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756472 ATOM PAIRS WERE FOUND FOR ATOM LIST 41745 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28737 from a total of 756472 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1797 -66.91604 -5.90217 0.56947 INTE EXTERN> -30.46776 -36.44828 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.916" Parameter: A <- "-66.916" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4678" Parameter: B <- "-30.4678" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4483" Parameter: C <- "-36.4483" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1797 TOTAL ENERGY = -66.916 RDTITL> * VAN DER WAALS = -30.4678 ELECTROSTATIC = -36.4483 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1797" Parameter: CONF_N -> "8002" Comparing "1797" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1798" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756472 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754756 ATOM PAIRS WERE FOUND FOR ATOM LIST 41458 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29376 from a total of 754756 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1798 -70.92705 4.01101 0.58908 INTE EXTERN> -29.76758 -41.15947 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9271" Parameter: A <- "-70.9271" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7676" Parameter: B <- "-29.7676" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1595" Parameter: C <- "-41.1595" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1798 TOTAL ENERGY = -70.9271 RDTITL> * VAN DER WAALS = -29.7676 ELECTROSTATIC = -41.1595 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1798" Parameter: CONF_N -> "8002" Comparing "1798" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1799" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754756 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759291 ATOM PAIRS WERE FOUND FOR ATOM LIST 41689 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28947 from a total of 759291 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1799 -67.57377 -3.35328 0.55176 INTE EXTERN> -32.79036 -34.78342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5738" Parameter: A <- "-67.5738" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7904" Parameter: B <- "-32.7904" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7834" Parameter: C <- "-34.7834" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1799 TOTAL ENERGY = -67.5738 RDTITL> * VAN DER WAALS = -32.7904 ELECTROSTATIC = -34.7834 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1799" Parameter: CONF_N -> "8002" Comparing "1799" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1800" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759291 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761042 ATOM PAIRS WERE FOUND FOR ATOM LIST 41877 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29305 from a total of 761042 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1800 -67.62269 0.04891 0.67112 INTE EXTERN> -31.59685 -36.02584 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6227" Parameter: A <- "-67.6227" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5968" Parameter: B <- "-31.5968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0258" Parameter: C <- "-36.0258" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1800 TOTAL ENERGY = -67.6227 RDTITL> * VAN DER WAALS = -31.5968 ELECTROSTATIC = -36.0258 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1800" Parameter: CONF_N -> "8002" Comparing "1800" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1801" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761042 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765468 ATOM PAIRS WERE FOUND FOR ATOM LIST 42089 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29219 from a total of 765468 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1801 -79.20500 11.58231 0.67510 INTE EXTERN> -33.05458 -46.15042 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.205" Parameter: A <- "-79.205" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0546" Parameter: B <- "-33.0546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1504" Parameter: C <- "-46.1504" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1801 TOTAL ENERGY = -79.205 RDTITL> * VAN DER WAALS = -33.0546 ELECTROSTATIC = -46.1504 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1801" Parameter: CONF_N -> "8002" Comparing "1801" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1802" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765468 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755495 ATOM PAIRS WERE FOUND FOR ATOM LIST 41755 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29197 from a total of 755495 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1802 -65.91485 -13.29014 0.60375 INTE EXTERN> -34.37726 -31.53759 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9149" Parameter: A <- "-65.9149" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3773" Parameter: B <- "-34.3773" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.5376" Parameter: C <- "-31.5376" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1802 TOTAL ENERGY = -65.9149 RDTITL> * VAN DER WAALS = -34.3773 ELECTROSTATIC = -31.5376 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1802" Parameter: CONF_N -> "8002" Comparing "1802" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1803" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755495 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754713 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29071 from a total of 754713 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1803 -69.98177 4.06692 0.64389 INTE EXTERN> -29.89541 -40.08636 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9818" Parameter: A <- "-69.9818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8954" Parameter: B <- "-29.8954" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0864" Parameter: C <- "-40.0864" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1803 TOTAL ENERGY = -69.9818 RDTITL> * VAN DER WAALS = -29.8954 ELECTROSTATIC = -40.0864 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1803" Parameter: CONF_N -> "8002" Comparing "1803" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1804" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754713 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753909 ATOM PAIRS WERE FOUND FOR ATOM LIST 41486 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28796 from a total of 753909 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1804 -62.74357 -7.23820 0.57926 INTE EXTERN> -31.95843 -30.78514 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7436" Parameter: A <- "-62.7436" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9584" Parameter: B <- "-31.9584" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.7851" Parameter: C <- "-30.7851" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1804 TOTAL ENERGY = -62.7436 RDTITL> * VAN DER WAALS = -31.9584 ELECTROSTATIC = -30.7851 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1804" Parameter: CONF_N -> "8002" Comparing "1804" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1805" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753909 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766015 ATOM PAIRS WERE FOUND FOR ATOM LIST 42372 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29553 from a total of 766015 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1805 -76.14395 13.40038 0.65472 INTE EXTERN> -32.41458 -43.72937 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.144" Parameter: A <- "-76.144" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4146" Parameter: B <- "-32.4146" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7294" Parameter: C <- "-43.7294" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1805 TOTAL ENERGY = -76.144 RDTITL> * VAN DER WAALS = -32.4146 ELECTROSTATIC = -43.7294 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1805" Parameter: CONF_N -> "8002" Comparing "1805" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1806" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766015 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761998 ATOM PAIRS WERE FOUND FOR ATOM LIST 41933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30052 from a total of 761998 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1806 -71.37398 -4.76997 0.76209 INTE EXTERN> -28.69605 -42.67793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.374" Parameter: A <- "-71.374" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6961" Parameter: B <- "-28.6961" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6779" Parameter: C <- "-42.6779" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1806 TOTAL ENERGY = -71.374 RDTITL> * VAN DER WAALS = -28.6961 ELECTROSTATIC = -42.6779 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1806" Parameter: CONF_N -> "8002" Comparing "1806" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1807" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761998 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760716 ATOM PAIRS WERE FOUND FOR ATOM LIST 42009 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28841 from a total of 760716 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1807 -66.11592 -5.25807 0.58483 INTE EXTERN> -33.76187 -32.35405 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1159" Parameter: A <- "-66.1159" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7619" Parameter: B <- "-33.7619" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.354" Parameter: C <- "-32.354" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1807 TOTAL ENERGY = -66.1159 RDTITL> * VAN DER WAALS = -33.7619 ELECTROSTATIC = -32.354 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1807" Parameter: CONF_N -> "8002" Comparing "1807" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1808" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760716 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760568 ATOM PAIRS WERE FOUND FOR ATOM LIST 41919 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28879 from a total of 760568 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1808 -73.90349 7.78758 0.62870 INTE EXTERN> -32.07791 -41.82558 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9035" Parameter: A <- "-73.9035" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0779" Parameter: B <- "-32.0779" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8256" Parameter: C <- "-41.8256" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1808 TOTAL ENERGY = -73.9035 RDTITL> * VAN DER WAALS = -32.0779 ELECTROSTATIC = -41.8256 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1808" Parameter: CONF_N -> "8002" Comparing "1808" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1809" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760568 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756737 ATOM PAIRS WERE FOUND FOR ATOM LIST 41692 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28624 from a total of 756737 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1809 -71.13580 -2.76770 0.69120 INTE EXTERN> -30.30909 -40.82671 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1358" Parameter: A <- "-71.1358" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3091" Parameter: B <- "-30.3091" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8267" Parameter: C <- "-40.8267" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1809 TOTAL ENERGY = -71.1358 RDTITL> * VAN DER WAALS = -30.3091 ELECTROSTATIC = -40.8267 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1809" Parameter: CONF_N -> "8002" Comparing "1809" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1810" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756737 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757242 ATOM PAIRS WERE FOUND FOR ATOM LIST 41621 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28737 from a total of 757242 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1810 -66.42448 -4.71132 0.70388 INTE EXTERN> -29.08853 -37.33595 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4245" Parameter: A <- "-66.4245" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0885" Parameter: B <- "-29.0885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.336" Parameter: C <- "-37.336" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1810 TOTAL ENERGY = -66.4245 RDTITL> * VAN DER WAALS = -29.0885 ELECTROSTATIC = -37.336 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1810" Parameter: CONF_N -> "8002" Comparing "1810" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1811" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757242 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756936 ATOM PAIRS WERE FOUND FOR ATOM LIST 41630 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28902 from a total of 756936 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1811 -71.99099 5.56651 0.65397 INTE EXTERN> -32.32431 -39.66668 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.991" Parameter: A <- "-71.991" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3243" Parameter: B <- "-32.3243" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6667" Parameter: C <- "-39.6667" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1811 TOTAL ENERGY = -71.991 RDTITL> * VAN DER WAALS = -32.3243 ELECTROSTATIC = -39.6667 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1811" Parameter: CONF_N -> "8002" Comparing "1811" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1812" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756936 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767591 ATOM PAIRS WERE FOUND FOR ATOM LIST 42088 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29975 from a total of 767591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1812 -73.64330 1.65232 0.75451 INTE EXTERN> -28.43649 -45.20681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6433" Parameter: A <- "-73.6433" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4365" Parameter: B <- "-28.4365" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2068" Parameter: C <- "-45.2068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1812 TOTAL ENERGY = -73.6433 RDTITL> * VAN DER WAALS = -28.4365 ELECTROSTATIC = -45.2068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1812" Parameter: CONF_N -> "8002" Comparing "1812" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1813" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756595 ATOM PAIRS WERE FOUND FOR ATOM LIST 41652 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28999 from a total of 756595 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1813 -68.02213 -5.62117 0.64128 INTE EXTERN> -30.90872 -37.11341 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0221" Parameter: A <- "-68.0221" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9087" Parameter: B <- "-30.9087" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1134" Parameter: C <- "-37.1134" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1813 TOTAL ENERGY = -68.0221 RDTITL> * VAN DER WAALS = -30.9087 ELECTROSTATIC = -37.1134 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1813" Parameter: CONF_N -> "8002" Comparing "1813" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1814" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756595 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760502 ATOM PAIRS WERE FOUND FOR ATOM LIST 41861 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29396 from a total of 760502 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1814 -69.70061 1.67847 0.72689 INTE EXTERN> -26.85713 -42.84347 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7006" Parameter: A <- "-69.7006" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8571" Parameter: B <- "-26.8571" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8435" Parameter: C <- "-42.8435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1814 TOTAL ENERGY = -69.7006 RDTITL> * VAN DER WAALS = -26.8571 ELECTROSTATIC = -42.8435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1814" Parameter: CONF_N -> "8002" Comparing "1814" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1815" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760502 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41734 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29157 from a total of 758586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1815 -69.93314 0.23253 0.63286 INTE EXTERN> -30.93095 -39.00219 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9331" Parameter: A <- "-69.9331" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.931" Parameter: B <- "-30.931" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0022" Parameter: C <- "-39.0022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1815 TOTAL ENERGY = -69.9331 RDTITL> * VAN DER WAALS = -30.931 ELECTROSTATIC = -39.0022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1815" Parameter: CONF_N -> "8002" Comparing "1815" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1816" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755491 ATOM PAIRS WERE FOUND FOR ATOM LIST 41498 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29694 from a total of 755491 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1816 -68.72333 -1.20981 0.53381 INTE EXTERN> -34.30433 -34.41900 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7233" Parameter: A <- "-68.7233" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3043" Parameter: B <- "-34.3043" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.419" Parameter: C <- "-34.419" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1816 TOTAL ENERGY = -68.7233 RDTITL> * VAN DER WAALS = -34.3043 ELECTROSTATIC = -34.419 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1816" Parameter: CONF_N -> "8002" Comparing "1816" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1817" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755491 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759571 ATOM PAIRS WERE FOUND FOR ATOM LIST 41712 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29597 from a total of 759571 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1817 -70.03119 1.30787 0.64062 INTE EXTERN> -29.32670 -40.70450 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0312" Parameter: A <- "-70.0312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3267" Parameter: B <- "-29.3267" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7045" Parameter: C <- "-40.7045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1817 TOTAL ENERGY = -70.0312 RDTITL> * VAN DER WAALS = -29.3267 ELECTROSTATIC = -40.7045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1817" Parameter: CONF_N -> "8002" Comparing "1817" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1818" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759571 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760732 ATOM PAIRS WERE FOUND FOR ATOM LIST 41746 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29917 from a total of 760732 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1818 -70.42719 0.39600 0.62567 INTE EXTERN> -30.12922 -40.29798 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4272" Parameter: A <- "-70.4272" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1292" Parameter: B <- "-30.1292" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.298" Parameter: C <- "-40.298" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1818 TOTAL ENERGY = -70.4272 RDTITL> * VAN DER WAALS = -30.1292 ELECTROSTATIC = -40.298 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1818" Parameter: CONF_N -> "8002" Comparing "1818" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1819" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760732 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757206 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29720 from a total of 757206 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1819 -68.87679 -1.55040 0.58770 INTE EXTERN> -31.11674 -37.76006 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8768" Parameter: A <- "-68.8768" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1167" Parameter: B <- "-31.1167" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7601" Parameter: C <- "-37.7601" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1819 TOTAL ENERGY = -68.8768 RDTITL> * VAN DER WAALS = -31.1167 ELECTROSTATIC = -37.7601 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1819" Parameter: CONF_N -> "8002" Comparing "1819" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1820" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757206 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764696 ATOM PAIRS WERE FOUND FOR ATOM LIST 41970 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29402 from a total of 764696 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1820 -66.76806 -2.10873 0.56136 INTE EXTERN> -33.97901 -32.78905 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7681" Parameter: A <- "-66.7681" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.979" Parameter: B <- "-33.979" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.7891" Parameter: C <- "-32.7891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1820 TOTAL ENERGY = -66.7681 RDTITL> * VAN DER WAALS = -33.979 ELECTROSTATIC = -32.7891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1820" Parameter: CONF_N -> "8002" Comparing "1820" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1821" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764696 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754891 ATOM PAIRS WERE FOUND FOR ATOM LIST 41543 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30118 from a total of 754891 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1821 -60.14234 -6.62572 0.53545 INTE EXTERN> -31.71720 -28.42514 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.1423" Parameter: A <- "-60.1423" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7172" Parameter: B <- "-31.7172" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.4251" Parameter: C <- "-28.4251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1821 TOTAL ENERGY = -60.1423 RDTITL> * VAN DER WAALS = -31.7172 ELECTROSTATIC = -28.4251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1821" Parameter: CONF_N -> "8002" Comparing "1821" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1822" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754891 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759619 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30088 from a total of 759619 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1822 -63.97123 3.82889 0.52687 INTE EXTERN> -32.75646 -31.21477 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.9712" Parameter: A <- "-63.9712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7565" Parameter: B <- "-32.7565" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.2148" Parameter: C <- "-31.2148" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1822 TOTAL ENERGY = -63.9712 RDTITL> * VAN DER WAALS = -32.7565 ELECTROSTATIC = -31.2148 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1822" Parameter: CONF_N -> "8002" Comparing "1822" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1823" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759619 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767763 ATOM PAIRS WERE FOUND FOR ATOM LIST 42216 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30575 from a total of 767763 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1823 -63.10882 -0.86241 0.62453 INTE EXTERN> -30.89012 -32.21871 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1088" Parameter: A <- "-63.1088" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8901" Parameter: B <- "-30.8901" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2187" Parameter: C <- "-32.2187" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1823 TOTAL ENERGY = -63.1088 RDTITL> * VAN DER WAALS = -30.8901 ELECTROSTATIC = -32.2187 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1823" Parameter: CONF_N -> "8002" Comparing "1823" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1824" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767763 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760365 ATOM PAIRS WERE FOUND FOR ATOM LIST 41842 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30179 from a total of 760365 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1824 -62.94194 -0.16688 0.59666 INTE EXTERN> -28.96489 -33.97706 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9419" Parameter: A <- "-62.9419" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9649" Parameter: B <- "-28.9649" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9771" Parameter: C <- "-33.9771" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1824 TOTAL ENERGY = -62.9419 RDTITL> * VAN DER WAALS = -28.9649 ELECTROSTATIC = -33.9771 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1824" Parameter: CONF_N -> "8002" Comparing "1824" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1825" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760365 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753381 ATOM PAIRS WERE FOUND FOR ATOM LIST 41579 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29920 from a total of 753381 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1825 -65.69648 2.75454 0.52678 INTE EXTERN> -34.93346 -30.76302 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6965" Parameter: A <- "-65.6965" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9335" Parameter: B <- "-34.9335" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.763" Parameter: C <- "-30.763" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1825 TOTAL ENERGY = -65.6965 RDTITL> * VAN DER WAALS = -34.9335 ELECTROSTATIC = -30.763 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1825" Parameter: CONF_N -> "8002" Comparing "1825" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1826" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753381 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758400 ATOM PAIRS WERE FOUND FOR ATOM LIST 41602 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30483 from a total of 758400 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1826 -66.09702 0.40055 0.52610 INTE EXTERN> -34.13170 -31.96533 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.097" Parameter: A <- "-66.097" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1317" Parameter: B <- "-34.1317" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.9653" Parameter: C <- "-31.9653" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1826 TOTAL ENERGY = -66.097 RDTITL> * VAN DER WAALS = -34.1317 ELECTROSTATIC = -31.9653 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1826" Parameter: CONF_N -> "8002" Comparing "1826" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1827" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758400 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757797 ATOM PAIRS WERE FOUND FOR ATOM LIST 41827 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29983 from a total of 757797 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1827 -66.79447 0.69745 0.75474 INTE EXTERN> -23.90014 -42.89433 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7945" Parameter: A <- "-66.7945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9001" Parameter: B <- "-23.9001" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8943" Parameter: C <- "-42.8943" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1827 TOTAL ENERGY = -66.7945 RDTITL> * VAN DER WAALS = -23.9001 ELECTROSTATIC = -42.8943 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1827" Parameter: CONF_N -> "8002" Comparing "1827" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1828" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757797 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759030 ATOM PAIRS WERE FOUND FOR ATOM LIST 41925 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29960 from a total of 759030 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1828 -69.17146 2.37698 0.57420 INTE EXTERN> -31.29936 -37.87210 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1715" Parameter: A <- "-69.1715" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2994" Parameter: B <- "-31.2994" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8721" Parameter: C <- "-37.8721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1828 TOTAL ENERGY = -69.1715 RDTITL> * VAN DER WAALS = -31.2994 ELECTROSTATIC = -37.8721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1828" Parameter: CONF_N -> "8002" Comparing "1828" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1829" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759030 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762434 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29732 from a total of 762434 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1829 -67.89793 -1.27353 0.60798 INTE EXTERN> -29.99913 -37.89879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8979" Parameter: A <- "-67.8979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9991" Parameter: B <- "-29.9991" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8988" Parameter: C <- "-37.8988" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1829 TOTAL ENERGY = -67.8979 RDTITL> * VAN DER WAALS = -29.9991 ELECTROSTATIC = -37.8988 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1829" Parameter: CONF_N -> "8002" Comparing "1829" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1830" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762434 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764534 ATOM PAIRS WERE FOUND FOR ATOM LIST 42036 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29951 from a total of 764534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1830 -68.95438 1.05645 0.68218 INTE EXTERN> -29.50734 -39.44704 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9544" Parameter: A <- "-68.9544" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5073" Parameter: B <- "-29.5073" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.447" Parameter: C <- "-39.447" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1830 TOTAL ENERGY = -68.9544 RDTITL> * VAN DER WAALS = -29.5073 ELECTROSTATIC = -39.447 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1830" Parameter: CONF_N -> "8002" Comparing "1830" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1831" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755811 ATOM PAIRS WERE FOUND FOR ATOM LIST 41565 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29046 from a total of 755811 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1831 -65.30874 -3.64563 0.65467 INTE EXTERN> -29.26473 -36.04401 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3087" Parameter: A <- "-65.3087" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2647" Parameter: B <- "-29.2647" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.044" Parameter: C <- "-36.044" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1831 TOTAL ENERGY = -65.3087 RDTITL> * VAN DER WAALS = -29.2647 ELECTROSTATIC = -36.044 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1831" Parameter: CONF_N -> "8002" Comparing "1831" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1832" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755811 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764127 ATOM PAIRS WERE FOUND FOR ATOM LIST 42008 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30014 from a total of 764127 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1832 -67.98261 2.67386 0.59528 INTE EXTERN> -33.71169 -34.27092 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9826" Parameter: A <- "-67.9826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7117" Parameter: B <- "-33.7117" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2709" Parameter: C <- "-34.2709" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1832 TOTAL ENERGY = -67.9826 RDTITL> * VAN DER WAALS = -33.7117 ELECTROSTATIC = -34.2709 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1832" Parameter: CONF_N -> "8002" Comparing "1832" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1833" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764127 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761546 ATOM PAIRS WERE FOUND FOR ATOM LIST 41996 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30067 from a total of 761546 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1833 -76.55830 8.57570 0.68403 INTE EXTERN> -30.18991 -46.36840 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5583" Parameter: A <- "-76.5583" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1899" Parameter: B <- "-30.1899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3684" Parameter: C <- "-46.3684" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1833 TOTAL ENERGY = -76.5583 RDTITL> * VAN DER WAALS = -30.1899 ELECTROSTATIC = -46.3684 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1833" Parameter: CONF_N -> "8002" Comparing "1833" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1834" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761546 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761511 ATOM PAIRS WERE FOUND FOR ATOM LIST 41937 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29907 from a total of 761511 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1834 -75.78475 -0.77356 0.78175 INTE EXTERN> -28.40718 -47.37756 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7847" Parameter: A <- "-75.7847" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4072" Parameter: B <- "-28.4072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3776" Parameter: C <- "-47.3776" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1834 TOTAL ENERGY = -75.7847 RDTITL> * VAN DER WAALS = -28.4072 ELECTROSTATIC = -47.3776 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1834" Parameter: CONF_N -> "8002" Comparing "1834" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1835" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761511 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764555 ATOM PAIRS WERE FOUND FOR ATOM LIST 42224 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30542 from a total of 764555 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1835 -75.97644 0.19169 0.62148 INTE EXTERN> -32.81150 -43.16494 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9764" Parameter: A <- "-75.9764" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8115" Parameter: B <- "-32.8115" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1649" Parameter: C <- "-43.1649" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1835 TOTAL ENERGY = -75.9764 RDTITL> * VAN DER WAALS = -32.8115 ELECTROSTATIC = -43.1649 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1835" Parameter: CONF_N -> "8002" Comparing "1835" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1836" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764555 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761682 ATOM PAIRS WERE FOUND FOR ATOM LIST 41859 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29746 from a total of 761682 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1836 -70.30448 -5.67196 0.70089 INTE EXTERN> -26.19702 -44.10746 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3045" Parameter: A <- "-70.3045" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.197" Parameter: B <- "-26.197" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1075" Parameter: C <- "-44.1075" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1836 TOTAL ENERGY = -70.3045 RDTITL> * VAN DER WAALS = -26.197 ELECTROSTATIC = -44.1075 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1836" Parameter: CONF_N -> "8002" Comparing "1836" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1837" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761682 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768911 ATOM PAIRS WERE FOUND FOR ATOM LIST 42185 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30346 from a total of 768911 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1837 -72.25430 1.94982 0.60174 INTE EXTERN> -32.44965 -39.80465 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2543" Parameter: A <- "-72.2543" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4497" Parameter: B <- "-32.4497" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8047" Parameter: C <- "-39.8047" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1837 TOTAL ENERGY = -72.2543 RDTITL> * VAN DER WAALS = -32.4497 ELECTROSTATIC = -39.8047 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1837" Parameter: CONF_N -> "8002" Comparing "1837" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1838" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768911 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763297 ATOM PAIRS WERE FOUND FOR ATOM LIST 41787 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29810 from a total of 763297 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1838 -71.82010 -0.43421 0.64979 INTE EXTERN> -29.08071 -42.73938 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8201" Parameter: A <- "-71.8201" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0807" Parameter: B <- "-29.0807" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7394" Parameter: C <- "-42.7394" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1838 TOTAL ENERGY = -71.8201 RDTITL> * VAN DER WAALS = -29.0807 ELECTROSTATIC = -42.7394 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1838" Parameter: CONF_N -> "8002" Comparing "1838" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1839" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763297 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766842 ATOM PAIRS WERE FOUND FOR ATOM LIST 42147 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30187 from a total of 766842 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1839 -70.72172 -1.09838 0.67889 INTE EXTERN> -28.20727 -42.51445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7217" Parameter: A <- "-70.7217" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2073" Parameter: B <- "-28.2073" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5145" Parameter: C <- "-42.5145" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1839 TOTAL ENERGY = -70.7217 RDTITL> * VAN DER WAALS = -28.2073 ELECTROSTATIC = -42.5145 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1839" Parameter: CONF_N -> "8002" Comparing "1839" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1840" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766842 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763682 ATOM PAIRS WERE FOUND FOR ATOM LIST 41957 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29983 from a total of 763682 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1840 -73.14310 2.42138 0.59361 INTE EXTERN> -31.39353 -41.74957 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1431" Parameter: A <- "-73.1431" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3935" Parameter: B <- "-31.3935" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7496" Parameter: C <- "-41.7496" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1840 TOTAL ENERGY = -73.1431 RDTITL> * VAN DER WAALS = -31.3935 ELECTROSTATIC = -41.7496 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1840" Parameter: CONF_N -> "8002" Comparing "1840" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1841" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763682 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768583 ATOM PAIRS WERE FOUND FOR ATOM LIST 42165 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29894 from a total of 768583 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1841 -73.40077 0.25767 0.71772 INTE EXTERN> -26.74400 -46.65676 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4008" Parameter: A <- "-73.4008" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.744" Parameter: B <- "-26.744" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6568" Parameter: C <- "-46.6568" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1841 TOTAL ENERGY = -73.4008 RDTITL> * VAN DER WAALS = -26.744 ELECTROSTATIC = -46.6568 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1841" Parameter: CONF_N -> "8002" Comparing "1841" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1842" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768583 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761770 ATOM PAIRS WERE FOUND FOR ATOM LIST 41999 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29790 from a total of 761770 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1842 -81.55791 8.15714 0.69850 INTE EXTERN> -30.07785 -51.48006 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5579" Parameter: A <- "-81.5579" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0778" Parameter: B <- "-30.0778" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4801" Parameter: C <- "-51.4801" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1842 TOTAL ENERGY = -81.5579 RDTITL> * VAN DER WAALS = -30.0778 ELECTROSTATIC = -51.4801 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1842" Parameter: CONF_N -> "8002" Comparing "1842" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1843" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761770 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765475 ATOM PAIRS WERE FOUND FOR ATOM LIST 42281 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30076 from a total of 765475 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1843 -75.62615 -5.93176 0.68154 INTE EXTERN> -30.09416 -45.53199 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6261" Parameter: A <- "-75.6261" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0942" Parameter: B <- "-30.0942" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.532" Parameter: C <- "-45.532" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1843 TOTAL ENERGY = -75.6261 RDTITL> * VAN DER WAALS = -30.0942 ELECTROSTATIC = -45.532 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1843" Parameter: CONF_N -> "8002" Comparing "1843" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1844" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765475 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765521 ATOM PAIRS WERE FOUND FOR ATOM LIST 42288 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29742 from a total of 765521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1844 -72.16106 -3.46508 0.65608 INTE EXTERN> -28.77211 -43.38895 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1611" Parameter: A <- "-72.1611" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7721" Parameter: B <- "-28.7721" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.389" Parameter: C <- "-43.389" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1844 TOTAL ENERGY = -72.1611 RDTITL> * VAN DER WAALS = -28.7721 ELECTROSTATIC = -43.389 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1844" Parameter: CONF_N -> "8002" Comparing "1844" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1845" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766406 ATOM PAIRS WERE FOUND FOR ATOM LIST 41971 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29644 from a total of 766406 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1845 -69.17737 -2.98369 0.57689 INTE EXTERN> -33.57671 -35.60067 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1774" Parameter: A <- "-69.1774" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5767" Parameter: B <- "-33.5767" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6007" Parameter: C <- "-35.6007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1845 TOTAL ENERGY = -69.1774 RDTITL> * VAN DER WAALS = -33.5767 ELECTROSTATIC = -35.6007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1845" Parameter: CONF_N -> "8002" Comparing "1845" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1846" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766406 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758647 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29464 from a total of 758647 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1846 -66.07312 -3.10425 0.48751 INTE EXTERN> -34.60879 -31.46433 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0731" Parameter: A <- "-66.0731" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6088" Parameter: B <- "-34.6088" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4643" Parameter: C <- "-31.4643" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1846 TOTAL ENERGY = -66.0731 RDTITL> * VAN DER WAALS = -34.6088 ELECTROSTATIC = -31.4643 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1846" Parameter: CONF_N -> "8002" Comparing "1846" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1847" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758647 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761778 ATOM PAIRS WERE FOUND FOR ATOM LIST 42050 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30747 from a total of 761778 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1847 -69.94815 3.87503 0.56587 INTE EXTERN> -35.04008 -34.90807 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9482" Parameter: A <- "-69.9482" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.0401" Parameter: B <- "-35.0401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9081" Parameter: C <- "-34.9081" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1847 TOTAL ENERGY = -69.9482 RDTITL> * VAN DER WAALS = -35.0401 ELECTROSTATIC = -34.9081 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1847" Parameter: CONF_N -> "8002" Comparing "1847" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1848" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761778 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764668 ATOM PAIRS WERE FOUND FOR ATOM LIST 42093 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30345 from a total of 764668 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1848 -70.61278 0.66462 0.57661 INTE EXTERN> -33.68595 -36.92683 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6128" Parameter: A <- "-70.6128" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.686" Parameter: B <- "-33.686" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9268" Parameter: C <- "-36.9268" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1848 TOTAL ENERGY = -70.6128 RDTITL> * VAN DER WAALS = -33.686 ELECTROSTATIC = -36.9268 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1848" Parameter: CONF_N -> "8002" Comparing "1848" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1849" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764668 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758917 ATOM PAIRS WERE FOUND FOR ATOM LIST 41845 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29903 from a total of 758917 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1849 -59.50894 -11.10384 0.65710 INTE EXTERN> -29.66561 -29.84333 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.5089" Parameter: A <- "-59.5089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6656" Parameter: B <- "-29.6656" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.8433" Parameter: C <- "-29.8433" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1849 TOTAL ENERGY = -59.5089 RDTITL> * VAN DER WAALS = -29.6656 ELECTROSTATIC = -29.8433 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1849" Parameter: CONF_N -> "8002" Comparing "1849" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1850" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758917 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760293 ATOM PAIRS WERE FOUND FOR ATOM LIST 41797 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30195 from a total of 760293 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1850 -66.69929 7.19035 0.61676 INTE EXTERN> -30.90600 -35.79329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6993" Parameter: A <- "-66.6993" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.906" Parameter: B <- "-30.906" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7933" Parameter: C <- "-35.7933" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1850 TOTAL ENERGY = -66.6993 RDTITL> * VAN DER WAALS = -30.906 ELECTROSTATIC = -35.7933 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1850" Parameter: CONF_N -> "8002" Comparing "1850" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1851" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760293 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762863 ATOM PAIRS WERE FOUND FOR ATOM LIST 42100 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30249 from a total of 762863 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1851 -63.40194 -3.29735 0.57117 INTE EXTERN> -30.14259 -33.25935 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4019" Parameter: A <- "-63.4019" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1426" Parameter: B <- "-30.1426" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2594" Parameter: C <- "-33.2594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1851 TOTAL ENERGY = -63.4019 RDTITL> * VAN DER WAALS = -30.1426 ELECTROSTATIC = -33.2594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1851" Parameter: CONF_N -> "8002" Comparing "1851" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1852" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762863 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760043 ATOM PAIRS WERE FOUND FOR ATOM LIST 41905 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30452 from a total of 760043 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1852 -74.41732 11.01538 0.61147 INTE EXTERN> -31.60710 -42.81022 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4173" Parameter: A <- "-74.4173" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6071" Parameter: B <- "-31.6071" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8102" Parameter: C <- "-42.8102" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1852 TOTAL ENERGY = -74.4173 RDTITL> * VAN DER WAALS = -31.6071 ELECTROSTATIC = -42.8102 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1852" Parameter: CONF_N -> "8002" Comparing "1852" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1853" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760043 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763882 ATOM PAIRS WERE FOUND FOR ATOM LIST 41867 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30003 from a total of 763882 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1853 -65.18236 -9.23496 0.62733 INTE EXTERN> -29.22231 -35.96005 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1824" Parameter: A <- "-65.1824" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2223" Parameter: B <- "-29.2223" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.96" Parameter: C <- "-35.96" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1853 TOTAL ENERGY = -65.1824 RDTITL> * VAN DER WAALS = -29.2223 ELECTROSTATIC = -35.96 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1853" Parameter: CONF_N -> "8002" Comparing "1853" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1854" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763882 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759300 ATOM PAIRS WERE FOUND FOR ATOM LIST 41881 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29877 from a total of 759300 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1854 -65.91267 0.73031 0.53768 INTE EXTERN> -32.62899 -33.28368 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9127" Parameter: A <- "-65.9127" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.629" Parameter: B <- "-32.629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2837" Parameter: C <- "-33.2837" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1854 TOTAL ENERGY = -65.9127 RDTITL> * VAN DER WAALS = -32.629 ELECTROSTATIC = -33.2837 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1854" Parameter: CONF_N -> "8002" Comparing "1854" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1855" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759300 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762901 ATOM PAIRS WERE FOUND FOR ATOM LIST 41909 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30134 from a total of 762901 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1855 -68.65754 2.74487 0.55675 INTE EXTERN> -33.51492 -35.14263 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6575" Parameter: A <- "-68.6575" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5149" Parameter: B <- "-33.5149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1426" Parameter: C <- "-35.1426" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1855 TOTAL ENERGY = -68.6575 RDTITL> * VAN DER WAALS = -33.5149 ELECTROSTATIC = -35.1426 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1855" Parameter: CONF_N -> "8002" Comparing "1855" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1856" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762901 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760955 ATOM PAIRS WERE FOUND FOR ATOM LIST 41941 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29739 from a total of 760955 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1856 -64.32441 -4.33313 0.65097 INTE EXTERN> -26.86932 -37.45510 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3244" Parameter: A <- "-64.3244" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8693" Parameter: B <- "-26.8693" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4551" Parameter: C <- "-37.4551" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1856 TOTAL ENERGY = -64.3244 RDTITL> * VAN DER WAALS = -26.8693 ELECTROSTATIC = -37.4551 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1856" Parameter: CONF_N -> "8002" Comparing "1856" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1857" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760955 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761984 ATOM PAIRS WERE FOUND FOR ATOM LIST 41825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29160 from a total of 761984 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1857 -65.74210 1.41768 0.56082 INTE EXTERN> -33.31296 -32.42913 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7421" Parameter: A <- "-65.7421" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.313" Parameter: B <- "-33.313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.4291" Parameter: C <- "-32.4291" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1857 TOTAL ENERGY = -65.7421 RDTITL> * VAN DER WAALS = -33.313 ELECTROSTATIC = -32.4291 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1857" Parameter: CONF_N -> "8002" Comparing "1857" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1858" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761984 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764960 ATOM PAIRS WERE FOUND FOR ATOM LIST 42176 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29390 from a total of 764960 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1858 -68.80856 3.06646 0.74892 INTE EXTERN> -28.00779 -40.80077 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8086" Parameter: A <- "-68.8086" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0078" Parameter: B <- "-28.0078" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8008" Parameter: C <- "-40.8008" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1858 TOTAL ENERGY = -68.8086 RDTITL> * VAN DER WAALS = -28.0078 ELECTROSTATIC = -40.8008 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1858" Parameter: CONF_N -> "8002" Comparing "1858" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1859" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764960 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758074 ATOM PAIRS WERE FOUND FOR ATOM LIST 41603 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29489 from a total of 758074 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1859 -67.49831 -1.31025 0.70124 INTE EXTERN> -29.22015 -38.27816 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4983" Parameter: A <- "-67.4983" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2201" Parameter: B <- "-29.2201" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2782" Parameter: C <- "-38.2782" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1859 TOTAL ENERGY = -67.4983 RDTITL> * VAN DER WAALS = -29.2201 ELECTROSTATIC = -38.2782 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1859" Parameter: CONF_N -> "8002" Comparing "1859" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1860" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758074 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758753 ATOM PAIRS WERE FOUND FOR ATOM LIST 41667 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29416 from a total of 758753 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1860 -70.57950 3.08119 0.64973 INTE EXTERN> -30.14830 -40.43120 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5795" Parameter: A <- "-70.5795" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1483" Parameter: B <- "-30.1483" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4312" Parameter: C <- "-40.4312" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1860 TOTAL ENERGY = -70.5795 RDTITL> * VAN DER WAALS = -30.1483 ELECTROSTATIC = -40.4312 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1860" Parameter: CONF_N -> "8002" Comparing "1860" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1861" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758753 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758064 ATOM PAIRS WERE FOUND FOR ATOM LIST 41817 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29427 from a total of 758064 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1861 -63.73028 -6.84922 0.55506 INTE EXTERN> -32.50158 -31.22870 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7303" Parameter: A <- "-63.7303" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5016" Parameter: B <- "-32.5016" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.2287" Parameter: C <- "-31.2287" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1861 TOTAL ENERGY = -63.7303 RDTITL> * VAN DER WAALS = -32.5016 ELECTROSTATIC = -31.2287 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1861" Parameter: CONF_N -> "8002" Comparing "1861" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1862" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758064 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757876 ATOM PAIRS WERE FOUND FOR ATOM LIST 41596 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29434 from a total of 757876 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1862 -64.12985 0.39957 0.53392 INTE EXTERN> -32.08692 -32.04293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1298" Parameter: A <- "-64.1298" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0869" Parameter: B <- "-32.0869" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.0429" Parameter: C <- "-32.0429" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1862 TOTAL ENERGY = -64.1298 RDTITL> * VAN DER WAALS = -32.0869 ELECTROSTATIC = -32.0429 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1862" Parameter: CONF_N -> "8002" Comparing "1862" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1863" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757876 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755951 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29391 from a total of 755951 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1863 -68.88824 4.75839 0.62985 INTE EXTERN> -31.05712 -37.83111 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8882" Parameter: A <- "-68.8882" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0571" Parameter: B <- "-31.0571" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8311" Parameter: C <- "-37.8311" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1863 TOTAL ENERGY = -68.8882 RDTITL> * VAN DER WAALS = -31.0571 ELECTROSTATIC = -37.8311 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1863" Parameter: CONF_N -> "8002" Comparing "1863" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1864" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755951 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759899 ATOM PAIRS WERE FOUND FOR ATOM LIST 41966 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30032 from a total of 759899 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1864 -75.74359 6.85535 0.64868 INTE EXTERN> -30.80345 -44.94014 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7436" Parameter: A <- "-75.7436" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8034" Parameter: B <- "-30.8034" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9401" Parameter: C <- "-44.9401" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1864 TOTAL ENERGY = -75.7436 RDTITL> * VAN DER WAALS = -30.8034 ELECTROSTATIC = -44.9401 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1864" Parameter: CONF_N -> "8002" Comparing "1864" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1865" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759899 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762185 ATOM PAIRS WERE FOUND FOR ATOM LIST 41775 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29900 from a total of 762185 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1865 -67.66997 -8.07362 0.58473 INTE EXTERN> -32.18402 -35.48595 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.67" Parameter: A <- "-67.67" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.184" Parameter: B <- "-32.184" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.486" Parameter: C <- "-35.486" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1865 TOTAL ENERGY = -67.67 RDTITL> * VAN DER WAALS = -32.184 ELECTROSTATIC = -35.486 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1865" Parameter: CONF_N -> "8002" Comparing "1865" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1866" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762185 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762002 ATOM PAIRS WERE FOUND FOR ATOM LIST 42094 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29806 from a total of 762002 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1866 -68.94106 1.27109 0.51246 INTE EXTERN> -36.68547 -32.25559 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9411" Parameter: A <- "-68.9411" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.6855" Parameter: B <- "-36.6855" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2556" Parameter: C <- "-32.2556" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1866 TOTAL ENERGY = -68.9411 RDTITL> * VAN DER WAALS = -36.6855 ELECTROSTATIC = -32.2556 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1866" Parameter: CONF_N -> "8002" Comparing "1866" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1867" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762002 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764132 ATOM PAIRS WERE FOUND FOR ATOM LIST 42071 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29976 from a total of 764132 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1867 -68.46714 -0.47392 0.71846 INTE EXTERN> -27.82663 -40.64051 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4671" Parameter: A <- "-68.4671" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8266" Parameter: B <- "-27.8266" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6405" Parameter: C <- "-40.6405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1867 TOTAL ENERGY = -68.4671 RDTITL> * VAN DER WAALS = -27.8266 ELECTROSTATIC = -40.6405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1867" Parameter: CONF_N -> "8002" Comparing "1867" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1868" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764132 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764088 ATOM PAIRS WERE FOUND FOR ATOM LIST 42044 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30048 from a total of 764088 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1868 -69.08690 0.61976 0.62156 INTE EXTERN> -29.29995 -39.78695 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0869" Parameter: A <- "-69.0869" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2999" Parameter: B <- "-29.2999" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.787" Parameter: C <- "-39.787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1868 TOTAL ENERGY = -69.0869 RDTITL> * VAN DER WAALS = -29.2999 ELECTROSTATIC = -39.787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1868" Parameter: CONF_N -> "8002" Comparing "1868" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1869" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764088 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761614 ATOM PAIRS WERE FOUND FOR ATOM LIST 42129 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29996 from a total of 761614 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1869 -64.86328 -4.22362 0.53440 INTE EXTERN> -30.81796 -34.04532 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8633" Parameter: A <- "-64.8633" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.818" Parameter: B <- "-30.818" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.0453" Parameter: C <- "-34.0453" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1869 TOTAL ENERGY = -64.8633 RDTITL> * VAN DER WAALS = -30.818 ELECTROSTATIC = -34.0453 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1869" Parameter: CONF_N -> "8002" Comparing "1869" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1870" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761614 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762406 ATOM PAIRS WERE FOUND FOR ATOM LIST 41848 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29937 from a total of 762406 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1870 -69.95122 5.08794 0.67733 INTE EXTERN> -29.54106 -40.41016 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9512" Parameter: A <- "-69.9512" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5411" Parameter: B <- "-29.5411" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4102" Parameter: C <- "-40.4102" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1870 TOTAL ENERGY = -69.9512 RDTITL> * VAN DER WAALS = -29.5411 ELECTROSTATIC = -40.4102 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1870" Parameter: CONF_N -> "8002" Comparing "1870" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1871" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762406 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760377 ATOM PAIRS WERE FOUND FOR ATOM LIST 41804 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29854 from a total of 760377 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1871 -66.74753 -3.20369 0.58067 INTE EXTERN> -31.27774 -35.46979 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7475" Parameter: A <- "-66.7475" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2777" Parameter: B <- "-31.2777" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4698" Parameter: C <- "-35.4698" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1871 TOTAL ENERGY = -66.7475 RDTITL> * VAN DER WAALS = -31.2777 ELECTROSTATIC = -35.4698 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1871" Parameter: CONF_N -> "8002" Comparing "1871" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1872" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760377 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759121 ATOM PAIRS WERE FOUND FOR ATOM LIST 41643 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29449 from a total of 759121 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1872 -70.21513 3.46760 0.55239 INTE EXTERN> -32.65420 -37.56094 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2151" Parameter: A <- "-70.2151" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6542" Parameter: B <- "-32.6542" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5609" Parameter: C <- "-37.5609" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1872 TOTAL ENERGY = -70.2151 RDTITL> * VAN DER WAALS = -32.6542 ELECTROSTATIC = -37.5609 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1872" Parameter: CONF_N -> "8002" Comparing "1872" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1873" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759121 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764687 ATOM PAIRS WERE FOUND FOR ATOM LIST 41842 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30347 from a total of 764687 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1873 -74.03885 3.82372 0.55652 INTE EXTERN> -33.85260 -40.18625 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0389" Parameter: A <- "-74.0389" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8526" Parameter: B <- "-33.8526" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1862" Parameter: C <- "-40.1862" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1873 TOTAL ENERGY = -74.0389 RDTITL> * VAN DER WAALS = -33.8526 ELECTROSTATIC = -40.1862 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1873" Parameter: CONF_N -> "8002" Comparing "1873" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1874" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764687 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763353 ATOM PAIRS WERE FOUND FOR ATOM LIST 42098 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29773 from a total of 763353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1874 -69.07185 -4.96701 0.69209 INTE EXTERN> -28.72787 -40.34398 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0718" Parameter: A <- "-69.0718" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7279" Parameter: B <- "-28.7279" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.344" Parameter: C <- "-40.344" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1874 TOTAL ENERGY = -69.0718 RDTITL> * VAN DER WAALS = -28.7279 ELECTROSTATIC = -40.344 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1874" Parameter: CONF_N -> "8002" Comparing "1874" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1875" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762513 ATOM PAIRS WERE FOUND FOR ATOM LIST 42095 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30019 from a total of 762513 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1875 -73.68440 4.61255 0.69525 INTE EXTERN> -28.54615 -45.13825 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6844" Parameter: A <- "-73.6844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5462" Parameter: B <- "-28.5462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1382" Parameter: C <- "-45.1382" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1875 TOTAL ENERGY = -73.6844 RDTITL> * VAN DER WAALS = -28.5462 ELECTROSTATIC = -45.1382 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1875" Parameter: CONF_N -> "8002" Comparing "1875" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1876" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762513 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761485 ATOM PAIRS WERE FOUND FOR ATOM LIST 41723 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29821 from a total of 761485 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1876 -67.10746 -6.57694 0.50932 INTE EXTERN> -32.87082 -34.23664 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1075" Parameter: A <- "-67.1075" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8708" Parameter: B <- "-32.8708" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2366" Parameter: C <- "-34.2366" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1876 TOTAL ENERGY = -67.1075 RDTITL> * VAN DER WAALS = -32.8708 ELECTROSTATIC = -34.2366 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1876" Parameter: CONF_N -> "8002" Comparing "1876" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1877" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761485 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760417 ATOM PAIRS WERE FOUND FOR ATOM LIST 41802 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29844 from a total of 760417 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1877 -67.67732 0.56987 0.55841 INTE EXTERN> -31.29626 -36.38106 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6773" Parameter: A <- "-67.6773" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2963" Parameter: B <- "-31.2963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3811" Parameter: C <- "-36.3811" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1877 TOTAL ENERGY = -67.6773 RDTITL> * VAN DER WAALS = -31.2963 ELECTROSTATIC = -36.3811 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1877" Parameter: CONF_N -> "8002" Comparing "1877" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1878" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760417 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763817 ATOM PAIRS WERE FOUND FOR ATOM LIST 41893 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29842 from a total of 763817 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1878 -67.39147 -0.28586 0.64110 INTE EXTERN> -30.21092 -37.18054 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3915" Parameter: A <- "-67.3915" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2109" Parameter: B <- "-30.2109" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1805" Parameter: C <- "-37.1805" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1878 TOTAL ENERGY = -67.3915 RDTITL> * VAN DER WAALS = -30.2109 ELECTROSTATIC = -37.1805 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1878" Parameter: CONF_N -> "8002" Comparing "1878" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1879" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763817 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758547 ATOM PAIRS WERE FOUND FOR ATOM LIST 41812 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30280 from a total of 758547 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1879 -70.76101 3.36955 0.71441 INTE EXTERN> -28.80094 -41.96008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.761" Parameter: A <- "-70.761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8009" Parameter: B <- "-28.8009" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9601" Parameter: C <- "-41.9601" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1879 TOTAL ENERGY = -70.761 RDTITL> * VAN DER WAALS = -28.8009 ELECTROSTATIC = -41.9601 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1879" Parameter: CONF_N -> "8002" Comparing "1879" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1880" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758547 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758600 ATOM PAIRS WERE FOUND FOR ATOM LIST 41829 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30148 from a total of 758600 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1880 -64.20363 -6.55738 0.51136 INTE EXTERN> -33.13687 -31.06676 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2036" Parameter: A <- "-64.2036" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1369" Parameter: B <- "-33.1369" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.0668" Parameter: C <- "-31.0668" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1880 TOTAL ENERGY = -64.2036 RDTITL> * VAN DER WAALS = -33.1369 ELECTROSTATIC = -31.0668 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1880" Parameter: CONF_N -> "8002" Comparing "1880" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1881" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758600 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762294 ATOM PAIRS WERE FOUND FOR ATOM LIST 41976 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30589 from a total of 762294 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1881 -69.71485 5.51122 0.64367 INTE EXTERN> -30.41829 -39.29656 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7148" Parameter: A <- "-69.7148" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4183" Parameter: B <- "-30.4183" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2966" Parameter: C <- "-39.2966" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1881 TOTAL ENERGY = -69.7148 RDTITL> * VAN DER WAALS = -30.4183 ELECTROSTATIC = -39.2966 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1881" Parameter: CONF_N -> "8002" Comparing "1881" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1882" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762294 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762495 ATOM PAIRS WERE FOUND FOR ATOM LIST 41933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30154 from a total of 762495 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1882 -69.21789 -0.49696 0.62391 INTE EXTERN> -29.22427 -39.99362 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2179" Parameter: A <- "-69.2179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2243" Parameter: B <- "-29.2243" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9936" Parameter: C <- "-39.9936" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1882 TOTAL ENERGY = -69.2179 RDTITL> * VAN DER WAALS = -29.2243 ELECTROSTATIC = -39.9936 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1882" Parameter: CONF_N -> "8002" Comparing "1882" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1883" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762495 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760044 ATOM PAIRS WERE FOUND FOR ATOM LIST 41584 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29760 from a total of 760044 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1883 -72.73143 3.51354 0.63724 INTE EXTERN> -31.41071 -41.32072 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7314" Parameter: A <- "-72.7314" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4107" Parameter: B <- "-31.4107" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3207" Parameter: C <- "-41.3207" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1883 TOTAL ENERGY = -72.7314 RDTITL> * VAN DER WAALS = -31.4107 ELECTROSTATIC = -41.3207 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1883" Parameter: CONF_N -> "8002" Comparing "1883" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1884" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760044 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764344 ATOM PAIRS WERE FOUND FOR ATOM LIST 41955 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30422 from a total of 764344 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1884 -74.44684 1.71540 0.73310 INTE EXTERN> -30.12246 -44.32438 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4468" Parameter: A <- "-74.4468" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1225" Parameter: B <- "-30.1225" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3244" Parameter: C <- "-44.3244" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1884 TOTAL ENERGY = -74.4468 RDTITL> * VAN DER WAALS = -30.1225 ELECTROSTATIC = -44.3244 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1884" Parameter: CONF_N -> "8002" Comparing "1884" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1885" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764344 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41986 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30418 from a total of 767794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1885 -74.14370 -0.30314 0.64531 INTE EXTERN> -31.01395 -43.12974 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1437" Parameter: A <- "-74.1437" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.014" Parameter: B <- "-31.014" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1297" Parameter: C <- "-43.1297" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1885 TOTAL ENERGY = -74.1437 RDTITL> * VAN DER WAALS = -31.014 ELECTROSTATIC = -43.1297 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1885" Parameter: CONF_N -> "8002" Comparing "1885" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1886" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763433 ATOM PAIRS WERE FOUND FOR ATOM LIST 41641 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29963 from a total of 763433 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1886 -68.39272 -5.75098 0.54174 INTE EXTERN> -33.55365 -34.83907 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3927" Parameter: A <- "-68.3927" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5536" Parameter: B <- "-33.5536" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8391" Parameter: C <- "-34.8391" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1886 TOTAL ENERGY = -68.3927 RDTITL> * VAN DER WAALS = -33.5536 ELECTROSTATIC = -34.8391 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1886" Parameter: CONF_N -> "8002" Comparing "1886" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1887" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763433 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765748 ATOM PAIRS WERE FOUND FOR ATOM LIST 42051 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30643 from a total of 765748 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1887 -75.91383 7.52111 0.58553 INTE EXTERN> -34.07342 -41.84041 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9138" Parameter: A <- "-75.9138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0734" Parameter: B <- "-34.0734" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8404" Parameter: C <- "-41.8404" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1887 TOTAL ENERGY = -75.9138 RDTITL> * VAN DER WAALS = -34.0734 ELECTROSTATIC = -41.8404 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1887" Parameter: CONF_N -> "8002" Comparing "1887" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1888" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765748 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760662 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29374 from a total of 760662 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1888 -73.08308 -2.83075 0.63926 INTE EXTERN> -27.36231 -45.72077 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0831" Parameter: A <- "-73.0831" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3623" Parameter: B <- "-27.3623" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7208" Parameter: C <- "-45.7208" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1888 TOTAL ENERGY = -73.0831 RDTITL> * VAN DER WAALS = -27.3623 ELECTROSTATIC = -45.7208 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1888" Parameter: CONF_N -> "8002" Comparing "1888" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1889" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760662 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761909 ATOM PAIRS WERE FOUND FOR ATOM LIST 41884 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29439 from a total of 761909 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1889 -74.32428 1.24120 0.65991 INTE EXTERN> -31.06017 -43.26411 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3243" Parameter: A <- "-74.3243" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0602" Parameter: B <- "-31.0602" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2641" Parameter: C <- "-43.2641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1889 TOTAL ENERGY = -74.3243 RDTITL> * VAN DER WAALS = -31.0602 ELECTROSTATIC = -43.2641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1889" Parameter: CONF_N -> "8002" Comparing "1889" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1890" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761909 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757513 ATOM PAIRS WERE FOUND FOR ATOM LIST 41408 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29201 from a total of 757513 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1890 -71.83671 -2.48757 0.71393 INTE EXTERN> -27.73082 -44.10589 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8367" Parameter: A <- "-71.8367" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7308" Parameter: B <- "-27.7308" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1059" Parameter: C <- "-44.1059" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1890 TOTAL ENERGY = -71.8367 RDTITL> * VAN DER WAALS = -27.7308 ELECTROSTATIC = -44.1059 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1890" Parameter: CONF_N -> "8002" Comparing "1890" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1891" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757513 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764151 ATOM PAIRS WERE FOUND FOR ATOM LIST 41981 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29784 from a total of 764151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1891 -65.88515 -5.95156 0.58663 INTE EXTERN> -29.92520 -35.95996 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8852" Parameter: A <- "-65.8852" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9252" Parameter: B <- "-29.9252" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.96" Parameter: C <- "-35.96" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1891 TOTAL ENERGY = -65.8852 RDTITL> * VAN DER WAALS = -29.9252 ELECTROSTATIC = -35.96 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1891" Parameter: CONF_N -> "8002" Comparing "1891" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1892" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765145 ATOM PAIRS WERE FOUND FOR ATOM LIST 42222 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29737 from a total of 765145 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1892 -69.54124 3.65609 0.60910 INTE EXTERN> -29.53872 -40.00253 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5412" Parameter: A <- "-69.5412" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5387" Parameter: B <- "-29.5387" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0025" Parameter: C <- "-40.0025" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1892 TOTAL ENERGY = -69.5412 RDTITL> * VAN DER WAALS = -29.5387 ELECTROSTATIC = -40.0025 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1892" Parameter: CONF_N -> "8002" Comparing "1892" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1893" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765145 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759520 ATOM PAIRS WERE FOUND FOR ATOM LIST 41844 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29375 from a total of 759520 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1893 -72.38705 2.84580 0.60622 INTE EXTERN> -33.34848 -39.03857 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.387" Parameter: A <- "-72.387" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3485" Parameter: B <- "-33.3485" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0386" Parameter: C <- "-39.0386" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1893 TOTAL ENERGY = -72.387 RDTITL> * VAN DER WAALS = -33.3485 ELECTROSTATIC = -39.0386 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1893" Parameter: CONF_N -> "8002" Comparing "1893" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1894" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759520 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764472 ATOM PAIRS WERE FOUND FOR ATOM LIST 42189 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30123 from a total of 764472 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1894 -71.14962 -1.23743 0.59342 INTE EXTERN> -32.27378 -38.87584 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1496" Parameter: A <- "-71.1496" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2738" Parameter: B <- "-32.2738" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8758" Parameter: C <- "-38.8758" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1894 TOTAL ENERGY = -71.1496 RDTITL> * VAN DER WAALS = -32.2738 ELECTROSTATIC = -38.8758 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1894" Parameter: CONF_N -> "8002" Comparing "1894" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1895" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764472 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766636 ATOM PAIRS WERE FOUND FOR ATOM LIST 42063 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30018 from a total of 766636 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1895 -74.00367 2.85405 0.66818 INTE EXTERN> -31.87134 -42.13234 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0037" Parameter: A <- "-74.0037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8713" Parameter: B <- "-31.8713" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1323" Parameter: C <- "-42.1323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1895 TOTAL ENERGY = -74.0037 RDTITL> * VAN DER WAALS = -31.8713 ELECTROSTATIC = -42.1323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1895" Parameter: CONF_N -> "8002" Comparing "1895" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1896" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766636 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763080 ATOM PAIRS WERE FOUND FOR ATOM LIST 41934 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30676 from a total of 763080 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1896 -61.48955 -12.51412 0.56234 INTE EXTERN> -32.85294 -28.63662 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.4896" Parameter: A <- "-61.4896" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8529" Parameter: B <- "-32.8529" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.6366" Parameter: C <- "-28.6366" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1896 TOTAL ENERGY = -61.4896 RDTITL> * VAN DER WAALS = -32.8529 ELECTROSTATIC = -28.6366 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1896" Parameter: CONF_N -> "8002" Comparing "1896" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1897" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763080 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767482 ATOM PAIRS WERE FOUND FOR ATOM LIST 41990 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30353 from a total of 767482 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1897 -72.81717 11.32762 0.57839 INTE EXTERN> -32.93995 -39.87723 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8172" Parameter: A <- "-72.8172" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9399" Parameter: B <- "-32.9399" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8772" Parameter: C <- "-39.8772" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1897 TOTAL ENERGY = -72.8172 RDTITL> * VAN DER WAALS = -32.9399 ELECTROSTATIC = -39.8772 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1897" Parameter: CONF_N -> "8002" Comparing "1897" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1898" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767482 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758626 ATOM PAIRS WERE FOUND FOR ATOM LIST 41687 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30147 from a total of 758626 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1898 -73.16854 0.35137 0.59092 INTE EXTERN> -31.84801 -41.32053 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1685" Parameter: A <- "-73.1685" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.848" Parameter: B <- "-31.848" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3205" Parameter: C <- "-41.3205" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1898 TOTAL ENERGY = -73.1685 RDTITL> * VAN DER WAALS = -31.848 ELECTROSTATIC = -41.3205 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1898" Parameter: CONF_N -> "8002" Comparing "1898" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1899" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758626 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765270 ATOM PAIRS WERE FOUND FOR ATOM LIST 42112 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30216 from a total of 765270 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1899 -67.93887 -5.22967 0.60564 INTE EXTERN> -33.70274 -34.23613 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9389" Parameter: A <- "-67.9389" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7027" Parameter: B <- "-33.7027" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2361" Parameter: C <- "-34.2361" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1899 TOTAL ENERGY = -67.9389 RDTITL> * VAN DER WAALS = -33.7027 ELECTROSTATIC = -34.2361 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1899" Parameter: CONF_N -> "8002" Comparing "1899" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1900" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765270 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763559 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29934 from a total of 763559 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1900 -62.81305 -5.12582 0.70682 INTE EXTERN> -26.75347 -36.05958 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.8131" Parameter: A <- "-62.8131" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7535" Parameter: B <- "-26.7535" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0596" Parameter: C <- "-36.0596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1900 TOTAL ENERGY = -62.8131 RDTITL> * VAN DER WAALS = -26.7535 ELECTROSTATIC = -36.0596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1900" Parameter: CONF_N -> "8002" Comparing "1900" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1901" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763559 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765827 ATOM PAIRS WERE FOUND FOR ATOM LIST 42120 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30040 from a total of 765827 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1901 -73.54983 10.73678 0.63373 INTE EXTERN> -29.67570 -43.87412 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5498" Parameter: A <- "-73.5498" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6757" Parameter: B <- "-29.6757" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8741" Parameter: C <- "-43.8741" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1901 TOTAL ENERGY = -73.5498 RDTITL> * VAN DER WAALS = -29.6757 ELECTROSTATIC = -43.8741 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1901" Parameter: CONF_N -> "8002" Comparing "1901" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1902" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765827 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766883 ATOM PAIRS WERE FOUND FOR ATOM LIST 42139 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30214 from a total of 766883 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1902 -71.12500 -2.42483 0.59406 INTE EXTERN> -35.50085 -35.62415 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.125" Parameter: A <- "-71.125" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.5008" Parameter: B <- "-35.5008" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6242" Parameter: C <- "-35.6242" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1902 TOTAL ENERGY = -71.125 RDTITL> * VAN DER WAALS = -35.5008 ELECTROSTATIC = -35.6242 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1902" Parameter: CONF_N -> "8002" Comparing "1902" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1903" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766883 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769401 ATOM PAIRS WERE FOUND FOR ATOM LIST 42294 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29660 from a total of 769401 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1903 -64.53687 -6.58812 0.49012 INTE EXTERN> -32.73726 -31.79961 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5369" Parameter: A <- "-64.5369" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7373" Parameter: B <- "-32.7373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.7996" Parameter: C <- "-31.7996" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1903 TOTAL ENERGY = -64.5369 RDTITL> * VAN DER WAALS = -32.7373 ELECTROSTATIC = -31.7996 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1903" Parameter: CONF_N -> "8002" Comparing "1903" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1904" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769401 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768749 ATOM PAIRS WERE FOUND FOR ATOM LIST 42175 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30345 from a total of 768749 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1904 -62.68015 -1.85673 0.67637 INTE EXTERN> -30.20238 -32.47777 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.6801" Parameter: A <- "-62.6801" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2024" Parameter: B <- "-30.2024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.4778" Parameter: C <- "-32.4778" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1904 TOTAL ENERGY = -62.6801 RDTITL> * VAN DER WAALS = -30.2024 ELECTROSTATIC = -32.4778 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1904" Parameter: CONF_N -> "8002" Comparing "1904" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1905" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768749 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765924 ATOM PAIRS WERE FOUND FOR ATOM LIST 42209 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30747 from a total of 765924 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1905 -71.23774 8.55759 0.61091 INTE EXTERN> -32.49615 -38.74160 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2377" Parameter: A <- "-71.2377" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4961" Parameter: B <- "-32.4961" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7416" Parameter: C <- "-38.7416" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1905 TOTAL ENERGY = -71.2377 RDTITL> * VAN DER WAALS = -32.4961 ELECTROSTATIC = -38.7416 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1905" Parameter: CONF_N -> "8002" Comparing "1905" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1906" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765924 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767581 ATOM PAIRS WERE FOUND FOR ATOM LIST 42079 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29941 from a total of 767581 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1906 -68.98304 -2.25470 0.60371 INTE EXTERN> -31.86727 -37.11577 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.983" Parameter: A <- "-68.983" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8673" Parameter: B <- "-31.8673" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1158" Parameter: C <- "-37.1158" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1906 TOTAL ENERGY = -68.983 RDTITL> * VAN DER WAALS = -31.8673 ELECTROSTATIC = -37.1158 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1906" Parameter: CONF_N -> "8002" Comparing "1906" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1907" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767581 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761138 ATOM PAIRS WERE FOUND FOR ATOM LIST 42056 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30128 from a total of 761138 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1907 -67.23027 -1.75277 0.65507 INTE EXTERN> -30.09713 -37.13314 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2303" Parameter: A <- "-67.2303" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0971" Parameter: B <- "-30.0971" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1331" Parameter: C <- "-37.1331" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1907 TOTAL ENERGY = -67.2303 RDTITL> * VAN DER WAALS = -30.0971 ELECTROSTATIC = -37.1331 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1907" Parameter: CONF_N -> "8002" Comparing "1907" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1908" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761138 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762881 ATOM PAIRS WERE FOUND FOR ATOM LIST 41868 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30043 from a total of 762881 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1908 -68.35639 1.12612 0.73773 INTE EXTERN> -28.50740 -39.84899 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3564" Parameter: A <- "-68.3564" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5074" Parameter: B <- "-28.5074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.849" Parameter: C <- "-39.849" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1908 TOTAL ENERGY = -68.3564 RDTITL> * VAN DER WAALS = -28.5074 ELECTROSTATIC = -39.849 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1908" Parameter: CONF_N -> "8002" Comparing "1908" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1909" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762881 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769925 ATOM PAIRS WERE FOUND FOR ATOM LIST 42454 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30756 from a total of 769925 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1909 -72.10345 3.74706 0.60870 INTE EXTERN> -31.75529 -40.34816 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1034" Parameter: A <- "-72.1034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7553" Parameter: B <- "-31.7553" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3482" Parameter: C <- "-40.3482" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1909 TOTAL ENERGY = -72.1034 RDTITL> * VAN DER WAALS = -31.7553 ELECTROSTATIC = -40.3482 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1909" Parameter: CONF_N -> "8002" Comparing "1909" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1910" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769925 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766940 ATOM PAIRS WERE FOUND FOR ATOM LIST 42117 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30248 from a total of 766940 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1910 -72.88145 0.77800 0.59277 INTE EXTERN> -35.36367 -37.51778 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8815" Parameter: A <- "-72.8815" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.3637" Parameter: B <- "-35.3637" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5178" Parameter: C <- "-37.5178" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1910 TOTAL ENERGY = -72.8815 RDTITL> * VAN DER WAALS = -35.3637 ELECTROSTATIC = -37.5178 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1910" Parameter: CONF_N -> "8002" Comparing "1910" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1911" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766940 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763015 ATOM PAIRS WERE FOUND FOR ATOM LIST 42029 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30405 from a total of 763015 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1911 -63.55704 -9.32441 0.63859 INTE EXTERN> -30.60710 -32.94995 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.557" Parameter: A <- "-63.557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6071" Parameter: B <- "-30.6071" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.9499" Parameter: C <- "-32.9499" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1911 TOTAL ENERGY = -63.557 RDTITL> * VAN DER WAALS = -30.6071 ELECTROSTATIC = -32.9499 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1911" Parameter: CONF_N -> "8002" Comparing "1911" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1912" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763015 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761523 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29915 from a total of 761523 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1912 -64.08294 0.52589 0.67446 INTE EXTERN> -26.29837 -37.78457 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0829" Parameter: A <- "-64.0829" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2984" Parameter: B <- "-26.2984" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7846" Parameter: C <- "-37.7846" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1912 TOTAL ENERGY = -64.0829 RDTITL> * VAN DER WAALS = -26.2984 ELECTROSTATIC = -37.7846 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1912" Parameter: CONF_N -> "8002" Comparing "1912" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1913" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761523 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757164 ATOM PAIRS WERE FOUND FOR ATOM LIST 41493 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29720 from a total of 757164 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1913 -64.99571 0.91278 0.57098 INTE EXTERN> -32.23846 -32.75725 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9957" Parameter: A <- "-64.9957" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2385" Parameter: B <- "-32.2385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.7573" Parameter: C <- "-32.7573" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1913 TOTAL ENERGY = -64.9957 RDTITL> * VAN DER WAALS = -32.2385 ELECTROSTATIC = -32.7573 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1913" Parameter: CONF_N -> "8002" Comparing "1913" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1914" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757164 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761147 ATOM PAIRS WERE FOUND FOR ATOM LIST 41973 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30298 from a total of 761147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1914 -67.55335 2.55764 0.60231 INTE EXTERN> -32.82349 -34.72986 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5534" Parameter: A <- "-67.5534" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8235" Parameter: B <- "-32.8235" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7299" Parameter: C <- "-34.7299" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1914 TOTAL ENERGY = -67.5534 RDTITL> * VAN DER WAALS = -32.8235 ELECTROSTATIC = -34.7299 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1914" Parameter: CONF_N -> "8002" Comparing "1914" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1915" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759900 ATOM PAIRS WERE FOUND FOR ATOM LIST 41472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29970 from a total of 759900 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1915 -67.60188 0.04853 0.58920 INTE EXTERN> -30.05271 -37.54917 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6019" Parameter: A <- "-67.6019" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0527" Parameter: B <- "-30.0527" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5492" Parameter: C <- "-37.5492" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1915 TOTAL ENERGY = -67.6019 RDTITL> * VAN DER WAALS = -30.0527 ELECTROSTATIC = -37.5492 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1915" Parameter: CONF_N -> "8002" Comparing "1915" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1916" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759900 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756301 ATOM PAIRS WERE FOUND FOR ATOM LIST 41629 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29539 from a total of 756301 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1916 -68.58420 0.98232 0.53316 INTE EXTERN> -34.84359 -33.74062 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5842" Parameter: A <- "-68.5842" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.8436" Parameter: B <- "-34.8436" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7406" Parameter: C <- "-33.7406" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1916 TOTAL ENERGY = -68.5842 RDTITL> * VAN DER WAALS = -34.8436 ELECTROSTATIC = -33.7406 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1916" Parameter: CONF_N -> "8002" Comparing "1916" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1917" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756301 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767800 ATOM PAIRS WERE FOUND FOR ATOM LIST 42051 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30015 from a total of 767800 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1917 -69.37082 0.78662 0.66197 INTE EXTERN> -30.88788 -38.48294 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3708" Parameter: A <- "-69.3708" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8879" Parameter: B <- "-30.8879" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4829" Parameter: C <- "-38.4829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1917 TOTAL ENERGY = -69.3708 RDTITL> * VAN DER WAALS = -30.8879 ELECTROSTATIC = -38.4829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1917" Parameter: CONF_N -> "8002" Comparing "1917" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1918" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767800 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766853 ATOM PAIRS WERE FOUND FOR ATOM LIST 42096 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29569 from a total of 766853 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1918 -71.47046 2.09965 0.58710 INTE EXTERN> -32.78877 -38.68169 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4705" Parameter: A <- "-71.4705" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7888" Parameter: B <- "-32.7888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6817" Parameter: C <- "-38.6817" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1918 TOTAL ENERGY = -71.4705 RDTITL> * VAN DER WAALS = -32.7888 ELECTROSTATIC = -38.6817 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1918" Parameter: CONF_N -> "8002" Comparing "1918" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1919" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766853 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765921 ATOM PAIRS WERE FOUND FOR ATOM LIST 41899 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29781 from a total of 765921 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1919 -67.62749 -3.84298 0.65552 INTE EXTERN> -30.94276 -36.68473 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6275" Parameter: A <- "-67.6275" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9428" Parameter: B <- "-30.9428" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6847" Parameter: C <- "-36.6847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1919 TOTAL ENERGY = -67.6275 RDTITL> * VAN DER WAALS = -30.9428 ELECTROSTATIC = -36.6847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1919" Parameter: CONF_N -> "8002" Comparing "1919" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1920" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765921 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763562 ATOM PAIRS WERE FOUND FOR ATOM LIST 42012 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30181 from a total of 763562 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1920 -69.43302 1.80553 0.66252 INTE EXTERN> -29.16840 -40.26462 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.433" Parameter: A <- "-69.433" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1684" Parameter: B <- "-29.1684" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2646" Parameter: C <- "-40.2646" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1920 TOTAL ENERGY = -69.433 RDTITL> * VAN DER WAALS = -29.1684 ELECTROSTATIC = -40.2646 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1920" Parameter: CONF_N -> "8002" Comparing "1920" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1921" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763562 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763000 ATOM PAIRS WERE FOUND FOR ATOM LIST 41692 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30168 from a total of 763000 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1921 -71.85642 2.42340 0.66037 INTE EXTERN> -30.69113 -41.16529 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8564" Parameter: A <- "-71.8564" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6911" Parameter: B <- "-30.6911" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1653" Parameter: C <- "-41.1653" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1921 TOTAL ENERGY = -71.8564 RDTITL> * VAN DER WAALS = -30.6911 ELECTROSTATIC = -41.1653 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1921" Parameter: CONF_N -> "8002" Comparing "1921" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1922" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763000 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765775 ATOM PAIRS WERE FOUND FOR ATOM LIST 41959 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29831 from a total of 765775 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1922 -66.57771 -5.27871 0.67596 INTE EXTERN> -30.64821 -35.92950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5777" Parameter: A <- "-66.5777" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6482" Parameter: B <- "-30.6482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9295" Parameter: C <- "-35.9295" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1922 TOTAL ENERGY = -66.5777 RDTITL> * VAN DER WAALS = -30.6482 ELECTROSTATIC = -35.9295 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1922" Parameter: CONF_N -> "8002" Comparing "1922" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1923" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765775 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765499 ATOM PAIRS WERE FOUND FOR ATOM LIST 42133 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29584 from a total of 765499 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1923 -68.16559 1.58788 0.50819 INTE EXTERN> -35.46183 -32.70376 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1656" Parameter: A <- "-68.1656" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.4618" Parameter: B <- "-35.4618" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.7038" Parameter: C <- "-32.7038" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1923 TOTAL ENERGY = -68.1656 RDTITL> * VAN DER WAALS = -35.4618 ELECTROSTATIC = -32.7038 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1923" Parameter: CONF_N -> "8002" Comparing "1923" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1924" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765499 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763014 ATOM PAIRS WERE FOUND FOR ATOM LIST 41814 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29931 from a total of 763014 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1924 -64.29918 -3.86641 0.56105 INTE EXTERN> -33.61681 -30.68237 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2992" Parameter: A <- "-64.2992" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6168" Parameter: B <- "-33.6168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.6824" Parameter: C <- "-30.6824" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1924 TOTAL ENERGY = -64.2992 RDTITL> * VAN DER WAALS = -33.6168 ELECTROSTATIC = -30.6824 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1924" Parameter: CONF_N -> "8002" Comparing "1924" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1925" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763014 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757665 ATOM PAIRS WERE FOUND FOR ATOM LIST 41486 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29093 from a total of 757665 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1925 -59.46034 -4.83884 0.56961 INTE EXTERN> -29.37633 -30.08400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.4603" Parameter: A <- "-59.4603" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3763" Parameter: B <- "-29.3763" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.084" Parameter: C <- "-30.084" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1925 TOTAL ENERGY = -59.4603 RDTITL> * VAN DER WAALS = -29.3763 ELECTROSTATIC = -30.084 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1925" Parameter: CONF_N -> "8002" Comparing "1925" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1926" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757665 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763884 ATOM PAIRS WERE FOUND FOR ATOM LIST 41869 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29583 from a total of 763884 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1926 -64.00600 4.54567 0.55347 INTE EXTERN> -31.62680 -32.37921 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.006" Parameter: A <- "-64.006" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6268" Parameter: B <- "-31.6268" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.3792" Parameter: C <- "-32.3792" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1926 TOTAL ENERGY = -64.006 RDTITL> * VAN DER WAALS = -31.6268 ELECTROSTATIC = -32.3792 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1926" Parameter: CONF_N -> "8002" Comparing "1926" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1927" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763884 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765513 ATOM PAIRS WERE FOUND FOR ATOM LIST 42097 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30087 from a total of 765513 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1927 -68.37599 4.36999 0.57911 INTE EXTERN> -32.22660 -36.14939 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.376" Parameter: A <- "-68.376" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2266" Parameter: B <- "-32.2266" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1494" Parameter: C <- "-36.1494" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1927 TOTAL ENERGY = -68.376 RDTITL> * VAN DER WAALS = -32.2266 ELECTROSTATIC = -36.1494 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1927" Parameter: CONF_N -> "8002" Comparing "1927" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1928" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765513 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771923 ATOM PAIRS WERE FOUND FOR ATOM LIST 42277 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30077 from a total of 771923 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1928 -74.48938 6.11339 0.67433 INTE EXTERN> -29.81464 -44.67474 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4894" Parameter: A <- "-74.4894" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8146" Parameter: B <- "-29.8146" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6747" Parameter: C <- "-44.6747" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1928 TOTAL ENERGY = -74.4894 RDTITL> * VAN DER WAALS = -29.8146 ELECTROSTATIC = -44.6747 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1928" Parameter: CONF_N -> "8002" Comparing "1928" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1929" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771923 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767996 ATOM PAIRS WERE FOUND FOR ATOM LIST 42066 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29280 from a total of 767996 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1929 -70.77673 -3.71265 0.62980 INTE EXTERN> -30.17227 -40.60446 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7767" Parameter: A <- "-70.7767" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1723" Parameter: B <- "-30.1723" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6045" Parameter: C <- "-40.6045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1929 TOTAL ENERGY = -70.7767 RDTITL> * VAN DER WAALS = -30.1723 ELECTROSTATIC = -40.6045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1929" Parameter: CONF_N -> "8002" Comparing "1929" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1930" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767996 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768135 ATOM PAIRS WERE FOUND FOR ATOM LIST 42110 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29670 from a total of 768135 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1930 -66.18265 -4.59408 0.54335 INTE EXTERN> -31.41117 -34.77147 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1826" Parameter: A <- "-66.1826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4112" Parameter: B <- "-31.4112" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7715" Parameter: C <- "-34.7715" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1930 TOTAL ENERGY = -66.1826 RDTITL> * VAN DER WAALS = -31.4112 ELECTROSTATIC = -34.7715 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1930" Parameter: CONF_N -> "8002" Comparing "1930" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1931" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768135 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764750 ATOM PAIRS WERE FOUND FOR ATOM LIST 41959 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29586 from a total of 764750 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1931 -62.94741 -3.23524 0.51393 INTE EXTERN> -30.16586 -32.78155 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9474" Parameter: A <- "-62.9474" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1659" Parameter: B <- "-30.1659" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.7815" Parameter: C <- "-32.7815" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1931 TOTAL ENERGY = -62.9474 RDTITL> * VAN DER WAALS = -30.1659 ELECTROSTATIC = -32.7815 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1931" Parameter: CONF_N -> "8002" Comparing "1931" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1932" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764750 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763809 ATOM PAIRS WERE FOUND FOR ATOM LIST 41816 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29598 from a total of 763809 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1932 -73.52874 10.58133 0.70520 INTE EXTERN> -25.45488 -48.07386 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5287" Parameter: A <- "-73.5287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4549" Parameter: B <- "-25.4549" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0739" Parameter: C <- "-48.0739" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1932 TOTAL ENERGY = -73.5287 RDTITL> * VAN DER WAALS = -25.4549 ELECTROSTATIC = -48.0739 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1932" Parameter: CONF_N -> "8002" Comparing "1932" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1933" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763809 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767244 ATOM PAIRS WERE FOUND FOR ATOM LIST 42199 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29600 from a total of 767244 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1933 -66.01078 -7.51796 0.56852 INTE EXTERN> -31.68915 -34.32163 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0108" Parameter: A <- "-66.0108" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6891" Parameter: B <- "-31.6891" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3216" Parameter: C <- "-34.3216" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1933 TOTAL ENERGY = -66.0108 RDTITL> * VAN DER WAALS = -31.6891 ELECTROSTATIC = -34.3216 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1933" Parameter: CONF_N -> "8002" Comparing "1933" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1934" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767244 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768359 ATOM PAIRS WERE FOUND FOR ATOM LIST 42023 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29801 from a total of 768359 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1934 -63.81206 -2.19872 0.59136 INTE EXTERN> -30.18250 -33.62956 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.8121" Parameter: A <- "-63.8121" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1825" Parameter: B <- "-30.1825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6296" Parameter: C <- "-33.6296" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1934 TOTAL ENERGY = -63.8121 RDTITL> * VAN DER WAALS = -30.1825 ELECTROSTATIC = -33.6296 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1934" Parameter: CONF_N -> "8002" Comparing "1934" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1935" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768359 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763978 ATOM PAIRS WERE FOUND FOR ATOM LIST 41848 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30086 from a total of 763978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1935 -69.74501 5.93295 0.55936 INTE EXTERN> -29.56091 -40.18411 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.745" Parameter: A <- "-69.745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5609" Parameter: B <- "-29.5609" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1841" Parameter: C <- "-40.1841" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1935 TOTAL ENERGY = -69.745 RDTITL> * VAN DER WAALS = -29.5609 ELECTROSTATIC = -40.1841 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1935" Parameter: CONF_N -> "8002" Comparing "1935" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1936" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768280 ATOM PAIRS WERE FOUND FOR ATOM LIST 42084 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30620 from a total of 768280 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1936 -73.97198 4.22696 0.56116 INTE EXTERN> -33.70293 -40.26905 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.972" Parameter: A <- "-73.972" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7029" Parameter: B <- "-33.7029" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.269" Parameter: C <- "-40.269" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1936 TOTAL ENERGY = -73.972 RDTITL> * VAN DER WAALS = -33.7029 ELECTROSTATIC = -40.269 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1936" Parameter: CONF_N -> "8002" Comparing "1936" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1937" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768280 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770583 ATOM PAIRS WERE FOUND FOR ATOM LIST 42077 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30709 from a total of 770583 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1937 -71.22708 -2.74490 0.66917 INTE EXTERN> -25.60458 -45.62250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2271" Parameter: A <- "-71.2271" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6046" Parameter: B <- "-25.6046" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6225" Parameter: C <- "-45.6225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1937 TOTAL ENERGY = -71.2271 RDTITL> * VAN DER WAALS = -25.6046 ELECTROSTATIC = -45.6225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1937" Parameter: CONF_N -> "8002" Comparing "1937" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1938" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770583 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771026 ATOM PAIRS WERE FOUND FOR ATOM LIST 42132 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30221 from a total of 771026 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1938 -73.49407 2.26699 0.67098 INTE EXTERN> -30.59654 -42.89753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4941" Parameter: A <- "-73.4941" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5965" Parameter: B <- "-30.5965" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8975" Parameter: C <- "-42.8975" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1938 TOTAL ENERGY = -73.4941 RDTITL> * VAN DER WAALS = -30.5965 ELECTROSTATIC = -42.8975 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1938" Parameter: CONF_N -> "8002" Comparing "1938" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1939" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771026 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772293 ATOM PAIRS WERE FOUND FOR ATOM LIST 42268 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30476 from a total of 772293 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1939 -78.93171 5.43764 0.67001 INTE EXTERN> -29.74988 -49.18183 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9317" Parameter: A <- "-78.9317" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7499" Parameter: B <- "-29.7499" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1818" Parameter: C <- "-49.1818" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1939 TOTAL ENERGY = -78.9317 RDTITL> * VAN DER WAALS = -29.7499 ELECTROSTATIC = -49.1818 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1939" Parameter: CONF_N -> "8002" Comparing "1939" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1940" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772293 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772068 ATOM PAIRS WERE FOUND FOR ATOM LIST 42201 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30314 from a total of 772068 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1940 -70.61308 -8.31863 0.60507 INTE EXTERN> -31.93470 -38.67838 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6131" Parameter: A <- "-70.6131" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9347" Parameter: B <- "-31.9347" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6784" Parameter: C <- "-38.6784" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1940 TOTAL ENERGY = -70.6131 RDTITL> * VAN DER WAALS = -31.9347 ELECTROSTATIC = -38.6784 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1940" Parameter: CONF_N -> "8002" Comparing "1940" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1941" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772068 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764402 ATOM PAIRS WERE FOUND FOR ATOM LIST 41970 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29611 from a total of 764402 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1941 -73.49817 2.88509 0.59856 INTE EXTERN> -30.88680 -42.61136 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4982" Parameter: A <- "-73.4982" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8868" Parameter: B <- "-30.8868" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6114" Parameter: C <- "-42.6114" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1941 TOTAL ENERGY = -73.4982 RDTITL> * VAN DER WAALS = -30.8868 ELECTROSTATIC = -42.6114 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1941" Parameter: CONF_N -> "8002" Comparing "1941" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1942" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764402 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766785 ATOM PAIRS WERE FOUND FOR ATOM LIST 42064 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29706 from a total of 766785 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1942 -66.24356 -7.25460 0.69126 INTE EXTERN> -26.76846 -39.47510 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2436" Parameter: A <- "-66.2436" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7685" Parameter: B <- "-26.7685" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4751" Parameter: C <- "-39.4751" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1942 TOTAL ENERGY = -66.2436 RDTITL> * VAN DER WAALS = -26.7685 ELECTROSTATIC = -39.4751 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1942" Parameter: CONF_N -> "8002" Comparing "1942" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1943" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766785 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764566 ATOM PAIRS WERE FOUND FOR ATOM LIST 42061 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29822 from a total of 764566 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1943 -62.63117 -3.61239 0.63704 INTE EXTERN> -29.14096 -33.49021 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.6312" Parameter: A <- "-62.6312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.141" Parameter: B <- "-29.141" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.4902" Parameter: C <- "-33.4902" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1943 TOTAL ENERGY = -62.6312 RDTITL> * VAN DER WAALS = -29.141 ELECTROSTATIC = -33.4902 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1943" Parameter: CONF_N -> "8002" Comparing "1943" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1944" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764566 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764146 ATOM PAIRS WERE FOUND FOR ATOM LIST 42065 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30492 from a total of 764146 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1944 -77.36564 14.73447 0.56497 INTE EXTERN> -33.54191 -43.82374 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3656" Parameter: A <- "-77.3656" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5419" Parameter: B <- "-33.5419" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8237" Parameter: C <- "-43.8237" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1944 TOTAL ENERGY = -77.3656 RDTITL> * VAN DER WAALS = -33.5419 ELECTROSTATIC = -43.8237 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1944" Parameter: CONF_N -> "8002" Comparing "1944" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1945" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764146 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760946 ATOM PAIRS WERE FOUND FOR ATOM LIST 41658 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29943 from a total of 760946 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1945 -63.36742 -13.99822 0.65285 INTE EXTERN> -26.12560 -37.24182 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3674" Parameter: A <- "-63.3674" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1256" Parameter: B <- "-26.1256" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2418" Parameter: C <- "-37.2418" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1945 TOTAL ENERGY = -63.3674 RDTITL> * VAN DER WAALS = -26.1256 ELECTROSTATIC = -37.2418 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1945" Parameter: CONF_N -> "8002" Comparing "1945" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1946" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760946 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766574 ATOM PAIRS WERE FOUND FOR ATOM LIST 42140 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30125 from a total of 766574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1946 -69.16432 5.79689 0.62503 INTE EXTERN> -30.79312 -38.37119 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1643" Parameter: A <- "-69.1643" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7931" Parameter: B <- "-30.7931" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3712" Parameter: C <- "-38.3712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1946 TOTAL ENERGY = -69.1643 RDTITL> * VAN DER WAALS = -30.7931 ELECTROSTATIC = -38.3712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1946" Parameter: CONF_N -> "8002" Comparing "1946" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1947" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766742 ATOM PAIRS WERE FOUND FOR ATOM LIST 42253 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30098 from a total of 766742 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1947 -75.10215 5.93783 0.70501 INTE EXTERN> -26.98856 -48.11359 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1022" Parameter: A <- "-75.1022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9886" Parameter: B <- "-26.9886" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1136" Parameter: C <- "-48.1136" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1947 TOTAL ENERGY = -75.1022 RDTITL> * VAN DER WAALS = -26.9886 ELECTROSTATIC = -48.1136 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1947" Parameter: CONF_N -> "8002" Comparing "1947" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1948" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766742 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761125 ATOM PAIRS WERE FOUND FOR ATOM LIST 41566 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30233 from a total of 761125 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1948 -70.27180 -4.83036 0.64674 INTE EXTERN> -29.29220 -40.97960 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2718" Parameter: A <- "-70.2718" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2922" Parameter: B <- "-29.2922" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9796" Parameter: C <- "-40.9796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1948 TOTAL ENERGY = -70.2718 RDTITL> * VAN DER WAALS = -29.2922 ELECTROSTATIC = -40.9796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1948" Parameter: CONF_N -> "8002" Comparing "1948" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1949" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761125 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760253 ATOM PAIRS WERE FOUND FOR ATOM LIST 41891 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29874 from a total of 760253 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1949 -69.50123 -0.77056 0.71596 INTE EXTERN> -28.09237 -41.40886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5012" Parameter: A <- "-69.5012" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0924" Parameter: B <- "-28.0924" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4089" Parameter: C <- "-41.4089" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1949 TOTAL ENERGY = -69.5012 RDTITL> * VAN DER WAALS = -28.0924 ELECTROSTATIC = -41.4089 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1949" Parameter: CONF_N -> "8002" Comparing "1949" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1950" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760253 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764573 ATOM PAIRS WERE FOUND FOR ATOM LIST 41877 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30332 from a total of 764573 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1950 -70.40919 0.90796 0.62591 INTE EXTERN> -29.95965 -40.44954 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4092" Parameter: A <- "-70.4092" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9596" Parameter: B <- "-29.9596" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4495" Parameter: C <- "-40.4495" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1950 TOTAL ENERGY = -70.4092 RDTITL> * VAN DER WAALS = -29.9596 ELECTROSTATIC = -40.4495 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1950" Parameter: CONF_N -> "8002" Comparing "1950" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1951" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764573 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766102 ATOM PAIRS WERE FOUND FOR ATOM LIST 42139 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30128 from a total of 766102 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1951 -66.97498 -3.43421 0.50221 INTE EXTERN> -32.23793 -34.73706 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.975" Parameter: A <- "-66.975" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2379" Parameter: B <- "-32.2379" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7371" Parameter: C <- "-34.7371" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1951 TOTAL ENERGY = -66.975 RDTITL> * VAN DER WAALS = -32.2379 ELECTROSTATIC = -34.7371 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1951" Parameter: CONF_N -> "8002" Comparing "1951" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1952" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766102 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761844 ATOM PAIRS WERE FOUND FOR ATOM LIST 41861 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29566 from a total of 761844 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1952 -73.24889 6.27390 0.59962 INTE EXTERN> -32.56184 -40.68705 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2489" Parameter: A <- "-73.2489" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5618" Parameter: B <- "-32.5618" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.687" Parameter: C <- "-40.687" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1952 TOTAL ENERGY = -73.2489 RDTITL> * VAN DER WAALS = -32.5618 ELECTROSTATIC = -40.687 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1952" Parameter: CONF_N -> "8002" Comparing "1952" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1953" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761844 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762672 ATOM PAIRS WERE FOUND FOR ATOM LIST 41673 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29824 from a total of 762672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1953 -74.61587 1.36699 0.69420 INTE EXTERN> -28.89996 -45.71592 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6159" Parameter: A <- "-74.6159" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9" Parameter: B <- "-28.9" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7159" Parameter: C <- "-45.7159" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1953 TOTAL ENERGY = -74.6159 RDTITL> * VAN DER WAALS = -28.9 ELECTROSTATIC = -45.7159 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1953" Parameter: CONF_N -> "8002" Comparing "1953" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1954" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767778 ATOM PAIRS WERE FOUND FOR ATOM LIST 42000 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30271 from a total of 767778 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1954 -76.77221 2.15634 0.63465 INTE EXTERN> -31.39349 -45.37872 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7722" Parameter: A <- "-76.7722" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3935" Parameter: B <- "-31.3935" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3787" Parameter: C <- "-45.3787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1954 TOTAL ENERGY = -76.7722 RDTITL> * VAN DER WAALS = -31.3935 ELECTROSTATIC = -45.3787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1954" Parameter: CONF_N -> "8002" Comparing "1954" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1955" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767778 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765007 ATOM PAIRS WERE FOUND FOR ATOM LIST 42082 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30605 from a total of 765007 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1955 -71.05869 -5.71352 0.52740 INTE EXTERN> -35.00120 -36.05750 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0587" Parameter: A <- "-71.0587" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.0012" Parameter: B <- "-35.0012" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0575" Parameter: C <- "-36.0575" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1955 TOTAL ENERGY = -71.0587 RDTITL> * VAN DER WAALS = -35.0012 ELECTROSTATIC = -36.0575 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1955" Parameter: CONF_N -> "8002" Comparing "1955" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1956" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765007 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770588 ATOM PAIRS WERE FOUND FOR ATOM LIST 42133 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30342 from a total of 770588 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1956 -73.28897 2.23028 0.57351 INTE EXTERN> -34.87949 -38.40948 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.289" Parameter: A <- "-73.289" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.8795" Parameter: B <- "-34.8795" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4095" Parameter: C <- "-38.4095" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1956 TOTAL ENERGY = -73.289 RDTITL> * VAN DER WAALS = -34.8795 ELECTROSTATIC = -38.4095 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1956" Parameter: CONF_N -> "8002" Comparing "1956" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1957" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770588 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767371 ATOM PAIRS WERE FOUND FOR ATOM LIST 42090 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30227 from a total of 767371 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1957 -73.30760 0.01863 0.67458 INTE EXTERN> -29.95809 -43.34951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3076" Parameter: A <- "-73.3076" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9581" Parameter: B <- "-29.9581" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3495" Parameter: C <- "-43.3495" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1957 TOTAL ENERGY = -73.3076 RDTITL> * VAN DER WAALS = -29.9581 ELECTROSTATIC = -43.3495 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1957" Parameter: CONF_N -> "8002" Comparing "1957" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1958" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767371 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765040 ATOM PAIRS WERE FOUND FOR ATOM LIST 42180 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30074 from a total of 765040 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1958 -70.14022 -3.16738 0.55333 INTE EXTERN> -32.56976 -37.57046 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1402" Parameter: A <- "-70.1402" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5698" Parameter: B <- "-32.5698" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5705" Parameter: C <- "-37.5705" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1958 TOTAL ENERGY = -70.1402 RDTITL> * VAN DER WAALS = -32.5698 ELECTROSTATIC = -37.5705 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1958" Parameter: CONF_N -> "8002" Comparing "1958" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1959" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765040 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765972 ATOM PAIRS WERE FOUND FOR ATOM LIST 42020 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29804 from a total of 765972 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1959 -72.03440 1.89418 0.59309 INTE EXTERN> -31.98085 -40.05356 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0344" Parameter: A <- "-72.0344" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9808" Parameter: B <- "-31.9808" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0536" Parameter: C <- "-40.0536" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1959 TOTAL ENERGY = -72.0344 RDTITL> * VAN DER WAALS = -31.9808 ELECTROSTATIC = -40.0536 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1959" Parameter: CONF_N -> "8002" Comparing "1959" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1960" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765972 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764261 ATOM PAIRS WERE FOUND FOR ATOM LIST 41892 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30195 from a total of 764261 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1960 -71.42541 -0.60899 0.60987 INTE EXTERN> -30.76143 -40.66398 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4254" Parameter: A <- "-71.4254" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7614" Parameter: B <- "-30.7614" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.664" Parameter: C <- "-40.664" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1960 TOTAL ENERGY = -71.4254 RDTITL> * VAN DER WAALS = -30.7614 ELECTROSTATIC = -40.664 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1960" Parameter: CONF_N -> "8002" Comparing "1960" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1961" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764261 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769106 ATOM PAIRS WERE FOUND FOR ATOM LIST 42190 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29822 from a total of 769106 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1961 -69.14526 -2.28015 0.54311 INTE EXTERN> -32.17250 -36.97276 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1453" Parameter: A <- "-69.1453" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1725" Parameter: B <- "-32.1725" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9728" Parameter: C <- "-36.9728" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1961 TOTAL ENERGY = -69.1453 RDTITL> * VAN DER WAALS = -32.1725 ELECTROSTATIC = -36.9728 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1961" Parameter: CONF_N -> "8002" Comparing "1961" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1962" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769106 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763780 ATOM PAIRS WERE FOUND FOR ATOM LIST 41935 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29988 from a total of 763780 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1962 -64.26223 -4.88303 0.66250 INTE EXTERN> -29.21056 -35.05167 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2622" Parameter: A <- "-64.2622" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2106" Parameter: B <- "-29.2106" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0517" Parameter: C <- "-35.0517" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1962 TOTAL ENERGY = -64.2622 RDTITL> * VAN DER WAALS = -29.2106 ELECTROSTATIC = -35.0517 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1962" Parameter: CONF_N -> "8002" Comparing "1962" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1963" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763780 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762826 ATOM PAIRS WERE FOUND FOR ATOM LIST 41881 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29628 from a total of 762826 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1963 -60.90009 -3.36214 0.53957 INTE EXTERN> -30.79483 -30.10525 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.9001" Parameter: A <- "-60.9001" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7948" Parameter: B <- "-30.7948" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.1053" Parameter: C <- "-30.1053" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1963 TOTAL ENERGY = -60.9001 RDTITL> * VAN DER WAALS = -30.7948 ELECTROSTATIC = -30.1053 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1963" Parameter: CONF_N -> "8002" Comparing "1963" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1964" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762826 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766754 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30631 from a total of 766754 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1964 -70.93908 10.03900 0.60491 INTE EXTERN> -32.69110 -38.24798 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9391" Parameter: A <- "-70.9391" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6911" Parameter: B <- "-32.6911" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.248" Parameter: C <- "-38.248" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1964 TOTAL ENERGY = -70.9391 RDTITL> * VAN DER WAALS = -32.6911 ELECTROSTATIC = -38.248 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1964" Parameter: CONF_N -> "8002" Comparing "1964" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1965" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766754 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763749 ATOM PAIRS WERE FOUND FOR ATOM LIST 41823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30568 from a total of 763749 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1965 -70.41947 -0.51961 0.51531 INTE EXTERN> -34.34560 -36.07387 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4195" Parameter: A <- "-70.4195" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3456" Parameter: B <- "-34.3456" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0739" Parameter: C <- "-36.0739" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1965 TOTAL ENERGY = -70.4195 RDTITL> * VAN DER WAALS = -34.3456 ELECTROSTATIC = -36.0739 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1965" Parameter: CONF_N -> "8002" Comparing "1965" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1966" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763749 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41791 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29276 from a total of 760586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1966 -63.97204 -6.44743 0.54885 INTE EXTERN> -32.43261 -31.53943 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.972" Parameter: A <- "-63.972" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4326" Parameter: B <- "-32.4326" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.5394" Parameter: C <- "-31.5394" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1966 TOTAL ENERGY = -63.972 RDTITL> * VAN DER WAALS = -32.4326 ELECTROSTATIC = -31.5394 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1966" Parameter: CONF_N -> "8002" Comparing "1966" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1967" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761669 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29864 from a total of 761669 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1967 -63.94272 -0.02932 0.51485 INTE EXTERN> -34.48685 -29.45587 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.9427" Parameter: A <- "-63.9427" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.4869" Parameter: B <- "-34.4869" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.4559" Parameter: C <- "-29.4559" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1967 TOTAL ENERGY = -63.9427 RDTITL> * VAN DER WAALS = -34.4869 ELECTROSTATIC = -29.4559 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1967" Parameter: CONF_N -> "8002" Comparing "1967" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1968" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761669 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759257 ATOM PAIRS WERE FOUND FOR ATOM LIST 41778 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30423 from a total of 759257 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1968 -68.40522 4.46250 0.49559 INTE EXTERN> -32.52835 -35.87687 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4052" Parameter: A <- "-68.4052" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5283" Parameter: B <- "-32.5283" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8769" Parameter: C <- "-35.8769" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1968 TOTAL ENERGY = -68.4052 RDTITL> * VAN DER WAALS = -32.5283 ELECTROSTATIC = -35.8769 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1968" Parameter: CONF_N -> "8002" Comparing "1968" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1969" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759257 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763058 ATOM PAIRS WERE FOUND FOR ATOM LIST 42089 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30251 from a total of 763058 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1969 -66.57058 -1.83463 0.56265 INTE EXTERN> -31.13240 -35.43818 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5706" Parameter: A <- "-66.5706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1324" Parameter: B <- "-31.1324" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4382" Parameter: C <- "-35.4382" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1969 TOTAL ENERGY = -66.5706 RDTITL> * VAN DER WAALS = -31.1324 ELECTROSTATIC = -35.4382 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1969" Parameter: CONF_N -> "8002" Comparing "1969" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1970" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763058 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763694 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29947 from a total of 763694 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1970 -63.53188 -3.03870 0.55972 INTE EXTERN> -31.90424 -31.62764 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5319" Parameter: A <- "-63.5319" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9042" Parameter: B <- "-31.9042" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.6276" Parameter: C <- "-31.6276" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1970 TOTAL ENERGY = -63.5319 RDTITL> * VAN DER WAALS = -31.9042 ELECTROSTATIC = -31.6276 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1970" Parameter: CONF_N -> "8002" Comparing "1970" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1971" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763694 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764373 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29844 from a total of 764373 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1971 -65.21545 1.68357 0.48491 INTE EXTERN> -33.73604 -31.47941 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2154" Parameter: A <- "-65.2154" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.736" Parameter: B <- "-33.736" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4794" Parameter: C <- "-31.4794" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1971 TOTAL ENERGY = -65.2154 RDTITL> * VAN DER WAALS = -33.736 ELECTROSTATIC = -31.4794 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1971" Parameter: CONF_N -> "8002" Comparing "1971" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1972" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764373 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766912 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29778 from a total of 766912 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1972 -66.41654 1.20109 0.49772 INTE EXTERN> -35.04327 -31.37327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4165" Parameter: A <- "-66.4165" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.0433" Parameter: B <- "-35.0433" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.3733" Parameter: C <- "-31.3733" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1972 TOTAL ENERGY = -66.4165 RDTITL> * VAN DER WAALS = -35.0433 ELECTROSTATIC = -31.3733 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1972" Parameter: CONF_N -> "8002" Comparing "1972" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1973" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766912 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772397 ATOM PAIRS WERE FOUND FOR ATOM LIST 42430 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30365 from a total of 772397 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1973 -66.62324 0.20670 0.69099 INTE EXTERN> -29.87225 -36.75099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6232" Parameter: A <- "-66.6232" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8722" Parameter: B <- "-29.8722" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.751" Parameter: C <- "-36.751" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1973 TOTAL ENERGY = -66.6232 RDTITL> * VAN DER WAALS = -29.8722 ELECTROSTATIC = -36.751 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1973" Parameter: CONF_N -> "8002" Comparing "1973" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1974" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772397 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769995 ATOM PAIRS WERE FOUND FOR ATOM LIST 42347 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29320 from a total of 769995 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1974 -66.66307 0.03983 0.57317 INTE EXTERN> -29.85036 -36.81271 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6631" Parameter: A <- "-66.6631" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8504" Parameter: B <- "-29.8504" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8127" Parameter: C <- "-36.8127" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1974 TOTAL ENERGY = -66.6631 RDTITL> * VAN DER WAALS = -29.8504 ELECTROSTATIC = -36.8127 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1974" Parameter: CONF_N -> "8002" Comparing "1974" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1975" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769995 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763521 ATOM PAIRS WERE FOUND FOR ATOM LIST 42012 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30009 from a total of 763521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1975 -67.45594 0.79287 0.62089 INTE EXTERN> -28.48380 -38.97214 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4559" Parameter: A <- "-67.4559" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4838" Parameter: B <- "-28.4838" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9721" Parameter: C <- "-38.9721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1975 TOTAL ENERGY = -67.4559 RDTITL> * VAN DER WAALS = -28.4838 ELECTROSTATIC = -38.9721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1975" Parameter: CONF_N -> "8002" Comparing "1975" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1976" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762847 ATOM PAIRS WERE FOUND FOR ATOM LIST 41844 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29227 from a total of 762847 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1976 -63.92245 -3.53349 0.52636 INTE EXTERN> -29.78364 -34.13881 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.9224" Parameter: A <- "-63.9224" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7836" Parameter: B <- "-29.7836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1388" Parameter: C <- "-34.1388" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1976 TOTAL ENERGY = -63.9224 RDTITL> * VAN DER WAALS = -29.7836 ELECTROSTATIC = -34.1388 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1976" Parameter: CONF_N -> "8002" Comparing "1976" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1977" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762847 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767005 ATOM PAIRS WERE FOUND FOR ATOM LIST 42157 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29709 from a total of 767005 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1977 -69.57802 5.65557 0.54048 INTE EXTERN> -33.24967 -36.32834 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.578" Parameter: A <- "-69.578" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2497" Parameter: B <- "-33.2497" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3283" Parameter: C <- "-36.3283" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1977 TOTAL ENERGY = -69.578 RDTITL> * VAN DER WAALS = -33.2497 ELECTROSTATIC = -36.3283 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1977" Parameter: CONF_N -> "8002" Comparing "1977" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1978" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767005 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766540 ATOM PAIRS WERE FOUND FOR ATOM LIST 42322 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30242 from a total of 766540 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1978 -73.33262 3.75461 0.61055 INTE EXTERN> -32.79155 -40.54107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3326" Parameter: A <- "-73.3326" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7916" Parameter: B <- "-32.7916" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5411" Parameter: C <- "-40.5411" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1978 TOTAL ENERGY = -73.3326 RDTITL> * VAN DER WAALS = -32.7916 ELECTROSTATIC = -40.5411 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1978" Parameter: CONF_N -> "8002" Comparing "1978" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1979" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766540 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766193 ATOM PAIRS WERE FOUND FOR ATOM LIST 42092 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29924 from a total of 766193 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1979 -66.62527 -6.70736 0.58771 INTE EXTERN> -31.53723 -35.08803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6253" Parameter: A <- "-66.6253" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5372" Parameter: B <- "-31.5372" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.088" Parameter: C <- "-35.088" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1979 TOTAL ENERGY = -66.6253 RDTITL> * VAN DER WAALS = -31.5372 ELECTROSTATIC = -35.088 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1979" Parameter: CONF_N -> "8002" Comparing "1979" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1980" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766193 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768591 ATOM PAIRS WERE FOUND FOR ATOM LIST 42290 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30115 from a total of 768591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1980 -70.79509 4.16983 0.58476 INTE EXTERN> -31.34755 -39.44755 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7951" Parameter: A <- "-70.7951" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3475" Parameter: B <- "-31.3475" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4475" Parameter: C <- "-39.4475" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1980 TOTAL ENERGY = -70.7951 RDTITL> * VAN DER WAALS = -31.3475 ELECTROSTATIC = -39.4475 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1980" Parameter: CONF_N -> "8002" Comparing "1980" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1981" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765663 ATOM PAIRS WERE FOUND FOR ATOM LIST 42131 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30066 from a total of 765663 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1981 -64.09181 -6.70328 0.54304 INTE EXTERN> -32.18152 -31.91029 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0918" Parameter: A <- "-64.0918" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1815" Parameter: B <- "-32.1815" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.9103" Parameter: C <- "-31.9103" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1981 TOTAL ENERGY = -64.0918 RDTITL> * VAN DER WAALS = -32.1815 ELECTROSTATIC = -31.9103 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1981" Parameter: CONF_N -> "8002" Comparing "1981" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1982" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765663 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762876 ATOM PAIRS WERE FOUND FOR ATOM LIST 41806 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29741 from a total of 762876 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1982 -64.03657 -0.05524 0.59540 INTE EXTERN> -32.58419 -31.45238 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0366" Parameter: A <- "-64.0366" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5842" Parameter: B <- "-32.5842" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4524" Parameter: C <- "-31.4524" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1982 TOTAL ENERGY = -64.0366 RDTITL> * VAN DER WAALS = -32.5842 ELECTROSTATIC = -31.4524 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1982" Parameter: CONF_N -> "8002" Comparing "1982" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1983" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762876 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770662 ATOM PAIRS WERE FOUND FOR ATOM LIST 42274 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30221 from a total of 770662 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1983 -73.24135 9.20478 0.68552 INTE EXTERN> -29.11920 -44.12214 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2413" Parameter: A <- "-73.2413" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1192" Parameter: B <- "-29.1192" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1221" Parameter: C <- "-44.1221" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1983 TOTAL ENERGY = -73.2413 RDTITL> * VAN DER WAALS = -29.1192 ELECTROSTATIC = -44.1221 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1983" Parameter: CONF_N -> "8002" Comparing "1983" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1984" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770662 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763890 ATOM PAIRS WERE FOUND FOR ATOM LIST 42003 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29300 from a total of 763890 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1984 -67.69715 -5.54420 0.46634 INTE EXTERN> -33.55909 -34.13806 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6971" Parameter: A <- "-67.6971" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5591" Parameter: B <- "-33.5591" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1381" Parameter: C <- "-34.1381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1984 TOTAL ENERGY = -67.6971 RDTITL> * VAN DER WAALS = -33.5591 ELECTROSTATIC = -34.1381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1984" Parameter: CONF_N -> "8002" Comparing "1984" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1985" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763890 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760001 ATOM PAIRS WERE FOUND FOR ATOM LIST 41800 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29252 from a total of 760001 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1985 -70.07478 2.37763 0.52698 INTE EXTERN> -34.97333 -35.10145 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0748" Parameter: A <- "-70.0748" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9733" Parameter: B <- "-34.9733" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1014" Parameter: C <- "-35.1014" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1985 TOTAL ENERGY = -70.0748 RDTITL> * VAN DER WAALS = -34.9733 ELECTROSTATIC = -35.1014 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1985" Parameter: CONF_N -> "8002" Comparing "1985" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1986" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760001 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772876 ATOM PAIRS WERE FOUND FOR ATOM LIST 42567 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30188 from a total of 772876 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1986 -66.14693 -3.92785 0.51488 INTE EXTERN> -34.67139 -31.47553 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1469" Parameter: A <- "-66.1469" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6714" Parameter: B <- "-34.6714" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4755" Parameter: C <- "-31.4755" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1986 TOTAL ENERGY = -66.1469 RDTITL> * VAN DER WAALS = -34.6714 ELECTROSTATIC = -31.4755 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1986" Parameter: CONF_N -> "8002" Comparing "1986" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1987" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772876 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771763 ATOM PAIRS WERE FOUND FOR ATOM LIST 42452 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30208 from a total of 771763 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1987 -66.05888 -0.08804 0.56946 INTE EXTERN> -32.57704 -33.48184 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0589" Parameter: A <- "-66.0589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.577" Parameter: B <- "-32.577" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.4818" Parameter: C <- "-33.4818" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1987 TOTAL ENERGY = -66.0589 RDTITL> * VAN DER WAALS = -32.577 ELECTROSTATIC = -33.4818 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1987" Parameter: CONF_N -> "8002" Comparing "1987" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1988" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771763 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765900 ATOM PAIRS WERE FOUND FOR ATOM LIST 42132 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30111 from a total of 765900 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1988 -66.85041 0.79152 0.50279 INTE EXTERN> -36.00144 -30.84897 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8504" Parameter: A <- "-66.8504" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.0014" Parameter: B <- "-36.0014" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.849" Parameter: C <- "-30.849" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1988 TOTAL ENERGY = -66.8504 RDTITL> * VAN DER WAALS = -36.0014 ELECTROSTATIC = -30.849 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1988" Parameter: CONF_N -> "8002" Comparing "1988" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1989" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765900 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766790 ATOM PAIRS WERE FOUND FOR ATOM LIST 42055 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29816 from a total of 766790 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1989 -70.33184 3.48143 0.63447 INTE EXTERN> -30.40425 -39.92759 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3318" Parameter: A <- "-70.3318" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4043" Parameter: B <- "-30.4043" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9276" Parameter: C <- "-39.9276" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1989 TOTAL ENERGY = -70.3318 RDTITL> * VAN DER WAALS = -30.4043 ELECTROSTATIC = -39.9276 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1989" Parameter: CONF_N -> "8002" Comparing "1989" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1990" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766790 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766751 ATOM PAIRS WERE FOUND FOR ATOM LIST 42080 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30203 from a total of 766751 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1990 -68.86225 -1.46958 0.58950 INTE EXTERN> -30.10161 -38.76064 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8623" Parameter: A <- "-68.8623" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1016" Parameter: B <- "-30.1016" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7606" Parameter: C <- "-38.7606" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1990 TOTAL ENERGY = -68.8623 RDTITL> * VAN DER WAALS = -30.1016 ELECTROSTATIC = -38.7606 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1990" Parameter: CONF_N -> "8002" Comparing "1990" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1991" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766751 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769085 ATOM PAIRS WERE FOUND FOR ATOM LIST 42324 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30626 from a total of 769085 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1991 -66.01446 -2.84779 0.57275 INTE EXTERN> -31.39347 -34.62099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0145" Parameter: A <- "-66.0145" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3935" Parameter: B <- "-31.3935" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.621" Parameter: C <- "-34.621" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1991 TOTAL ENERGY = -66.0145 RDTITL> * VAN DER WAALS = -31.3935 ELECTROSTATIC = -34.621 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1991" Parameter: CONF_N -> "8002" Comparing "1991" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1992" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769085 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766987 ATOM PAIRS WERE FOUND FOR ATOM LIST 42299 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29969 from a total of 766987 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1992 -68.97669 2.96223 0.73255 INTE EXTERN> -28.12632 -40.85037 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9767" Parameter: A <- "-68.9767" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1263" Parameter: B <- "-28.1263" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8504" Parameter: C <- "-40.8504" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1992 TOTAL ENERGY = -68.9767 RDTITL> * VAN DER WAALS = -28.1263 ELECTROSTATIC = -40.8504 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1992" Parameter: CONF_N -> "8002" Comparing "1992" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1993" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766987 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764138 ATOM PAIRS WERE FOUND FOR ATOM LIST 42121 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29743 from a total of 764138 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1993 -75.61612 6.63943 0.59641 INTE EXTERN> -31.73716 -43.87896 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6161" Parameter: A <- "-75.6161" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7372" Parameter: B <- "-31.7372" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.879" Parameter: C <- "-43.879" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1993 TOTAL ENERGY = -75.6161 RDTITL> * VAN DER WAALS = -31.7372 ELECTROSTATIC = -43.879 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1993" Parameter: CONF_N -> "8002" Comparing "1993" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1994" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764138 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766525 ATOM PAIRS WERE FOUND FOR ATOM LIST 42024 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30264 from a total of 766525 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1994 -77.98402 2.36790 0.67612 INTE EXTERN> -30.94002 -47.04400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.984" Parameter: A <- "-77.984" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.94" Parameter: B <- "-30.94" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.044" Parameter: C <- "-47.044" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1994 TOTAL ENERGY = -77.984 RDTITL> * VAN DER WAALS = -30.94 ELECTROSTATIC = -47.044 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1994" Parameter: CONF_N -> "8002" Comparing "1994" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1995" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766525 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771784 ATOM PAIRS WERE FOUND FOR ATOM LIST 42352 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30678 from a total of 771784 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1995 -78.59574 0.61172 0.65305 INTE EXTERN> -32.05663 -46.53911 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5957" Parameter: A <- "-78.5957" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0566" Parameter: B <- "-32.0566" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5391" Parameter: C <- "-46.5391" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1995 TOTAL ENERGY = -78.5957 RDTITL> * VAN DER WAALS = -32.0566 ELECTROSTATIC = -46.5391 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1995" Parameter: CONF_N -> "8002" Comparing "1995" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1996" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771784 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767819 ATOM PAIRS WERE FOUND FOR ATOM LIST 42155 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30429 from a total of 767819 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1996 -77.65584 -0.93989 0.65554 INTE EXTERN> -30.32163 -47.33422 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6558" Parameter: A <- "-77.6558" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3216" Parameter: B <- "-30.3216" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3342" Parameter: C <- "-47.3342" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1996 TOTAL ENERGY = -77.6558 RDTITL> * VAN DER WAALS = -30.3216 ELECTROSTATIC = -47.3342 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1996" Parameter: CONF_N -> "8002" Comparing "1996" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1997" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767819 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767829 ATOM PAIRS WERE FOUND FOR ATOM LIST 42172 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30093 from a total of 767829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1997 -75.81070 -1.84515 0.71698 INTE EXTERN> -28.53409 -47.27661 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8107" Parameter: A <- "-75.8107" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5341" Parameter: B <- "-28.5341" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2766" Parameter: C <- "-47.2766" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1997 TOTAL ENERGY = -75.8107 RDTITL> * VAN DER WAALS = -28.5341 ELECTROSTATIC = -47.2766 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1997" Parameter: CONF_N -> "8002" Comparing "1997" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1998" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770500 ATOM PAIRS WERE FOUND FOR ATOM LIST 42427 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30364 from a total of 770500 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1998 -74.63510 -1.17560 0.58653 INTE EXTERN> -31.92032 -42.71478 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6351" Parameter: A <- "-74.6351" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9203" Parameter: B <- "-31.9203" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7148" Parameter: C <- "-42.7148" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1998 TOTAL ENERGY = -74.6351 RDTITL> * VAN DER WAALS = -31.9203 ELECTROSTATIC = -42.7148 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1998" Parameter: CONF_N -> "8002" Comparing "1998" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "1999" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770500 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764624 ATOM PAIRS WERE FOUND FOR ATOM LIST 42150 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29753 from a total of 764624 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 1999 -76.89051 2.25541 0.64426 INTE EXTERN> -30.36013 -46.53038 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8905" Parameter: A <- "-76.8905" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3601" Parameter: B <- "-30.3601" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5304" Parameter: C <- "-46.5304" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 1999 TOTAL ENERGY = -76.8905 RDTITL> * VAN DER WAALS = -30.3601 ELECTROSTATIC = -46.5304 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "1999" Parameter: CONF_N -> "8002" Comparing "1999" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2000" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764624 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761181 ATOM PAIRS WERE FOUND FOR ATOM LIST 41756 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29465 from a total of 761181 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2000 -72.63854 -4.25196 0.62930 INTE EXTERN> -30.42234 -42.21620 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6385" Parameter: A <- "-72.6385" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4223" Parameter: B <- "-30.4223" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2162" Parameter: C <- "-42.2162" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2000 TOTAL ENERGY = -72.6385 RDTITL> * VAN DER WAALS = -30.4223 ELECTROSTATIC = -42.2162 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2000" Parameter: CONF_N -> "8002" Comparing "2000" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2001" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761181 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 773643 ATOM PAIRS WERE FOUND FOR ATOM LIST 42511 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30197 from a total of 773643 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2001 -73.08223 0.44368 0.62297 INTE EXTERN> -32.54468 -40.53755 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0822" Parameter: A <- "-73.0822" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5447" Parameter: B <- "-32.5447" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5375" Parameter: C <- "-40.5375" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2001 TOTAL ENERGY = -73.0822 RDTITL> * VAN DER WAALS = -32.5447 ELECTROSTATIC = -40.5375 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2001" Parameter: CONF_N -> "8002" Comparing "2001" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2002" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 773643 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768372 ATOM PAIRS WERE FOUND FOR ATOM LIST 42361 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29372 from a total of 768372 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2002 -70.31750 -2.76472 0.58136 INTE EXTERN> -27.82961 -42.48789 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3175" Parameter: A <- "-70.3175" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8296" Parameter: B <- "-27.8296" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4879" Parameter: C <- "-42.4879" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2002 TOTAL ENERGY = -70.3175 RDTITL> * VAN DER WAALS = -27.8296 ELECTROSTATIC = -42.4879 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2002" Parameter: CONF_N -> "8002" Comparing "2002" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2003" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768372 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758585 ATOM PAIRS WERE FOUND FOR ATOM LIST 41789 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29815 from a total of 758585 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2003 -68.99770 -1.31980 0.63755 INTE EXTERN> -30.34041 -38.65729 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9977" Parameter: A <- "-68.9977" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3404" Parameter: B <- "-30.3404" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6573" Parameter: C <- "-38.6573" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2003 TOTAL ENERGY = -68.9977 RDTITL> * VAN DER WAALS = -30.3404 ELECTROSTATIC = -38.6573 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2003" Parameter: CONF_N -> "8002" Comparing "2003" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2004" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758585 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761347 ATOM PAIRS WERE FOUND FOR ATOM LIST 41956 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30034 from a total of 761347 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2004 -72.63747 3.63976 0.58313 INTE EXTERN> -34.89683 -37.74064 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6375" Parameter: A <- "-72.6375" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.8968" Parameter: B <- "-34.8968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7406" Parameter: C <- "-37.7406" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2004 TOTAL ENERGY = -72.6375 RDTITL> * VAN DER WAALS = -34.8968 ELECTROSTATIC = -37.7406 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2004" Parameter: CONF_N -> "8002" Comparing "2004" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2005" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761347 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767944 ATOM PAIRS WERE FOUND FOR ATOM LIST 42288 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29959 from a total of 767944 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2005 -73.61364 0.97617 0.64601 INTE EXTERN> -29.00995 -44.60369 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6136" Parameter: A <- "-73.6136" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0099" Parameter: B <- "-29.0099" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6037" Parameter: C <- "-44.6037" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2005 TOTAL ENERGY = -73.6136 RDTITL> * VAN DER WAALS = -29.0099 ELECTROSTATIC = -44.6037 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2005" Parameter: CONF_N -> "8002" Comparing "2005" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2006" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767944 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764196 ATOM PAIRS WERE FOUND FOR ATOM LIST 42057 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30181 from a total of 764196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2006 -71.76211 -1.85153 0.66372 INTE EXTERN> -31.55722 -40.20489 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7621" Parameter: A <- "-71.7621" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5572" Parameter: B <- "-31.5572" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2049" Parameter: C <- "-40.2049" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2006 TOTAL ENERGY = -71.7621 RDTITL> * VAN DER WAALS = -31.5572 ELECTROSTATIC = -40.2049 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2006" Parameter: CONF_N -> "8002" Comparing "2006" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2007" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767310 ATOM PAIRS WERE FOUND FOR ATOM LIST 42187 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30302 from a total of 767310 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2007 -64.80639 -6.95572 0.58985 INTE EXTERN> -31.63239 -33.17400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8064" Parameter: A <- "-64.8064" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6324" Parameter: B <- "-31.6324" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.174" Parameter: C <- "-33.174" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2007 TOTAL ENERGY = -64.8064 RDTITL> * VAN DER WAALS = -31.6324 ELECTROSTATIC = -33.174 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2007" Parameter: CONF_N -> "8002" Comparing "2007" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2008" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767310 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765073 ATOM PAIRS WERE FOUND FOR ATOM LIST 42020 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29674 from a total of 765073 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2008 -65.57791 0.77152 0.56034 INTE EXTERN> -30.15613 -35.42179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5779" Parameter: A <- "-65.5779" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1561" Parameter: B <- "-30.1561" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4218" Parameter: C <- "-35.4218" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2008 TOTAL ENERGY = -65.5779 RDTITL> * VAN DER WAALS = -30.1561 ELECTROSTATIC = -35.4218 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2008" Parameter: CONF_N -> "8002" Comparing "2008" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2009" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765073 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772105 ATOM PAIRS WERE FOUND FOR ATOM LIST 42511 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30143 from a total of 772105 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2009 -73.66708 8.08917 0.56519 INTE EXTERN> -33.28025 -40.38683 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6671" Parameter: A <- "-73.6671" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2802" Parameter: B <- "-33.2802" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3868" Parameter: C <- "-40.3868" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2009 TOTAL ENERGY = -73.6671 RDTITL> * VAN DER WAALS = -33.2802 ELECTROSTATIC = -40.3868 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2009" Parameter: CONF_N -> "8002" Comparing "2009" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2010" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772105 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768074 ATOM PAIRS WERE FOUND FOR ATOM LIST 42155 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30138 from a total of 768074 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2010 -66.77880 -6.88828 0.56971 INTE EXTERN> -31.42616 -35.35263 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7788" Parameter: A <- "-66.7788" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4262" Parameter: B <- "-31.4262" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3526" Parameter: C <- "-35.3526" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2010 TOTAL ENERGY = -66.7788 RDTITL> * VAN DER WAALS = -31.4262 ELECTROSTATIC = -35.3526 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2010" Parameter: CONF_N -> "8002" Comparing "2010" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2011" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768074 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766097 ATOM PAIRS WERE FOUND FOR ATOM LIST 42356 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29740 from a total of 766097 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2011 -65.35293 -1.42587 0.50153 INTE EXTERN> -33.22193 -32.13100 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3529" Parameter: A <- "-65.3529" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2219" Parameter: B <- "-33.2219" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.131" Parameter: C <- "-32.131" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2011 TOTAL ENERGY = -65.3529 RDTITL> * VAN DER WAALS = -33.2219 ELECTROSTATIC = -32.131 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2011" Parameter: CONF_N -> "8002" Comparing "2011" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2012" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766097 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767783 ATOM PAIRS WERE FOUND FOR ATOM LIST 42101 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29964 from a total of 767783 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2012 -63.72184 -1.63108 0.59229 INTE EXTERN> -31.65942 -32.06242 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7218" Parameter: A <- "-63.7218" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6594" Parameter: B <- "-31.6594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.0624" Parameter: C <- "-32.0624" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2012 TOTAL ENERGY = -63.7218 RDTITL> * VAN DER WAALS = -31.6594 ELECTROSTATIC = -32.0624 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2012" Parameter: CONF_N -> "8002" Comparing "2012" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2013" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767783 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766941 ATOM PAIRS WERE FOUND FOR ATOM LIST 42048 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30303 from a total of 766941 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2013 -67.21079 3.48894 0.71621 INTE EXTERN> -29.01525 -38.19554 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2108" Parameter: A <- "-67.2108" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0153" Parameter: B <- "-29.0153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1955" Parameter: C <- "-38.1955" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2013 TOTAL ENERGY = -67.2108 RDTITL> * VAN DER WAALS = -29.0153 ELECTROSTATIC = -38.1955 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2013" Parameter: CONF_N -> "8002" Comparing "2013" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2014" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766941 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 773664 ATOM PAIRS WERE FOUND FOR ATOM LIST 42472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 31003 from a total of 773664 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2014 -65.79308 -1.41771 0.70342 INTE EXTERN> -24.94229 -40.85079 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7931" Parameter: A <- "-65.7931" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9423" Parameter: B <- "-24.9423" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8508" Parameter: C <- "-40.8508" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2014 TOTAL ENERGY = -65.7931 RDTITL> * VAN DER WAALS = -24.9423 ELECTROSTATIC = -40.8508 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2014" Parameter: CONF_N -> "8002" Comparing "2014" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2015" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 773664 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763748 ATOM PAIRS WERE FOUND FOR ATOM LIST 42039 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29168 from a total of 763748 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2015 -67.36879 1.57571 0.54490 INTE EXTERN> -30.52589 -36.84290 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3688" Parameter: A <- "-67.3688" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5259" Parameter: B <- "-30.5259" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8429" Parameter: C <- "-36.8429" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2015 TOTAL ENERGY = -67.3688 RDTITL> * VAN DER WAALS = -30.5259 ELECTROSTATIC = -36.8429 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2015" Parameter: CONF_N -> "8002" Comparing "2015" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2016" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763748 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758575 ATOM PAIRS WERE FOUND FOR ATOM LIST 41814 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30082 from a total of 758575 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2016 -66.48336 -0.88543 0.58117 INTE EXTERN> -30.68825 -35.79511 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4834" Parameter: A <- "-66.4834" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6882" Parameter: B <- "-30.6882" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7951" Parameter: C <- "-35.7951" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2016 TOTAL ENERGY = -66.4834 RDTITL> * VAN DER WAALS = -30.6882 ELECTROSTATIC = -35.7951 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2016" Parameter: CONF_N -> "8002" Comparing "2016" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2017" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758575 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761742 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29671 from a total of 761742 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2017 -69.77337 3.29001 0.64874 INTE EXTERN> -28.57469 -41.19868 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7734" Parameter: A <- "-69.7734" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5747" Parameter: B <- "-28.5747" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1987" Parameter: C <- "-41.1987" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2017 TOTAL ENERGY = -69.7734 RDTITL> * VAN DER WAALS = -28.5747 ELECTROSTATIC = -41.1987 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2017" Parameter: CONF_N -> "8002" Comparing "2017" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2018" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761742 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766360 ATOM PAIRS WERE FOUND FOR ATOM LIST 42229 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30263 from a total of 766360 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2018 -76.30197 6.52860 0.78400 INTE EXTERN> -26.03439 -50.26758 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.302" Parameter: A <- "-76.302" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0344" Parameter: B <- "-26.0344" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2676" Parameter: C <- "-50.2676" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2018 TOTAL ENERGY = -76.302 RDTITL> * VAN DER WAALS = -26.0344 ELECTROSTATIC = -50.2676 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2018" Parameter: CONF_N -> "8002" Comparing "2018" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2019" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766360 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759632 ATOM PAIRS WERE FOUND FOR ATOM LIST 41758 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30247 from a total of 759632 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2019 -75.68239 -0.61958 0.74135 INTE EXTERN> -29.93511 -45.74728 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6824" Parameter: A <- "-75.6824" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9351" Parameter: B <- "-29.9351" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7473" Parameter: C <- "-45.7473" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2019 TOTAL ENERGY = -75.6824 RDTITL> * VAN DER WAALS = -29.9351 ELECTROSTATIC = -45.7473 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2019" Parameter: CONF_N -> "8002" Comparing "2019" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2020" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759632 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756568 ATOM PAIRS WERE FOUND FOR ATOM LIST 41622 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29994 from a total of 756568 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2020 -65.15139 -10.53100 0.65109 INTE EXTERN> -30.08100 -35.07038 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1514" Parameter: A <- "-65.1514" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.081" Parameter: B <- "-30.081" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0704" Parameter: C <- "-35.0704" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2020 TOTAL ENERGY = -65.1514 RDTITL> * VAN DER WAALS = -30.081 ELECTROSTATIC = -35.0704 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2020" Parameter: CONF_N -> "8002" Comparing "2020" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2021" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756568 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764372 ATOM PAIRS WERE FOUND FOR ATOM LIST 42131 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30114 from a total of 764372 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2021 -70.05912 4.90773 0.64748 INTE EXTERN> -33.06552 -36.99360 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0591" Parameter: A <- "-70.0591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0655" Parameter: B <- "-33.0655" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9936" Parameter: C <- "-36.9936" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2021 TOTAL ENERGY = -70.0591 RDTITL> * VAN DER WAALS = -33.0655 ELECTROSTATIC = -36.9936 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2021" Parameter: CONF_N -> "8002" Comparing "2021" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2022" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764372 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764561 ATOM PAIRS WERE FOUND FOR ATOM LIST 42010 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30623 from a total of 764561 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2022 -72.92039 2.86128 0.67403 INTE EXTERN> -28.46352 -44.45687 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9204" Parameter: A <- "-72.9204" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4635" Parameter: B <- "-28.4635" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4569" Parameter: C <- "-44.4569" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2022 TOTAL ENERGY = -72.9204 RDTITL> * VAN DER WAALS = -28.4635 ELECTROSTATIC = -44.4569 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2022" Parameter: CONF_N -> "8002" Comparing "2022" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2023" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764561 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41890 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30545 from a total of 760118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2023 -67.16599 -5.75441 0.66991 INTE EXTERN> -26.84842 -40.31757 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.166" Parameter: A <- "-67.166" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8484" Parameter: B <- "-26.8484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3176" Parameter: C <- "-40.3176" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2023 TOTAL ENERGY = -67.166 RDTITL> * VAN DER WAALS = -26.8484 ELECTROSTATIC = -40.3176 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2023" Parameter: CONF_N -> "8002" Comparing "2023" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2024" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762579 ATOM PAIRS WERE FOUND FOR ATOM LIST 42018 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30423 from a total of 762579 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2024 -73.80393 6.63795 0.53940 INTE EXTERN> -34.91044 -38.89349 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8039" Parameter: A <- "-73.8039" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9104" Parameter: B <- "-34.9104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8935" Parameter: C <- "-38.8935" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2024 TOTAL ENERGY = -73.8039 RDTITL> * VAN DER WAALS = -34.9104 ELECTROSTATIC = -38.8935 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2024" Parameter: CONF_N -> "8002" Comparing "2024" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2025" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762579 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758462 ATOM PAIRS WERE FOUND FOR ATOM LIST 41583 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30201 from a total of 758462 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2025 -66.64727 -7.15667 0.69345 INTE EXTERN> -25.97168 -40.67559 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6473" Parameter: A <- "-66.6473" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9717" Parameter: B <- "-25.9717" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6756" Parameter: C <- "-40.6756" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2025 TOTAL ENERGY = -66.6473 RDTITL> * VAN DER WAALS = -25.9717 ELECTROSTATIC = -40.6756 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2025" Parameter: CONF_N -> "8002" Comparing "2025" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2026" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758462 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761705 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29962 from a total of 761705 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2026 -75.61068 8.96341 0.77227 INTE EXTERN> -26.19071 -49.41997 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6107" Parameter: A <- "-75.6107" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1907" Parameter: B <- "-26.1907" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.42" Parameter: C <- "-49.42" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2026 TOTAL ENERGY = -75.6107 RDTITL> * VAN DER WAALS = -26.1907 ELECTROSTATIC = -49.42 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2026" Parameter: CONF_N -> "8002" Comparing "2026" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2027" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761705 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766210 ATOM PAIRS WERE FOUND FOR ATOM LIST 42270 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30288 from a total of 766210 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2027 -70.56760 -5.04308 0.62694 INTE EXTERN> -31.68877 -38.87883 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5676" Parameter: A <- "-70.5676" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6888" Parameter: B <- "-31.6888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8788" Parameter: C <- "-38.8788" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2027 TOTAL ENERGY = -70.5676 RDTITL> * VAN DER WAALS = -31.6888 ELECTROSTATIC = -38.8788 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2027" Parameter: CONF_N -> "8002" Comparing "2027" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2028" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766210 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765594 ATOM PAIRS WERE FOUND FOR ATOM LIST 42078 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29621 from a total of 765594 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2028 -68.77272 -1.79488 0.82387 INTE EXTERN> -22.60096 -46.17177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7727" Parameter: A <- "-68.7727" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.601" Parameter: B <- "-22.601" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1718" Parameter: C <- "-46.1718" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2028 TOTAL ENERGY = -68.7727 RDTITL> * VAN DER WAALS = -22.601 ELECTROSTATIC = -46.1718 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2028" Parameter: CONF_N -> "8002" Comparing "2028" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2029" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765594 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759606 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29931 from a total of 759606 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2029 -67.38437 -1.38835 0.68814 INTE EXTERN> -27.86714 -39.51723 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3844" Parameter: A <- "-67.3844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8671" Parameter: B <- "-27.8671" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5172" Parameter: C <- "-39.5172" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2029 TOTAL ENERGY = -67.3844 RDTITL> * VAN DER WAALS = -27.8671 ELECTROSTATIC = -39.5172 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2029" Parameter: CONF_N -> "8002" Comparing "2029" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2030" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759606 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767360 ATOM PAIRS WERE FOUND FOR ATOM LIST 41930 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29940 from a total of 767360 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2030 -67.27281 -0.11156 0.60281 INTE EXTERN> -32.41390 -34.85891 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2728" Parameter: A <- "-67.2728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4139" Parameter: B <- "-32.4139" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8589" Parameter: C <- "-34.8589" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2030 TOTAL ENERGY = -67.2728 RDTITL> * VAN DER WAALS = -32.4139 ELECTROSTATIC = -34.8589 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2030" Parameter: CONF_N -> "8002" Comparing "2030" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2031" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767360 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766593 ATOM PAIRS WERE FOUND FOR ATOM LIST 41860 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30211 from a total of 766593 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2031 -74.01432 6.74151 0.67361 INTE EXTERN> -30.92148 -43.09284 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0143" Parameter: A <- "-74.0143" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9215" Parameter: B <- "-30.9215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0928" Parameter: C <- "-43.0928" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2031 TOTAL ENERGY = -74.0143 RDTITL> * VAN DER WAALS = -30.9215 ELECTROSTATIC = -43.0928 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2031" Parameter: CONF_N -> "8002" Comparing "2031" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2032" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766593 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768352 ATOM PAIRS WERE FOUND FOR ATOM LIST 42062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30263 from a total of 768352 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2032 -71.30850 -2.70582 0.66594 INTE EXTERN> -28.24954 -43.05895 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3085" Parameter: A <- "-71.3085" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2495" Parameter: B <- "-28.2495" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.059" Parameter: C <- "-43.059" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2032 TOTAL ENERGY = -71.3085 RDTITL> * VAN DER WAALS = -28.2495 ELECTROSTATIC = -43.059 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2032" Parameter: CONF_N -> "8002" Comparing "2032" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2033" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768352 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770925 ATOM PAIRS WERE FOUND FOR ATOM LIST 42247 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30242 from a total of 770925 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2033 -71.08182 -0.22667 0.64507 INTE EXTERN> -31.38031 -39.70152 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0818" Parameter: A <- "-71.0818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3803" Parameter: B <- "-31.3803" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7015" Parameter: C <- "-39.7015" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2033 TOTAL ENERGY = -71.0818 RDTITL> * VAN DER WAALS = -31.3803 ELECTROSTATIC = -39.7015 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2033" Parameter: CONF_N -> "8002" Comparing "2033" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2034" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770925 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762859 ATOM PAIRS WERE FOUND FOR ATOM LIST 41876 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29390 from a total of 762859 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2034 -72.21196 1.13014 0.71188 INTE EXTERN> -29.22859 -42.98337 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.212" Parameter: A <- "-72.212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2286" Parameter: B <- "-29.2286" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9834" Parameter: C <- "-42.9834" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2034 TOTAL ENERGY = -72.212 RDTITL> * VAN DER WAALS = -29.2286 ELECTROSTATIC = -42.9834 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2034" Parameter: CONF_N -> "8002" Comparing "2034" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2035" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762859 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765546 ATOM PAIRS WERE FOUND FOR ATOM LIST 41898 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30303 from a total of 765546 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2035 -74.74163 2.52967 0.76114 INTE EXTERN> -26.78314 -47.95849 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7416" Parameter: A <- "-74.7416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7831" Parameter: B <- "-26.7831" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9585" Parameter: C <- "-47.9585" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2035 TOTAL ENERGY = -74.7416 RDTITL> * VAN DER WAALS = -26.7831 ELECTROSTATIC = -47.9585 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2035" Parameter: CONF_N -> "8002" Comparing "2035" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2036" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765546 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772179 ATOM PAIRS WERE FOUND FOR ATOM LIST 42449 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30201 from a total of 772179 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2036 -75.35925 0.61762 0.70852 INTE EXTERN> -27.92867 -47.43058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3593" Parameter: A <- "-75.3593" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9287" Parameter: B <- "-27.9287" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4306" Parameter: C <- "-47.4306" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2036 TOTAL ENERGY = -75.3593 RDTITL> * VAN DER WAALS = -27.9287 ELECTROSTATIC = -47.4306 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2036" Parameter: CONF_N -> "8002" Comparing "2036" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2037" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772179 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767174 ATOM PAIRS WERE FOUND FOR ATOM LIST 42072 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30072 from a total of 767174 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2037 -68.69478 -6.66447 0.71756 INTE EXTERN> -27.91794 -40.77684 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6948" Parameter: A <- "-68.6948" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9179" Parameter: B <- "-27.9179" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7768" Parameter: C <- "-40.7768" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2037 TOTAL ENERGY = -68.6948 RDTITL> * VAN DER WAALS = -27.9179 ELECTROSTATIC = -40.7768 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2037" Parameter: CONF_N -> "8002" Comparing "2037" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2038" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767174 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760439 ATOM PAIRS WERE FOUND FOR ATOM LIST 41849 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29732 from a total of 760439 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2038 -68.65839 -0.03639 0.60493 INTE EXTERN> -31.06353 -37.59486 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6584" Parameter: A <- "-68.6584" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0635" Parameter: B <- "-31.0635" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5949" Parameter: C <- "-37.5949" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2038 TOTAL ENERGY = -68.6584 RDTITL> * VAN DER WAALS = -31.0635 ELECTROSTATIC = -37.5949 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2038" Parameter: CONF_N -> "8002" Comparing "2038" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2039" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760439 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761353 ATOM PAIRS WERE FOUND FOR ATOM LIST 41680 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29557 from a total of 761353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2039 -69.74930 1.09091 0.70996 INTE EXTERN> -27.62506 -42.12424 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7493" Parameter: A <- "-69.7493" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6251" Parameter: B <- "-27.6251" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1242" Parameter: C <- "-42.1242" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2039 TOTAL ENERGY = -69.7493 RDTITL> * VAN DER WAALS = -27.6251 ELECTROSTATIC = -42.1242 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2039" Parameter: CONF_N -> "8002" Comparing "2039" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2040" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767909 ATOM PAIRS WERE FOUND FOR ATOM LIST 42083 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30168 from a total of 767909 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2040 -71.14886 1.39955 0.69531 INTE EXTERN> -26.18804 -44.96082 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1489" Parameter: A <- "-71.1489" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.188" Parameter: B <- "-26.188" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9608" Parameter: C <- "-44.9608" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2040 TOTAL ENERGY = -71.1489 RDTITL> * VAN DER WAALS = -26.188 ELECTROSTATIC = -44.9608 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2040" Parameter: CONF_N -> "8002" Comparing "2040" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2041" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767909 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770626 ATOM PAIRS WERE FOUND FOR ATOM LIST 42073 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30061 from a total of 770626 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2041 -64.12314 -7.02571 0.70728 INTE EXTERN> -25.14916 -38.97398 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1231" Parameter: A <- "-64.1231" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1492" Parameter: B <- "-25.1492" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.974" Parameter: C <- "-38.974" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2041 TOTAL ENERGY = -64.1231 RDTITL> * VAN DER WAALS = -25.1492 ELECTROSTATIC = -38.974 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2041" Parameter: CONF_N -> "8002" Comparing "2041" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2042" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770626 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767682 ATOM PAIRS WERE FOUND FOR ATOM LIST 42159 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29744 from a total of 767682 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2042 -76.20219 12.07905 0.70434 INTE EXTERN> -30.85808 -45.34411 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2022" Parameter: A <- "-76.2022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8581" Parameter: B <- "-30.8581" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3441" Parameter: C <- "-45.3441" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2042 TOTAL ENERGY = -76.2022 RDTITL> * VAN DER WAALS = -30.8581 ELECTROSTATIC = -45.3441 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2042" Parameter: CONF_N -> "8002" Comparing "2042" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2043" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767682 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761386 ATOM PAIRS WERE FOUND FOR ATOM LIST 41715 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29674 from a total of 761386 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2043 -71.95107 -4.25112 0.66511 INTE EXTERN> -26.75437 -45.19670 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9511" Parameter: A <- "-71.9511" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7544" Parameter: B <- "-26.7544" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1967" Parameter: C <- "-45.1967" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2043 TOTAL ENERGY = -71.9511 RDTITL> * VAN DER WAALS = -26.7544 ELECTROSTATIC = -45.1967 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2043" Parameter: CONF_N -> "8002" Comparing "2043" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2044" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761386 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767782 ATOM PAIRS WERE FOUND FOR ATOM LIST 41975 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29993 from a total of 767782 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2044 -64.54021 -7.41086 0.53340 INTE EXTERN> -31.38742 -33.15279 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5402" Parameter: A <- "-64.5402" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3874" Parameter: B <- "-31.3874" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1528" Parameter: C <- "-33.1528" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2044 TOTAL ENERGY = -64.5402 RDTITL> * VAN DER WAALS = -31.3874 ELECTROSTATIC = -33.1528 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2044" Parameter: CONF_N -> "8002" Comparing "2044" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2045" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767782 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766750 ATOM PAIRS WERE FOUND FOR ATOM LIST 42091 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29585 from a total of 766750 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2045 -70.79930 6.25909 0.62176 INTE EXTERN> -29.44867 -41.35063 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7993" Parameter: A <- "-70.7993" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4487" Parameter: B <- "-29.4487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3506" Parameter: C <- "-41.3506" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2045 TOTAL ENERGY = -70.7993 RDTITL> * VAN DER WAALS = -29.4487 ELECTROSTATIC = -41.3506 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2045" Parameter: CONF_N -> "8002" Comparing "2045" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2046" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766750 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764875 ATOM PAIRS WERE FOUND FOR ATOM LIST 42145 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29592 from a total of 764875 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2046 -70.99663 0.19733 0.66754 INTE EXTERN> -28.72147 -42.27516 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9966" Parameter: A <- "-70.9966" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7215" Parameter: B <- "-28.7215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2752" Parameter: C <- "-42.2752" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2046 TOTAL ENERGY = -70.9966 RDTITL> * VAN DER WAALS = -28.7215 ELECTROSTATIC = -42.2752 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2046" Parameter: CONF_N -> "8002" Comparing "2046" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2047" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764875 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765721 ATOM PAIRS WERE FOUND FOR ATOM LIST 41876 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29849 from a total of 765721 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2047 -77.16065 6.16402 0.61783 INTE EXTERN> -31.41874 -45.74191 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1606" Parameter: A <- "-77.1606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4187" Parameter: B <- "-31.4187" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7419" Parameter: C <- "-45.7419" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2047 TOTAL ENERGY = -77.1606 RDTITL> * VAN DER WAALS = -31.4187 ELECTROSTATIC = -45.7419 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2047" Parameter: CONF_N -> "8002" Comparing "2047" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2048" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765721 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759458 ATOM PAIRS WERE FOUND FOR ATOM LIST 41710 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29156 from a total of 759458 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2048 -78.26963 1.10899 0.73535 INTE EXTERN> -28.60174 -49.66789 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2696" Parameter: A <- "-78.2696" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6017" Parameter: B <- "-28.6017" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6679" Parameter: C <- "-49.6679" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2048 TOTAL ENERGY = -78.2696 RDTITL> * VAN DER WAALS = -28.6017 ELECTROSTATIC = -49.6679 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2048" Parameter: CONF_N -> "8002" Comparing "2048" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2049" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759458 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752480 ATOM PAIRS WERE FOUND FOR ATOM LIST 41338 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29264 from a total of 752480 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2049 -69.08319 -9.18644 0.64867 INTE EXTERN> -29.10650 -39.97669 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0832" Parameter: A <- "-69.0832" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1065" Parameter: B <- "-29.1065" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9767" Parameter: C <- "-39.9767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2049 TOTAL ENERGY = -69.0832 RDTITL> * VAN DER WAALS = -29.1065 ELECTROSTATIC = -39.9767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2049" Parameter: CONF_N -> "8002" Comparing "2049" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2050" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752480 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762041 ATOM PAIRS WERE FOUND FOR ATOM LIST 41921 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29639 from a total of 762041 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2050 -78.96525 9.88206 0.74022 INTE EXTERN> -25.84636 -53.11889 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9652" Parameter: A <- "-78.9652" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8464" Parameter: B <- "-25.8464" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.1189" Parameter: C <- "-53.1189" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2050 TOTAL ENERGY = -78.9652 RDTITL> * VAN DER WAALS = -25.8464 ELECTROSTATIC = -53.1189 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2050" Parameter: CONF_N -> "8002" Comparing "2050" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2051" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762041 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764725 ATOM PAIRS WERE FOUND FOR ATOM LIST 42048 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29639 from a total of 764725 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2051 -71.89376 -7.07149 0.62384 INTE EXTERN> -32.23710 -39.65666 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8938" Parameter: A <- "-71.8938" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2371" Parameter: B <- "-32.2371" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6567" Parameter: C <- "-39.6567" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2051 TOTAL ENERGY = -71.8938 RDTITL> * VAN DER WAALS = -32.2371 ELECTROSTATIC = -39.6567 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2051" Parameter: CONF_N -> "8002" Comparing "2051" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2052" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764725 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765772 ATOM PAIRS WERE FOUND FOR ATOM LIST 42219 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30057 from a total of 765772 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2052 -73.86424 1.97047 0.60960 INTE EXTERN> -33.78468 -40.07956 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8642" Parameter: A <- "-73.8642" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7847" Parameter: B <- "-33.7847" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0796" Parameter: C <- "-40.0796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2052 TOTAL ENERGY = -73.8642 RDTITL> * VAN DER WAALS = -33.7847 ELECTROSTATIC = -40.0796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2052" Parameter: CONF_N -> "8002" Comparing "2052" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2053" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765772 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758451 ATOM PAIRS WERE FOUND FOR ATOM LIST 41561 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29566 from a total of 758451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2053 -71.65157 -2.21266 0.64196 INTE EXTERN> -29.76249 -41.88909 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6516" Parameter: A <- "-71.6516" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7625" Parameter: B <- "-29.7625" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8891" Parameter: C <- "-41.8891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2053 TOTAL ENERGY = -71.6516 RDTITL> * VAN DER WAALS = -29.7625 ELECTROSTATIC = -41.8891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2053" Parameter: CONF_N -> "8002" Comparing "2053" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2054" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763569 ATOM PAIRS WERE FOUND FOR ATOM LIST 41593 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29486 from a total of 763569 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2054 -72.24771 0.59614 0.71560 INTE EXTERN> -26.47480 -45.77291 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2477" Parameter: A <- "-72.2477" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4748" Parameter: B <- "-26.4748" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7729" Parameter: C <- "-45.7729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2054 TOTAL ENERGY = -72.2477 RDTITL> * VAN DER WAALS = -26.4748 ELECTROSTATIC = -45.7729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2054" Parameter: CONF_N -> "8002" Comparing "2054" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2055" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763569 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766208 ATOM PAIRS WERE FOUND FOR ATOM LIST 42102 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29558 from a total of 766208 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2055 -75.34524 3.09753 0.63655 INTE EXTERN> -33.04071 -42.30453 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3452" Parameter: A <- "-75.3452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0407" Parameter: B <- "-33.0407" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3045" Parameter: C <- "-42.3045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2055 TOTAL ENERGY = -75.3452 RDTITL> * VAN DER WAALS = -33.0407 ELECTROSTATIC = -42.3045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2055" Parameter: CONF_N -> "8002" Comparing "2055" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2056" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766208 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761100 ATOM PAIRS WERE FOUND FOR ATOM LIST 41802 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29749 from a total of 761100 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2056 -78.88322 3.53797 0.63821 INTE EXTERN> -32.93732 -45.94590 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8832" Parameter: A <- "-78.8832" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9373" Parameter: B <- "-32.9373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9459" Parameter: C <- "-45.9459" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2056 TOTAL ENERGY = -78.8832 RDTITL> * VAN DER WAALS = -32.9373 ELECTROSTATIC = -45.9459 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2056" Parameter: CONF_N -> "8002" Comparing "2056" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2057" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761100 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757400 ATOM PAIRS WERE FOUND FOR ATOM LIST 41644 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29008 from a total of 757400 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2057 -70.02339 -8.85982 0.63848 INTE EXTERN> -31.21462 -38.80878 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0234" Parameter: A <- "-70.0234" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2146" Parameter: B <- "-31.2146" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8088" Parameter: C <- "-38.8088" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2057 TOTAL ENERGY = -70.0234 RDTITL> * VAN DER WAALS = -31.2146 ELECTROSTATIC = -38.8088 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2057" Parameter: CONF_N -> "8002" Comparing "2057" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2058" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757400 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760334 ATOM PAIRS WERE FOUND FOR ATOM LIST 41635 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29157 from a total of 760334 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2058 -73.60063 3.57724 0.54428 INTE EXTERN> -32.75145 -40.84918 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6006" Parameter: A <- "-73.6006" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7514" Parameter: B <- "-32.7514" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8492" Parameter: C <- "-40.8492" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2058 TOTAL ENERGY = -73.6006 RDTITL> * VAN DER WAALS = -32.7514 ELECTROSTATIC = -40.8492 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2058" Parameter: CONF_N -> "8002" Comparing "2058" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2059" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760334 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764008 ATOM PAIRS WERE FOUND FOR ATOM LIST 41824 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29328 from a total of 764008 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2059 -80.24033 6.63969 0.58759 INTE EXTERN> -33.90309 -46.33724 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2403" Parameter: A <- "-80.2403" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9031" Parameter: B <- "-33.9031" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3372" Parameter: C <- "-46.3372" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2059 TOTAL ENERGY = -80.2403 RDTITL> * VAN DER WAALS = -33.9031 ELECTROSTATIC = -46.3372 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2059" Parameter: CONF_N -> "8002" Comparing "2059" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2060" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764008 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753789 ATOM PAIRS WERE FOUND FOR ATOM LIST 41455 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28535 from a total of 753789 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2060 -76.43495 -3.80538 0.62843 INTE EXTERN> -30.11969 -46.31526 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4349" Parameter: A <- "-76.4349" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1197" Parameter: B <- "-30.1197" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3153" Parameter: C <- "-46.3153" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2060 TOTAL ENERGY = -76.4349 RDTITL> * VAN DER WAALS = -30.1197 ELECTROSTATIC = -46.3153 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2060" Parameter: CONF_N -> "8002" Comparing "2060" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2061" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753789 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758440 ATOM PAIRS WERE FOUND FOR ATOM LIST 41811 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29429 from a total of 758440 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2061 -77.16216 0.72721 0.68781 INTE EXTERN> -28.02638 -49.13578 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1622" Parameter: A <- "-77.1622" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0264" Parameter: B <- "-28.0264" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1358" Parameter: C <- "-49.1358" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2061 TOTAL ENERGY = -77.1622 RDTITL> * VAN DER WAALS = -28.0264 ELECTROSTATIC = -49.1358 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2061" Parameter: CONF_N -> "8002" Comparing "2061" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2062" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758440 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762960 ATOM PAIRS WERE FOUND FOR ATOM LIST 41773 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30023 from a total of 762960 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2062 -79.69806 2.53590 0.71869 INTE EXTERN> -28.74604 -50.95202 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6981" Parameter: A <- "-79.6981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.746" Parameter: B <- "-28.746" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.952" Parameter: C <- "-50.952" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2062 TOTAL ENERGY = -79.6981 RDTITL> * VAN DER WAALS = -28.746 ELECTROSTATIC = -50.952 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2062" Parameter: CONF_N -> "8002" Comparing "2062" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2063" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762960 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760114 ATOM PAIRS WERE FOUND FOR ATOM LIST 41728 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29503 from a total of 760114 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2063 -81.06386 1.36580 0.69292 INTE EXTERN> -30.97802 -50.08583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.0639" Parameter: A <- "-81.0639" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.978" Parameter: B <- "-30.978" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0858" Parameter: C <- "-50.0858" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2063 TOTAL ENERGY = -81.0639 RDTITL> * VAN DER WAALS = -30.978 ELECTROSTATIC = -50.0858 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2063" Parameter: CONF_N -> "8002" Comparing "2063" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2064" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760114 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763430 ATOM PAIRS WERE FOUND FOR ATOM LIST 41861 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29655 from a total of 763430 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2064 -79.11432 -1.94954 0.68060 INTE EXTERN> -32.63165 -46.48267 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1143" Parameter: A <- "-79.1143" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6317" Parameter: B <- "-32.6317" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4827" Parameter: C <- "-46.4827" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2064 TOTAL ENERGY = -79.1143 RDTITL> * VAN DER WAALS = -32.6317 ELECTROSTATIC = -46.4827 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2064" Parameter: CONF_N -> "8002" Comparing "2064" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2065" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763430 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765494 ATOM PAIRS WERE FOUND FOR ATOM LIST 42169 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29461 from a total of 765494 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2065 -70.85973 -8.25458 0.76634 INTE EXTERN> -26.52432 -44.33541 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8597" Parameter: A <- "-70.8597" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5243" Parameter: B <- "-26.5243" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3354" Parameter: C <- "-44.3354" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2065 TOTAL ENERGY = -70.8597 RDTITL> * VAN DER WAALS = -26.5243 ELECTROSTATIC = -44.3354 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2065" Parameter: CONF_N -> "8002" Comparing "2065" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2066" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765494 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768278 ATOM PAIRS WERE FOUND FOR ATOM LIST 42162 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30373 from a total of 768278 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2066 -82.01369 11.15396 0.72615 INTE EXTERN> -32.57769 -49.43600 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.0137" Parameter: A <- "-82.0137" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5777" Parameter: B <- "-32.5777" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.436" Parameter: C <- "-49.436" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2066 TOTAL ENERGY = -82.0137 RDTITL> * VAN DER WAALS = -32.5777 ELECTROSTATIC = -49.436 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2066" Parameter: CONF_N -> "8002" Comparing "2066" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2067" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768278 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767174 ATOM PAIRS WERE FOUND FOR ATOM LIST 42075 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30309 from a total of 767174 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2067 -85.25954 3.24585 0.76732 INTE EXTERN> -30.51509 -54.74445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.2595" Parameter: A <- "-85.2595" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5151" Parameter: B <- "-30.5151" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.7444" Parameter: C <- "-54.7444" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2067 TOTAL ENERGY = -85.2595 RDTITL> * VAN DER WAALS = -30.5151 ELECTROSTATIC = -54.7444 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2067" Parameter: CONF_N -> "8002" Comparing "2067" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2068" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767174 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770769 ATOM PAIRS WERE FOUND FOR ATOM LIST 42204 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30260 from a total of 770769 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2068 -74.87240 -10.38714 0.79016 INTE EXTERN> -26.61526 -48.25714 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8724" Parameter: A <- "-74.8724" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6153" Parameter: B <- "-26.6153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2571" Parameter: C <- "-48.2571" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2068 TOTAL ENERGY = -74.8724 RDTITL> * VAN DER WAALS = -26.6153 ELECTROSTATIC = -48.2571 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2068" Parameter: CONF_N -> "8002" Comparing "2068" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2069" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770769 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761386 ATOM PAIRS WERE FOUND FOR ATOM LIST 41906 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29670 from a total of 761386 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2069 -77.15203 2.27963 0.73969 INTE EXTERN> -28.97871 -48.17332 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.152" Parameter: A <- "-77.152" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9787" Parameter: B <- "-28.9787" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1733" Parameter: C <- "-48.1733" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2069 TOTAL ENERGY = -77.152 RDTITL> * VAN DER WAALS = -28.9787 ELECTROSTATIC = -48.1733 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2069" Parameter: CONF_N -> "8002" Comparing "2069" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2070" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761386 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761657 ATOM PAIRS WERE FOUND FOR ATOM LIST 41920 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29169 from a total of 761657 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2070 -79.65425 2.50222 0.69745 INTE EXTERN> -32.21814 -47.43611 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6543" Parameter: A <- "-79.6543" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2181" Parameter: B <- "-32.2181" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4361" Parameter: C <- "-47.4361" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2070 TOTAL ENERGY = -79.6543 RDTITL> * VAN DER WAALS = -32.2181 ELECTROSTATIC = -47.4361 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2070" Parameter: CONF_N -> "8002" Comparing "2070" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2071" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761657 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758596 ATOM PAIRS WERE FOUND FOR ATOM LIST 41763 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30023 from a total of 758596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2071 -77.23607 -2.41818 0.77509 INTE EXTERN> -26.67932 -50.55675 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2361" Parameter: A <- "-77.2361" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6793" Parameter: B <- "-26.6793" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5567" Parameter: C <- "-50.5567" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2071 TOTAL ENERGY = -77.2361 RDTITL> * VAN DER WAALS = -26.6793 ELECTROSTATIC = -50.5567 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2071" Parameter: CONF_N -> "8002" Comparing "2071" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2072" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762251 ATOM PAIRS WERE FOUND FOR ATOM LIST 42061 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29766 from a total of 762251 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2072 -73.33160 -3.90447 0.71680 INTE EXTERN> -29.98029 -43.35131 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3316" Parameter: A <- "-73.3316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9803" Parameter: B <- "-29.9803" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3513" Parameter: C <- "-43.3513" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2072 TOTAL ENERGY = -73.3316 RDTITL> * VAN DER WAALS = -29.9803 ELECTROSTATIC = -43.3513 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2072" Parameter: CONF_N -> "8002" Comparing "2072" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2073" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762251 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761839 ATOM PAIRS WERE FOUND FOR ATOM LIST 42014 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30288 from a total of 761839 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2073 -69.94224 -3.38936 0.61683 INTE EXTERN> -32.53739 -37.40485 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9422" Parameter: A <- "-69.9422" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5374" Parameter: B <- "-32.5374" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4049" Parameter: C <- "-37.4049" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2073 TOTAL ENERGY = -69.9422 RDTITL> * VAN DER WAALS = -32.5374 ELECTROSTATIC = -37.4049 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2073" Parameter: CONF_N -> "8002" Comparing "2073" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2074" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761839 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760637 ATOM PAIRS WERE FOUND FOR ATOM LIST 41624 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30325 from a total of 760637 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2074 -76.35400 6.41176 0.66718 INTE EXTERN> -34.46616 -41.88785 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.354" Parameter: A <- "-76.354" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.4662" Parameter: B <- "-34.4662" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8878" Parameter: C <- "-41.8878" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2074 TOTAL ENERGY = -76.354 RDTITL> * VAN DER WAALS = -34.4662 ELECTROSTATIC = -41.8878 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2074" Parameter: CONF_N -> "8002" Comparing "2074" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2075" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760637 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768493 ATOM PAIRS WERE FOUND FOR ATOM LIST 42301 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30417 from a total of 768493 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2075 -81.59579 5.24179 0.71806 INTE EXTERN> -30.76443 -50.83137 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5958" Parameter: A <- "-81.5958" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7644" Parameter: B <- "-30.7644" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8314" Parameter: C <- "-50.8314" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2075 TOTAL ENERGY = -81.5958 RDTITL> * VAN DER WAALS = -30.7644 ELECTROSTATIC = -50.8314 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2075" Parameter: CONF_N -> "8002" Comparing "2075" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2076" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768493 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767323 ATOM PAIRS WERE FOUND FOR ATOM LIST 42262 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29725 from a total of 767323 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2076 -74.18344 -7.41236 0.65323 INTE EXTERN> -30.89908 -43.28436 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1834" Parameter: A <- "-74.1834" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8991" Parameter: B <- "-30.8991" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2844" Parameter: C <- "-43.2844" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2076 TOTAL ENERGY = -74.1834 RDTITL> * VAN DER WAALS = -30.8991 ELECTROSTATIC = -43.2844 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2076" Parameter: CONF_N -> "8002" Comparing "2076" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2077" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767323 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766497 ATOM PAIRS WERE FOUND FOR ATOM LIST 42115 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29662 from a total of 766497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2077 -80.72068 6.53724 0.70382 INTE EXTERN> -31.18367 -49.53701 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7207" Parameter: A <- "-80.7207" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1837" Parameter: B <- "-31.1837" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.537" Parameter: C <- "-49.537" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2077 TOTAL ENERGY = -80.7207 RDTITL> * VAN DER WAALS = -31.1837 ELECTROSTATIC = -49.537 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2077" Parameter: CONF_N -> "8002" Comparing "2077" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2078" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762759 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29826 from a total of 762759 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2078 -71.22857 -9.49211 0.68477 INTE EXTERN> -26.76151 -44.46707 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2286" Parameter: A <- "-71.2286" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7615" Parameter: B <- "-26.7615" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4671" Parameter: C <- "-44.4671" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2078 TOTAL ENERGY = -71.2286 RDTITL> * VAN DER WAALS = -26.7615 ELECTROSTATIC = -44.4671 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2078" Parameter: CONF_N -> "8002" Comparing "2078" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2079" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762759 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765598 ATOM PAIRS WERE FOUND FOR ATOM LIST 42216 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29869 from a total of 765598 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2079 -69.32195 -1.90663 0.55457 INTE EXTERN> -31.71566 -37.60629 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3219" Parameter: A <- "-69.3219" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7157" Parameter: B <- "-31.7157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6063" Parameter: C <- "-37.6063" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2079 TOTAL ENERGY = -69.3219 RDTITL> * VAN DER WAALS = -31.7157 ELECTROSTATIC = -37.6063 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2079" Parameter: CONF_N -> "8002" Comparing "2079" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2080" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765598 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763105 ATOM PAIRS WERE FOUND FOR ATOM LIST 41921 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30248 from a total of 763105 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2080 -71.47139 2.14944 0.66155 INTE EXTERN> -29.07780 -42.39359 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4714" Parameter: A <- "-71.4714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0778" Parameter: B <- "-29.0778" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3936" Parameter: C <- "-42.3936" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2080 TOTAL ENERGY = -71.4714 RDTITL> * VAN DER WAALS = -29.0778 ELECTROSTATIC = -42.3936 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2080" Parameter: CONF_N -> "8002" Comparing "2080" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2081" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763105 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768326 ATOM PAIRS WERE FOUND FOR ATOM LIST 42247 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30067 from a total of 768326 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2081 -71.37554 -0.09585 0.55047 INTE EXTERN> -31.35786 -40.01768 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3755" Parameter: A <- "-71.3755" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3579" Parameter: B <- "-31.3579" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0177" Parameter: C <- "-40.0177" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2081 TOTAL ENERGY = -71.3755 RDTITL> * VAN DER WAALS = -31.3579 ELECTROSTATIC = -40.0177 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2081" Parameter: CONF_N -> "8002" Comparing "2081" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2082" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768326 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766020 ATOM PAIRS WERE FOUND FOR ATOM LIST 42329 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29550 from a total of 766020 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2082 -72.05535 0.67980 0.64975 INTE EXTERN> -29.74949 -42.30586 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0553" Parameter: A <- "-72.0553" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7495" Parameter: B <- "-29.7495" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3059" Parameter: C <- "-42.3059" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2082 TOTAL ENERGY = -72.0553 RDTITL> * VAN DER WAALS = -29.7495 ELECTROSTATIC = -42.3059 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2082" Parameter: CONF_N -> "8002" Comparing "2082" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2083" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766020 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762587 ATOM PAIRS WERE FOUND FOR ATOM LIST 42004 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30266 from a total of 762587 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2083 -75.92193 3.86658 0.81767 INTE EXTERN> -25.12209 -50.79984 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9219" Parameter: A <- "-75.9219" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1221" Parameter: B <- "-25.1221" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7998" Parameter: C <- "-50.7998" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2083 TOTAL ENERGY = -75.9219 RDTITL> * VAN DER WAALS = -25.1221 ELECTROSTATIC = -50.7998 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2083" Parameter: CONF_N -> "8002" Comparing "2083" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2084" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762587 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757447 ATOM PAIRS WERE FOUND FOR ATOM LIST 41579 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29662 from a total of 757447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2084 -72.42311 -3.49882 0.73488 INTE EXTERN> -25.91741 -46.50569 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4231" Parameter: A <- "-72.4231" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9174" Parameter: B <- "-25.9174" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5057" Parameter: C <- "-46.5057" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2084 TOTAL ENERGY = -72.4231 RDTITL> * VAN DER WAALS = -25.9174 ELECTROSTATIC = -46.5057 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2084" Parameter: CONF_N -> "8002" Comparing "2084" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2085" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758053 ATOM PAIRS WERE FOUND FOR ATOM LIST 41652 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29442 from a total of 758053 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2085 -76.56286 4.13976 0.62544 INTE EXTERN> -30.09041 -46.47245 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5629" Parameter: A <- "-76.5629" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0904" Parameter: B <- "-30.0904" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4725" Parameter: C <- "-46.4725" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2085 TOTAL ENERGY = -76.5629 RDTITL> * VAN DER WAALS = -30.0904 ELECTROSTATIC = -46.4725 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2085" Parameter: CONF_N -> "8002" Comparing "2085" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2086" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758053 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763104 ATOM PAIRS WERE FOUND FOR ATOM LIST 41868 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29520 from a total of 763104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2086 -70.54189 -6.02098 0.68202 INTE EXTERN> -27.83242 -42.70947 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5419" Parameter: A <- "-70.5419" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8324" Parameter: B <- "-27.8324" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7095" Parameter: C <- "-42.7095" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2086 TOTAL ENERGY = -70.5419 RDTITL> * VAN DER WAALS = -27.8324 ELECTROSTATIC = -42.7095 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2086" Parameter: CONF_N -> "8002" Comparing "2086" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2087" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763419 ATOM PAIRS WERE FOUND FOR ATOM LIST 41779 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29593 from a total of 763419 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2087 -78.60989 8.06800 0.64352 INTE EXTERN> -30.45940 -48.15048 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6099" Parameter: A <- "-78.6099" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4594" Parameter: B <- "-30.4594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1505" Parameter: C <- "-48.1505" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2087 TOTAL ENERGY = -78.6099 RDTITL> * VAN DER WAALS = -30.4594 ELECTROSTATIC = -48.1505 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2087" Parameter: CONF_N -> "8002" Comparing "2087" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2088" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763419 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763947 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29885 from a total of 763947 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2088 -73.16828 -5.44161 0.68119 INTE EXTERN> -27.81157 -45.35670 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1683" Parameter: A <- "-73.1683" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8116" Parameter: B <- "-27.8116" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3567" Parameter: C <- "-45.3567" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2088 TOTAL ENERGY = -73.1683 RDTITL> * VAN DER WAALS = -27.8116 ELECTROSTATIC = -45.3567 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2088" Parameter: CONF_N -> "8002" Comparing "2088" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2089" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763947 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755377 ATOM PAIRS WERE FOUND FOR ATOM LIST 41481 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29245 from a total of 755377 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2089 -74.15981 0.99153 0.64340 INTE EXTERN> -29.59185 -44.56795 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1598" Parameter: A <- "-74.1598" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5919" Parameter: B <- "-29.5919" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.568" Parameter: C <- "-44.568" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2089 TOTAL ENERGY = -74.1598 RDTITL> * VAN DER WAALS = -29.5919 ELECTROSTATIC = -44.568 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2089" Parameter: CONF_N -> "8002" Comparing "2089" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2090" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755377 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759261 ATOM PAIRS WERE FOUND FOR ATOM LIST 41789 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29178 from a total of 759261 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2090 -71.67780 -2.48201 0.51522 INTE EXTERN> -33.61486 -38.06294 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6778" Parameter: A <- "-71.6778" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6149" Parameter: B <- "-33.6149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0629" Parameter: C <- "-38.0629" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2090 TOTAL ENERGY = -71.6778 RDTITL> * VAN DER WAALS = -33.6149 ELECTROSTATIC = -38.0629 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2090" Parameter: CONF_N -> "8002" Comparing "2090" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2091" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759261 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756428 ATOM PAIRS WERE FOUND FOR ATOM LIST 41847 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29353 from a total of 756428 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2091 -82.44085 10.76305 0.72239 INTE EXTERN> -29.71077 -52.73008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.4409" Parameter: A <- "-82.4409" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7108" Parameter: B <- "-29.7108" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.7301" Parameter: C <- "-52.7301" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2091 TOTAL ENERGY = -82.4409 RDTITL> * VAN DER WAALS = -29.7108 ELECTROSTATIC = -52.7301 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2091" Parameter: CONF_N -> "8002" Comparing "2091" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2092" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756428 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759360 ATOM PAIRS WERE FOUND FOR ATOM LIST 41689 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29825 from a total of 759360 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2092 -79.72997 -2.71088 0.80512 INTE EXTERN> -24.34773 -55.38225 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.73" Parameter: A <- "-79.73" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3477" Parameter: B <- "-24.3477" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.3822" Parameter: C <- "-55.3822" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2092 TOTAL ENERGY = -79.73 RDTITL> * VAN DER WAALS = -24.3477 ELECTROSTATIC = -55.3822 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2092" Parameter: CONF_N -> "8002" Comparing "2092" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2093" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759360 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767803 ATOM PAIRS WERE FOUND FOR ATOM LIST 42280 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30304 from a total of 767803 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2093 -84.94511 5.21513 0.91195 INTE EXTERN> -24.33402 -60.61109 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.9451" Parameter: A <- "-84.9451" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.334" Parameter: B <- "-24.334" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-60.6111" Parameter: C <- "-60.6111" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2093 TOTAL ENERGY = -84.9451 RDTITL> * VAN DER WAALS = -24.334 ELECTROSTATIC = -60.6111 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2093" Parameter: CONF_N -> "8002" Comparing "2093" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2094" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767803 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769672 ATOM PAIRS WERE FOUND FOR ATOM LIST 42192 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30249 from a total of 769672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2094 -76.17195 -8.77316 0.62676 INTE EXTERN> -31.71579 -44.45615 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1719" Parameter: A <- "-76.1719" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7158" Parameter: B <- "-31.7158" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4562" Parameter: C <- "-44.4562" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2094 TOTAL ENERGY = -76.1719 RDTITL> * VAN DER WAALS = -31.7158 ELECTROSTATIC = -44.4562 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2094" Parameter: CONF_N -> "8002" Comparing "2094" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2095" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758445 ATOM PAIRS WERE FOUND FOR ATOM LIST 41745 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29845 from a total of 758445 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2095 -73.91998 -2.25197 0.59118 INTE EXTERN> -32.04337 -41.87661 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.92" Parameter: A <- "-73.92" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0434" Parameter: B <- "-32.0434" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8766" Parameter: C <- "-41.8766" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2095 TOTAL ENERGY = -73.92 RDTITL> * VAN DER WAALS = -32.0434 ELECTROSTATIC = -41.8766 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2095" Parameter: CONF_N -> "8002" Comparing "2095" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2096" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758445 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756274 ATOM PAIRS WERE FOUND FOR ATOM LIST 41693 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29870 from a total of 756274 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2096 -68.19576 -5.72422 0.62784 INTE EXTERN> -29.42581 -38.76995 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1958" Parameter: A <- "-68.1958" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4258" Parameter: B <- "-29.4258" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7699" Parameter: C <- "-38.7699" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2096 TOTAL ENERGY = -68.1958 RDTITL> * VAN DER WAALS = -29.4258 ELECTROSTATIC = -38.7699 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2096" Parameter: CONF_N -> "8002" Comparing "2096" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2097" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756274 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758170 ATOM PAIRS WERE FOUND FOR ATOM LIST 41716 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29788 from a total of 758170 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2097 -70.35415 2.15838 0.63041 INTE EXTERN> -30.28254 -40.07161 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3541" Parameter: A <- "-70.3541" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2825" Parameter: B <- "-30.2825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0716" Parameter: C <- "-40.0716" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2097 TOTAL ENERGY = -70.3541 RDTITL> * VAN DER WAALS = -30.2825 ELECTROSTATIC = -40.0716 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2097" Parameter: CONF_N -> "8002" Comparing "2097" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2098" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758170 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759272 ATOM PAIRS WERE FOUND FOR ATOM LIST 41772 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30167 from a total of 759272 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2098 -66.62201 -3.73213 0.52447 INTE EXTERN> -32.27499 -34.34702 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.622" Parameter: A <- "-66.622" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.275" Parameter: B <- "-32.275" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.347" Parameter: C <- "-34.347" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2098 TOTAL ENERGY = -66.622 RDTITL> * VAN DER WAALS = -32.275 ELECTROSTATIC = -34.347 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2098" Parameter: CONF_N -> "8002" Comparing "2098" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2099" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759272 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755821 ATOM PAIRS WERE FOUND FOR ATOM LIST 41691 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29358 from a total of 755821 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2099 -63.44427 -3.17774 0.58247 INTE EXTERN> -29.88897 -33.55530 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4443" Parameter: A <- "-63.4443" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.889" Parameter: B <- "-29.889" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.5553" Parameter: C <- "-33.5553" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2099 TOTAL ENERGY = -63.4443 RDTITL> * VAN DER WAALS = -29.889 ELECTROSTATIC = -33.5553 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2099" Parameter: CONF_N -> "8002" Comparing "2099" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2100" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755821 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755242 ATOM PAIRS WERE FOUND FOR ATOM LIST 41580 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29282 from a total of 755242 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2100 -63.54299 0.09871 0.37507 INTE EXTERN> -33.87233 -29.67065 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.543" Parameter: A <- "-63.543" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8723" Parameter: B <- "-33.8723" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.6707" Parameter: C <- "-29.6707" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2100 TOTAL ENERGY = -63.543 RDTITL> * VAN DER WAALS = -33.8723 ELECTROSTATIC = -29.6707 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2100" Parameter: CONF_N -> "8002" Comparing "2100" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2101" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755242 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760768 ATOM PAIRS WERE FOUND FOR ATOM LIST 41760 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29537 from a total of 760768 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2101 -63.36715 -0.17583 0.61419 INTE EXTERN> -25.96543 -37.40172 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3672" Parameter: A <- "-63.3672" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9654" Parameter: B <- "-25.9654" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4017" Parameter: C <- "-37.4017" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2101 TOTAL ENERGY = -63.3672 RDTITL> * VAN DER WAALS = -25.9654 ELECTROSTATIC = -37.4017 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2101" Parameter: CONF_N -> "8002" Comparing "2101" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2102" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760768 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763728 ATOM PAIRS WERE FOUND FOR ATOM LIST 42051 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29782 from a total of 763728 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2102 -66.59832 3.23117 0.62249 INTE EXTERN> -32.01269 -34.58563 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5983" Parameter: A <- "-66.5983" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0127" Parameter: B <- "-32.0127" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5856" Parameter: C <- "-34.5856" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2102 TOTAL ENERGY = -66.5983 RDTITL> * VAN DER WAALS = -32.0127 ELECTROSTATIC = -34.5856 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2102" Parameter: CONF_N -> "8002" Comparing "2102" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2103" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763728 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765668 ATOM PAIRS WERE FOUND FOR ATOM LIST 42036 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30117 from a total of 765668 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2103 -64.08906 -2.50927 0.59884 INTE EXTERN> -27.94535 -36.14371 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0891" Parameter: A <- "-64.0891" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9453" Parameter: B <- "-27.9453" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1437" Parameter: C <- "-36.1437" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2103 TOTAL ENERGY = -64.0891 RDTITL> * VAN DER WAALS = -27.9453 ELECTROSTATIC = -36.1437 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2103" Parameter: CONF_N -> "8002" Comparing "2103" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2104" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765668 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756647 ATOM PAIRS WERE FOUND FOR ATOM LIST 41796 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29446 from a total of 756647 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2104 -63.54931 -0.53974 0.47934 INTE EXTERN> -32.54571 -31.00360 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5493" Parameter: A <- "-63.5493" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5457" Parameter: B <- "-32.5457" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.0036" Parameter: C <- "-31.0036" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2104 TOTAL ENERGY = -63.5493 RDTITL> * VAN DER WAALS = -32.5457 ELECTROSTATIC = -31.0036 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2104" Parameter: CONF_N -> "8002" Comparing "2104" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2105" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756647 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760359 ATOM PAIRS WERE FOUND FOR ATOM LIST 42025 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30039 from a total of 760359 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2105 -67.47723 3.92792 0.67083 INTE EXTERN> -28.27415 -39.20308 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4772" Parameter: A <- "-67.4772" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2742" Parameter: B <- "-28.2742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2031" Parameter: C <- "-39.2031" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2105 TOTAL ENERGY = -67.4772 RDTITL> * VAN DER WAALS = -28.2742 ELECTROSTATIC = -39.2031 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2105" Parameter: CONF_N -> "8002" Comparing "2105" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2106" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760359 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767135 ATOM PAIRS WERE FOUND FOR ATOM LIST 42035 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29809 from a total of 767135 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2106 -67.04279 -0.43444 0.49956 INTE EXTERN> -34.81556 -32.22723 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0428" Parameter: A <- "-67.0428" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.8156" Parameter: B <- "-34.8156" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2272" Parameter: C <- "-32.2272" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2106 TOTAL ENERGY = -67.0428 RDTITL> * VAN DER WAALS = -34.8156 ELECTROSTATIC = -32.2272 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2106" Parameter: CONF_N -> "8002" Comparing "2106" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2107" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767135 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762423 ATOM PAIRS WERE FOUND FOR ATOM LIST 41904 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29497 from a total of 762423 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2107 -63.39548 -3.64730 0.53775 INTE EXTERN> -33.01683 -30.37866 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3955" Parameter: A <- "-63.3955" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0168" Parameter: B <- "-33.0168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.3787" Parameter: C <- "-30.3787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2107 TOTAL ENERGY = -63.3955 RDTITL> * VAN DER WAALS = -33.0168 ELECTROSTATIC = -30.3787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2107" Parameter: CONF_N -> "8002" Comparing "2107" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2108" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762423 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764451 ATOM PAIRS WERE FOUND FOR ATOM LIST 42000 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30109 from a total of 764451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2108 -67.67632 4.28083 0.52515 INTE EXTERN> -31.34987 -36.32644 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6763" Parameter: A <- "-67.6763" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3499" Parameter: B <- "-31.3499" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3264" Parameter: C <- "-36.3264" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2108 TOTAL ENERGY = -67.6763 RDTITL> * VAN DER WAALS = -31.3499 ELECTROSTATIC = -36.3264 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2108" Parameter: CONF_N -> "8002" Comparing "2108" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2109" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765293 ATOM PAIRS WERE FOUND FOR ATOM LIST 42118 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29871 from a total of 765293 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2109 -64.63501 -3.04131 0.53372 INTE EXTERN> -32.06743 -32.56757 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.635" Parameter: A <- "-64.635" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0674" Parameter: B <- "-32.0674" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5676" Parameter: C <- "-32.5676" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2109 TOTAL ENERGY = -64.635 RDTITL> * VAN DER WAALS = -32.0674 ELECTROSTATIC = -32.5676 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2109" Parameter: CONF_N -> "8002" Comparing "2109" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2110" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765293 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 774295 ATOM PAIRS WERE FOUND FOR ATOM LIST 42492 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30105 from a total of 774295 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2110 -63.41350 -1.22150 0.54831 INTE EXTERN> -29.06542 -34.34808 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4135" Parameter: A <- "-63.4135" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0654" Parameter: B <- "-29.0654" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3481" Parameter: C <- "-34.3481" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2110 TOTAL ENERGY = -63.4135 RDTITL> * VAN DER WAALS = -29.0654 ELECTROSTATIC = -34.3481 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2110" Parameter: CONF_N -> "8002" Comparing "2110" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2111" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 774295 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762123 ATOM PAIRS WERE FOUND FOR ATOM LIST 41871 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29526 from a total of 762123 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2111 -70.80604 7.39254 0.60516 INTE EXTERN> -33.52757 -37.27847 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.806" Parameter: A <- "-70.806" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5276" Parameter: B <- "-33.5276" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2785" Parameter: C <- "-37.2785" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2111 TOTAL ENERGY = -70.806 RDTITL> * VAN DER WAALS = -33.5276 ELECTROSTATIC = -37.2785 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2111" Parameter: CONF_N -> "8002" Comparing "2111" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2112" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762123 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766028 ATOM PAIRS WERE FOUND FOR ATOM LIST 42167 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29663 from a total of 766028 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2112 -73.01883 2.21279 0.84257 INTE EXTERN> -25.59005 -47.42878 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0188" Parameter: A <- "-73.0188" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.59" Parameter: B <- "-25.59" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4288" Parameter: C <- "-47.4288" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2112 TOTAL ENERGY = -73.0188 RDTITL> * VAN DER WAALS = -25.59 ELECTROSTATIC = -47.4288 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2112" Parameter: CONF_N -> "8002" Comparing "2112" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2113" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766028 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764485 ATOM PAIRS WERE FOUND FOR ATOM LIST 42013 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29064 from a total of 764485 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2113 -76.32572 3.30689 0.65033 INTE EXTERN> -32.42962 -43.89610 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3257" Parameter: A <- "-76.3257" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4296" Parameter: B <- "-32.4296" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8961" Parameter: C <- "-43.8961" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2113 TOTAL ENERGY = -76.3257 RDTITL> * VAN DER WAALS = -32.4296 ELECTROSTATIC = -43.8961 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2113" Parameter: CONF_N -> "8002" Comparing "2113" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2114" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764485 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769192 ATOM PAIRS WERE FOUND FOR ATOM LIST 42332 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29634 from a total of 769192 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2114 -76.14874 -0.17698 0.62734 INTE EXTERN> -33.70291 -42.44584 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1487" Parameter: A <- "-76.1487" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7029" Parameter: B <- "-33.7029" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4458" Parameter: C <- "-42.4458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2114 TOTAL ENERGY = -76.1487 RDTITL> * VAN DER WAALS = -33.7029 ELECTROSTATIC = -42.4458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2114" Parameter: CONF_N -> "8002" Comparing "2114" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2115" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769192 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764201 ATOM PAIRS WERE FOUND FOR ATOM LIST 42003 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29833 from a total of 764201 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2115 -73.28896 -2.85978 0.67109 INTE EXTERN> -30.59496 -42.69400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.289" Parameter: A <- "-73.289" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.595" Parameter: B <- "-30.595" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.694" Parameter: C <- "-42.694" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2115 TOTAL ENERGY = -73.289 RDTITL> * VAN DER WAALS = -30.595 ELECTROSTATIC = -42.694 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2115" Parameter: CONF_N -> "8002" Comparing "2115" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2116" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764201 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765950 ATOM PAIRS WERE FOUND FOR ATOM LIST 41961 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29947 from a total of 765950 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2116 -74.47198 1.18302 0.70149 INTE EXTERN> -30.71240 -43.75958 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.472" Parameter: A <- "-74.472" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7124" Parameter: B <- "-30.7124" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7596" Parameter: C <- "-43.7596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2116 TOTAL ENERGY = -74.472 RDTITL> * VAN DER WAALS = -30.7124 ELECTROSTATIC = -43.7596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2116" Parameter: CONF_N -> "8002" Comparing "2116" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2117" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765950 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762964 ATOM PAIRS WERE FOUND FOR ATOM LIST 41868 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29343 from a total of 762964 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2117 -78.08662 3.61464 0.60861 INTE EXTERN> -33.79492 -44.29170 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0866" Parameter: A <- "-78.0866" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7949" Parameter: B <- "-33.7949" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2917" Parameter: C <- "-44.2917" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2117 TOTAL ENERGY = -78.0866 RDTITL> * VAN DER WAALS = -33.7949 ELECTROSTATIC = -44.2917 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2117" Parameter: CONF_N -> "8002" Comparing "2117" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2118" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762964 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769567 ATOM PAIRS WERE FOUND FOR ATOM LIST 42303 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29369 from a total of 769567 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2118 -67.65449 -10.43213 0.65645 INTE EXTERN> -30.23009 -37.42440 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6545" Parameter: A <- "-67.6545" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2301" Parameter: B <- "-30.2301" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4244" Parameter: C <- "-37.4244" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2118 TOTAL ENERGY = -67.6545 RDTITL> * VAN DER WAALS = -30.2301 ELECTROSTATIC = -37.4244 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2118" Parameter: CONF_N -> "8002" Comparing "2118" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2119" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769567 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767958 ATOM PAIRS WERE FOUND FOR ATOM LIST 42190 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30293 from a total of 767958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2119 -65.04162 -2.61287 0.56728 INTE EXTERN> -31.24854 -33.79308 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0416" Parameter: A <- "-65.0416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2485" Parameter: B <- "-31.2485" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7931" Parameter: C <- "-33.7931" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2119 TOTAL ENERGY = -65.0416 RDTITL> * VAN DER WAALS = -31.2485 ELECTROSTATIC = -33.7931 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2119" Parameter: CONF_N -> "8002" Comparing "2119" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2120" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764228 ATOM PAIRS WERE FOUND FOR ATOM LIST 41970 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30697 from a total of 764228 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2120 -74.14923 9.10761 0.60634 INTE EXTERN> -32.45747 -41.69176 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1492" Parameter: A <- "-74.1492" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4575" Parameter: B <- "-32.4575" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6918" Parameter: C <- "-41.6918" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2120 TOTAL ENERGY = -74.1492 RDTITL> * VAN DER WAALS = -32.4575 ELECTROSTATIC = -41.6918 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2120" Parameter: CONF_N -> "8002" Comparing "2120" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2121" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764228 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768265 ATOM PAIRS WERE FOUND FOR ATOM LIST 42019 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30236 from a total of 768265 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2121 -75.11379 0.96456 0.66647 INTE EXTERN> -28.28789 -46.82591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1138" Parameter: A <- "-75.1138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2879" Parameter: B <- "-28.2879" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8259" Parameter: C <- "-46.8259" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2121 TOTAL ENERGY = -75.1138 RDTITL> * VAN DER WAALS = -28.2879 ELECTROSTATIC = -46.8259 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2121" Parameter: CONF_N -> "8002" Comparing "2121" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2122" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768265 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764264 ATOM PAIRS WERE FOUND FOR ATOM LIST 42244 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30084 from a total of 764264 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2122 -64.62409 -10.48970 0.73308 INTE EXTERN> -24.05497 -40.56912 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6241" Parameter: A <- "-64.6241" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.055" Parameter: B <- "-24.055" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5691" Parameter: C <- "-40.5691" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2122 TOTAL ENERGY = -64.6241 RDTITL> * VAN DER WAALS = -24.055 ELECTROSTATIC = -40.5691 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2122" Parameter: CONF_N -> "8002" Comparing "2122" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2123" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764264 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766735 ATOM PAIRS WERE FOUND FOR ATOM LIST 41981 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29609 from a total of 766735 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2123 -77.63903 13.01494 0.76507 INTE EXTERN> -27.28597 -50.35306 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.639" Parameter: A <- "-77.639" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.286" Parameter: B <- "-27.286" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3531" Parameter: C <- "-50.3531" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2123 TOTAL ENERGY = -77.639 RDTITL> * VAN DER WAALS = -27.286 ELECTROSTATIC = -50.3531 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2123" Parameter: CONF_N -> "8002" Comparing "2123" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2124" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766735 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766474 ATOM PAIRS WERE FOUND FOR ATOM LIST 42095 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30205 from a total of 766474 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2124 -79.58085 1.94182 0.76846 INTE EXTERN> -29.68357 -49.89728 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5808" Parameter: A <- "-79.5808" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6836" Parameter: B <- "-29.6836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8973" Parameter: C <- "-49.8973" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2124 TOTAL ENERGY = -79.5808 RDTITL> * VAN DER WAALS = -29.6836 ELECTROSTATIC = -49.8973 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2124" Parameter: CONF_N -> "8002" Comparing "2124" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2125" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766474 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767459 ATOM PAIRS WERE FOUND FOR ATOM LIST 42054 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29680 from a total of 767459 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2125 -72.54364 -7.03721 0.67832 INTE EXTERN> -30.19922 -42.34442 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5436" Parameter: A <- "-72.5436" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1992" Parameter: B <- "-30.1992" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3444" Parameter: C <- "-42.3444" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2125 TOTAL ENERGY = -72.5436 RDTITL> * VAN DER WAALS = -30.1992 ELECTROSTATIC = -42.3444 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2125" Parameter: CONF_N -> "8002" Comparing "2125" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2126" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767459 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764136 ATOM PAIRS WERE FOUND FOR ATOM LIST 41919 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29441 from a total of 764136 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2126 -79.03787 6.49424 0.72102 INTE EXTERN> -30.90823 -48.12964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0379" Parameter: A <- "-79.0379" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9082" Parameter: B <- "-30.9082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1296" Parameter: C <- "-48.1296" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2126 TOTAL ENERGY = -79.0379 RDTITL> * VAN DER WAALS = -30.9082 ELECTROSTATIC = -48.1296 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2126" Parameter: CONF_N -> "8002" Comparing "2126" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2127" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764136 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760787 ATOM PAIRS WERE FOUND FOR ATOM LIST 41976 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29795 from a total of 760787 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2127 -74.82004 -4.21783 0.65922 INTE EXTERN> -30.90663 -43.91342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.82" Parameter: A <- "-74.82" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9066" Parameter: B <- "-30.9066" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9134" Parameter: C <- "-43.9134" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2127 TOTAL ENERGY = -74.82 RDTITL> * VAN DER WAALS = -30.9066 ELECTROSTATIC = -43.9134 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2127" Parameter: CONF_N -> "8002" Comparing "2127" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2128" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760787 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765018 ATOM PAIRS WERE FOUND FOR ATOM LIST 42138 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29314 from a total of 765018 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2128 -67.26993 -7.55012 0.78934 INTE EXTERN> -27.24777 -40.02216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2699" Parameter: A <- "-67.2699" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2478" Parameter: B <- "-27.2478" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0222" Parameter: C <- "-40.0222" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2128 TOTAL ENERGY = -67.2699 RDTITL> * VAN DER WAALS = -27.2478 ELECTROSTATIC = -40.0222 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2128" Parameter: CONF_N -> "8002" Comparing "2128" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2129" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765018 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763272 ATOM PAIRS WERE FOUND FOR ATOM LIST 41908 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29594 from a total of 763272 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2129 -76.09304 8.82311 0.75374 INTE EXTERN> -30.54842 -45.54462 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.093" Parameter: A <- "-76.093" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5484" Parameter: B <- "-30.5484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5446" Parameter: C <- "-45.5446" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2129 TOTAL ENERGY = -76.093 RDTITL> * VAN DER WAALS = -30.5484 ELECTROSTATIC = -45.5446 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2129" Parameter: CONF_N -> "8002" Comparing "2129" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2130" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763272 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762037 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29264 from a total of 762037 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2130 -77.80669 1.71365 0.64042 INTE EXTERN> -32.04529 -45.76140 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8067" Parameter: A <- "-77.8067" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0453" Parameter: B <- "-32.0453" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7614" Parameter: C <- "-45.7614" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2130 TOTAL ENERGY = -77.8067 RDTITL> * VAN DER WAALS = -32.0453 ELECTROSTATIC = -45.7614 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2130" Parameter: CONF_N -> "8002" Comparing "2130" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2131" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762037 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761634 ATOM PAIRS WERE FOUND FOR ATOM LIST 41832 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28978 from a total of 761634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2131 -73.46780 -4.33889 0.81307 INTE EXTERN> -22.83527 -50.63252 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4678" Parameter: A <- "-73.4678" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.8353" Parameter: B <- "-22.8353" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6325" Parameter: C <- "-50.6325" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2131 TOTAL ENERGY = -73.4678 RDTITL> * VAN DER WAALS = -22.8353 ELECTROSTATIC = -50.6325 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2131" Parameter: CONF_N -> "8002" Comparing "2131" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2132" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760770 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29411 from a total of 760770 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2132 -77.34994 3.88215 0.67456 INTE EXTERN> -30.75171 -46.59824 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3499" Parameter: A <- "-77.3499" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7517" Parameter: B <- "-30.7517" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5982" Parameter: C <- "-46.5982" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2132 TOTAL ENERGY = -77.3499 RDTITL> * VAN DER WAALS = -30.7517 ELECTROSTATIC = -46.5982 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2132" Parameter: CONF_N -> "8002" Comparing "2132" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2133" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760770 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770751 ATOM PAIRS WERE FOUND FOR ATOM LIST 42422 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30190 from a total of 770751 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2133 -75.09262 -2.25733 0.68590 INTE EXTERN> -29.06893 -46.02369 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0926" Parameter: A <- "-75.0926" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0689" Parameter: B <- "-29.0689" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0237" Parameter: C <- "-46.0237" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2133 TOTAL ENERGY = -75.0926 RDTITL> * VAN DER WAALS = -29.0689 ELECTROSTATIC = -46.0237 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2133" Parameter: CONF_N -> "8002" Comparing "2133" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2134" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770751 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765030 ATOM PAIRS WERE FOUND FOR ATOM LIST 42019 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29105 from a total of 765030 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2134 -74.48115 -0.61147 0.67559 INTE EXTERN> -31.10367 -43.37748 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4811" Parameter: A <- "-74.4811" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1037" Parameter: B <- "-31.1037" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3775" Parameter: C <- "-43.3775" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2134 TOTAL ENERGY = -74.4811 RDTITL> * VAN DER WAALS = -31.1037 ELECTROSTATIC = -43.3775 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2134" Parameter: CONF_N -> "8002" Comparing "2134" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2135" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765030 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766314 ATOM PAIRS WERE FOUND FOR ATOM LIST 42091 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29372 from a total of 766314 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2135 -77.72520 3.24406 0.83069 INTE EXTERN> -23.83516 -53.89004 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7252" Parameter: A <- "-77.7252" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8352" Parameter: B <- "-23.8352" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.89" Parameter: C <- "-53.89" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2135 TOTAL ENERGY = -77.7252 RDTITL> * VAN DER WAALS = -23.8352 ELECTROSTATIC = -53.89 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2135" Parameter: CONF_N -> "8002" Comparing "2135" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2136" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766314 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762248 ATOM PAIRS WERE FOUND FOR ATOM LIST 41896 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29134 from a total of 762248 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2136 -75.54593 -2.17927 0.69479 INTE EXTERN> -32.30773 -43.23820 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5459" Parameter: A <- "-75.5459" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3077" Parameter: B <- "-32.3077" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2382" Parameter: C <- "-43.2382" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2136 TOTAL ENERGY = -75.5459 RDTITL> * VAN DER WAALS = -32.3077 ELECTROSTATIC = -43.2382 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2136" Parameter: CONF_N -> "8002" Comparing "2136" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2137" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762248 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763869 ATOM PAIRS WERE FOUND FOR ATOM LIST 42001 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29612 from a total of 763869 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2137 -76.15910 0.61317 0.72349 INTE EXTERN> -29.03393 -47.12517 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1591" Parameter: A <- "-76.1591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0339" Parameter: B <- "-29.0339" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1252" Parameter: C <- "-47.1252" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2137 TOTAL ENERGY = -76.1591 RDTITL> * VAN DER WAALS = -29.0339 ELECTROSTATIC = -47.1252 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2137" Parameter: CONF_N -> "8002" Comparing "2137" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2138" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763869 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756712 ATOM PAIRS WERE FOUND FOR ATOM LIST 41531 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29046 from a total of 756712 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2138 -75.57656 -0.58254 0.59288 INTE EXTERN> -34.68614 -40.89042 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5766" Parameter: A <- "-75.5766" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6861" Parameter: B <- "-34.6861" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8904" Parameter: C <- "-40.8904" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2138 TOTAL ENERGY = -75.5766 RDTITL> * VAN DER WAALS = -34.6861 ELECTROSTATIC = -40.8904 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2138" Parameter: CONF_N -> "8002" Comparing "2138" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2139" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756712 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757908 ATOM PAIRS WERE FOUND FOR ATOM LIST 41759 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29520 from a total of 757908 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2139 -77.44196 1.86539 0.67620 INTE EXTERN> -29.16084 -48.28112 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.442" Parameter: A <- "-77.442" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1608" Parameter: B <- "-29.1608" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2811" Parameter: C <- "-48.2811" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2139 TOTAL ENERGY = -77.442 RDTITL> * VAN DER WAALS = -29.1608 ELECTROSTATIC = -48.2811 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2139" Parameter: CONF_N -> "8002" Comparing "2139" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2140" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757908 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755566 ATOM PAIRS WERE FOUND FOR ATOM LIST 41750 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29518 from a total of 755566 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2140 -74.05981 -3.38215 0.66984 INTE EXTERN> -29.38296 -44.67685 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0598" Parameter: A <- "-74.0598" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.383" Parameter: B <- "-29.383" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6768" Parameter: C <- "-44.6768" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2140 TOTAL ENERGY = -74.0598 RDTITL> * VAN DER WAALS = -29.383 ELECTROSTATIC = -44.6768 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2140" Parameter: CONF_N -> "8002" Comparing "2140" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2141" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755566 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763741 ATOM PAIRS WERE FOUND FOR ATOM LIST 42020 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29407 from a total of 763741 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2141 -81.77595 7.71615 0.70780 INTE EXTERN> -29.18284 -52.59311 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.776" Parameter: A <- "-81.776" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1828" Parameter: B <- "-29.1828" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5931" Parameter: C <- "-52.5931" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2141 TOTAL ENERGY = -81.776 RDTITL> * VAN DER WAALS = -29.1828 ELECTROSTATIC = -52.5931 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2141" Parameter: CONF_N -> "8002" Comparing "2141" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2142" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763741 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769171 ATOM PAIRS WERE FOUND FOR ATOM LIST 42298 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29707 from a total of 769171 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2142 -82.28040 0.50445 0.73243 INTE EXTERN> -27.20431 -55.07609 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.2804" Parameter: A <- "-82.2804" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2043" Parameter: B <- "-27.2043" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.0761" Parameter: C <- "-55.0761" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2142 TOTAL ENERGY = -82.2804 RDTITL> * VAN DER WAALS = -27.2043 ELECTROSTATIC = -55.0761 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2142" Parameter: CONF_N -> "8002" Comparing "2142" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2143" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769171 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765108 ATOM PAIRS WERE FOUND FOR ATOM LIST 42190 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29627 from a total of 765108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2143 -77.98960 -4.29080 0.71758 INTE EXTERN> -27.89626 -50.09334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9896" Parameter: A <- "-77.9896" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8963" Parameter: B <- "-27.8963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0933" Parameter: C <- "-50.0933" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2143 TOTAL ENERGY = -77.9896 RDTITL> * VAN DER WAALS = -27.8963 ELECTROSTATIC = -50.0933 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2143" Parameter: CONF_N -> "8002" Comparing "2143" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2144" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764339 ATOM PAIRS WERE FOUND FOR ATOM LIST 41933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29315 from a total of 764339 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2144 -76.23449 -1.75511 0.61336 INTE EXTERN> -31.95195 -44.28254 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2345" Parameter: A <- "-76.2345" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9519" Parameter: B <- "-31.9519" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2825" Parameter: C <- "-44.2825" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2144 TOTAL ENERGY = -76.2345 RDTITL> * VAN DER WAALS = -31.9519 ELECTROSTATIC = -44.2825 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2144" Parameter: CONF_N -> "8002" Comparing "2144" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2145" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764339 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767128 ATOM PAIRS WERE FOUND FOR ATOM LIST 42166 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29529 from a total of 767128 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2145 -77.39996 1.16547 0.68238 INTE EXTERN> -31.23791 -46.16205 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4" Parameter: A <- "-77.4" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2379" Parameter: B <- "-31.2379" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.162" Parameter: C <- "-46.162" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2145 TOTAL ENERGY = -77.4 RDTITL> * VAN DER WAALS = -31.2379 ELECTROSTATIC = -46.162 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2145" Parameter: CONF_N -> "8002" Comparing "2145" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2146" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767128 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763897 ATOM PAIRS WERE FOUND FOR ATOM LIST 41708 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29358 from a total of 763897 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2146 -72.00108 -5.39888 0.75215 INTE EXTERN> -25.32066 -46.68042 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0011" Parameter: A <- "-72.0011" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3207" Parameter: B <- "-25.3207" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6804" Parameter: C <- "-46.6804" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2146 TOTAL ENERGY = -72.0011 RDTITL> * VAN DER WAALS = -25.3207 ELECTROSTATIC = -46.6804 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2146" Parameter: CONF_N -> "8002" Comparing "2146" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2147" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763897 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761373 ATOM PAIRS WERE FOUND FOR ATOM LIST 41864 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29155 from a total of 761373 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2147 -74.60715 2.60607 0.66439 INTE EXTERN> -30.95521 -43.65195 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6072" Parameter: A <- "-74.6072" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9552" Parameter: B <- "-30.9552" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6519" Parameter: C <- "-43.6519" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2147 TOTAL ENERGY = -74.6072 RDTITL> * VAN DER WAALS = -30.9552 ELECTROSTATIC = -43.6519 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2147" Parameter: CONF_N -> "8002" Comparing "2147" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2148" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761373 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764146 ATOM PAIRS WERE FOUND FOR ATOM LIST 41898 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29869 from a total of 764146 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2148 -77.89039 3.28324 0.69130 INTE EXTERN> -30.19648 -47.69392 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8904" Parameter: A <- "-77.8904" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1965" Parameter: B <- "-30.1965" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6939" Parameter: C <- "-47.6939" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2148 TOTAL ENERGY = -77.8904 RDTITL> * VAN DER WAALS = -30.1965 ELECTROSTATIC = -47.6939 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2148" Parameter: CONF_N -> "8002" Comparing "2148" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2149" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764146 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763288 ATOM PAIRS WERE FOUND FOR ATOM LIST 41803 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28931 from a total of 763288 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2149 -74.00131 -3.88908 0.67607 INTE EXTERN> -29.88933 -44.11199 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0013" Parameter: A <- "-74.0013" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8893" Parameter: B <- "-29.8893" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.112" Parameter: C <- "-44.112" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2149 TOTAL ENERGY = -74.0013 RDTITL> * VAN DER WAALS = -29.8893 ELECTROSTATIC = -44.112 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2149" Parameter: CONF_N -> "8002" Comparing "2149" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2150" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763288 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761654 ATOM PAIRS WERE FOUND FOR ATOM LIST 41761 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28917 from a total of 761654 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2150 -68.75936 -5.24196 0.73231 INTE EXTERN> -25.28660 -43.47276 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7594" Parameter: A <- "-68.7594" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2866" Parameter: B <- "-25.2866" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4728" Parameter: C <- "-43.4728" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2150 TOTAL ENERGY = -68.7594 RDTITL> * VAN DER WAALS = -25.2866 ELECTROSTATIC = -43.4728 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2150" Parameter: CONF_N -> "8002" Comparing "2150" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2151" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761654 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763838 ATOM PAIRS WERE FOUND FOR ATOM LIST 42024 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29456 from a total of 763838 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2151 -73.22522 4.46587 0.69297 INTE EXTERN> -29.77083 -43.45439 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2252" Parameter: A <- "-73.2252" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7708" Parameter: B <- "-29.7708" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4544" Parameter: C <- "-43.4544" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2151 TOTAL ENERGY = -73.2252 RDTITL> * VAN DER WAALS = -29.7708 ELECTROSTATIC = -43.4544 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2151" Parameter: CONF_N -> "8002" Comparing "2151" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2152" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763838 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765215 ATOM PAIRS WERE FOUND FOR ATOM LIST 41890 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29453 from a total of 765215 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2152 -77.11118 3.88596 0.75493 INTE EXTERN> -28.58778 -48.52340 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1112" Parameter: A <- "-77.1112" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5878" Parameter: B <- "-28.5878" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5234" Parameter: C <- "-48.5234" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2152 TOTAL ENERGY = -77.1112 RDTITL> * VAN DER WAALS = -28.5878 ELECTROSTATIC = -48.5234 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2152" Parameter: CONF_N -> "8002" Comparing "2152" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2153" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765215 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770108 ATOM PAIRS WERE FOUND FOR ATOM LIST 42313 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29097 from a total of 770108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2153 -70.88391 -6.22727 0.73448 INTE EXTERN> -27.20481 -43.67910 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8839" Parameter: A <- "-70.8839" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2048" Parameter: B <- "-27.2048" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6791" Parameter: C <- "-43.6791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2153 TOTAL ENERGY = -70.8839 RDTITL> * VAN DER WAALS = -27.2048 ELECTROSTATIC = -43.6791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2153" Parameter: CONF_N -> "8002" Comparing "2153" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2154" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768216 ATOM PAIRS WERE FOUND FOR ATOM LIST 42006 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29796 from a total of 768216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2154 -72.39919 1.51528 0.67789 INTE EXTERN> -29.67697 -42.72222 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3992" Parameter: A <- "-72.3992" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.677" Parameter: B <- "-29.677" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7222" Parameter: C <- "-42.7222" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2154 TOTAL ENERGY = -72.3992 RDTITL> * VAN DER WAALS = -29.677 ELECTROSTATIC = -42.7222 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2154" Parameter: CONF_N -> "8002" Comparing "2154" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2155" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772788 ATOM PAIRS WERE FOUND FOR ATOM LIST 42397 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29622 from a total of 772788 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2155 -75.31523 2.91604 0.60937 INTE EXTERN> -32.58769 -42.72754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3152" Parameter: A <- "-75.3152" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5877" Parameter: B <- "-32.5877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7275" Parameter: C <- "-42.7275" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2155 TOTAL ENERGY = -75.3152 RDTITL> * VAN DER WAALS = -32.5877 ELECTROSTATIC = -42.7275 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2155" Parameter: CONF_N -> "8002" Comparing "2155" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2156" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772788 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762668 ATOM PAIRS WERE FOUND FOR ATOM LIST 41890 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29336 from a total of 762668 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2156 -80.36613 5.05089 0.78527 INTE EXTERN> -27.13269 -53.23343 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3661" Parameter: A <- "-80.3661" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1327" Parameter: B <- "-27.1327" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.2334" Parameter: C <- "-53.2334" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2156 TOTAL ENERGY = -80.3661 RDTITL> * VAN DER WAALS = -27.1327 ELECTROSTATIC = -53.2334 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2156" Parameter: CONF_N -> "8002" Comparing "2156" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2157" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762668 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760819 ATOM PAIRS WERE FOUND FOR ATOM LIST 41890 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29102 from a total of 760819 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2157 -79.15746 -1.20866 0.59281 INTE EXTERN> -34.29946 -44.85800 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1575" Parameter: A <- "-79.1575" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.2995" Parameter: B <- "-34.2995" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.858" Parameter: C <- "-44.858" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2157 TOTAL ENERGY = -79.1575 RDTITL> * VAN DER WAALS = -34.2995 ELECTROSTATIC = -44.858 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2157" Parameter: CONF_N -> "8002" Comparing "2157" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2158" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760819 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760962 ATOM PAIRS WERE FOUND FOR ATOM LIST 41629 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29351 from a total of 760962 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2158 -77.06296 -2.09450 0.62869 INTE EXTERN> -35.51387 -41.54909 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.063" Parameter: A <- "-77.063" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.5139" Parameter: B <- "-35.5139" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5491" Parameter: C <- "-41.5491" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2158 TOTAL ENERGY = -77.063 RDTITL> * VAN DER WAALS = -35.5139 ELECTROSTATIC = -41.5491 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2158" Parameter: CONF_N -> "8002" Comparing "2158" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2159" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760962 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762608 ATOM PAIRS WERE FOUND FOR ATOM LIST 41995 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29695 from a total of 762608 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2159 -71.06206 -6.00090 0.66467 INTE EXTERN> -29.32412 -41.73794 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0621" Parameter: A <- "-71.0621" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3241" Parameter: B <- "-29.3241" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7379" Parameter: C <- "-41.7379" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2159 TOTAL ENERGY = -71.0621 RDTITL> * VAN DER WAALS = -29.3241 ELECTROSTATIC = -41.7379 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2159" Parameter: CONF_N -> "8002" Comparing "2159" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2160" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762608 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758309 ATOM PAIRS WERE FOUND FOR ATOM LIST 41729 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29226 from a total of 758309 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2160 -76.46084 5.39878 0.67814 INTE EXTERN> -29.63819 -46.82266 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4608" Parameter: A <- "-76.4608" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6382" Parameter: B <- "-29.6382" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8227" Parameter: C <- "-46.8227" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2160 TOTAL ENERGY = -76.4608 RDTITL> * VAN DER WAALS = -29.6382 ELECTROSTATIC = -46.8227 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2160" Parameter: CONF_N -> "8002" Comparing "2160" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2161" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758309 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756098 ATOM PAIRS WERE FOUND FOR ATOM LIST 41649 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29306 from a total of 756098 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2161 -69.88116 -6.57968 0.67078 INTE EXTERN> -29.33701 -40.54415 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8812" Parameter: A <- "-69.8812" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.337" Parameter: B <- "-29.337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5442" Parameter: C <- "-40.5442" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2161 TOTAL ENERGY = -69.8812 RDTITL> * VAN DER WAALS = -29.337 ELECTROSTATIC = -40.5442 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2161" Parameter: CONF_N -> "8002" Comparing "2161" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2162" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756098 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760625 ATOM PAIRS WERE FOUND FOR ATOM LIST 42023 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29716 from a total of 760625 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2162 -73.79746 3.91629 0.65901 INTE EXTERN> -30.53304 -43.26442 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7975" Parameter: A <- "-73.7975" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.533" Parameter: B <- "-30.533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2644" Parameter: C <- "-43.2644" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2162 TOTAL ENERGY = -73.7975 RDTITL> * VAN DER WAALS = -30.533 ELECTROSTATIC = -43.2644 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2162" Parameter: CONF_N -> "8002" Comparing "2162" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2163" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760625 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758203 ATOM PAIRS WERE FOUND FOR ATOM LIST 41680 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29076 from a total of 758203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2163 -70.88604 -2.91142 0.67825 INTE EXTERN> -27.81808 -43.06796 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.886" Parameter: A <- "-70.886" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8181" Parameter: B <- "-27.8181" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.068" Parameter: C <- "-43.068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2163 TOTAL ENERGY = -70.886 RDTITL> * VAN DER WAALS = -27.8181 ELECTROSTATIC = -43.068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2163" Parameter: CONF_N -> "8002" Comparing "2163" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2164" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753902 ATOM PAIRS WERE FOUND FOR ATOM LIST 41650 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28656 from a total of 753902 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2164 -72.58248 1.69645 0.64967 INTE EXTERN> -30.56923 -42.01326 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5825" Parameter: A <- "-72.5825" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5692" Parameter: B <- "-30.5692" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0133" Parameter: C <- "-42.0133" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2164 TOTAL ENERGY = -72.5825 RDTITL> * VAN DER WAALS = -30.5692 ELECTROSTATIC = -42.0133 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2164" Parameter: CONF_N -> "8002" Comparing "2164" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2165" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753902 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759120 ATOM PAIRS WERE FOUND FOR ATOM LIST 41510 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29709 from a total of 759120 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2165 -78.03334 5.45086 0.77348 INTE EXTERN> -25.78926 -52.24409 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0333" Parameter: A <- "-78.0333" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7893" Parameter: B <- "-25.7893" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2441" Parameter: C <- "-52.2441" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2165 TOTAL ENERGY = -78.0333 RDTITL> * VAN DER WAALS = -25.7893 ELECTROSTATIC = -52.2441 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2165" Parameter: CONF_N -> "8002" Comparing "2165" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2166" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759120 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755810 ATOM PAIRS WERE FOUND FOR ATOM LIST 41505 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29010 from a total of 755810 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2166 -77.98405 -0.04930 0.68780 INTE EXTERN> -27.94937 -50.03468 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.984" Parameter: A <- "-77.984" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9494" Parameter: B <- "-27.9494" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0347" Parameter: C <- "-50.0347" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2166 TOTAL ENERGY = -77.984 RDTITL> * VAN DER WAALS = -27.9494 ELECTROSTATIC = -50.0347 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2166" Parameter: CONF_N -> "8002" Comparing "2166" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2167" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755810 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752966 ATOM PAIRS WERE FOUND FOR ATOM LIST 41307 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28752 from a total of 752966 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2167 -64.74124 -13.24281 0.57877 INTE EXTERN> -28.30253 -36.43871 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7412" Parameter: A <- "-64.7412" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3025" Parameter: B <- "-28.3025" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4387" Parameter: C <- "-36.4387" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2167 TOTAL ENERGY = -64.7412 RDTITL> * VAN DER WAALS = -28.3025 ELECTROSTATIC = -36.4387 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2167" Parameter: CONF_N -> "8002" Comparing "2167" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2168" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752966 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758681 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28901 from a total of 758681 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2168 -70.08566 5.34442 0.60003 INTE EXTERN> -30.60010 -39.48556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0857" Parameter: A <- "-70.0857" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6001" Parameter: B <- "-30.6001" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4856" Parameter: C <- "-39.4856" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2168 TOTAL ENERGY = -70.0857 RDTITL> * VAN DER WAALS = -30.6001 ELECTROSTATIC = -39.4856 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2168" Parameter: CONF_N -> "8002" Comparing "2168" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2169" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758681 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755348 ATOM PAIRS WERE FOUND FOR ATOM LIST 41643 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28852 from a total of 755348 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2169 -74.16942 4.08376 0.61551 INTE EXTERN> -29.17227 -44.99716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1694" Parameter: A <- "-74.1694" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1723" Parameter: B <- "-29.1723" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9972" Parameter: C <- "-44.9972" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2169 TOTAL ENERGY = -74.1694 RDTITL> * VAN DER WAALS = -29.1723 ELECTROSTATIC = -44.9972 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2169" Parameter: CONF_N -> "8002" Comparing "2169" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2170" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755348 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763070 ATOM PAIRS WERE FOUND FOR ATOM LIST 41972 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29275 from a total of 763070 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2170 -71.94808 -2.22134 0.63260 INTE EXTERN> -32.01324 -39.93484 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9481" Parameter: A <- "-71.9481" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0132" Parameter: B <- "-32.0132" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9348" Parameter: C <- "-39.9348" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2170 TOTAL ENERGY = -71.9481 RDTITL> * VAN DER WAALS = -32.0132 ELECTROSTATIC = -39.9348 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2170" Parameter: CONF_N -> "8002" Comparing "2170" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2171" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763070 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753702 ATOM PAIRS WERE FOUND FOR ATOM LIST 41476 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29314 from a total of 753702 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2171 -71.77307 -0.17501 0.68157 INTE EXTERN> -28.46463 -43.30844 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7731" Parameter: A <- "-71.7731" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4646" Parameter: B <- "-28.4646" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3084" Parameter: C <- "-43.3084" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2171 TOTAL ENERGY = -71.7731 RDTITL> * VAN DER WAALS = -28.4646 ELECTROSTATIC = -43.3084 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2171" Parameter: CONF_N -> "8002" Comparing "2171" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2172" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753702 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761509 ATOM PAIRS WERE FOUND FOR ATOM LIST 42056 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29605 from a total of 761509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2172 -75.17549 3.40242 0.65466 INTE EXTERN> -32.45343 -42.72206 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1755" Parameter: A <- "-75.1755" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4534" Parameter: B <- "-32.4534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7221" Parameter: C <- "-42.7221" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2172 TOTAL ENERGY = -75.1755 RDTITL> * VAN DER WAALS = -32.4534 ELECTROSTATIC = -42.7221 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2172" Parameter: CONF_N -> "8002" Comparing "2172" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2173" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759990 ATOM PAIRS WERE FOUND FOR ATOM LIST 41874 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29037 from a total of 759990 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2173 -72.52101 -2.65448 0.70669 INTE EXTERN> -28.31878 -44.20223 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.521" Parameter: A <- "-72.521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3188" Parameter: B <- "-28.3188" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2022" Parameter: C <- "-44.2022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2173 TOTAL ENERGY = -72.521 RDTITL> * VAN DER WAALS = -28.3188 ELECTROSTATIC = -44.2022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2173" Parameter: CONF_N -> "8002" Comparing "2173" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2174" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759990 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754479 ATOM PAIRS WERE FOUND FOR ATOM LIST 41579 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29350 from a total of 754479 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2174 -81.98788 9.46687 0.73697 INTE EXTERN> -27.39315 -54.59473 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9879" Parameter: A <- "-81.9879" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3932" Parameter: B <- "-27.3932" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.5947" Parameter: C <- "-54.5947" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2174 TOTAL ENERGY = -81.9879 RDTITL> * VAN DER WAALS = -27.3932 ELECTROSTATIC = -54.5947 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2174" Parameter: CONF_N -> "8002" Comparing "2174" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2175" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754479 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763444 ATOM PAIRS WERE FOUND FOR ATOM LIST 42193 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29123 from a total of 763444 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2175 -76.33272 -5.65516 0.69836 INTE EXTERN> -27.22347 -49.10925 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3327" Parameter: A <- "-76.3327" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2235" Parameter: B <- "-27.2235" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1092" Parameter: C <- "-49.1092" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2175 TOTAL ENERGY = -76.3327 RDTITL> * VAN DER WAALS = -27.2235 ELECTROSTATIC = -49.1092 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2175" Parameter: CONF_N -> "8002" Comparing "2175" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2176" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763444 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762924 ATOM PAIRS WERE FOUND FOR ATOM LIST 42017 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29815 from a total of 762924 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2176 -80.51927 4.18656 0.65050 INTE EXTERN> -29.85461 -50.66466 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5193" Parameter: A <- "-80.5193" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8546" Parameter: B <- "-29.8546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6647" Parameter: C <- "-50.6647" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2176 TOTAL ENERGY = -80.5193 RDTITL> * VAN DER WAALS = -29.8546 ELECTROSTATIC = -50.6647 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2176" Parameter: CONF_N -> "8002" Comparing "2176" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2177" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762924 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763005 ATOM PAIRS WERE FOUND FOR ATOM LIST 42097 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29737 from a total of 763005 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2177 -82.74785 2.22858 0.76322 INTE EXTERN> -29.70662 -53.04123 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7478" Parameter: A <- "-82.7478" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7066" Parameter: B <- "-29.7066" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0412" Parameter: C <- "-53.0412" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2177 TOTAL ENERGY = -82.7478 RDTITL> * VAN DER WAALS = -29.7066 ELECTROSTATIC = -53.0412 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2177" Parameter: CONF_N -> "8002" Comparing "2177" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2178" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763005 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 773421 ATOM PAIRS WERE FOUND FOR ATOM LIST 42362 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30458 from a total of 773421 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2178 -77.43792 -5.30993 0.75107 INTE EXTERN> -27.61249 -49.82543 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4379" Parameter: A <- "-77.4379" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6125" Parameter: B <- "-27.6125" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8254" Parameter: C <- "-49.8254" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2178 TOTAL ENERGY = -77.4379 RDTITL> * VAN DER WAALS = -27.6125 ELECTROSTATIC = -49.8254 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2178" Parameter: CONF_N -> "8002" Comparing "2178" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2179" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 773421 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766266 ATOM PAIRS WERE FOUND FOR ATOM LIST 42295 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29947 from a total of 766266 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2179 -93.64275 16.20483 0.81610 INTE EXTERN> -30.75833 -62.88442 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-93.6427" Parameter: A <- "-93.6427" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7583" Parameter: B <- "-30.7583" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-62.8844" Parameter: C <- "-62.8844" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2179 TOTAL ENERGY = -93.6427 RDTITL> * VAN DER WAALS = -30.7583 ELECTROSTATIC = -62.8844 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2179" Parameter: CONF_N -> "8002" Comparing "2179" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2180" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766266 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766497 ATOM PAIRS WERE FOUND FOR ATOM LIST 42227 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30157 from a total of 766497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2180 -83.83477 -9.80798 0.85847 INTE EXTERN> -25.43118 -58.40359 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.8348" Parameter: A <- "-83.8348" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4312" Parameter: B <- "-25.4312" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.4036" Parameter: C <- "-58.4036" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2180 TOTAL ENERGY = -83.8348 RDTITL> * VAN DER WAALS = -25.4312 ELECTROSTATIC = -58.4036 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2180" Parameter: CONF_N -> "8002" Comparing "2180" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2181" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767592 ATOM PAIRS WERE FOUND FOR ATOM LIST 42307 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29874 from a total of 767592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2181 -83.92643 0.09166 0.65029 INTE EXTERN> -29.08540 -54.84104 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.9264" Parameter: A <- "-83.9264" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0854" Parameter: B <- "-29.0854" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.841" Parameter: C <- "-54.841" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2181 TOTAL ENERGY = -83.9264 RDTITL> * VAN DER WAALS = -29.0854 ELECTROSTATIC = -54.841 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2181" Parameter: CONF_N -> "8002" Comparing "2181" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2182" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759430 ATOM PAIRS WERE FOUND FOR ATOM LIST 41872 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29775 from a total of 759430 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2182 -74.53786 -9.38857 0.74767 INTE EXTERN> -26.39556 -48.14231 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5379" Parameter: A <- "-74.5379" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3956" Parameter: B <- "-26.3956" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1423" Parameter: C <- "-48.1423" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2182 TOTAL ENERGY = -74.5379 RDTITL> * VAN DER WAALS = -26.3956 ELECTROSTATIC = -48.1423 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2182" Parameter: CONF_N -> "8002" Comparing "2182" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2183" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759430 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761290 ATOM PAIRS WERE FOUND FOR ATOM LIST 42047 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30519 from a total of 761290 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2183 -82.07754 7.53968 0.70456 INTE EXTERN> -29.10908 -52.96846 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.0775" Parameter: A <- "-82.0775" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1091" Parameter: B <- "-29.1091" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9685" Parameter: C <- "-52.9685" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2183 TOTAL ENERGY = -82.0775 RDTITL> * VAN DER WAALS = -29.1091 ELECTROSTATIC = -52.9685 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2183" Parameter: CONF_N -> "8002" Comparing "2183" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2184" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761290 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761718 ATOM PAIRS WERE FOUND FOR ATOM LIST 42010 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29838 from a total of 761718 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2184 -82.52195 0.44442 0.78781 INTE EXTERN> -27.18245 -55.33950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.522" Parameter: A <- "-82.522" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1825" Parameter: B <- "-27.1825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.3395" Parameter: C <- "-55.3395" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2184 TOTAL ENERGY = -82.522 RDTITL> * VAN DER WAALS = -27.1825 ELECTROSTATIC = -55.3395 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2184" Parameter: CONF_N -> "8002" Comparing "2184" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2185" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761718 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764118 ATOM PAIRS WERE FOUND FOR ATOM LIST 42086 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30693 from a total of 764118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2185 -83.58441 1.06245 0.67843 INTE EXTERN> -32.50325 -51.08115 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.5844" Parameter: A <- "-83.5844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5033" Parameter: B <- "-32.5033" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0812" Parameter: C <- "-51.0812" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2185 TOTAL ENERGY = -83.5844 RDTITL> * VAN DER WAALS = -32.5033 ELECTROSTATIC = -51.0812 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2185" Parameter: CONF_N -> "8002" Comparing "2185" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2186" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772483 ATOM PAIRS WERE FOUND FOR ATOM LIST 42610 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30833 from a total of 772483 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2186 -84.66925 1.08485 0.74912 INTE EXTERN> -31.88973 -52.77953 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.6693" Parameter: A <- "-84.6693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8897" Parameter: B <- "-31.8897" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.7795" Parameter: C <- "-52.7795" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2186 TOTAL ENERGY = -84.6693 RDTITL> * VAN DER WAALS = -31.8897 ELECTROSTATIC = -52.7795 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2186" Parameter: CONF_N -> "8002" Comparing "2186" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2187" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772483 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765547 ATOM PAIRS WERE FOUND FOR ATOM LIST 42101 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30101 from a total of 765547 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2187 -77.57727 -7.09198 0.70053 INTE EXTERN> -27.94281 -49.63446 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5773" Parameter: A <- "-77.5773" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9428" Parameter: B <- "-27.9428" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6345" Parameter: C <- "-49.6345" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2187 TOTAL ENERGY = -77.5773 RDTITL> * VAN DER WAALS = -27.9428 ELECTROSTATIC = -49.6345 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2187" Parameter: CONF_N -> "8002" Comparing "2187" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2188" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765547 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763133 ATOM PAIRS WERE FOUND FOR ATOM LIST 41939 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30370 from a total of 763133 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2188 -86.71445 9.13718 0.86906 INTE EXTERN> -25.16715 -61.54730 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.7144" Parameter: A <- "-86.7144" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1672" Parameter: B <- "-25.1672" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-61.5473" Parameter: C <- "-61.5473" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2188 TOTAL ENERGY = -86.7144 RDTITL> * VAN DER WAALS = -25.1672 ELECTROSTATIC = -61.5473 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2188" Parameter: CONF_N -> "8002" Comparing "2188" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2189" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763133 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762647 ATOM PAIRS WERE FOUND FOR ATOM LIST 42015 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29671 from a total of 762647 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2189 -77.74253 -8.97192 0.66711 INTE EXTERN> -30.48938 -47.25315 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7425" Parameter: A <- "-77.7425" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4894" Parameter: B <- "-30.4894" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2531" Parameter: C <- "-47.2531" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2189 TOTAL ENERGY = -77.7425 RDTITL> * VAN DER WAALS = -30.4894 ELECTROSTATIC = -47.2531 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2189" Parameter: CONF_N -> "8002" Comparing "2189" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2190" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762647 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763405 ATOM PAIRS WERE FOUND FOR ATOM LIST 42145 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29802 from a total of 763405 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2190 -85.87437 8.13184 0.68810 INTE EXTERN> -32.91467 -52.95970 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.8744" Parameter: A <- "-85.8744" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9147" Parameter: B <- "-32.9147" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9597" Parameter: C <- "-52.9597" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2190 TOTAL ENERGY = -85.8744 RDTITL> * VAN DER WAALS = -32.9147 ELECTROSTATIC = -52.9597 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2190" Parameter: CONF_N -> "8002" Comparing "2190" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2191" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763405 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765707 ATOM PAIRS WERE FOUND FOR ATOM LIST 42218 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30299 from a total of 765707 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2191 -82.94460 -2.92977 0.74853 INTE EXTERN> -29.62016 -53.32443 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9446" Parameter: A <- "-82.9446" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6202" Parameter: B <- "-29.6202" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3244" Parameter: C <- "-53.3244" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2191 TOTAL ENERGY = -82.9446 RDTITL> * VAN DER WAALS = -29.6202 ELECTROSTATIC = -53.3244 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2191" Parameter: CONF_N -> "8002" Comparing "2191" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2192" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765707 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762912 ATOM PAIRS WERE FOUND FOR ATOM LIST 42327 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29741 from a total of 762912 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2192 -82.53578 -0.40882 0.72590 INTE EXTERN> -31.29039 -51.24539 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5358" Parameter: A <- "-82.5358" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2904" Parameter: B <- "-31.2904" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2454" Parameter: C <- "-51.2454" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2192 TOTAL ENERGY = -82.5358 RDTITL> * VAN DER WAALS = -31.2904 ELECTROSTATIC = -51.2454 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2192" Parameter: CONF_N -> "8002" Comparing "2192" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2193" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762912 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764080 ATOM PAIRS WERE FOUND FOR ATOM LIST 42045 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30104 from a total of 764080 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2193 -87.46740 4.93162 0.73068 INTE EXTERN> -26.77394 -60.69346 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.4674" Parameter: A <- "-87.4674" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7739" Parameter: B <- "-26.7739" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-60.6935" Parameter: C <- "-60.6935" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2193 TOTAL ENERGY = -87.4674 RDTITL> * VAN DER WAALS = -26.7739 ELECTROSTATIC = -60.6935 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2193" Parameter: CONF_N -> "8002" Comparing "2193" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2194" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764080 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762079 ATOM PAIRS WERE FOUND FOR ATOM LIST 41970 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29428 from a total of 762079 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2194 -77.17109 -10.29630 0.65523 INTE EXTERN> -30.47197 -46.69913 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1711" Parameter: A <- "-77.1711" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.472" Parameter: B <- "-30.472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6991" Parameter: C <- "-46.6991" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2194 TOTAL ENERGY = -77.1711 RDTITL> * VAN DER WAALS = -30.472 ELECTROSTATIC = -46.6991 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2194" Parameter: CONF_N -> "8002" Comparing "2194" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2195" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762079 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761770 ATOM PAIRS WERE FOUND FOR ATOM LIST 41934 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29847 from a total of 761770 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2195 -77.93794 0.76685 0.79701 INTE EXTERN> -24.93556 -53.00238 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9379" Parameter: A <- "-77.9379" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9356" Parameter: B <- "-24.9356" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0024" Parameter: C <- "-53.0024" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2195 TOTAL ENERGY = -77.9379 RDTITL> * VAN DER WAALS = -24.9356 ELECTROSTATIC = -53.0024 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2195" Parameter: CONF_N -> "8002" Comparing "2195" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2196" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761770 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767091 ATOM PAIRS WERE FOUND FOR ATOM LIST 42082 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29789 from a total of 767091 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2196 -79.21693 1.27899 0.76438 INTE EXTERN> -28.16791 -51.04903 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2169" Parameter: A <- "-79.2169" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1679" Parameter: B <- "-28.1679" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.049" Parameter: C <- "-51.049" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2196 TOTAL ENERGY = -79.2169 RDTITL> * VAN DER WAALS = -28.1679 ELECTROSTATIC = -51.049 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2196" Parameter: CONF_N -> "8002" Comparing "2196" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2197" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767091 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762885 ATOM PAIRS WERE FOUND FOR ATOM LIST 41975 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29605 from a total of 762885 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2197 -82.38892 3.17198 0.79800 INTE EXTERN> -27.01923 -55.36969 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3889" Parameter: A <- "-82.3889" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0192" Parameter: B <- "-27.0192" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.3697" Parameter: C <- "-55.3697" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2197 TOTAL ENERGY = -82.3889 RDTITL> * VAN DER WAALS = -27.0192 ELECTROSTATIC = -55.3697 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2197" Parameter: CONF_N -> "8002" Comparing "2197" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2198" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762885 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769509 ATOM PAIRS WERE FOUND FOR ATOM LIST 42325 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29689 from a total of 769509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2198 -78.06688 -4.32204 0.66819 INTE EXTERN> -31.10854 -46.95834 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0669" Parameter: A <- "-78.0669" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1085" Parameter: B <- "-31.1085" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9583" Parameter: C <- "-46.9583" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2198 TOTAL ENERGY = -78.0669 RDTITL> * VAN DER WAALS = -31.1085 ELECTROSTATIC = -46.9583 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2198" Parameter: CONF_N -> "8002" Comparing "2198" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2199" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764308 ATOM PAIRS WERE FOUND FOR ATOM LIST 41916 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29887 from a total of 764308 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2199 -85.67010 7.60322 0.78495 INTE EXTERN> -27.74198 -57.92811 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.6701" Parameter: A <- "-85.6701" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.742" Parameter: B <- "-27.742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.9281" Parameter: C <- "-57.9281" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2199 TOTAL ENERGY = -85.6701 RDTITL> * VAN DER WAALS = -27.742 ELECTROSTATIC = -57.9281 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2199" Parameter: CONF_N -> "8002" Comparing "2199" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2200" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764308 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767145 ATOM PAIRS WERE FOUND FOR ATOM LIST 42021 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30301 from a total of 767145 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2200 -87.59092 1.92082 0.67977 INTE EXTERN> -32.35754 -55.23338 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.5909" Parameter: A <- "-87.5909" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3575" Parameter: B <- "-32.3575" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.2334" Parameter: C <- "-55.2334" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2200 TOTAL ENERGY = -87.5909 RDTITL> * VAN DER WAALS = -32.3575 ELECTROSTATIC = -55.2334 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2200" Parameter: CONF_N -> "8002" Comparing "2200" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2201" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767145 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766614 ATOM PAIRS WERE FOUND FOR ATOM LIST 42163 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29914 from a total of 766614 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2201 -86.09040 -1.50052 0.70651 INTE EXTERN> -30.12787 -55.96253 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.0904" Parameter: A <- "-86.0904" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1279" Parameter: B <- "-30.1279" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.9625" Parameter: C <- "-55.9625" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2201 TOTAL ENERGY = -86.0904 RDTITL> * VAN DER WAALS = -30.1279 ELECTROSTATIC = -55.9625 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2201" Parameter: CONF_N -> "8002" Comparing "2201" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2202" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766614 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763188 ATOM PAIRS WERE FOUND FOR ATOM LIST 42049 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30008 from a total of 763188 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2202 -77.58019 -8.51021 0.70433 INTE EXTERN> -31.11086 -46.46933 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5802" Parameter: A <- "-77.5802" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1109" Parameter: B <- "-31.1109" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4693" Parameter: C <- "-46.4693" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2202 TOTAL ENERGY = -77.5802 RDTITL> * VAN DER WAALS = -31.1109 ELECTROSTATIC = -46.4693 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2202" Parameter: CONF_N -> "8002" Comparing "2202" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2203" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763188 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766427 ATOM PAIRS WERE FOUND FOR ATOM LIST 42103 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30220 from a total of 766427 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2203 -77.50844 -0.07175 0.64369 INTE EXTERN> -31.74149 -45.76695 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5084" Parameter: A <- "-77.5084" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7415" Parameter: B <- "-31.7415" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7669" Parameter: C <- "-45.7669" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2203 TOTAL ENERGY = -77.5084 RDTITL> * VAN DER WAALS = -31.7415 ELECTROSTATIC = -45.7669 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2203" Parameter: CONF_N -> "8002" Comparing "2203" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2204" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766427 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768142 ATOM PAIRS WERE FOUND FOR ATOM LIST 42110 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30294 from a total of 768142 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2204 -72.73604 -4.77240 0.68114 INTE EXTERN> -29.49940 -43.23664 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.736" Parameter: A <- "-72.736" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4994" Parameter: B <- "-29.4994" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2366" Parameter: C <- "-43.2366" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2204 TOTAL ENERGY = -72.736 RDTITL> * VAN DER WAALS = -29.4994 ELECTROSTATIC = -43.2366 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2204" Parameter: CONF_N -> "8002" Comparing "2204" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2205" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768142 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767232 ATOM PAIRS WERE FOUND FOR ATOM LIST 42328 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29917 from a total of 767232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2205 -74.95989 2.22385 0.63423 INTE EXTERN> -32.84952 -42.11037 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9599" Parameter: A <- "-74.9599" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8495" Parameter: B <- "-32.8495" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1104" Parameter: C <- "-42.1104" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2205 TOTAL ENERGY = -74.9599 RDTITL> * VAN DER WAALS = -32.8495 ELECTROSTATIC = -42.1104 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2205" Parameter: CONF_N -> "8002" Comparing "2205" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2206" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768902 ATOM PAIRS WERE FOUND FOR ATOM LIST 42231 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29684 from a total of 768902 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2206 -79.48269 4.52279 0.72510 INTE EXTERN> -29.39781 -50.08488 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4827" Parameter: A <- "-79.4827" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3978" Parameter: B <- "-29.3978" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0849" Parameter: C <- "-50.0849" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2206 TOTAL ENERGY = -79.4827 RDTITL> * VAN DER WAALS = -29.3978 ELECTROSTATIC = -50.0849 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2206" Parameter: CONF_N -> "8002" Comparing "2206" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2207" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768902 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769147 ATOM PAIRS WERE FOUND FOR ATOM LIST 42393 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30340 from a total of 769147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2207 -77.69896 -1.78372 0.67037 INTE EXTERN> -32.39075 -45.30821 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.699" Parameter: A <- "-77.699" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3908" Parameter: B <- "-32.3908" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3082" Parameter: C <- "-45.3082" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2207 TOTAL ENERGY = -77.699 RDTITL> * VAN DER WAALS = -32.3908 ELECTROSTATIC = -45.3082 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2207" Parameter: CONF_N -> "8002" Comparing "2207" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2208" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770424 ATOM PAIRS WERE FOUND FOR ATOM LIST 42398 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30803 from a total of 770424 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2208 -75.95278 -1.74618 0.64138 INTE EXTERN> -32.27314 -43.67964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9528" Parameter: A <- "-75.9528" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2731" Parameter: B <- "-32.2731" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6796" Parameter: C <- "-43.6796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2208 TOTAL ENERGY = -75.9528 RDTITL> * VAN DER WAALS = -32.2731 ELECTROSTATIC = -43.6796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2208" Parameter: CONF_N -> "8002" Comparing "2208" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2209" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770424 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758270 ATOM PAIRS WERE FOUND FOR ATOM LIST 41715 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30301 from a total of 758270 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2209 -75.67912 -0.27366 0.77112 INTE EXTERN> -26.11747 -49.56165 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6791" Parameter: A <- "-75.6791" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1175" Parameter: B <- "-26.1175" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5617" Parameter: C <- "-49.5617" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2209 TOTAL ENERGY = -75.6791 RDTITL> * VAN DER WAALS = -26.1175 ELECTROSTATIC = -49.5617 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2209" Parameter: CONF_N -> "8002" Comparing "2209" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2210" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758270 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760489 ATOM PAIRS WERE FOUND FOR ATOM LIST 41531 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29690 from a total of 760489 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2210 -84.40701 8.72789 0.63825 INTE EXTERN> -32.13846 -52.26855 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.407" Parameter: A <- "-84.407" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1385" Parameter: B <- "-32.1385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2686" Parameter: C <- "-52.2686" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2210 TOTAL ENERGY = -84.407 RDTITL> * VAN DER WAALS = -32.1385 ELECTROSTATIC = -52.2686 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2210" Parameter: CONF_N -> "8002" Comparing "2210" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2211" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760489 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763610 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30161 from a total of 763610 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2211 -85.16216 0.75515 0.63154 INTE EXTERN> -34.92603 -50.23613 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.1622" Parameter: A <- "-85.1622" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.926" Parameter: B <- "-34.926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2361" Parameter: C <- "-50.2361" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2211 TOTAL ENERGY = -85.1622 RDTITL> * VAN DER WAALS = -34.926 ELECTROSTATIC = -50.2361 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2211" Parameter: CONF_N -> "8002" Comparing "2211" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2212" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763610 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765180 ATOM PAIRS WERE FOUND FOR ATOM LIST 41902 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30010 from a total of 765180 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2212 -78.68634 -6.47582 0.72956 INTE EXTERN> -28.27893 -50.40741 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6863" Parameter: A <- "-78.6863" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2789" Parameter: B <- "-28.2789" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4074" Parameter: C <- "-50.4074" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2212 TOTAL ENERGY = -78.6863 RDTITL> * VAN DER WAALS = -28.2789 ELECTROSTATIC = -50.4074 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2212" Parameter: CONF_N -> "8002" Comparing "2212" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2213" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765180 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765388 ATOM PAIRS WERE FOUND FOR ATOM LIST 41975 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30228 from a total of 765388 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2213 -82.68066 3.99433 0.66507 INTE EXTERN> -33.50337 -49.17730 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.6807" Parameter: A <- "-82.6807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5034" Parameter: B <- "-33.5034" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1773" Parameter: C <- "-49.1773" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2213 TOTAL ENERGY = -82.6807 RDTITL> * VAN DER WAALS = -33.5034 ELECTROSTATIC = -49.1773 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2213" Parameter: CONF_N -> "8002" Comparing "2213" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2214" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765388 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763982 ATOM PAIRS WERE FOUND FOR ATOM LIST 41878 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30424 from a total of 763982 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2214 -81.61291 -1.06776 0.77842 INTE EXTERN> -29.50570 -52.10721 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6129" Parameter: A <- "-81.6129" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5057" Parameter: B <- "-29.5057" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1072" Parameter: C <- "-52.1072" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2214 TOTAL ENERGY = -81.6129 RDTITL> * VAN DER WAALS = -29.5057 ELECTROSTATIC = -52.1072 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2214" Parameter: CONF_N -> "8002" Comparing "2214" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2215" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763982 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757913 ATOM PAIRS WERE FOUND FOR ATOM LIST 41518 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29718 from a total of 757913 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2215 -77.93156 -3.68135 0.70976 INTE EXTERN> -30.24012 -47.69144 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9316" Parameter: A <- "-77.9316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2401" Parameter: B <- "-30.2401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6914" Parameter: C <- "-47.6914" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2215 TOTAL ENERGY = -77.9316 RDTITL> * VAN DER WAALS = -30.2401 ELECTROSTATIC = -47.6914 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2215" Parameter: CONF_N -> "8002" Comparing "2215" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2216" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757913 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763637 ATOM PAIRS WERE FOUND FOR ATOM LIST 42065 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29931 from a total of 763637 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2216 -83.42122 5.48966 0.71041 INTE EXTERN> -30.30017 -53.12105 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.4212" Parameter: A <- "-83.4212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3002" Parameter: B <- "-30.3002" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.1211" Parameter: C <- "-53.1211" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2216 TOTAL ENERGY = -83.4212 RDTITL> * VAN DER WAALS = -30.3002 ELECTROSTATIC = -53.1211 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2216" Parameter: CONF_N -> "8002" Comparing "2216" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2217" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763637 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767190 ATOM PAIRS WERE FOUND FOR ATOM LIST 42128 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29651 from a total of 767190 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2217 -82.12168 -1.29954 0.68549 INTE EXTERN> -31.67934 -50.44234 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.1217" Parameter: A <- "-82.1217" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6793" Parameter: B <- "-31.6793" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4423" Parameter: C <- "-50.4423" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2217 TOTAL ENERGY = -82.1217 RDTITL> * VAN DER WAALS = -31.6793 ELECTROSTATIC = -50.4423 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2217" Parameter: CONF_N -> "8002" Comparing "2217" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2218" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767190 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765353 ATOM PAIRS WERE FOUND FOR ATOM LIST 42085 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29821 from a total of 765353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2218 -85.40162 3.27995 0.72480 INTE EXTERN> -31.23451 -54.16711 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.4016" Parameter: A <- "-85.4016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2345" Parameter: B <- "-31.2345" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.1671" Parameter: C <- "-54.1671" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2218 TOTAL ENERGY = -85.4016 RDTITL> * VAN DER WAALS = -31.2345 ELECTROSTATIC = -54.1671 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2218" Parameter: CONF_N -> "8002" Comparing "2218" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2219" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769867 ATOM PAIRS WERE FOUND FOR ATOM LIST 42242 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29808 from a total of 769867 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2219 -74.96889 -10.43273 0.75890 INTE EXTERN> -27.57939 -47.38950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9689" Parameter: A <- "-74.9689" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5794" Parameter: B <- "-27.5794" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3895" Parameter: C <- "-47.3895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2219 TOTAL ENERGY = -74.9689 RDTITL> * VAN DER WAALS = -27.5794 ELECTROSTATIC = -47.3895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2219" Parameter: CONF_N -> "8002" Comparing "2219" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2220" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769867 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762101 ATOM PAIRS WERE FOUND FOR ATOM LIST 41893 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29655 from a total of 762101 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2220 -75.69446 0.72557 0.62144 INTE EXTERN> -33.46549 -42.22897 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6945" Parameter: A <- "-75.6945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4655" Parameter: B <- "-33.4655" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.229" Parameter: C <- "-42.229" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2220 TOTAL ENERGY = -75.6945 RDTITL> * VAN DER WAALS = -33.4655 ELECTROSTATIC = -42.229 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2220" Parameter: CONF_N -> "8002" Comparing "2220" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2221" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762101 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765427 ATOM PAIRS WERE FOUND FOR ATOM LIST 41914 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30359 from a total of 765427 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2221 -75.23163 -0.46284 0.69265 INTE EXTERN> -29.29650 -45.93513 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2316" Parameter: A <- "-75.2316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2965" Parameter: B <- "-29.2965" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9351" Parameter: C <- "-45.9351" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2221 TOTAL ENERGY = -75.2316 RDTITL> * VAN DER WAALS = -29.2965 ELECTROSTATIC = -45.9351 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2221" Parameter: CONF_N -> "8002" Comparing "2221" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2222" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765427 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765354 ATOM PAIRS WERE FOUND FOR ATOM LIST 42082 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29909 from a total of 765354 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2222 -83.01681 7.78519 0.71167 INTE EXTERN> -32.48045 -50.53636 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.0168" Parameter: A <- "-83.0168" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4805" Parameter: B <- "-32.4805" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5364" Parameter: C <- "-50.5364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2222 TOTAL ENERGY = -83.0168 RDTITL> * VAN DER WAALS = -32.4805 ELECTROSTATIC = -50.5364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2222" Parameter: CONF_N -> "8002" Comparing "2222" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2223" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765354 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762464 ATOM PAIRS WERE FOUND FOR ATOM LIST 42023 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29953 from a total of 762464 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2223 -79.20127 -3.81554 0.81480 INTE EXTERN> -23.60703 -55.59424 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2013" Parameter: A <- "-79.2013" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.607" Parameter: B <- "-23.607" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.5942" Parameter: C <- "-55.5942" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2223 TOTAL ENERGY = -79.2013 RDTITL> * VAN DER WAALS = -23.607 ELECTROSTATIC = -55.5942 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2223" Parameter: CONF_N -> "8002" Comparing "2223" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2224" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762464 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759924 ATOM PAIRS WERE FOUND FOR ATOM LIST 41801 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29208 from a total of 759924 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2224 -73.49255 -5.70872 0.63345 INTE EXTERN> -32.37590 -41.11665 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4926" Parameter: A <- "-73.4926" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3759" Parameter: B <- "-32.3759" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1167" Parameter: C <- "-41.1167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2224 TOTAL ENERGY = -73.4926 RDTITL> * VAN DER WAALS = -32.3759 ELECTROSTATIC = -41.1167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2224" Parameter: CONF_N -> "8002" Comparing "2224" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2225" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759924 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763514 ATOM PAIRS WERE FOUND FOR ATOM LIST 41816 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 763514 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2225 -83.58312 10.09057 0.70331 INTE EXTERN> -32.11533 -51.46780 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.5831" Parameter: A <- "-83.5831" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1153" Parameter: B <- "-32.1153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4678" Parameter: C <- "-51.4678" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2225 TOTAL ENERGY = -83.5831 RDTITL> * VAN DER WAALS = -32.1153 ELECTROSTATIC = -51.4678 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2225" Parameter: CONF_N -> "8002" Comparing "2225" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2226" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763514 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759426 ATOM PAIRS WERE FOUND FOR ATOM LIST 41761 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29603 from a total of 759426 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2226 -86.47398 2.89085 0.72631 INTE EXTERN> -31.20613 -55.26784 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.474" Parameter: A <- "-86.474" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2061" Parameter: B <- "-31.2061" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.2678" Parameter: C <- "-55.2678" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2226 TOTAL ENERGY = -86.474 RDTITL> * VAN DER WAALS = -31.2061 ELECTROSTATIC = -55.2678 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2226" Parameter: CONF_N -> "8002" Comparing "2226" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2227" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759426 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761646 ATOM PAIRS WERE FOUND FOR ATOM LIST 41907 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29985 from a total of 761646 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2227 -69.81492 -16.65906 0.82800 INTE EXTERN> -26.00846 -43.80646 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8149" Parameter: A <- "-69.8149" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0085" Parameter: B <- "-26.0085" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8065" Parameter: C <- "-43.8065" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2227 TOTAL ENERGY = -69.8149 RDTITL> * VAN DER WAALS = -26.0085 ELECTROSTATIC = -43.8065 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2227" Parameter: CONF_N -> "8002" Comparing "2227" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2228" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761646 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764845 ATOM PAIRS WERE FOUND FOR ATOM LIST 42095 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29972 from a total of 764845 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2228 -82.93504 13.12012 0.67768 INTE EXTERN> -32.17566 -50.75938 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.935" Parameter: A <- "-82.935" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1757" Parameter: B <- "-32.1757" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7594" Parameter: C <- "-50.7594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2228 TOTAL ENERGY = -82.935 RDTITL> * VAN DER WAALS = -32.1757 ELECTROSTATIC = -50.7594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2228" Parameter: CONF_N -> "8002" Comparing "2228" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2229" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764845 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761653 ATOM PAIRS WERE FOUND FOR ATOM LIST 42038 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29722 from a total of 761653 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2229 -74.30525 -8.62979 0.71563 INTE EXTERN> -30.95489 -43.35036 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3052" Parameter: A <- "-74.3052" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9549" Parameter: B <- "-30.9549" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3504" Parameter: C <- "-43.3504" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2229 TOTAL ENERGY = -74.3052 RDTITL> * VAN DER WAALS = -30.9549 ELECTROSTATIC = -43.3504 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2229" Parameter: CONF_N -> "8002" Comparing "2229" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2230" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761653 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761680 ATOM PAIRS WERE FOUND FOR ATOM LIST 41691 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30002 from a total of 761680 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2230 -79.21332 4.90807 0.78993 INTE EXTERN> -27.50126 -51.71206 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2133" Parameter: A <- "-79.2133" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5013" Parameter: B <- "-27.5013" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7121" Parameter: C <- "-51.7121" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2230 TOTAL ENERGY = -79.2133 RDTITL> * VAN DER WAALS = -27.5013 ELECTROSTATIC = -51.7121 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2230" Parameter: CONF_N -> "8002" Comparing "2230" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2231" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761680 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765488 ATOM PAIRS WERE FOUND FOR ATOM LIST 42051 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30282 from a total of 765488 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2231 -80.80323 1.58991 0.73176 INTE EXTERN> -30.55332 -50.24991 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.8032" Parameter: A <- "-80.8032" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5533" Parameter: B <- "-30.5533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2499" Parameter: C <- "-50.2499" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2231 TOTAL ENERGY = -80.8032 RDTITL> * VAN DER WAALS = -30.5533 ELECTROSTATIC = -50.2499 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2231" Parameter: CONF_N -> "8002" Comparing "2231" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2232" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765488 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757211 ATOM PAIRS WERE FOUND FOR ATOM LIST 41575 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29294 from a total of 757211 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2232 -81.50462 0.70139 0.78513 INTE EXTERN> -29.87467 -51.62995 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5046" Parameter: A <- "-81.5046" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8747" Parameter: B <- "-29.8747" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.63" Parameter: C <- "-51.63" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2232 TOTAL ENERGY = -81.5046 RDTITL> * VAN DER WAALS = -29.8747 ELECTROSTATIC = -51.63 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2232" Parameter: CONF_N -> "8002" Comparing "2232" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2233" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757211 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756202 ATOM PAIRS WERE FOUND FOR ATOM LIST 41636 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29684 from a total of 756202 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2233 -77.61156 -3.89306 0.69483 INTE EXTERN> -30.45904 -47.15252 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6116" Parameter: A <- "-77.6116" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.459" Parameter: B <- "-30.459" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1525" Parameter: C <- "-47.1525" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2233 TOTAL ENERGY = -77.6116 RDTITL> * VAN DER WAALS = -30.459 ELECTROSTATIC = -47.1525 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2233" Parameter: CONF_N -> "8002" Comparing "2233" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2234" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756202 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759938 ATOM PAIRS WERE FOUND FOR ATOM LIST 41813 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29773 from a total of 759938 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2234 -77.99431 0.38276 0.59667 INTE EXTERN> -34.89206 -43.10225 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9943" Parameter: A <- "-77.9943" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.8921" Parameter: B <- "-34.8921" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1022" Parameter: C <- "-43.1022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2234 TOTAL ENERGY = -77.9943 RDTITL> * VAN DER WAALS = -34.8921 ELECTROSTATIC = -43.1022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2234" Parameter: CONF_N -> "8002" Comparing "2234" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2235" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759938 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761635 ATOM PAIRS WERE FOUND FOR ATOM LIST 41932 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29990 from a total of 761635 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2235 -83.36069 5.36638 0.73771 INTE EXTERN> -31.11035 -52.25034 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.3607" Parameter: A <- "-83.3607" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1104" Parameter: B <- "-31.1104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2503" Parameter: C <- "-52.2503" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2235 TOTAL ENERGY = -83.3607 RDTITL> * VAN DER WAALS = -31.1104 ELECTROSTATIC = -52.2503 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2235" Parameter: CONF_N -> "8002" Comparing "2235" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2236" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761635 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756551 ATOM PAIRS WERE FOUND FOR ATOM LIST 41682 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29261 from a total of 756551 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2236 -82.81017 -0.55052 0.71591 INTE EXTERN> -31.48393 -51.32624 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.8102" Parameter: A <- "-82.8102" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4839" Parameter: B <- "-31.4839" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3262" Parameter: C <- "-51.3262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2236 TOTAL ENERGY = -82.8102 RDTITL> * VAN DER WAALS = -31.4839 ELECTROSTATIC = -51.3262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2236" Parameter: CONF_N -> "8002" Comparing "2236" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2237" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756551 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41667 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29419 from a total of 759110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2237 -81.19000 -1.62017 0.65132 INTE EXTERN> -32.11480 -49.07520 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.19" Parameter: A <- "-81.19" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1148" Parameter: B <- "-32.1148" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0752" Parameter: C <- "-49.0752" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2237 TOTAL ENERGY = -81.19 RDTITL> * VAN DER WAALS = -32.1148 ELECTROSTATIC = -49.0752 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2237" Parameter: CONF_N -> "8002" Comparing "2237" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2238" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760973 ATOM PAIRS WERE FOUND FOR ATOM LIST 41778 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29939 from a total of 760973 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2238 -71.31426 -9.87574 0.69704 INTE EXTERN> -26.14188 -45.17238 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3143" Parameter: A <- "-71.3143" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1419" Parameter: B <- "-26.1419" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1724" Parameter: C <- "-45.1724" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2238 TOTAL ENERGY = -71.3143 RDTITL> * VAN DER WAALS = -26.1419 ELECTROSTATIC = -45.1724 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2238" Parameter: CONF_N -> "8002" Comparing "2238" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2239" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760973 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755439 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29911 from a total of 755439 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2239 -75.50911 4.19485 0.66110 INTE EXTERN> -29.04947 -46.45964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5091" Parameter: A <- "-75.5091" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0495" Parameter: B <- "-29.0495" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4596" Parameter: C <- "-46.4596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2239 TOTAL ENERGY = -75.5091 RDTITL> * VAN DER WAALS = -29.0495 ELECTROSTATIC = -46.4596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2239" Parameter: CONF_N -> "8002" Comparing "2239" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2240" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755439 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757160 ATOM PAIRS WERE FOUND FOR ATOM LIST 41566 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30023 from a total of 757160 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2240 -80.68062 5.17151 0.64570 INTE EXTERN> -33.67846 -47.00216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6806" Parameter: A <- "-80.6806" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6785" Parameter: B <- "-33.6785" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0022" Parameter: C <- "-47.0022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2240 TOTAL ENERGY = -80.6806 RDTITL> * VAN DER WAALS = -33.6785 ELECTROSTATIC = -47.0022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2240" Parameter: CONF_N -> "8002" Comparing "2240" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2241" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757160 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756327 ATOM PAIRS WERE FOUND FOR ATOM LIST 41669 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29604 from a total of 756327 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2241 -76.32995 -4.35067 0.71657 INTE EXTERN> -29.18505 -47.14490 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3299" Parameter: A <- "-76.3299" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1851" Parameter: B <- "-29.1851" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1449" Parameter: C <- "-47.1449" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2241 TOTAL ENERGY = -76.3299 RDTITL> * VAN DER WAALS = -29.1851 ELECTROSTATIC = -47.1449 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2241" Parameter: CONF_N -> "8002" Comparing "2241" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2242" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756327 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753130 ATOM PAIRS WERE FOUND FOR ATOM LIST 41403 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29557 from a total of 753130 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2242 -79.34524 3.01529 0.71419 INTE EXTERN> -30.16565 -49.17959 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.3452" Parameter: A <- "-79.3452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1656" Parameter: B <- "-30.1656" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1796" Parameter: C <- "-49.1796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2242 TOTAL ENERGY = -79.3452 RDTITL> * VAN DER WAALS = -30.1656 ELECTROSTATIC = -49.1796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2242" Parameter: CONF_N -> "8002" Comparing "2242" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2243" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753130 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756821 ATOM PAIRS WERE FOUND FOR ATOM LIST 41554 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29295 from a total of 756821 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2243 -76.98983 -2.35541 0.75431 INTE EXTERN> -27.05479 -49.93504 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9898" Parameter: A <- "-76.9898" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0548" Parameter: B <- "-27.0548" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.935" Parameter: C <- "-49.935" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2243 TOTAL ENERGY = -76.9898 RDTITL> * VAN DER WAALS = -27.0548 ELECTROSTATIC = -49.935 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2243" Parameter: CONF_N -> "8002" Comparing "2243" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2244" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756821 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758540 ATOM PAIRS WERE FOUND FOR ATOM LIST 41828 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29737 from a total of 758540 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2244 -77.29672 0.30689 0.75308 INTE EXTERN> -27.88562 -49.41110 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2967" Parameter: A <- "-77.2967" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8856" Parameter: B <- "-27.8856" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4111" Parameter: C <- "-49.4111" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2244 TOTAL ENERGY = -77.2967 RDTITL> * VAN DER WAALS = -27.8856 ELECTROSTATIC = -49.4111 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2244" Parameter: CONF_N -> "8002" Comparing "2244" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2245" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758540 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758725 ATOM PAIRS WERE FOUND FOR ATOM LIST 41666 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29290 from a total of 758725 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2245 -75.47174 -1.82498 0.61874 INTE EXTERN> -30.75608 -44.71566 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4717" Parameter: A <- "-75.4717" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7561" Parameter: B <- "-30.7561" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7157" Parameter: C <- "-44.7157" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2245 TOTAL ENERGY = -75.4717 RDTITL> * VAN DER WAALS = -30.7561 ELECTROSTATIC = -44.7157 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2245" Parameter: CONF_N -> "8002" Comparing "2245" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2246" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758725 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769893 ATOM PAIRS WERE FOUND FOR ATOM LIST 42411 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29994 from a total of 769893 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2246 -77.75019 2.27845 0.66403 INTE EXTERN> -33.31075 -44.43944 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7502" Parameter: A <- "-77.7502" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3108" Parameter: B <- "-33.3108" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4394" Parameter: C <- "-44.4394" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2246 TOTAL ENERGY = -77.7502 RDTITL> * VAN DER WAALS = -33.3108 ELECTROSTATIC = -44.4394 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2246" Parameter: CONF_N -> "8002" Comparing "2246" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2247" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769893 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764274 ATOM PAIRS WERE FOUND FOR ATOM LIST 42124 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30680 from a total of 764274 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2247 -81.48485 3.73465 0.68482 INTE EXTERN> -30.20982 -51.27503 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4848" Parameter: A <- "-81.4848" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2098" Parameter: B <- "-30.2098" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.275" Parameter: C <- "-51.275" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2247 TOTAL ENERGY = -81.4848 RDTITL> * VAN DER WAALS = -30.2098 ELECTROSTATIC = -51.275 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2247" Parameter: CONF_N -> "8002" Comparing "2247" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2248" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764274 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762880 ATOM PAIRS WERE FOUND FOR ATOM LIST 41835 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29310 from a total of 762880 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2248 -75.96102 -5.52383 0.75056 INTE EXTERN> -23.71131 -52.24970 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.961" Parameter: A <- "-75.961" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7113" Parameter: B <- "-23.7113" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2497" Parameter: C <- "-52.2497" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2248 TOTAL ENERGY = -75.961 RDTITL> * VAN DER WAALS = -23.7113 ELECTROSTATIC = -52.2497 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2248" Parameter: CONF_N -> "8002" Comparing "2248" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2249" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762880 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759176 ATOM PAIRS WERE FOUND FOR ATOM LIST 41819 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29949 from a total of 759176 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2249 -81.67512 5.71410 0.67091 INTE EXTERN> -32.44671 -49.22842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6751" Parameter: A <- "-81.6751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4467" Parameter: B <- "-32.4467" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2284" Parameter: C <- "-49.2284" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2249 TOTAL ENERGY = -81.6751 RDTITL> * VAN DER WAALS = -32.4467 ELECTROSTATIC = -49.2284 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2249" Parameter: CONF_N -> "8002" Comparing "2249" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2250" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759176 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760603 ATOM PAIRS WERE FOUND FOR ATOM LIST 41902 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29589 from a total of 760603 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2250 -79.92210 -1.75302 0.70328 INTE EXTERN> -30.72224 -49.19986 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9221" Parameter: A <- "-79.9221" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7222" Parameter: B <- "-30.7222" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1999" Parameter: C <- "-49.1999" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2250 TOTAL ENERGY = -79.9221 RDTITL> * VAN DER WAALS = -30.7222 ELECTROSTATIC = -49.1999 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2250" Parameter: CONF_N -> "8002" Comparing "2250" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2251" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760603 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759467 ATOM PAIRS WERE FOUND FOR ATOM LIST 41876 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29874 from a total of 759467 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2251 -84.03906 4.11696 0.73677 INTE EXTERN> -30.41281 -53.62625 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.0391" Parameter: A <- "-84.0391" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4128" Parameter: B <- "-30.4128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6262" Parameter: C <- "-53.6262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2251 TOTAL ENERGY = -84.0391 RDTITL> * VAN DER WAALS = -30.4128 ELECTROSTATIC = -53.6262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2251" Parameter: CONF_N -> "8002" Comparing "2251" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2252" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759467 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760886 ATOM PAIRS WERE FOUND FOR ATOM LIST 41707 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29517 from a total of 760886 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2252 -80.16063 -3.87842 0.66196 INTE EXTERN> -31.71169 -48.44895 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1606" Parameter: A <- "-80.1606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7117" Parameter: B <- "-31.7117" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4489" Parameter: C <- "-48.4489" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2252 TOTAL ENERGY = -80.1606 RDTITL> * VAN DER WAALS = -31.7117 ELECTROSTATIC = -48.4489 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2252" Parameter: CONF_N -> "8002" Comparing "2252" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2253" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760886 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762587 ATOM PAIRS WERE FOUND FOR ATOM LIST 42001 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29915 from a total of 762587 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2253 -85.03088 4.87025 0.68014 INTE EXTERN> -30.67309 -54.35779 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.0309" Parameter: A <- "-85.0309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6731" Parameter: B <- "-30.6731" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.3578" Parameter: C <- "-54.3578" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2253 TOTAL ENERGY = -85.0309 RDTITL> * VAN DER WAALS = -30.6731 ELECTROSTATIC = -54.3578 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2253" Parameter: CONF_N -> "8002" Comparing "2253" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2254" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762587 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759227 ATOM PAIRS WERE FOUND FOR ATOM LIST 41663 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29870 from a total of 759227 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2254 -82.00246 -3.02842 0.75660 INTE EXTERN> -25.54214 -56.46032 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.0025" Parameter: A <- "-82.0025" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5421" Parameter: B <- "-25.5421" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.4603" Parameter: C <- "-56.4603" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2254 TOTAL ENERGY = -82.0025 RDTITL> * VAN DER WAALS = -25.5421 ELECTROSTATIC = -56.4603 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2254" Parameter: CONF_N -> "8002" Comparing "2254" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2255" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759227 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762808 ATOM PAIRS WERE FOUND FOR ATOM LIST 41918 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29629 from a total of 762808 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2255 -79.96023 -2.04223 0.80710 INTE EXTERN> -26.86846 -53.09176 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9602" Parameter: A <- "-79.9602" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8685" Parameter: B <- "-26.8685" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0918" Parameter: C <- "-53.0918" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2255 TOTAL ENERGY = -79.9602 RDTITL> * VAN DER WAALS = -26.8685 ELECTROSTATIC = -53.0918 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2255" Parameter: CONF_N -> "8002" Comparing "2255" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2256" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762808 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766415 ATOM PAIRS WERE FOUND FOR ATOM LIST 42093 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29638 from a total of 766415 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2256 -80.57248 0.61225 0.70056 INTE EXTERN> -30.72785 -49.84463 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5725" Parameter: A <- "-80.5725" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7278" Parameter: B <- "-30.7278" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8446" Parameter: C <- "-49.8446" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2256 TOTAL ENERGY = -80.5725 RDTITL> * VAN DER WAALS = -30.7278 ELECTROSTATIC = -49.8446 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2256" Parameter: CONF_N -> "8002" Comparing "2256" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2257" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766415 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764448 ATOM PAIRS WERE FOUND FOR ATOM LIST 42020 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29594 from a total of 764448 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2257 -78.62419 -1.94829 0.61734 INTE EXTERN> -32.32373 -46.30045 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6242" Parameter: A <- "-78.6242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3237" Parameter: B <- "-32.3237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3005" Parameter: C <- "-46.3005" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2257 TOTAL ENERGY = -78.6242 RDTITL> * VAN DER WAALS = -32.3237 ELECTROSTATIC = -46.3005 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2257" Parameter: CONF_N -> "8002" Comparing "2257" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2258" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764448 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764234 ATOM PAIRS WERE FOUND FOR ATOM LIST 42053 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29988 from a total of 764234 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2258 -82.83114 4.20696 0.73829 INTE EXTERN> -29.80069 -53.03045 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.8311" Parameter: A <- "-82.8311" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8007" Parameter: B <- "-29.8007" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0305" Parameter: C <- "-53.0305" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2258 TOTAL ENERGY = -82.8311 RDTITL> * VAN DER WAALS = -29.8007 ELECTROSTATIC = -53.0305 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2258" Parameter: CONF_N -> "8002" Comparing "2258" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2259" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764234 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765476 ATOM PAIRS WERE FOUND FOR ATOM LIST 42009 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29866 from a total of 765476 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2259 -81.82418 -1.00696 0.75546 INTE EXTERN> -26.21172 -55.61246 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8242" Parameter: A <- "-81.8242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2117" Parameter: B <- "-26.2117" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.6125" Parameter: C <- "-55.6125" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2259 TOTAL ENERGY = -81.8242 RDTITL> * VAN DER WAALS = -26.2117 ELECTROSTATIC = -55.6125 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2259" Parameter: CONF_N -> "8002" Comparing "2259" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2260" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765476 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761080 ATOM PAIRS WERE FOUND FOR ATOM LIST 42078 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29776 from a total of 761080 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2260 -83.78636 1.96218 0.73190 INTE EXTERN> -30.95015 -52.83621 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.7864" Parameter: A <- "-83.7864" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9501" Parameter: B <- "-30.9501" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8362" Parameter: C <- "-52.8362" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2260 TOTAL ENERGY = -83.7864 RDTITL> * VAN DER WAALS = -30.9501 ELECTROSTATIC = -52.8362 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2260" Parameter: CONF_N -> "8002" Comparing "2260" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2261" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761080 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760818 ATOM PAIRS WERE FOUND FOR ATOM LIST 41999 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29787 from a total of 760818 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2261 -81.32530 -2.46106 0.68544 INTE EXTERN> -28.59732 -52.72798 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.3253" Parameter: A <- "-81.3253" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5973" Parameter: B <- "-28.5973" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.728" Parameter: C <- "-52.728" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2261 TOTAL ENERGY = -81.3253 RDTITL> * VAN DER WAALS = -28.5973 ELECTROSTATIC = -52.728 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2261" Parameter: CONF_N -> "8002" Comparing "2261" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2262" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760818 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769366 ATOM PAIRS WERE FOUND FOR ATOM LIST 42404 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30398 from a total of 769366 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2262 -79.83983 -1.48547 0.77940 INTE EXTERN> -26.93833 -52.90150 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8398" Parameter: A <- "-79.8398" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9383" Parameter: B <- "-26.9383" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9015" Parameter: C <- "-52.9015" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2262 TOTAL ENERGY = -79.8398 RDTITL> * VAN DER WAALS = -26.9383 ELECTROSTATIC = -52.9015 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2262" Parameter: CONF_N -> "8002" Comparing "2262" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2263" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769366 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769132 ATOM PAIRS WERE FOUND FOR ATOM LIST 42242 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30093 from a total of 769132 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2263 -79.03675 -0.80308 0.84656 INTE EXTERN> -25.53025 -53.50650 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0367" Parameter: A <- "-79.0367" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5302" Parameter: B <- "-25.5302" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.5065" Parameter: C <- "-53.5065" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2263 TOTAL ENERGY = -79.0367 RDTITL> * VAN DER WAALS = -25.5302 ELECTROSTATIC = -53.5065 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2263" Parameter: CONF_N -> "8002" Comparing "2263" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2264" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769132 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763841 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29852 from a total of 763841 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2264 -80.37478 1.33804 0.64965 INTE EXTERN> -31.93548 -48.43930 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3748" Parameter: A <- "-80.3748" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9355" Parameter: B <- "-31.9355" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4393" Parameter: C <- "-48.4393" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2264 TOTAL ENERGY = -80.3748 RDTITL> * VAN DER WAALS = -31.9355 ELECTROSTATIC = -48.4393 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2264" Parameter: CONF_N -> "8002" Comparing "2264" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2265" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763841 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766127 ATOM PAIRS WERE FOUND FOR ATOM LIST 42192 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30073 from a total of 766127 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2265 -76.04237 -4.33241 0.69936 INTE EXTERN> -28.37767 -47.66470 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0424" Parameter: A <- "-76.0424" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3777" Parameter: B <- "-28.3777" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6647" Parameter: C <- "-47.6647" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2265 TOTAL ENERGY = -76.0424 RDTITL> * VAN DER WAALS = -28.3777 ELECTROSTATIC = -47.6647 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2265" Parameter: CONF_N -> "8002" Comparing "2265" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2266" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766127 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766501 ATOM PAIRS WERE FOUND FOR ATOM LIST 42180 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30196 from a total of 766501 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2266 -84.65916 8.61679 0.85940 INTE EXTERN> -25.12082 -59.53834 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.6592" Parameter: A <- "-84.6592" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1208" Parameter: B <- "-25.1208" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.5383" Parameter: C <- "-59.5383" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2266 TOTAL ENERGY = -84.6592 RDTITL> * VAN DER WAALS = -25.1208 ELECTROSTATIC = -59.5383 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2266" Parameter: CONF_N -> "8002" Comparing "2266" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2267" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766501 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41857 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30191 from a total of 760601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2267 -84.83402 0.17487 0.63532 INTE EXTERN> -34.86271 -49.97131 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.834" Parameter: A <- "-84.834" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.8627" Parameter: B <- "-34.8627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9713" Parameter: C <- "-49.9713" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2267 TOTAL ENERGY = -84.834 RDTITL> * VAN DER WAALS = -34.8627 ELECTROSTATIC = -49.9713 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2267" Parameter: CONF_N -> "8002" Comparing "2267" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2268" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766631 ATOM PAIRS WERE FOUND FOR ATOM LIST 41973 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30469 from a total of 766631 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2268 -76.10989 -8.72414 0.64421 INTE EXTERN> -34.39695 -41.71294 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1099" Parameter: A <- "-76.1099" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3969" Parameter: B <- "-34.3969" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7129" Parameter: C <- "-41.7129" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2268 TOTAL ENERGY = -76.1099 RDTITL> * VAN DER WAALS = -34.3969 ELECTROSTATIC = -41.7129 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2268" Parameter: CONF_N -> "8002" Comparing "2268" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2269" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766631 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763615 ATOM PAIRS WERE FOUND FOR ATOM LIST 41897 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30675 from a total of 763615 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2269 -73.76324 -2.34664 0.82260 INTE EXTERN> -25.74737 -48.01588 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7632" Parameter: A <- "-73.7632" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7474" Parameter: B <- "-25.7474" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0159" Parameter: C <- "-48.0159" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2269 TOTAL ENERGY = -73.7632 RDTITL> * VAN DER WAALS = -25.7474 ELECTROSTATIC = -48.0159 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2269" Parameter: CONF_N -> "8002" Comparing "2269" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2270" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763615 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753904 ATOM PAIRS WERE FOUND FOR ATOM LIST 41532 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29468 from a total of 753904 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2270 -85.11180 11.34856 0.75099 INTE EXTERN> -28.38101 -56.73080 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.1118" Parameter: A <- "-85.1118" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.381" Parameter: B <- "-28.381" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.7308" Parameter: C <- "-56.7308" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2270 TOTAL ENERGY = -85.1118 RDTITL> * VAN DER WAALS = -28.381 ELECTROSTATIC = -56.7308 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2270" Parameter: CONF_N -> "8002" Comparing "2270" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2271" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753904 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757783 ATOM PAIRS WERE FOUND FOR ATOM LIST 41804 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29940 from a total of 757783 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2271 -81.90388 -3.20793 0.72584 INTE EXTERN> -29.86015 -52.04372 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9039" Parameter: A <- "-81.9039" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8602" Parameter: B <- "-29.8602" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0437" Parameter: C <- "-52.0437" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2271 TOTAL ENERGY = -81.9039 RDTITL> * VAN DER WAALS = -29.8602 ELECTROSTATIC = -52.0437 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2271" Parameter: CONF_N -> "8002" Comparing "2271" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2272" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757783 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758742 ATOM PAIRS WERE FOUND FOR ATOM LIST 41836 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29883 from a total of 758742 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2272 -76.94057 -4.96330 0.81377 INTE EXTERN> -22.04300 -54.89757 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9406" Parameter: A <- "-76.9406" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.043" Parameter: B <- "-22.043" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8976" Parameter: C <- "-54.8976" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2272 TOTAL ENERGY = -76.9406 RDTITL> * VAN DER WAALS = -22.043 ELECTROSTATIC = -54.8976 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2272" Parameter: CONF_N -> "8002" Comparing "2272" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2273" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758742 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756201 ATOM PAIRS WERE FOUND FOR ATOM LIST 41563 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28976 from a total of 756201 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2273 -81.12693 4.18636 0.67996 INTE EXTERN> -30.30580 -50.82113 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1269" Parameter: A <- "-81.1269" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3058" Parameter: B <- "-30.3058" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8211" Parameter: C <- "-50.8211" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2273 TOTAL ENERGY = -81.1269 RDTITL> * VAN DER WAALS = -30.3058 ELECTROSTATIC = -50.8211 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2273" Parameter: CONF_N -> "8002" Comparing "2273" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2274" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756201 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756043 ATOM PAIRS WERE FOUND FOR ATOM LIST 41636 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29796 from a total of 756043 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2274 -81.69647 0.56954 0.72929 INTE EXTERN> -28.20669 -53.48979 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6965" Parameter: A <- "-81.6965" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2067" Parameter: B <- "-28.2067" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4898" Parameter: C <- "-53.4898" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2274 TOTAL ENERGY = -81.6965 RDTITL> * VAN DER WAALS = -28.2067 ELECTROSTATIC = -53.4898 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2274" Parameter: CONF_N -> "8002" Comparing "2274" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2275" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756043 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754599 ATOM PAIRS WERE FOUND FOR ATOM LIST 41568 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29647 from a total of 754599 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2275 -69.18258 -12.51389 0.63033 INTE EXTERN> -28.77376 -40.40882 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1826" Parameter: A <- "-69.1826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7738" Parameter: B <- "-28.7738" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4088" Parameter: C <- "-40.4088" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2275 TOTAL ENERGY = -69.1826 RDTITL> * VAN DER WAALS = -28.7738 ELECTROSTATIC = -40.4088 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2275" Parameter: CONF_N -> "8002" Comparing "2275" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2276" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754599 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765529 ATOM PAIRS WERE FOUND FOR ATOM LIST 41961 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30217 from a total of 765529 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2276 -68.80190 -0.38068 0.57236 INTE EXTERN> -32.70930 -36.09259 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8019" Parameter: A <- "-68.8019" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7093" Parameter: B <- "-32.7093" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0926" Parameter: C <- "-36.0926" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2276 TOTAL ENERGY = -68.8019 RDTITL> * VAN DER WAALS = -32.7093 ELECTROSTATIC = -36.0926 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2276" Parameter: CONF_N -> "8002" Comparing "2276" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2277" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765529 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764647 ATOM PAIRS WERE FOUND FOR ATOM LIST 42023 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29837 from a total of 764647 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2277 -70.89143 2.08953 0.57687 INTE EXTERN> -32.50402 -38.38741 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8914" Parameter: A <- "-70.8914" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.504" Parameter: B <- "-32.504" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3874" Parameter: C <- "-38.3874" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2277 TOTAL ENERGY = -70.8914 RDTITL> * VAN DER WAALS = -32.504 ELECTROSTATIC = -38.3874 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2277" Parameter: CONF_N -> "8002" Comparing "2277" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2278" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764647 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764207 ATOM PAIRS WERE FOUND FOR ATOM LIST 42017 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29915 from a total of 764207 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2278 -66.42544 -4.46599 0.58598 INTE EXTERN> -31.04559 -35.37985 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4254" Parameter: A <- "-66.4254" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0456" Parameter: B <- "-31.0456" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3799" Parameter: C <- "-35.3799" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2278 TOTAL ENERGY = -66.4254 RDTITL> * VAN DER WAALS = -31.0456 ELECTROSTATIC = -35.3799 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2278" Parameter: CONF_N -> "8002" Comparing "2278" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2279" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764207 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763770 ATOM PAIRS WERE FOUND FOR ATOM LIST 41983 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29699 from a total of 763770 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2279 -66.98292 0.55748 0.53416 INTE EXTERN> -32.81793 -34.16499 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9829" Parameter: A <- "-66.9829" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8179" Parameter: B <- "-32.8179" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.165" Parameter: C <- "-34.165" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2279 TOTAL ENERGY = -66.9829 RDTITL> * VAN DER WAALS = -32.8179 ELECTROSTATIC = -34.165 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2279" Parameter: CONF_N -> "8002" Comparing "2279" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2280" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763770 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768319 ATOM PAIRS WERE FOUND FOR ATOM LIST 42322 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30312 from a total of 768319 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2280 -66.21244 -0.77048 0.57616 INTE EXTERN> -30.87589 -35.33655 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2124" Parameter: A <- "-66.2124" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8759" Parameter: B <- "-30.8759" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3365" Parameter: C <- "-35.3365" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2280 TOTAL ENERGY = -66.2124 RDTITL> * VAN DER WAALS = -30.8759 ELECTROSTATIC = -35.3365 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2280" Parameter: CONF_N -> "8002" Comparing "2280" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2281" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768319 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761913 ATOM PAIRS WERE FOUND FOR ATOM LIST 41999 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29731 from a total of 761913 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2281 -70.47397 4.26153 0.62983 INTE EXTERN> -29.81235 -40.66162 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.474" Parameter: A <- "-70.474" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8123" Parameter: B <- "-29.8123" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6616" Parameter: C <- "-40.6616" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2281 TOTAL ENERGY = -70.474 RDTITL> * VAN DER WAALS = -29.8123 ELECTROSTATIC = -40.6616 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2281" Parameter: CONF_N -> "8002" Comparing "2281" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2282" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761913 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764759 ATOM PAIRS WERE FOUND FOR ATOM LIST 41955 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30025 from a total of 764759 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2282 -73.72704 3.25307 0.59388 INTE EXTERN> -34.73515 -38.99189 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.727" Parameter: A <- "-73.727" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.7352" Parameter: B <- "-34.7352" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9919" Parameter: C <- "-38.9919" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2282 TOTAL ENERGY = -73.727 RDTITL> * VAN DER WAALS = -34.7352 ELECTROSTATIC = -38.9919 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2282" Parameter: CONF_N -> "8002" Comparing "2282" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2283" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764759 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767612 ATOM PAIRS WERE FOUND FOR ATOM LIST 41956 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29762 from a total of 767612 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2283 -74.83377 1.10673 0.61880 INTE EXTERN> -30.53992 -44.29385 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8338" Parameter: A <- "-74.8338" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5399" Parameter: B <- "-30.5399" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2938" Parameter: C <- "-44.2938" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2283 TOTAL ENERGY = -74.8338 RDTITL> * VAN DER WAALS = -30.5399 ELECTROSTATIC = -44.2938 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2283" Parameter: CONF_N -> "8002" Comparing "2283" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2284" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767612 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765191 ATOM PAIRS WERE FOUND FOR ATOM LIST 42132 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28997 from a total of 765191 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2284 -77.77361 2.93985 0.64811 INTE EXTERN> -32.64488 -45.12874 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7736" Parameter: A <- "-77.7736" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6449" Parameter: B <- "-32.6449" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1287" Parameter: C <- "-45.1287" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2284 TOTAL ENERGY = -77.7736 RDTITL> * VAN DER WAALS = -32.6449 ELECTROSTATIC = -45.1287 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2284" Parameter: CONF_N -> "8002" Comparing "2284" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2285" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765191 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768704 ATOM PAIRS WERE FOUND FOR ATOM LIST 42340 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29193 from a total of 768704 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2285 -72.97644 -4.79718 0.59541 INTE EXTERN> -31.27841 -41.69803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9764" Parameter: A <- "-72.9764" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2784" Parameter: B <- "-31.2784" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.698" Parameter: C <- "-41.698" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2285 TOTAL ENERGY = -72.9764 RDTITL> * VAN DER WAALS = -31.2784 ELECTROSTATIC = -41.698 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2285" Parameter: CONF_N -> "8002" Comparing "2285" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2286" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768704 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769713 ATOM PAIRS WERE FOUND FOR ATOM LIST 42307 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29207 from a total of 769713 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2286 -72.19677 -0.77967 0.59585 INTE EXTERN> -32.18348 -40.01329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1968" Parameter: A <- "-72.1968" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1835" Parameter: B <- "-32.1835" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0133" Parameter: C <- "-40.0133" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2286 TOTAL ENERGY = -72.1968 RDTITL> * VAN DER WAALS = -32.1835 ELECTROSTATIC = -40.0133 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2286" Parameter: CONF_N -> "8002" Comparing "2286" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2287" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769713 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761268 ATOM PAIRS WERE FOUND FOR ATOM LIST 42053 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29587 from a total of 761268 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2287 -67.84537 -4.35140 0.76743 INTE EXTERN> -19.92469 -47.92068 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8454" Parameter: A <- "-67.8454" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-19.9247" Parameter: B <- "-19.9247" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9207" Parameter: C <- "-47.9207" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2287 TOTAL ENERGY = -67.8454 RDTITL> * VAN DER WAALS = -19.9247 ELECTROSTATIC = -47.9207 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2287" Parameter: CONF_N -> "8002" Comparing "2287" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2288" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761268 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766299 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29825 from a total of 766299 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2288 -78.90013 11.05476 0.61350 INTE EXTERN> -30.98859 -47.91154 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9001" Parameter: A <- "-78.9001" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9886" Parameter: B <- "-30.9886" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9115" Parameter: C <- "-47.9115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2288 TOTAL ENERGY = -78.9001 RDTITL> * VAN DER WAALS = -30.9886 ELECTROSTATIC = -47.9115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2288" Parameter: CONF_N -> "8002" Comparing "2288" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2289" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766299 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770514 ATOM PAIRS WERE FOUND FOR ATOM LIST 42543 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29242 from a total of 770514 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2289 -64.21920 -14.68092 0.64107 INTE EXTERN> -27.50695 -36.71226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2192" Parameter: A <- "-64.2192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5069" Parameter: B <- "-27.5069" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7123" Parameter: C <- "-36.7123" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2289 TOTAL ENERGY = -64.2192 RDTITL> * VAN DER WAALS = -27.5069 ELECTROSTATIC = -36.7123 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2289" Parameter: CONF_N -> "8002" Comparing "2289" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2290" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770514 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771582 ATOM PAIRS WERE FOUND FOR ATOM LIST 42365 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29768 from a total of 771582 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2290 -71.08503 6.86583 0.60524 INTE EXTERN> -29.91229 -41.17274 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.085" Parameter: A <- "-71.085" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9123" Parameter: B <- "-29.9123" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1727" Parameter: C <- "-41.1727" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2290 TOTAL ENERGY = -71.085 RDTITL> * VAN DER WAALS = -29.9123 ELECTROSTATIC = -41.1727 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2290" Parameter: CONF_N -> "8002" Comparing "2290" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2291" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771582 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763290 ATOM PAIRS WERE FOUND FOR ATOM LIST 42107 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29441 from a total of 763290 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2291 -69.80261 -1.28242 0.58884 INTE EXTERN> -31.78765 -38.01495 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8026" Parameter: A <- "-69.8026" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7877" Parameter: B <- "-31.7877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.015" Parameter: C <- "-38.015" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2291 TOTAL ENERGY = -69.8026 RDTITL> * VAN DER WAALS = -31.7877 ELECTROSTATIC = -38.015 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2291" Parameter: CONF_N -> "8002" Comparing "2291" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2292" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763290 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764187 ATOM PAIRS WERE FOUND FOR ATOM LIST 41985 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29492 from a total of 764187 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2292 -68.53367 -1.26894 0.54235 INTE EXTERN> -30.27872 -38.25495 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5337" Parameter: A <- "-68.5337" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2787" Parameter: B <- "-30.2787" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.255" Parameter: C <- "-38.255" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2292 TOTAL ENERGY = -68.5337 RDTITL> * VAN DER WAALS = -30.2787 ELECTROSTATIC = -38.255 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2292" Parameter: CONF_N -> "8002" Comparing "2292" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2293" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764187 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763177 ATOM PAIRS WERE FOUND FOR ATOM LIST 41885 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29950 from a total of 763177 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2293 -73.38209 4.84842 0.62132 INTE EXTERN> -29.53071 -43.85138 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3821" Parameter: A <- "-73.3821" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5307" Parameter: B <- "-29.5307" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8514" Parameter: C <- "-43.8514" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2293 TOTAL ENERGY = -73.3821 RDTITL> * VAN DER WAALS = -29.5307 ELECTROSTATIC = -43.8514 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2293" Parameter: CONF_N -> "8002" Comparing "2293" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2294" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763177 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763984 ATOM PAIRS WERE FOUND FOR ATOM LIST 41864 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30144 from a total of 763984 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2294 -71.29050 -2.09160 0.68101 INTE EXTERN> -29.08721 -42.20329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2905" Parameter: A <- "-71.2905" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0872" Parameter: B <- "-29.0872" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2033" Parameter: C <- "-42.2033" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2294 TOTAL ENERGY = -71.2905 RDTITL> * VAN DER WAALS = -29.0872 ELECTROSTATIC = -42.2033 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2294" Parameter: CONF_N -> "8002" Comparing "2294" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2295" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763984 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768817 ATOM PAIRS WERE FOUND FOR ATOM LIST 42421 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30167 from a total of 768817 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2295 -70.90241 -0.38809 0.63252 INTE EXTERN> -32.28167 -38.62075 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9024" Parameter: A <- "-70.9024" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2817" Parameter: B <- "-32.2817" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6207" Parameter: C <- "-38.6207" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2295 TOTAL ENERGY = -70.9024 RDTITL> * VAN DER WAALS = -32.2817 ELECTROSTATIC = -38.6207 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2295" Parameter: CONF_N -> "8002" Comparing "2295" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2296" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768817 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761627 ATOM PAIRS WERE FOUND FOR ATOM LIST 41941 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29699 from a total of 761627 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2296 -71.41325 0.51083 0.56101 INTE EXTERN> -32.76355 -38.64969 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4132" Parameter: A <- "-71.4132" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7636" Parameter: B <- "-32.7636" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6497" Parameter: C <- "-38.6497" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2296 TOTAL ENERGY = -71.4132 RDTITL> * VAN DER WAALS = -32.7636 ELECTROSTATIC = -38.6497 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2296" Parameter: CONF_N -> "8002" Comparing "2296" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2297" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761627 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765204 ATOM PAIRS WERE FOUND FOR ATOM LIST 42087 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30313 from a total of 765204 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2297 -70.24958 -1.16366 0.72506 INTE EXTERN> -25.81891 -44.43067 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2496" Parameter: A <- "-70.2496" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8189" Parameter: B <- "-25.8189" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4307" Parameter: C <- "-44.4307" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2297 TOTAL ENERGY = -70.2496 RDTITL> * VAN DER WAALS = -25.8189 ELECTROSTATIC = -44.4307 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2297" Parameter: CONF_N -> "8002" Comparing "2297" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2298" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765204 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761981 ATOM PAIRS WERE FOUND FOR ATOM LIST 41913 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29347 from a total of 761981 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2298 -79.22560 8.97602 0.62834 INTE EXTERN> -32.53466 -46.69094 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2256" Parameter: A <- "-79.2256" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5347" Parameter: B <- "-32.5347" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6909" Parameter: C <- "-46.6909" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2298 TOTAL ENERGY = -79.2256 RDTITL> * VAN DER WAALS = -32.5347 ELECTROSTATIC = -46.6909 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2298" Parameter: CONF_N -> "8002" Comparing "2298" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2299" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761981 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761135 ATOM PAIRS WERE FOUND FOR ATOM LIST 41645 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29477 from a total of 761135 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2299 -67.03272 -12.19288 0.62578 INTE EXTERN> -32.98306 -34.04966 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0327" Parameter: A <- "-67.0327" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9831" Parameter: B <- "-32.9831" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.0497" Parameter: C <- "-34.0497" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2299 TOTAL ENERGY = -67.0327 RDTITL> * VAN DER WAALS = -32.9831 ELECTROSTATIC = -34.0497 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2299" Parameter: CONF_N -> "8002" Comparing "2299" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2300" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761135 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767460 ATOM PAIRS WERE FOUND FOR ATOM LIST 42123 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29952 from a total of 767460 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2300 -71.94510 4.91237 0.74462 INTE EXTERN> -26.14576 -45.79934 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9451" Parameter: A <- "-71.9451" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1458" Parameter: B <- "-26.1458" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7993" Parameter: C <- "-45.7993" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2300 TOTAL ENERGY = -71.9451 RDTITL> * VAN DER WAALS = -26.1458 ELECTROSTATIC = -45.7993 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2300" Parameter: CONF_N -> "8002" Comparing "2300" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2301" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767460 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766772 ATOM PAIRS WERE FOUND FOR ATOM LIST 42108 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29982 from a total of 766772 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2301 -78.75274 6.80765 0.68854 INTE EXTERN> -32.51493 -46.23781 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7527" Parameter: A <- "-78.7527" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5149" Parameter: B <- "-32.5149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2378" Parameter: C <- "-46.2378" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2301 TOTAL ENERGY = -78.7527 RDTITL> * VAN DER WAALS = -32.5149 ELECTROSTATIC = -46.2378 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2301" Parameter: CONF_N -> "8002" Comparing "2301" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2302" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766772 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762132 ATOM PAIRS WERE FOUND FOR ATOM LIST 41834 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29408 from a total of 762132 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2302 -74.30637 -4.44637 0.88213 INTE EXTERN> -23.51669 -50.78967 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3064" Parameter: A <- "-74.3064" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.5167" Parameter: B <- "-23.5167" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7897" Parameter: C <- "-50.7897" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2302 TOTAL ENERGY = -74.3064 RDTITL> * VAN DER WAALS = -23.5167 ELECTROSTATIC = -50.7897 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2302" Parameter: CONF_N -> "8002" Comparing "2302" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2303" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762132 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772208 ATOM PAIRS WERE FOUND FOR ATOM LIST 42270 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30316 from a total of 772208 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2303 -78.42584 4.11947 0.65376 INTE EXTERN> -31.67798 -46.74786 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4258" Parameter: A <- "-78.4258" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.678" Parameter: B <- "-31.678" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7479" Parameter: C <- "-46.7479" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2303 TOTAL ENERGY = -78.4258 RDTITL> * VAN DER WAALS = -31.678 ELECTROSTATIC = -46.7479 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2303" Parameter: CONF_N -> "8002" Comparing "2303" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2304" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772208 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769208 ATOM PAIRS WERE FOUND FOR ATOM LIST 42425 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29798 from a total of 769208 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2304 -77.81787 -0.60798 0.77353 INTE EXTERN> -26.20129 -51.61658 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8179" Parameter: A <- "-77.8179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2013" Parameter: B <- "-26.2013" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6166" Parameter: C <- "-51.6166" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2304 TOTAL ENERGY = -77.8179 RDTITL> * VAN DER WAALS = -26.2013 ELECTROSTATIC = -51.6166 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2304" Parameter: CONF_N -> "8002" Comparing "2304" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2305" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769208 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770339 ATOM PAIRS WERE FOUND FOR ATOM LIST 42305 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30113 from a total of 770339 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2305 -81.83801 4.02015 0.58677 INTE EXTERN> -36.01510 -45.82292 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.838" Parameter: A <- "-81.838" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.0151" Parameter: B <- "-36.0151" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8229" Parameter: C <- "-45.8229" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2305 TOTAL ENERGY = -81.838 RDTITL> * VAN DER WAALS = -36.0151 ELECTROSTATIC = -45.8229 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2305" Parameter: CONF_N -> "8002" Comparing "2305" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2306" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770339 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763248 ATOM PAIRS WERE FOUND FOR ATOM LIST 42028 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29836 from a total of 763248 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2306 -83.45072 1.61270 0.70235 INTE EXTERN> -29.17757 -54.27315 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.4507" Parameter: A <- "-83.4507" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1776" Parameter: B <- "-29.1776" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2731" Parameter: C <- "-54.2731" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2306 TOTAL ENERGY = -83.4507 RDTITL> * VAN DER WAALS = -29.1776 ELECTROSTATIC = -54.2731 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2306" Parameter: CONF_N -> "8002" Comparing "2306" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2307" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763248 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765130 ATOM PAIRS WERE FOUND FOR ATOM LIST 42261 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29821 from a total of 765130 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2307 -81.13494 -2.31578 0.73731 INTE EXTERN> -27.28318 -53.85176 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1349" Parameter: A <- "-81.1349" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2832" Parameter: B <- "-27.2832" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8518" Parameter: C <- "-53.8518" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2307 TOTAL ENERGY = -81.1349 RDTITL> * VAN DER WAALS = -27.2832 ELECTROSTATIC = -53.8518 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2307" Parameter: CONF_N -> "8002" Comparing "2307" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2308" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765130 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762950 ATOM PAIRS WERE FOUND FOR ATOM LIST 42088 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30209 from a total of 762950 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2308 -79.18648 -1.94846 0.76155 INTE EXTERN> -29.24730 -49.93917 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1865" Parameter: A <- "-79.1865" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2473" Parameter: B <- "-29.2473" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9392" Parameter: C <- "-49.9392" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2308 TOTAL ENERGY = -79.1865 RDTITL> * VAN DER WAALS = -29.2473 ELECTROSTATIC = -49.9392 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2308" Parameter: CONF_N -> "8002" Comparing "2308" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2309" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762950 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766608 ATOM PAIRS WERE FOUND FOR ATOM LIST 42075 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30135 from a total of 766608 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2309 -79.14483 -0.04165 0.78661 INTE EXTERN> -26.67416 -52.47067 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1448" Parameter: A <- "-79.1448" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6742" Parameter: B <- "-26.6742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.4707" Parameter: C <- "-52.4707" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2309 TOTAL ENERGY = -79.1448 RDTITL> * VAN DER WAALS = -26.6742 ELECTROSTATIC = -52.4707 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2309" Parameter: CONF_N -> "8002" Comparing "2309" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2310" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766608 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762420 ATOM PAIRS WERE FOUND FOR ATOM LIST 42070 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30292 from a total of 762420 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2310 -79.57218 0.42736 0.71821 INTE EXTERN> -30.11964 -49.45255 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5722" Parameter: A <- "-79.5722" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1196" Parameter: B <- "-30.1196" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4525" Parameter: C <- "-49.4525" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2310 TOTAL ENERGY = -79.5722 RDTITL> * VAN DER WAALS = -30.1196 ELECTROSTATIC = -49.4525 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2310" Parameter: CONF_N -> "8002" Comparing "2310" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2311" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762420 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761063 ATOM PAIRS WERE FOUND FOR ATOM LIST 41909 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29579 from a total of 761063 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2311 -79.58262 0.01044 0.64913 INTE EXTERN> -33.13371 -46.44892 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5826" Parameter: A <- "-79.5826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1337" Parameter: B <- "-33.1337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4489" Parameter: C <- "-46.4489" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2311 TOTAL ENERGY = -79.5826 RDTITL> * VAN DER WAALS = -33.1337 ELECTROSTATIC = -46.4489 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2311" Parameter: CONF_N -> "8002" Comparing "2311" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2312" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761063 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766038 ATOM PAIRS WERE FOUND FOR ATOM LIST 42246 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30020 from a total of 766038 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2312 -83.19151 3.60889 0.71234 INTE EXTERN> -28.29399 -54.89753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.1915" Parameter: A <- "-83.1915" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.294" Parameter: B <- "-28.294" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8975" Parameter: C <- "-54.8975" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2312 TOTAL ENERGY = -83.1915 RDTITL> * VAN DER WAALS = -28.294 ELECTROSTATIC = -54.8975 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2312" Parameter: CONF_N -> "8002" Comparing "2312" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2313" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766038 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770103 ATOM PAIRS WERE FOUND FOR ATOM LIST 42469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30726 from a total of 770103 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2313 -74.42109 -8.77042 0.72590 INTE EXTERN> -26.41555 -48.00554 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4211" Parameter: A <- "-74.4211" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4156" Parameter: B <- "-26.4156" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0055" Parameter: C <- "-48.0055" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2313 TOTAL ENERGY = -74.4211 RDTITL> * VAN DER WAALS = -26.4156 ELECTROSTATIC = -48.0055 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2313" Parameter: CONF_N -> "8002" Comparing "2313" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2314" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770103 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764369 ATOM PAIRS WERE FOUND FOR ATOM LIST 42063 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30267 from a total of 764369 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2314 -74.95099 0.52989 0.65645 INTE EXTERN> -29.74875 -45.20224 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.951" Parameter: A <- "-74.951" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7488" Parameter: B <- "-29.7488" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2022" Parameter: C <- "-45.2022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2314 TOTAL ENERGY = -74.951 RDTITL> * VAN DER WAALS = -29.7488 ELECTROSTATIC = -45.2022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2314" Parameter: CONF_N -> "8002" Comparing "2314" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2315" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764369 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764251 ATOM PAIRS WERE FOUND FOR ATOM LIST 42145 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29387 from a total of 764251 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2315 -76.57059 1.61960 0.66200 INTE EXTERN> -29.81451 -46.75608 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5706" Parameter: A <- "-76.5706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8145" Parameter: B <- "-29.8145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7561" Parameter: C <- "-46.7561" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2315 TOTAL ENERGY = -76.5706 RDTITL> * VAN DER WAALS = -29.8145 ELECTROSTATIC = -46.7561 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2315" Parameter: CONF_N -> "8002" Comparing "2315" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2316" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764251 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760991 ATOM PAIRS WERE FOUND FOR ATOM LIST 41957 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29297 from a total of 760991 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2316 -77.92280 1.35221 0.77567 INTE EXTERN> -25.90100 -52.02179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9228" Parameter: A <- "-77.9228" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.901" Parameter: B <- "-25.901" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0218" Parameter: C <- "-52.0218" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2316 TOTAL ENERGY = -77.9228 RDTITL> * VAN DER WAALS = -25.901 ELECTROSTATIC = -52.0218 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2316" Parameter: CONF_N -> "8002" Comparing "2316" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2317" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760991 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761134 ATOM PAIRS WERE FOUND FOR ATOM LIST 42026 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29812 from a total of 761134 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2317 -82.52121 4.59841 0.74012 INTE EXTERN> -29.44207 -53.07914 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5212" Parameter: A <- "-82.5212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4421" Parameter: B <- "-29.4421" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0791" Parameter: C <- "-53.0791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2317 TOTAL ENERGY = -82.5212 RDTITL> * VAN DER WAALS = -29.4421 ELECTROSTATIC = -53.0791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2317" Parameter: CONF_N -> "8002" Comparing "2317" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2318" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761134 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757464 ATOM PAIRS WERE FOUND FOR ATOM LIST 41758 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30012 from a total of 757464 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2318 -84.37109 1.84988 0.77232 INTE EXTERN> -25.33707 -59.03402 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.3711" Parameter: A <- "-84.3711" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3371" Parameter: B <- "-25.3371" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.034" Parameter: C <- "-59.034" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2318 TOTAL ENERGY = -84.3711 RDTITL> * VAN DER WAALS = -25.3371 ELECTROSTATIC = -59.034 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2318" Parameter: CONF_N -> "8002" Comparing "2318" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2319" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757464 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760407 ATOM PAIRS WERE FOUND FOR ATOM LIST 41885 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29858 from a total of 760407 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2319 -76.41964 -7.95146 0.67050 INTE EXTERN> -28.44261 -47.97703 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4196" Parameter: A <- "-76.4196" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4426" Parameter: B <- "-28.4426" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.977" Parameter: C <- "-47.977" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2319 TOTAL ENERGY = -76.4196 RDTITL> * VAN DER WAALS = -28.4426 ELECTROSTATIC = -47.977 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2319" Parameter: CONF_N -> "8002" Comparing "2319" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2320" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760407 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763829 ATOM PAIRS WERE FOUND FOR ATOM LIST 41929 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30191 from a total of 763829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2320 -81.92056 5.50092 0.78246 INTE EXTERN> -27.37268 -54.54788 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9206" Parameter: A <- "-81.9206" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3727" Parameter: B <- "-27.3727" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.5479" Parameter: C <- "-54.5479" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2320 TOTAL ENERGY = -81.9206 RDTITL> * VAN DER WAALS = -27.3727 ELECTROSTATIC = -54.5479 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2320" Parameter: CONF_N -> "8002" Comparing "2320" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2321" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768995 ATOM PAIRS WERE FOUND FOR ATOM LIST 42351 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29998 from a total of 768995 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2321 -78.43789 -3.48267 0.66328 INTE EXTERN> -30.27395 -48.16394 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4379" Parameter: A <- "-78.4379" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2739" Parameter: B <- "-30.2739" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1639" Parameter: C <- "-48.1639" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2321 TOTAL ENERGY = -78.4379 RDTITL> * VAN DER WAALS = -30.2739 ELECTROSTATIC = -48.1639 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2321" Parameter: CONF_N -> "8002" Comparing "2321" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2322" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768995 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766004 ATOM PAIRS WERE FOUND FOR ATOM LIST 42112 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30220 from a total of 766004 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2322 -81.07748 2.63959 0.73589 INTE EXTERN> -29.69120 -51.38628 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.0775" Parameter: A <- "-81.0775" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6912" Parameter: B <- "-29.6912" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3863" Parameter: C <- "-51.3863" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2322 TOTAL ENERGY = -81.0775 RDTITL> * VAN DER WAALS = -29.6912 ELECTROSTATIC = -51.3863 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2322" Parameter: CONF_N -> "8002" Comparing "2322" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2323" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766004 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764762 ATOM PAIRS WERE FOUND FOR ATOM LIST 42207 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29953 from a total of 764762 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2323 -74.16603 -6.91145 0.59963 INTE EXTERN> -32.97596 -41.19007 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.166" Parameter: A <- "-74.166" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.976" Parameter: B <- "-32.976" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1901" Parameter: C <- "-41.1901" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2323 TOTAL ENERGY = -74.166 RDTITL> * VAN DER WAALS = -32.976 ELECTROSTATIC = -41.1901 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2323" Parameter: CONF_N -> "8002" Comparing "2323" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2324" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764762 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762418 ATOM PAIRS WERE FOUND FOR ATOM LIST 42119 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29966 from a total of 762418 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2324 -79.74044 5.57442 0.79103 INTE EXTERN> -27.70307 -52.03737 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7404" Parameter: A <- "-79.7404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7031" Parameter: B <- "-27.7031" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0374" Parameter: C <- "-52.0374" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2324 TOTAL ENERGY = -79.7404 RDTITL> * VAN DER WAALS = -27.7031 ELECTROSTATIC = -52.0374 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2324" Parameter: CONF_N -> "8002" Comparing "2324" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2325" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762418 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761243 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30118 from a total of 761243 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2325 -74.85115 -4.88929 0.74695 INTE EXTERN> -27.53060 -47.32055 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8512" Parameter: A <- "-74.8512" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5306" Parameter: B <- "-27.5306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3205" Parameter: C <- "-47.3205" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2325 TOTAL ENERGY = -74.8512 RDTITL> * VAN DER WAALS = -27.5306 ELECTROSTATIC = -47.3205 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2325" Parameter: CONF_N -> "8002" Comparing "2325" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2326" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761243 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762928 ATOM PAIRS WERE FOUND FOR ATOM LIST 41893 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30123 from a total of 762928 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2326 -74.88396 0.03281 0.66614 INTE EXTERN> -29.36209 -45.52186 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.884" Parameter: A <- "-74.884" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3621" Parameter: B <- "-29.3621" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5219" Parameter: C <- "-45.5219" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2326 TOTAL ENERGY = -74.884 RDTITL> * VAN DER WAALS = -29.3621 ELECTROSTATIC = -45.5219 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2326" Parameter: CONF_N -> "8002" Comparing "2326" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2327" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762928 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765653 ATOM PAIRS WERE FOUND FOR ATOM LIST 42046 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29668 from a total of 765653 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2327 -72.21700 -2.66696 0.68506 INTE EXTERN> -27.98061 -44.23639 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.217" Parameter: A <- "-72.217" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9806" Parameter: B <- "-27.9806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2364" Parameter: C <- "-44.2364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2327 TOTAL ENERGY = -72.217 RDTITL> * VAN DER WAALS = -27.9806 ELECTROSTATIC = -44.2364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2327" Parameter: CONF_N -> "8002" Comparing "2327" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2328" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765653 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759739 ATOM PAIRS WERE FOUND FOR ATOM LIST 41748 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29549 from a total of 759739 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2328 -75.75408 3.53709 0.62617 INTE EXTERN> -31.96228 -43.79181 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7541" Parameter: A <- "-75.7541" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9623" Parameter: B <- "-31.9623" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7918" Parameter: C <- "-43.7918" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2328 TOTAL ENERGY = -75.7541 RDTITL> * VAN DER WAALS = -31.9623 ELECTROSTATIC = -43.7918 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2328" Parameter: CONF_N -> "8002" Comparing "2328" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2329" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759739 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756039 ATOM PAIRS WERE FOUND FOR ATOM LIST 41658 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29083 from a total of 756039 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2329 -78.27747 2.52339 0.73656 INTE EXTERN> -27.30167 -50.97580 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2775" Parameter: A <- "-78.2775" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3017" Parameter: B <- "-27.3017" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9758" Parameter: C <- "-50.9758" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2329 TOTAL ENERGY = -78.2775 RDTITL> * VAN DER WAALS = -27.3017 ELECTROSTATIC = -50.9758 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2329" Parameter: CONF_N -> "8002" Comparing "2329" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2330" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756039 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768229 ATOM PAIRS WERE FOUND FOR ATOM LIST 42149 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29780 from a total of 768229 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2330 -74.90960 -3.36787 0.76802 INTE EXTERN> -26.14501 -48.76459 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9096" Parameter: A <- "-74.9096" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.145" Parameter: B <- "-26.145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7646" Parameter: C <- "-48.7646" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2330 TOTAL ENERGY = -74.9096 RDTITL> * VAN DER WAALS = -26.145 ELECTROSTATIC = -48.7646 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2330" Parameter: CONF_N -> "8002" Comparing "2330" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2331" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768229 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762532 ATOM PAIRS WERE FOUND FOR ATOM LIST 42059 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29374 from a total of 762532 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2331 -83.72110 8.81150 0.76932 INTE EXTERN> -27.06540 -56.65570 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.7211" Parameter: A <- "-83.7211" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0654" Parameter: B <- "-27.0654" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.6557" Parameter: C <- "-56.6557" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2331 TOTAL ENERGY = -83.7211 RDTITL> * VAN DER WAALS = -27.0654 ELECTROSTATIC = -56.6557 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2331" Parameter: CONF_N -> "8002" Comparing "2331" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2332" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762532 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762681 ATOM PAIRS WERE FOUND FOR ATOM LIST 42062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28418 from a total of 762681 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2332 -67.19971 -16.52139 0.80578 INTE EXTERN> -22.71650 -44.48321 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1997" Parameter: A <- "-67.1997" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.7165" Parameter: B <- "-22.7165" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4832" Parameter: C <- "-44.4832" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2332 TOTAL ENERGY = -67.1997 RDTITL> * VAN DER WAALS = -22.7165 ELECTROSTATIC = -44.4832 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2332" Parameter: CONF_N -> "8002" Comparing "2332" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2333" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762681 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758513 ATOM PAIRS WERE FOUND FOR ATOM LIST 41610 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28929 from a total of 758513 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2333 -69.26061 2.06090 0.65933 INTE EXTERN> -27.78339 -41.47722 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2606" Parameter: A <- "-69.2606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7834" Parameter: B <- "-27.7834" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4772" Parameter: C <- "-41.4772" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2333 TOTAL ENERGY = -69.2606 RDTITL> * VAN DER WAALS = -27.7834 ELECTROSTATIC = -41.4772 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2333" Parameter: CONF_N -> "8002" Comparing "2333" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2334" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758513 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760073 ATOM PAIRS WERE FOUND FOR ATOM LIST 41825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29703 from a total of 760073 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2334 -67.60216 -1.65845 0.68555 INTE EXTERN> -28.89535 -38.70680 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6022" Parameter: A <- "-67.6022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8954" Parameter: B <- "-28.8954" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7068" Parameter: C <- "-38.7068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2334 TOTAL ENERGY = -67.6022 RDTITL> * VAN DER WAALS = -28.8954 ELECTROSTATIC = -38.7068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2334" Parameter: CONF_N -> "8002" Comparing "2334" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2335" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760073 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757553 ATOM PAIRS WERE FOUND FOR ATOM LIST 41715 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29117 from a total of 757553 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2335 -77.35100 9.74885 0.73932 INTE EXTERN> -28.38940 -48.96161 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.351" Parameter: A <- "-77.351" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3894" Parameter: B <- "-28.3894" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9616" Parameter: C <- "-48.9616" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2335 TOTAL ENERGY = -77.351 RDTITL> * VAN DER WAALS = -28.3894 ELECTROSTATIC = -48.9616 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2335" Parameter: CONF_N -> "8002" Comparing "2335" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2336" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757553 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755220 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29390 from a total of 755220 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2336 -76.86748 -0.48353 0.74226 INTE EXTERN> -26.20797 -50.65951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8675" Parameter: A <- "-76.8675" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.208" Parameter: B <- "-26.208" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6595" Parameter: C <- "-50.6595" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2336 TOTAL ENERGY = -76.8675 RDTITL> * VAN DER WAALS = -26.208 ELECTROSTATIC = -50.6595 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2336" Parameter: CONF_N -> "8002" Comparing "2336" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2337" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755220 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760648 ATOM PAIRS WERE FOUND FOR ATOM LIST 41825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30234 from a total of 760648 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2337 -70.78746 -6.08002 0.74784 INTE EXTERN> -24.04839 -46.73908 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7875" Parameter: A <- "-70.7875" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0484" Parameter: B <- "-24.0484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7391" Parameter: C <- "-46.7391" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2337 TOTAL ENERGY = -70.7875 RDTITL> * VAN DER WAALS = -24.0484 ELECTROSTATIC = -46.7391 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2337" Parameter: CONF_N -> "8002" Comparing "2337" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2338" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760648 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758031 ATOM PAIRS WERE FOUND FOR ATOM LIST 41669 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29632 from a total of 758031 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2338 -76.59703 5.80956 0.79478 INTE EXTERN> -24.27924 -52.31779 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.597" Parameter: A <- "-76.597" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2792" Parameter: B <- "-24.2792" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3178" Parameter: C <- "-52.3178" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2338 TOTAL ENERGY = -76.597 RDTITL> * VAN DER WAALS = -24.2792 ELECTROSTATIC = -52.3178 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2338" Parameter: CONF_N -> "8002" Comparing "2338" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2339" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758031 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764961 ATOM PAIRS WERE FOUND FOR ATOM LIST 42153 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29850 from a total of 764961 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2339 -69.78664 -6.81039 0.61379 INTE EXTERN> -30.95045 -38.83619 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7866" Parameter: A <- "-69.7866" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9505" Parameter: B <- "-30.9505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8362" Parameter: C <- "-38.8362" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2339 TOTAL ENERGY = -69.7866 RDTITL> * VAN DER WAALS = -30.9505 ELECTROSTATIC = -38.8362 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2339" Parameter: CONF_N -> "8002" Comparing "2339" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2340" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764961 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760686 ATOM PAIRS WERE FOUND FOR ATOM LIST 41954 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29714 from a total of 760686 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2340 -77.06234 7.27570 0.62142 INTE EXTERN> -32.43928 -44.62306 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0623" Parameter: A <- "-77.0623" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4393" Parameter: B <- "-32.4393" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6231" Parameter: C <- "-44.6231" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2340 TOTAL ENERGY = -77.0623 RDTITL> * VAN DER WAALS = -32.4393 ELECTROSTATIC = -44.6231 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2340" Parameter: CONF_N -> "8002" Comparing "2340" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2341" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760686 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758197 ATOM PAIRS WERE FOUND FOR ATOM LIST 41740 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30028 from a total of 758197 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2341 -75.24935 -1.81299 0.65530 INTE EXTERN> -28.25065 -46.99870 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2494" Parameter: A <- "-75.2494" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2507" Parameter: B <- "-28.2507" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9987" Parameter: C <- "-46.9987" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2341 TOTAL ENERGY = -75.2494 RDTITL> * VAN DER WAALS = -28.2507 ELECTROSTATIC = -46.9987 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2341" Parameter: CONF_N -> "8002" Comparing "2341" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2342" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758197 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752887 ATOM PAIRS WERE FOUND FOR ATOM LIST 41469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29517 from a total of 752887 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2342 -72.68875 -2.56061 0.60302 INTE EXTERN> -30.81465 -41.87410 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6887" Parameter: A <- "-72.6887" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8146" Parameter: B <- "-30.8146" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8741" Parameter: C <- "-41.8741" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2342 TOTAL ENERGY = -72.6887 RDTITL> * VAN DER WAALS = -30.8146 ELECTROSTATIC = -41.8741 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2342" Parameter: CONF_N -> "8002" Comparing "2342" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2343" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752887 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759486 ATOM PAIRS WERE FOUND FOR ATOM LIST 41822 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29433 from a total of 759486 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2343 -71.09936 -1.58938 0.65608 INTE EXTERN> -28.81700 -42.28237 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0994" Parameter: A <- "-71.0994" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.817" Parameter: B <- "-28.817" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2824" Parameter: C <- "-42.2824" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2343 TOTAL ENERGY = -71.0994 RDTITL> * VAN DER WAALS = -28.817 ELECTROSTATIC = -42.2824 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2343" Parameter: CONF_N -> "8002" Comparing "2343" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2344" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759486 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760983 ATOM PAIRS WERE FOUND FOR ATOM LIST 41792 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29736 from a total of 760983 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2344 -76.34057 5.24121 0.65177 INTE EXTERN> -30.99977 -45.34080 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3406" Parameter: A <- "-76.3406" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9998" Parameter: B <- "-30.9998" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3408" Parameter: C <- "-45.3408" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2344 TOTAL ENERGY = -76.3406 RDTITL> * VAN DER WAALS = -30.9998 ELECTROSTATIC = -45.3408 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2344" Parameter: CONF_N -> "8002" Comparing "2344" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2345" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760983 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761635 ATOM PAIRS WERE FOUND FOR ATOM LIST 41984 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29290 from a total of 761635 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2345 -64.83448 -11.50610 0.62525 INTE EXTERN> -29.27145 -35.56302 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8345" Parameter: A <- "-64.8345" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2715" Parameter: B <- "-29.2715" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.563" Parameter: C <- "-35.563" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2345 TOTAL ENERGY = -64.8345 RDTITL> * VAN DER WAALS = -29.2715 ELECTROSTATIC = -35.563 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2345" Parameter: CONF_N -> "8002" Comparing "2345" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2346" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761635 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761360 ATOM PAIRS WERE FOUND FOR ATOM LIST 41893 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29297 from a total of 761360 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2346 -76.46723 11.63276 0.71337 INTE EXTERN> -28.67895 -47.78828 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4672" Parameter: A <- "-76.4672" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.679" Parameter: B <- "-28.679" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7883" Parameter: C <- "-47.7883" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2346 TOTAL ENERGY = -76.4672 RDTITL> * VAN DER WAALS = -28.679 ELECTROSTATIC = -47.7883 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2346" Parameter: CONF_N -> "8002" Comparing "2346" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2347" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761360 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757434 ATOM PAIRS WERE FOUND FOR ATOM LIST 41582 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29259 from a total of 757434 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2347 -72.50940 -3.95783 0.74400 INTE EXTERN> -25.84774 -46.66167 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5094" Parameter: A <- "-72.5094" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8477" Parameter: B <- "-25.8477" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6617" Parameter: C <- "-46.6617" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2347 TOTAL ENERGY = -72.5094 RDTITL> * VAN DER WAALS = -25.8477 ELECTROSTATIC = -46.6617 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2347" Parameter: CONF_N -> "8002" Comparing "2347" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2348" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757434 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758559 ATOM PAIRS WERE FOUND FOR ATOM LIST 41712 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29590 from a total of 758559 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2348 -80.83056 8.32116 0.58379 INTE EXTERN> -34.14841 -46.68215 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.8306" Parameter: A <- "-80.8306" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1484" Parameter: B <- "-34.1484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6822" Parameter: C <- "-46.6822" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2348 TOTAL ENERGY = -80.8306 RDTITL> * VAN DER WAALS = -34.1484 ELECTROSTATIC = -46.6822 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2348" Parameter: CONF_N -> "8002" Comparing "2348" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2349" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758559 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761659 ATOM PAIRS WERE FOUND FOR ATOM LIST 41742 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29887 from a total of 761659 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2349 -71.99443 -8.83613 0.71278 INTE EXTERN> -26.70928 -45.28515 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9944" Parameter: A <- "-71.9944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7093" Parameter: B <- "-26.7093" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2852" Parameter: C <- "-45.2852" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2349 TOTAL ENERGY = -71.9944 RDTITL> * VAN DER WAALS = -26.7093 ELECTROSTATIC = -45.2852 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2349" Parameter: CONF_N -> "8002" Comparing "2349" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2350" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761659 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761493 ATOM PAIRS WERE FOUND FOR ATOM LIST 41880 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29242 from a total of 761493 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2350 -76.63689 4.64246 0.67772 INTE EXTERN> -27.32735 -49.30954 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6369" Parameter: A <- "-76.6369" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3274" Parameter: B <- "-27.3274" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3095" Parameter: C <- "-49.3095" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2350 TOTAL ENERGY = -76.6369 RDTITL> * VAN DER WAALS = -27.3274 ELECTROSTATIC = -49.3095 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2350" Parameter: CONF_N -> "8002" Comparing "2350" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2351" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761493 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758245 ATOM PAIRS WERE FOUND FOR ATOM LIST 41690 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30053 from a total of 758245 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2351 -76.19422 -0.44268 0.67619 INTE EXTERN> -27.81423 -48.37999 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1942" Parameter: A <- "-76.1942" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8142" Parameter: B <- "-27.8142" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.38" Parameter: C <- "-48.38" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2351 TOTAL ENERGY = -76.1942 RDTITL> * VAN DER WAALS = -27.8142 ELECTROSTATIC = -48.38 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2351" Parameter: CONF_N -> "8002" Comparing "2351" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2352" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758245 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755880 ATOM PAIRS WERE FOUND FOR ATOM LIST 41558 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29873 from a total of 755880 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2352 -74.43027 -1.76394 0.72832 INTE EXTERN> -26.25763 -48.17264 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4303" Parameter: A <- "-74.4303" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2576" Parameter: B <- "-26.2576" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1726" Parameter: C <- "-48.1726" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2352 TOTAL ENERGY = -74.4303 RDTITL> * VAN DER WAALS = -26.2576 ELECTROSTATIC = -48.1726 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2352" Parameter: CONF_N -> "8002" Comparing "2352" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2353" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755880 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760270 ATOM PAIRS WERE FOUND FOR ATOM LIST 41414 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29822 from a total of 760270 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2353 -76.16590 1.73563 0.73383 INTE EXTERN> -26.28891 -49.87699 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1659" Parameter: A <- "-76.1659" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2889" Parameter: B <- "-26.2889" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.877" Parameter: C <- "-49.877" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2353 TOTAL ENERGY = -76.1659 RDTITL> * VAN DER WAALS = -26.2889 ELECTROSTATIC = -49.877 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2353" Parameter: CONF_N -> "8002" Comparing "2353" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2354" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760270 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761965 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29953 from a total of 761965 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2354 -80.60461 4.43871 0.64406 INTE EXTERN> -31.07532 -49.52929 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6046" Parameter: A <- "-80.6046" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0753" Parameter: B <- "-31.0753" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5293" Parameter: C <- "-49.5293" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2354 TOTAL ENERGY = -80.6046 RDTITL> * VAN DER WAALS = -31.0753 ELECTROSTATIC = -49.5293 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2354" Parameter: CONF_N -> "8002" Comparing "2354" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2355" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761965 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29580 from a total of 758422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2355 -71.60596 -8.99866 0.57580 INTE EXTERN> -31.09528 -40.51068 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.606" Parameter: A <- "-71.606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0953" Parameter: B <- "-31.0953" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5107" Parameter: C <- "-40.5107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2355 TOTAL ENERGY = -71.606 RDTITL> * VAN DER WAALS = -31.0953 ELECTROSTATIC = -40.5107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2355" Parameter: CONF_N -> "8002" Comparing "2355" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2356" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761771 ATOM PAIRS WERE FOUND FOR ATOM LIST 41679 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29595 from a total of 761771 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2356 -73.24578 1.63982 0.59035 INTE EXTERN> -31.33923 -41.90655 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2458" Parameter: A <- "-73.2458" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3392" Parameter: B <- "-31.3392" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9066" Parameter: C <- "-41.9066" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2356 TOTAL ENERGY = -73.2458 RDTITL> * VAN DER WAALS = -31.3392 ELECTROSTATIC = -41.9066 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2356" Parameter: CONF_N -> "8002" Comparing "2356" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2357" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761771 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756931 ATOM PAIRS WERE FOUND FOR ATOM LIST 41576 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29538 from a total of 756931 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2357 -78.88940 5.64362 0.62976 INTE EXTERN> -34.25497 -44.63443 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8894" Parameter: A <- "-78.8894" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.255" Parameter: B <- "-34.255" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6344" Parameter: C <- "-44.6344" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2357 TOTAL ENERGY = -78.8894 RDTITL> * VAN DER WAALS = -34.255 ELECTROSTATIC = -44.6344 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2357" Parameter: CONF_N -> "8002" Comparing "2357" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2358" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756931 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756757 ATOM PAIRS WERE FOUND FOR ATOM LIST 41625 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29717 from a total of 756757 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2358 -75.76893 -3.12047 0.76576 INTE EXTERN> -24.61606 -51.15287 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7689" Parameter: A <- "-75.7689" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6161" Parameter: B <- "-24.6161" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1529" Parameter: C <- "-51.1529" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2358 TOTAL ENERGY = -75.7689 RDTITL> * VAN DER WAALS = -24.6161 ELECTROSTATIC = -51.1529 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2358" Parameter: CONF_N -> "8002" Comparing "2358" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2359" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756757 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752343 ATOM PAIRS WERE FOUND FOR ATOM LIST 41428 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29263 from a total of 752343 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2359 -77.50126 1.73233 0.68972 INTE EXTERN> -29.05175 -48.44950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5013" Parameter: A <- "-77.5013" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0518" Parameter: B <- "-29.0518" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4495" Parameter: C <- "-48.4495" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2359 TOTAL ENERGY = -77.5013 RDTITL> * VAN DER WAALS = -29.0518 ELECTROSTATIC = -48.4495 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2359" Parameter: CONF_N -> "8002" Comparing "2359" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2360" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752343 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758438 ATOM PAIRS WERE FOUND FOR ATOM LIST 41695 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29408 from a total of 758438 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2360 -71.62814 -5.87312 0.72526 INTE EXTERN> -26.11148 -45.51666 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6281" Parameter: A <- "-71.6281" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1115" Parameter: B <- "-26.1115" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5167" Parameter: C <- "-45.5167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2360 TOTAL ENERGY = -71.6281 RDTITL> * VAN DER WAALS = -26.1115 ELECTROSTATIC = -45.5167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2360" Parameter: CONF_N -> "8002" Comparing "2360" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2361" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758438 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756602 ATOM PAIRS WERE FOUND FOR ATOM LIST 41695 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30020 from a total of 756602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2361 -76.37876 4.75063 0.63206 INTE EXTERN> -30.34693 -46.03183 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3788" Parameter: A <- "-76.3788" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3469" Parameter: B <- "-30.3469" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0318" Parameter: C <- "-46.0318" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2361 TOTAL ENERGY = -76.3788 RDTITL> * VAN DER WAALS = -30.3469 ELECTROSTATIC = -46.0318 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2361" Parameter: CONF_N -> "8002" Comparing "2361" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2362" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754700 ATOM PAIRS WERE FOUND FOR ATOM LIST 41711 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28891 from a total of 754700 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2362 -73.89004 -2.48872 0.62897 INTE EXTERN> -30.11113 -43.77892 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.89" Parameter: A <- "-73.89" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1111" Parameter: B <- "-30.1111" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7789" Parameter: C <- "-43.7789" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2362 TOTAL ENERGY = -73.89 RDTITL> * VAN DER WAALS = -30.1111 ELECTROSTATIC = -43.7789 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2362" Parameter: CONF_N -> "8002" Comparing "2362" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2363" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754700 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757415 ATOM PAIRS WERE FOUND FOR ATOM LIST 41624 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29643 from a total of 757415 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2363 -80.27187 6.38183 0.61146 INTE EXTERN> -32.79521 -47.47666 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2719" Parameter: A <- "-80.2719" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7952" Parameter: B <- "-32.7952" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4767" Parameter: C <- "-47.4767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2363 TOTAL ENERGY = -80.2719 RDTITL> * VAN DER WAALS = -32.7952 ELECTROSTATIC = -47.4767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2363" Parameter: CONF_N -> "8002" Comparing "2363" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2364" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757415 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30123 from a total of 761958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2364 -76.60440 -3.66747 0.76903 INTE EXTERN> -25.68908 -50.91532 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6044" Parameter: A <- "-76.6044" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6891" Parameter: B <- "-25.6891" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9153" Parameter: C <- "-50.9153" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2364 TOTAL ENERGY = -76.6044 RDTITL> * VAN DER WAALS = -25.6891 ELECTROSTATIC = -50.9153 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2364" Parameter: CONF_N -> "8002" Comparing "2364" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2365" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759787 ATOM PAIRS WERE FOUND FOR ATOM LIST 41942 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30077 from a total of 759787 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2365 -65.05882 -11.54558 0.70061 INTE EXTERN> -26.10845 -38.95037 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0588" Parameter: A <- "-65.0588" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1084" Parameter: B <- "-26.1084" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9504" Parameter: C <- "-38.9504" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2365 TOTAL ENERGY = -65.0588 RDTITL> * VAN DER WAALS = -26.1084 ELECTROSTATIC = -38.9504 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2365" Parameter: CONF_N -> "8002" Comparing "2365" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2366" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759787 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758524 ATOM PAIRS WERE FOUND FOR ATOM LIST 41830 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30019 from a total of 758524 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2366 -64.81414 -0.24468 0.88012 INTE EXTERN> -19.10749 -45.70666 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8141" Parameter: A <- "-64.8141" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-19.1075" Parameter: B <- "-19.1075" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7067" Parameter: C <- "-45.7067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2366 TOTAL ENERGY = -64.8141 RDTITL> * VAN DER WAALS = -19.1075 ELECTROSTATIC = -45.7067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2366" Parameter: CONF_N -> "8002" Comparing "2366" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2367" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758524 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757113 ATOM PAIRS WERE FOUND FOR ATOM LIST 41611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29541 from a total of 757113 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2367 -71.72440 6.91026 0.59728 INTE EXTERN> -31.44773 -40.27667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7244" Parameter: A <- "-71.7244" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4477" Parameter: B <- "-31.4477" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2767" Parameter: C <- "-40.2767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2367 TOTAL ENERGY = -71.7244 RDTITL> * VAN DER WAALS = -31.4477 ELECTROSTATIC = -40.2767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2367" Parameter: CONF_N -> "8002" Comparing "2367" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2368" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757113 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755559 ATOM PAIRS WERE FOUND FOR ATOM LIST 41557 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30435 from a total of 755559 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2368 -73.40264 1.67823 0.62344 INTE EXTERN> -29.90816 -43.49448 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4026" Parameter: A <- "-73.4026" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9082" Parameter: B <- "-29.9082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4945" Parameter: C <- "-43.4945" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2368 TOTAL ENERGY = -73.4026 RDTITL> * VAN DER WAALS = -29.9082 ELECTROSTATIC = -43.4945 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2368" Parameter: CONF_N -> "8002" Comparing "2368" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2369" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755559 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758672 ATOM PAIRS WERE FOUND FOR ATOM LIST 41713 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29245 from a total of 758672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2369 -74.53625 1.13361 0.66791 INTE EXTERN> -27.54332 -46.99293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5362" Parameter: A <- "-74.5362" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5433" Parameter: B <- "-27.5433" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9929" Parameter: C <- "-46.9929" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2369 TOTAL ENERGY = -74.5362 RDTITL> * VAN DER WAALS = -27.5433 ELECTROSTATIC = -46.9929 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2369" Parameter: CONF_N -> "8002" Comparing "2369" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2370" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752808 ATOM PAIRS WERE FOUND FOR ATOM LIST 41444 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30001 from a total of 752808 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2370 -80.52512 5.98888 0.65593 INTE EXTERN> -30.40216 -50.12297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5251" Parameter: A <- "-80.5251" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4022" Parameter: B <- "-30.4022" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.123" Parameter: C <- "-50.123" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2370 TOTAL ENERGY = -80.5251 RDTITL> * VAN DER WAALS = -30.4022 ELECTROSTATIC = -50.123 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2370" Parameter: CONF_N -> "8002" Comparing "2370" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2371" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752808 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757614 ATOM PAIRS WERE FOUND FOR ATOM LIST 41751 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29881 from a total of 757614 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2371 -79.86225 -0.66287 0.68810 INTE EXTERN> -28.76745 -51.09480 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8623" Parameter: A <- "-79.8623" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7675" Parameter: B <- "-28.7675" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0948" Parameter: C <- "-51.0948" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2371 TOTAL ENERGY = -79.8623 RDTITL> * VAN DER WAALS = -28.7675 ELECTROSTATIC = -51.0948 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2371" Parameter: CONF_N -> "8002" Comparing "2371" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2372" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757614 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759161 ATOM PAIRS WERE FOUND FOR ATOM LIST 41801 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29772 from a total of 759161 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2372 -86.70766 6.84541 0.74835 INTE EXTERN> -29.50414 -57.20353 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.7077" Parameter: A <- "-86.7077" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5041" Parameter: B <- "-29.5041" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.2035" Parameter: C <- "-57.2035" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2372 TOTAL ENERGY = -86.7077 RDTITL> * VAN DER WAALS = -29.5041 ELECTROSTATIC = -57.2035 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2372" Parameter: CONF_N -> "8002" Comparing "2372" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2373" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759161 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757935 ATOM PAIRS WERE FOUND FOR ATOM LIST 41774 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30520 from a total of 757935 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2373 -77.35483 -9.35284 0.76173 INTE EXTERN> -29.64448 -47.71035 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3548" Parameter: A <- "-77.3548" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6445" Parameter: B <- "-29.6445" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7103" Parameter: C <- "-47.7103" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2373 TOTAL ENERGY = -77.3548 RDTITL> * VAN DER WAALS = -29.6445 ELECTROSTATIC = -47.7103 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2373" Parameter: CONF_N -> "8002" Comparing "2373" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2374" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757935 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41829 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30255 from a total of 761958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2374 -76.89329 -0.46154 0.72096 INTE EXTERN> -24.78234 -52.11095 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8933" Parameter: A <- "-76.8933" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7823" Parameter: B <- "-24.7823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.111" Parameter: C <- "-52.111" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2374 TOTAL ENERGY = -76.8933 RDTITL> * VAN DER WAALS = -24.7823 ELECTROSTATIC = -52.111 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2374" Parameter: CONF_N -> "8002" Comparing "2374" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2375" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757821 ATOM PAIRS WERE FOUND FOR ATOM LIST 41416 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29519 from a total of 757821 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2375 -71.51953 -5.37376 0.83375 INTE EXTERN> -23.68945 -47.83009 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5195" Parameter: A <- "-71.5195" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6894" Parameter: B <- "-23.6894" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8301" Parameter: C <- "-47.8301" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2375 TOTAL ENERGY = -71.5195 RDTITL> * VAN DER WAALS = -23.6894 ELECTROSTATIC = -47.8301 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2375" Parameter: CONF_N -> "8002" Comparing "2375" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2376" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757821 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755511 ATOM PAIRS WERE FOUND FOR ATOM LIST 41549 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29006 from a total of 755511 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2376 -75.73595 4.21642 0.79093 INTE EXTERN> -27.38180 -48.35415 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7359" Parameter: A <- "-75.7359" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3818" Parameter: B <- "-27.3818" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3542" Parameter: C <- "-48.3542" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2376 TOTAL ENERGY = -75.7359 RDTITL> * VAN DER WAALS = -27.3818 ELECTROSTATIC = -48.3542 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2376" Parameter: CONF_N -> "8002" Comparing "2376" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2377" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755511 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758453 ATOM PAIRS WERE FOUND FOR ATOM LIST 41742 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29964 from a total of 758453 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2377 -77.56633 1.83038 0.66777 INTE EXTERN> -30.61891 -46.94743 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5663" Parameter: A <- "-77.5663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6189" Parameter: B <- "-30.6189" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9474" Parameter: C <- "-46.9474" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2377 TOTAL ENERGY = -77.5663 RDTITL> * VAN DER WAALS = -30.6189 ELECTROSTATIC = -46.9474 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2377" Parameter: CONF_N -> "8002" Comparing "2377" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2378" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758453 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759435 ATOM PAIRS WERE FOUND FOR ATOM LIST 41490 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29855 from a total of 759435 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2378 -75.05952 -2.50681 0.57108 INTE EXTERN> -32.10951 -42.95001 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0595" Parameter: A <- "-75.0595" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1095" Parameter: B <- "-32.1095" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.95" Parameter: C <- "-42.95" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2378 TOTAL ENERGY = -75.0595 RDTITL> * VAN DER WAALS = -32.1095 ELECTROSTATIC = -42.95 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2378" Parameter: CONF_N -> "8002" Comparing "2378" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2379" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759435 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759354 ATOM PAIRS WERE FOUND FOR ATOM LIST 41675 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29466 from a total of 759354 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2379 -72.80701 -2.25252 0.60538 INTE EXTERN> -30.25865 -42.54836 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.807" Parameter: A <- "-72.807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2586" Parameter: B <- "-30.2586" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5484" Parameter: C <- "-42.5484" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2379 TOTAL ENERGY = -72.807 RDTITL> * VAN DER WAALS = -30.2586 ELECTROSTATIC = -42.5484 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2379" Parameter: CONF_N -> "8002" Comparing "2379" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2380" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759354 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757263 ATOM PAIRS WERE FOUND FOR ATOM LIST 41670 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29898 from a total of 757263 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2380 -76.32200 3.51500 0.60693 INTE EXTERN> -32.76268 -43.55932 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.322" Parameter: A <- "-76.322" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7627" Parameter: B <- "-32.7627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5593" Parameter: C <- "-43.5593" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2380 TOTAL ENERGY = -76.322 RDTITL> * VAN DER WAALS = -32.7627 ELECTROSTATIC = -43.5593 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2380" Parameter: CONF_N -> "8002" Comparing "2380" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2381" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757263 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757755 ATOM PAIRS WERE FOUND FOR ATOM LIST 41615 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30401 from a total of 757755 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2381 -76.18702 -0.13498 0.69825 INTE EXTERN> -27.45191 -48.73511 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.187" Parameter: A <- "-76.187" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4519" Parameter: B <- "-27.4519" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7351" Parameter: C <- "-48.7351" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2381 TOTAL ENERGY = -76.187 RDTITL> * VAN DER WAALS = -27.4519 ELECTROSTATIC = -48.7351 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2381" Parameter: CONF_N -> "8002" Comparing "2381" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2382" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757755 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41417 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30060 from a total of 754794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2382 -62.50306 -13.68396 0.46704 INTE EXTERN> -32.73110 -29.77196 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5031" Parameter: A <- "-62.5031" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7311" Parameter: B <- "-32.7311" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.772" Parameter: C <- "-29.772" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2382 TOTAL ENERGY = -62.5031 RDTITL> * VAN DER WAALS = -32.7311 ELECTROSTATIC = -29.772 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2382" Parameter: CONF_N -> "8002" Comparing "2382" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2383" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750187 ATOM PAIRS WERE FOUND FOR ATOM LIST 41219 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29176 from a total of 750187 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2383 -78.65261 16.14955 0.65087 INTE EXTERN> -31.02500 -47.62761 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6526" Parameter: A <- "-78.6526" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.025" Parameter: B <- "-31.025" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6276" Parameter: C <- "-47.6276" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2383 TOTAL ENERGY = -78.6526 RDTITL> * VAN DER WAALS = -31.025 ELECTROSTATIC = -47.6276 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2383" Parameter: CONF_N -> "8002" Comparing "2383" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2384" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750187 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748903 ATOM PAIRS WERE FOUND FOR ATOM LIST 41199 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29288 from a total of 748903 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2384 -66.45597 -12.19664 0.74399 INTE EXTERN> -20.18635 -46.26962 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.456" Parameter: A <- "-66.456" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.1864" Parameter: B <- "-20.1864" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2696" Parameter: C <- "-46.2696" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2384 TOTAL ENERGY = -66.456 RDTITL> * VAN DER WAALS = -20.1864 ELECTROSTATIC = -46.2696 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2384" Parameter: CONF_N -> "8002" Comparing "2384" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2385" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748903 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751617 ATOM PAIRS WERE FOUND FOR ATOM LIST 41289 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29713 from a total of 751617 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2385 -71.55894 5.10297 0.62637 INTE EXTERN> -30.69931 -40.85963 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5589" Parameter: A <- "-71.5589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6993" Parameter: B <- "-30.6993" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8596" Parameter: C <- "-40.8596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2385 TOTAL ENERGY = -71.5589 RDTITL> * VAN DER WAALS = -30.6993 ELECTROSTATIC = -40.8596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2385" Parameter: CONF_N -> "8002" Comparing "2385" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2386" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751617 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754314 ATOM PAIRS WERE FOUND FOR ATOM LIST 41614 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29253 from a total of 754314 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2386 -74.15352 2.59458 0.63547 INTE EXTERN> -29.87431 -44.27921 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1535" Parameter: A <- "-74.1535" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8743" Parameter: B <- "-29.8743" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2792" Parameter: C <- "-44.2792" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2386 TOTAL ENERGY = -74.1535 RDTITL> * VAN DER WAALS = -29.8743 ELECTROSTATIC = -44.2792 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2386" Parameter: CONF_N -> "8002" Comparing "2386" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2387" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754314 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758389 ATOM PAIRS WERE FOUND FOR ATOM LIST 41795 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29728 from a total of 758389 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2387 -72.49062 -1.66290 0.67144 INTE EXTERN> -25.68796 -46.80266 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4906" Parameter: A <- "-72.4906" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.688" Parameter: B <- "-25.688" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8027" Parameter: C <- "-46.8027" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2387 TOTAL ENERGY = -72.4906 RDTITL> * VAN DER WAALS = -25.688 ELECTROSTATIC = -46.8027 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2387" Parameter: CONF_N -> "8002" Comparing "2387" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2388" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758389 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756632 ATOM PAIRS WERE FOUND FOR ATOM LIST 41528 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30149 from a total of 756632 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2388 -75.48439 2.99377 0.75067 INTE EXTERN> -26.48129 -49.00310 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4844" Parameter: A <- "-75.4844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4813" Parameter: B <- "-26.4813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0031" Parameter: C <- "-49.0031" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2388 TOTAL ENERGY = -75.4844 RDTITL> * VAN DER WAALS = -26.4813 ELECTROSTATIC = -49.0031 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2388" Parameter: CONF_N -> "8002" Comparing "2388" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2389" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756632 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756071 ATOM PAIRS WERE FOUND FOR ATOM LIST 41860 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29802 from a total of 756071 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2389 -79.77754 4.29316 0.64383 INTE EXTERN> -32.76585 -47.01169 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7775" Parameter: A <- "-79.7775" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7659" Parameter: B <- "-32.7659" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0117" Parameter: C <- "-47.0117" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2389 TOTAL ENERGY = -79.7775 RDTITL> * VAN DER WAALS = -32.7659 ELECTROSTATIC = -47.0117 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2389" Parameter: CONF_N -> "8002" Comparing "2389" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2390" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756071 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760602 ATOM PAIRS WERE FOUND FOR ATOM LIST 41994 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30285 from a total of 760602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2390 -74.23782 -5.53972 0.61696 INTE EXTERN> -30.92505 -43.31277 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2378" Parameter: A <- "-74.2378" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9251" Parameter: B <- "-30.9251" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3128" Parameter: C <- "-43.3128" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2390 TOTAL ENERGY = -74.2378 RDTITL> * VAN DER WAALS = -30.9251 ELECTROSTATIC = -43.3128 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2390" Parameter: CONF_N -> "8002" Comparing "2390" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2391" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759214 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30602 from a total of 759214 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2391 -75.80474 1.56691 0.67786 INTE EXTERN> -32.13818 -43.66656 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8047" Parameter: A <- "-75.8047" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1382" Parameter: B <- "-32.1382" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6666" Parameter: C <- "-43.6666" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2391 TOTAL ENERGY = -75.8047 RDTITL> * VAN DER WAALS = -32.1382 ELECTROSTATIC = -43.6666 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2391" Parameter: CONF_N -> "8002" Comparing "2391" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2392" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759214 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753767 ATOM PAIRS WERE FOUND FOR ATOM LIST 41461 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29963 from a total of 753767 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2392 -70.31150 -5.49323 0.71788 INTE EXTERN> -25.58555 -44.72595 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3115" Parameter: A <- "-70.3115" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5855" Parameter: B <- "-25.5855" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.726" Parameter: C <- "-44.726" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2392 TOTAL ENERGY = -70.3115 RDTITL> * VAN DER WAALS = -25.5855 ELECTROSTATIC = -44.726 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2392" Parameter: CONF_N -> "8002" Comparing "2392" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2393" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753767 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756577 ATOM PAIRS WERE FOUND FOR ATOM LIST 41610 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30046 from a total of 756577 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2393 -74.45388 4.14238 0.61832 INTE EXTERN> -28.99451 -45.45937 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4539" Parameter: A <- "-74.4539" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9945" Parameter: B <- "-28.9945" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4594" Parameter: C <- "-45.4594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2393 TOTAL ENERGY = -74.4539 RDTITL> * VAN DER WAALS = -28.9945 ELECTROSTATIC = -45.4594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2393" Parameter: CONF_N -> "8002" Comparing "2393" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2394" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756577 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760026 ATOM PAIRS WERE FOUND FOR ATOM LIST 41721 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30865 from a total of 760026 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2394 -74.00508 -0.44880 0.67874 INTE EXTERN> -28.59343 -45.41165 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0051" Parameter: A <- "-74.0051" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5934" Parameter: B <- "-28.5934" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4117" Parameter: C <- "-45.4117" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2394 TOTAL ENERGY = -74.0051 RDTITL> * VAN DER WAALS = -28.5934 ELECTROSTATIC = -45.4117 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2394" Parameter: CONF_N -> "8002" Comparing "2394" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2395" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760026 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753048 ATOM PAIRS WERE FOUND FOR ATOM LIST 41351 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29839 from a total of 753048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2395 -69.39527 -4.60981 0.58982 INTE EXTERN> -30.81934 -38.57593 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3953" Parameter: A <- "-69.3953" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8193" Parameter: B <- "-30.8193" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5759" Parameter: C <- "-38.5759" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2395 TOTAL ENERGY = -69.3953 RDTITL> * VAN DER WAALS = -30.8193 ELECTROSTATIC = -38.5759 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2395" Parameter: CONF_N -> "8002" Comparing "2395" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2396" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757186 ATOM PAIRS WERE FOUND FOR ATOM LIST 41562 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30088 from a total of 757186 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2396 -73.99126 4.59599 0.56950 INTE EXTERN> -30.67162 -43.31964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9913" Parameter: A <- "-73.9913" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6716" Parameter: B <- "-30.6716" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3196" Parameter: C <- "-43.3196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2396 TOTAL ENERGY = -73.9913 RDTITL> * VAN DER WAALS = -30.6716 ELECTROSTATIC = -43.3196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2396" Parameter: CONF_N -> "8002" Comparing "2396" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2397" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757186 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761574 ATOM PAIRS WERE FOUND FOR ATOM LIST 42063 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30143 from a total of 761574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2397 -66.20582 -7.78544 0.46570 INTE EXTERN> -35.47630 -30.72952 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2058" Parameter: A <- "-66.2058" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.4763" Parameter: B <- "-35.4763" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.7295" Parameter: C <- "-30.7295" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2397 TOTAL ENERGY = -66.2058 RDTITL> * VAN DER WAALS = -35.4763 ELECTROSTATIC = -30.7295 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2397" Parameter: CONF_N -> "8002" Comparing "2397" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2398" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758679 ATOM PAIRS WERE FOUND FOR ATOM LIST 41770 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30340 from a total of 758679 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2398 -68.44659 2.24077 0.66284 INTE EXTERN> -29.60668 -38.83991 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4466" Parameter: A <- "-68.4466" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6067" Parameter: B <- "-29.6067" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8399" Parameter: C <- "-38.8399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2398 TOTAL ENERGY = -68.4466 RDTITL> * VAN DER WAALS = -29.6067 ELECTROSTATIC = -38.8399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2398" Parameter: CONF_N -> "8002" Comparing "2398" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2399" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758679 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756426 ATOM PAIRS WERE FOUND FOR ATOM LIST 41626 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29739 from a total of 756426 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2399 -67.18444 -1.26215 0.56127 INTE EXTERN> -32.39399 -34.79046 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1844" Parameter: A <- "-67.1844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.394" Parameter: B <- "-32.394" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7905" Parameter: C <- "-34.7905" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2399 TOTAL ENERGY = -67.1844 RDTITL> * VAN DER WAALS = -32.394 ELECTROSTATIC = -34.7905 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2399" Parameter: CONF_N -> "8002" Comparing "2399" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2400" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756426 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755483 ATOM PAIRS WERE FOUND FOR ATOM LIST 41527 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29927 from a total of 755483 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2400 -68.48300 1.29856 0.58368 INTE EXTERN> -28.91286 -39.57014 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.483" Parameter: A <- "-68.483" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9129" Parameter: B <- "-28.9129" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5701" Parameter: C <- "-39.5701" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2400 TOTAL ENERGY = -68.483 RDTITL> * VAN DER WAALS = -28.9129 ELECTROSTATIC = -39.5701 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2400" Parameter: CONF_N -> "8002" Comparing "2400" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2401" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755483 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758402 ATOM PAIRS WERE FOUND FOR ATOM LIST 41703 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29647 from a total of 758402 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2401 -68.09376 -0.38924 0.51331 INTE EXTERN> -32.79932 -35.29444 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0938" Parameter: A <- "-68.0938" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7993" Parameter: B <- "-32.7993" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2944" Parameter: C <- "-35.2944" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2401 TOTAL ENERGY = -68.0938 RDTITL> * VAN DER WAALS = -32.7993 ELECTROSTATIC = -35.2944 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2401" Parameter: CONF_N -> "8002" Comparing "2401" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2402" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758402 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759855 ATOM PAIRS WERE FOUND FOR ATOM LIST 41829 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29891 from a total of 759855 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2402 -70.96218 2.86842 0.63593 INTE EXTERN> -30.78060 -40.18159 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9622" Parameter: A <- "-70.9622" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7806" Parameter: B <- "-30.7806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1816" Parameter: C <- "-40.1816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2402 TOTAL ENERGY = -70.9622 RDTITL> * VAN DER WAALS = -30.7806 ELECTROSTATIC = -40.1816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2402" Parameter: CONF_N -> "8002" Comparing "2402" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2403" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759855 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761384 ATOM PAIRS WERE FOUND FOR ATOM LIST 41871 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30507 from a total of 761384 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2403 -55.20963 -15.75256 0.64068 INTE EXTERN> -25.33679 -29.87284 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.2096" Parameter: A <- "-55.2096" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3368" Parameter: B <- "-25.3368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.8728" Parameter: C <- "-29.8728" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2403 TOTAL ENERGY = -55.2096 RDTITL> * VAN DER WAALS = -25.3368 ELECTROSTATIC = -29.8728 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2403" Parameter: CONF_N -> "8002" Comparing "2403" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2404" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761384 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758625 ATOM PAIRS WERE FOUND FOR ATOM LIST 41582 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30045 from a total of 758625 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2404 -70.44026 15.23063 0.54782 INTE EXTERN> -32.59860 -37.84165 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4403" Parameter: A <- "-70.4403" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5986" Parameter: B <- "-32.5986" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8417" Parameter: C <- "-37.8417" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2404 TOTAL ENERGY = -70.4403 RDTITL> * VAN DER WAALS = -32.5986 ELECTROSTATIC = -37.8417 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2404" Parameter: CONF_N -> "8002" Comparing "2404" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2405" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758625 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755946 ATOM PAIRS WERE FOUND FOR ATOM LIST 41548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30203 from a total of 755946 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2405 -70.96485 0.52460 0.60286 INTE EXTERN> -29.13851 -41.82634 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9649" Parameter: A <- "-70.9649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1385" Parameter: B <- "-29.1385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8263" Parameter: C <- "-41.8263" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2405 TOTAL ENERGY = -70.9649 RDTITL> * VAN DER WAALS = -29.1385 ELECTROSTATIC = -41.8263 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2405" Parameter: CONF_N -> "8002" Comparing "2405" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2406" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755946 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758664 ATOM PAIRS WERE FOUND FOR ATOM LIST 41760 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30298 from a total of 758664 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2406 -67.47661 -3.48824 0.59859 INTE EXTERN> -30.40758 -37.06903 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4766" Parameter: A <- "-67.4766" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4076" Parameter: B <- "-30.4076" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.069" Parameter: C <- "-37.069" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2406 TOTAL ENERGY = -67.4766 RDTITL> * VAN DER WAALS = -30.4076 ELECTROSTATIC = -37.069 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2406" Parameter: CONF_N -> "8002" Comparing "2406" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2407" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758664 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761178 ATOM PAIRS WERE FOUND FOR ATOM LIST 41893 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 31025 from a total of 761178 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2407 -73.32511 5.84850 0.62486 INTE EXTERN> -30.26553 -43.05959 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3251" Parameter: A <- "-73.3251" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2655" Parameter: B <- "-30.2655" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0596" Parameter: C <- "-43.0596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2407 TOTAL ENERGY = -73.3251 RDTITL> * VAN DER WAALS = -30.2655 ELECTROSTATIC = -43.0596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2407" Parameter: CONF_N -> "8002" Comparing "2407" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2408" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761178 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761138 ATOM PAIRS WERE FOUND FOR ATOM LIST 41908 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29958 from a total of 761138 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2408 -73.65239 0.32727 0.64839 INTE EXTERN> -28.31787 -45.33452 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6524" Parameter: A <- "-73.6524" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3179" Parameter: B <- "-28.3179" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3345" Parameter: C <- "-45.3345" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2408 TOTAL ENERGY = -73.6524 RDTITL> * VAN DER WAALS = -28.3179 ELECTROSTATIC = -45.3345 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2408" Parameter: CONF_N -> "8002" Comparing "2408" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2409" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761138 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758413 ATOM PAIRS WERE FOUND FOR ATOM LIST 41664 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30570 from a total of 758413 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2409 -69.68951 -3.96288 0.67859 INTE EXTERN> -27.51276 -42.17675 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6895" Parameter: A <- "-69.6895" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5128" Parameter: B <- "-27.5128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1767" Parameter: C <- "-42.1767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2409 TOTAL ENERGY = -69.6895 RDTITL> * VAN DER WAALS = -27.5128 ELECTROSTATIC = -42.1767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2409" Parameter: CONF_N -> "8002" Comparing "2409" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2410" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758413 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760389 ATOM PAIRS WERE FOUND FOR ATOM LIST 41749 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30591 from a total of 760389 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2410 -75.63910 5.94960 0.62250 INTE EXTERN> -31.78343 -43.85568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6391" Parameter: A <- "-75.6391" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7834" Parameter: B <- "-31.7834" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8557" Parameter: C <- "-43.8557" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2410 TOTAL ENERGY = -75.6391 RDTITL> * VAN DER WAALS = -31.7834 ELECTROSTATIC = -43.8557 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2410" Parameter: CONF_N -> "8002" Comparing "2410" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2411" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760389 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757608 ATOM PAIRS WERE FOUND FOR ATOM LIST 41676 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29866 from a total of 757608 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2411 -71.04685 -4.59226 0.62985 INTE EXTERN> -28.27806 -42.76879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0468" Parameter: A <- "-71.0468" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2781" Parameter: B <- "-28.2781" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7688" Parameter: C <- "-42.7688" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2411 TOTAL ENERGY = -71.0468 RDTITL> * VAN DER WAALS = -28.2781 ELECTROSTATIC = -42.7688 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2411" Parameter: CONF_N -> "8002" Comparing "2411" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2412" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757608 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762330 ATOM PAIRS WERE FOUND FOR ATOM LIST 41972 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30035 from a total of 762330 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2412 -75.11878 4.07193 0.70380 INTE EXTERN> -29.75161 -45.36717 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1188" Parameter: A <- "-75.1188" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7516" Parameter: B <- "-29.7516" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3672" Parameter: C <- "-45.3672" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2412 TOTAL ENERGY = -75.1188 RDTITL> * VAN DER WAALS = -29.7516 ELECTROSTATIC = -45.3672 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2412" Parameter: CONF_N -> "8002" Comparing "2412" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2413" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762330 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760928 ATOM PAIRS WERE FOUND FOR ATOM LIST 41982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30060 from a total of 760928 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2413 -79.30892 4.19014 0.61994 INTE EXTERN> -30.42723 -48.88170 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.3089" Parameter: A <- "-79.3089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4272" Parameter: B <- "-30.4272" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8817" Parameter: C <- "-48.8817" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2413 TOTAL ENERGY = -79.3089 RDTITL> * VAN DER WAALS = -30.4272 ELECTROSTATIC = -48.8817 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2413" Parameter: CONF_N -> "8002" Comparing "2413" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2414" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760928 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760173 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29310 from a total of 760173 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2414 -72.57214 -6.73678 0.67238 INTE EXTERN> -29.63541 -42.93673 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5721" Parameter: A <- "-72.5721" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6354" Parameter: B <- "-29.6354" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9367" Parameter: C <- "-42.9367" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2414 TOTAL ENERGY = -72.5721 RDTITL> * VAN DER WAALS = -29.6354 ELECTROSTATIC = -42.9367 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2414" Parameter: CONF_N -> "8002" Comparing "2414" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2415" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760173 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756517 ATOM PAIRS WERE FOUND FOR ATOM LIST 41825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29101 from a total of 756517 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2415 -82.67446 10.10232 0.67773 INTE EXTERN> -29.09480 -53.57966 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.6745" Parameter: A <- "-82.6745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0948" Parameter: B <- "-29.0948" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.5797" Parameter: C <- "-53.5797" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2415 TOTAL ENERGY = -82.6745 RDTITL> * VAN DER WAALS = -29.0948 ELECTROSTATIC = -53.5797 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2415" Parameter: CONF_N -> "8002" Comparing "2415" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2416" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756517 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759318 ATOM PAIRS WERE FOUND FOR ATOM LIST 41752 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29020 from a total of 759318 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2416 -77.96999 -4.70447 0.69071 INTE EXTERN> -30.25328 -47.71672 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.97" Parameter: A <- "-77.97" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2533" Parameter: B <- "-30.2533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7167" Parameter: C <- "-47.7167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2416 TOTAL ENERGY = -77.97 RDTITL> * VAN DER WAALS = -30.2533 ELECTROSTATIC = -47.7167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2416" Parameter: CONF_N -> "8002" Comparing "2416" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2417" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759318 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763462 ATOM PAIRS WERE FOUND FOR ATOM LIST 41898 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29284 from a total of 763462 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2417 -77.70008 -0.26991 0.76640 INTE EXTERN> -28.98328 -48.71679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7001" Parameter: A <- "-77.7001" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9833" Parameter: B <- "-28.9833" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7168" Parameter: C <- "-48.7168" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2417 TOTAL ENERGY = -77.7001 RDTITL> * VAN DER WAALS = -28.9833 ELECTROSTATIC = -48.7168 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2417" Parameter: CONF_N -> "8002" Comparing "2417" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2418" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763462 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760155 ATOM PAIRS WERE FOUND FOR ATOM LIST 41893 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29879 from a total of 760155 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2418 -78.54069 0.84061 0.82823 INTE EXTERN> -25.23661 -53.30408 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5407" Parameter: A <- "-78.5407" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2366" Parameter: B <- "-25.2366" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3041" Parameter: C <- "-53.3041" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2418 TOTAL ENERGY = -78.5407 RDTITL> * VAN DER WAALS = -25.2366 ELECTROSTATIC = -53.3041 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2418" Parameter: CONF_N -> "8002" Comparing "2418" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2419" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760155 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757764 ATOM PAIRS WERE FOUND FOR ATOM LIST 41822 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29221 from a total of 757764 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2419 -75.09272 -3.44797 0.60287 INTE EXTERN> -32.08816 -43.00456 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0927" Parameter: A <- "-75.0927" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0882" Parameter: B <- "-32.0882" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0046" Parameter: C <- "-43.0046" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2419 TOTAL ENERGY = -75.0927 RDTITL> * VAN DER WAALS = -32.0882 ELECTROSTATIC = -43.0046 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2419" Parameter: CONF_N -> "8002" Comparing "2419" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2420" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757764 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757065 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29146 from a total of 757065 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2420 -73.42304 -1.66968 0.63959 INTE EXTERN> -31.49209 -41.93095 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.423" Parameter: A <- "-73.423" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4921" Parameter: B <- "-31.4921" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9309" Parameter: C <- "-41.9309" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2420 TOTAL ENERGY = -73.423 RDTITL> * VAN DER WAALS = -31.4921 ELECTROSTATIC = -41.9309 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2420" Parameter: CONF_N -> "8002" Comparing "2420" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2421" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757065 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763784 ATOM PAIRS WERE FOUND FOR ATOM LIST 42023 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29753 from a total of 763784 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2421 -78.88793 5.46489 0.68449 INTE EXTERN> -30.82149 -48.06644 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8879" Parameter: A <- "-78.8879" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8215" Parameter: B <- "-30.8215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0664" Parameter: C <- "-48.0664" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2421 TOTAL ENERGY = -78.8879 RDTITL> * VAN DER WAALS = -30.8215 ELECTROSTATIC = -48.0664 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2421" Parameter: CONF_N -> "8002" Comparing "2421" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2422" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763784 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757976 ATOM PAIRS WERE FOUND FOR ATOM LIST 41619 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28396 from a total of 757976 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2422 -69.36572 -9.52221 0.61292 INTE EXTERN> -29.17267 -40.19305 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3657" Parameter: A <- "-69.3657" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1727" Parameter: B <- "-29.1727" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1931" Parameter: C <- "-40.1931" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2422 TOTAL ENERGY = -69.3657 RDTITL> * VAN DER WAALS = -29.1727 ELECTROSTATIC = -40.1931 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2422" Parameter: CONF_N -> "8002" Comparing "2422" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2423" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757976 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755593 ATOM PAIRS WERE FOUND FOR ATOM LIST 41592 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28914 from a total of 755593 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2423 -80.12923 10.76350 0.75320 INTE EXTERN> -26.17064 -53.95859 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1292" Parameter: A <- "-80.1292" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1706" Parameter: B <- "-26.1706" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.9586" Parameter: C <- "-53.9586" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2423 TOTAL ENERGY = -80.1292 RDTITL> * VAN DER WAALS = -26.1706 ELECTROSTATIC = -53.9586 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2423" Parameter: CONF_N -> "8002" Comparing "2423" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2424" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755593 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758634 ATOM PAIRS WERE FOUND FOR ATOM LIST 41600 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28661 from a total of 758634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2424 -81.12258 0.99335 0.81278 INTE EXTERN> -26.07147 -55.05111 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1226" Parameter: A <- "-81.1226" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0715" Parameter: B <- "-26.0715" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.0511" Parameter: C <- "-55.0511" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2424 TOTAL ENERGY = -81.1226 RDTITL> * VAN DER WAALS = -26.0715 ELECTROSTATIC = -55.0511 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2424" Parameter: CONF_N -> "8002" Comparing "2424" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2425" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763142 ATOM PAIRS WERE FOUND FOR ATOM LIST 41953 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29247 from a total of 763142 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2425 -80.56360 -0.55898 0.71222 INTE EXTERN> -27.42965 -53.13395 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5636" Parameter: A <- "-80.5636" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4297" Parameter: B <- "-27.4297" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.134" Parameter: C <- "-53.134" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2425 TOTAL ENERGY = -80.5636 RDTITL> * VAN DER WAALS = -27.4297 ELECTROSTATIC = -53.134 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2425" Parameter: CONF_N -> "8002" Comparing "2425" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2426" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763142 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761546 ATOM PAIRS WERE FOUND FOR ATOM LIST 41888 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30061 from a total of 761546 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2426 -84.10159 3.53799 0.67386 INTE EXTERN> -28.64052 -55.46107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.1016" Parameter: A <- "-84.1016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6405" Parameter: B <- "-28.6405" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.4611" Parameter: C <- "-55.4611" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2426 TOTAL ENERGY = -84.1016 RDTITL> * VAN DER WAALS = -28.6405 ELECTROSTATIC = -55.4611 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2426" Parameter: CONF_N -> "8002" Comparing "2426" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2427" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761546 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758176 ATOM PAIRS WERE FOUND FOR ATOM LIST 41808 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29103 from a total of 758176 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2427 -81.25756 -2.84404 0.80884 INTE EXTERN> -28.28978 -52.96778 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.2576" Parameter: A <- "-81.2576" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2898" Parameter: B <- "-28.2898" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9678" Parameter: C <- "-52.9678" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2427 TOTAL ENERGY = -81.2576 RDTITL> * VAN DER WAALS = -28.2898 ELECTROSTATIC = -52.9678 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2427" Parameter: CONF_N -> "8002" Comparing "2427" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2428" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758176 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758204 ATOM PAIRS WERE FOUND FOR ATOM LIST 41857 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30023 from a total of 758204 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2428 -88.13890 6.88134 0.66024 INTE EXTERN> -32.39009 -55.74881 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.1389" Parameter: A <- "-88.1389" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3901" Parameter: B <- "-32.3901" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.7488" Parameter: C <- "-55.7488" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2428 TOTAL ENERGY = -88.1389 RDTITL> * VAN DER WAALS = -32.3901 ELECTROSTATIC = -55.7488 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2428" Parameter: CONF_N -> "8002" Comparing "2428" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2429" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758204 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755264 ATOM PAIRS WERE FOUND FOR ATOM LIST 41631 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29932 from a total of 755264 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2429 -80.91756 -7.22134 0.59441 INTE EXTERN> -33.29429 -47.62326 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9176" Parameter: A <- "-80.9176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2943" Parameter: B <- "-33.2943" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6233" Parameter: C <- "-47.6233" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2429 TOTAL ENERGY = -80.9176 RDTITL> * VAN DER WAALS = -33.2943 ELECTROSTATIC = -47.6233 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2429" Parameter: CONF_N -> "8002" Comparing "2429" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2430" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755264 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756531 ATOM PAIRS WERE FOUND FOR ATOM LIST 41616 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29282 from a total of 756531 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2430 -81.32162 0.40406 0.68764 INTE EXTERN> -29.05256 -52.26906 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.3216" Parameter: A <- "-81.3216" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0526" Parameter: B <- "-29.0526" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2691" Parameter: C <- "-52.2691" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2430 TOTAL ENERGY = -81.3216 RDTITL> * VAN DER WAALS = -29.0526 ELECTROSTATIC = -52.2691 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2430" Parameter: CONF_N -> "8002" Comparing "2430" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2431" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756531 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761183 ATOM PAIRS WERE FOUND FOR ATOM LIST 41810 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29964 from a total of 761183 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2431 -81.19755 -0.12406 0.73949 INTE EXTERN> -27.14813 -54.04942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1976" Parameter: A <- "-81.1976" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1481" Parameter: B <- "-27.1481" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0494" Parameter: C <- "-54.0494" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2431 TOTAL ENERGY = -81.1976 RDTITL> * VAN DER WAALS = -27.1481 ELECTROSTATIC = -54.0494 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2431" Parameter: CONF_N -> "8002" Comparing "2431" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2432" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761183 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759430 ATOM PAIRS WERE FOUND FOR ATOM LIST 41769 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30254 from a total of 759430 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2432 -79.25534 -1.94221 0.60923 INTE EXTERN> -34.01466 -45.24069 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2553" Parameter: A <- "-79.2553" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0147" Parameter: B <- "-34.0147" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2407" Parameter: C <- "-45.2407" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2432 TOTAL ENERGY = -79.2553 RDTITL> * VAN DER WAALS = -34.0147 ELECTROSTATIC = -45.2407 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2432" Parameter: CONF_N -> "8002" Comparing "2432" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2433" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759430 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768456 ATOM PAIRS WERE FOUND FOR ATOM LIST 42379 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30560 from a total of 768456 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2433 -78.43630 -0.81904 0.69040 INTE EXTERN> -29.06044 -49.37587 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4363" Parameter: A <- "-78.4363" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0604" Parameter: B <- "-29.0604" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3759" Parameter: C <- "-49.3759" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2433 TOTAL ENERGY = -78.4363 RDTITL> * VAN DER WAALS = -29.0604 ELECTROSTATIC = -49.3759 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2433" Parameter: CONF_N -> "8002" Comparing "2433" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2434" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768456 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760702 ATOM PAIRS WERE FOUND FOR ATOM LIST 42085 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29606 from a total of 760702 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2434 -80.14000 1.70370 0.63782 INTE EXTERN> -32.21989 -47.92012 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.14" Parameter: A <- "-80.14" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2199" Parameter: B <- "-32.2199" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9201" Parameter: C <- "-47.9201" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2434 TOTAL ENERGY = -80.14 RDTITL> * VAN DER WAALS = -32.2199 ELECTROSTATIC = -47.9201 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2434" Parameter: CONF_N -> "8002" Comparing "2434" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2435" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760702 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762128 ATOM PAIRS WERE FOUND FOR ATOM LIST 42146 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29716 from a total of 762128 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2435 -76.42074 -3.71927 0.61511 INTE EXTERN> -31.56524 -44.85550 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4207" Parameter: A <- "-76.4207" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5652" Parameter: B <- "-31.5652" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8555" Parameter: C <- "-44.8555" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2435 TOTAL ENERGY = -76.4207 RDTITL> * VAN DER WAALS = -31.5652 ELECTROSTATIC = -44.8555 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2435" Parameter: CONF_N -> "8002" Comparing "2435" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2436" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762128 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759113 ATOM PAIRS WERE FOUND FOR ATOM LIST 41721 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29189 from a total of 759113 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2436 -74.57748 -1.84326 0.55648 INTE EXTERN> -32.12070 -42.45678 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5775" Parameter: A <- "-74.5775" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1207" Parameter: B <- "-32.1207" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4568" Parameter: C <- "-42.4568" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2436 TOTAL ENERGY = -74.5775 RDTITL> * VAN DER WAALS = -32.1207 ELECTROSTATIC = -42.4568 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2436" Parameter: CONF_N -> "8002" Comparing "2436" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2437" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759113 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748270 ATOM PAIRS WERE FOUND FOR ATOM LIST 41483 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29093 from a total of 748270 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2437 -77.84007 3.26259 0.59422 INTE EXTERN> -34.75850 -43.08157 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8401" Parameter: A <- "-77.8401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.7585" Parameter: B <- "-34.7585" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0816" Parameter: C <- "-43.0816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2437 TOTAL ENERGY = -77.8401 RDTITL> * VAN DER WAALS = -34.7585 ELECTROSTATIC = -43.0816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2437" Parameter: CONF_N -> "8002" Comparing "2437" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2438" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748270 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754466 ATOM PAIRS WERE FOUND FOR ATOM LIST 41868 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29470 from a total of 754466 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2438 -81.17050 3.33043 0.67331 INTE EXTERN> -31.41592 -49.75458 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1705" Parameter: A <- "-81.1705" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4159" Parameter: B <- "-31.4159" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7546" Parameter: C <- "-49.7546" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2438 TOTAL ENERGY = -81.1705 RDTITL> * VAN DER WAALS = -31.4159 ELECTROSTATIC = -49.7546 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2438" Parameter: CONF_N -> "8002" Comparing "2438" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2439" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754466 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756793 ATOM PAIRS WERE FOUND FOR ATOM LIST 41766 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29542 from a total of 756793 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2439 -72.51765 -8.65285 0.75809 INTE EXTERN> -29.17418 -43.34347 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5177" Parameter: A <- "-72.5177" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1742" Parameter: B <- "-29.1742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3435" Parameter: C <- "-43.3435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2439 TOTAL ENERGY = -72.5177 RDTITL> * VAN DER WAALS = -29.1742 ELECTROSTATIC = -43.3435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2439" Parameter: CONF_N -> "8002" Comparing "2439" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2440" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756793 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761356 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29847 from a total of 761356 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2440 -79.78223 7.26458 0.68784 INTE EXTERN> -31.28301 -48.49922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7822" Parameter: A <- "-79.7822" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.283" Parameter: B <- "-31.283" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4992" Parameter: C <- "-48.4992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2440 TOTAL ENERGY = -79.7822 RDTITL> * VAN DER WAALS = -31.283 ELECTROSTATIC = -48.4992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2440" Parameter: CONF_N -> "8002" Comparing "2440" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2441" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761356 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760077 ATOM PAIRS WERE FOUND FOR ATOM LIST 41811 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29811 from a total of 760077 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2441 -70.33722 -9.44501 0.82320 INTE EXTERN> -21.26289 -49.07432 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3372" Parameter: A <- "-70.3372" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.2629" Parameter: B <- "-21.2629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0743" Parameter: C <- "-49.0743" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2441 TOTAL ENERGY = -70.3372 RDTITL> * VAN DER WAALS = -21.2629 ELECTROSTATIC = -49.0743 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2441" Parameter: CONF_N -> "8002" Comparing "2441" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2442" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760077 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753808 ATOM PAIRS WERE FOUND FOR ATOM LIST 41320 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29312 from a total of 753808 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2442 -73.32288 2.98566 0.61397 INTE EXTERN> -31.89227 -41.43061 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3229" Parameter: A <- "-73.3229" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8923" Parameter: B <- "-31.8923" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4306" Parameter: C <- "-41.4306" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2442 TOTAL ENERGY = -73.3229 RDTITL> * VAN DER WAALS = -31.8923 ELECTROSTATIC = -41.4306 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2442" Parameter: CONF_N -> "8002" Comparing "2442" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2443" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753808 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750285 ATOM PAIRS WERE FOUND FOR ATOM LIST 41382 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29050 from a total of 750285 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2443 -70.39776 -2.92512 0.74639 INTE EXTERN> -24.36604 -46.03172 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3978" Parameter: A <- "-70.3978" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.366" Parameter: B <- "-24.366" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0317" Parameter: C <- "-46.0317" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2443 TOTAL ENERGY = -70.3978 RDTITL> * VAN DER WAALS = -24.366 ELECTROSTATIC = -46.0317 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2443" Parameter: CONF_N -> "8002" Comparing "2443" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2444" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750285 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752000 ATOM PAIRS WERE FOUND FOR ATOM LIST 41415 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29891 from a total of 752000 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2444 -74.93481 4.53704 0.59574 INTE EXTERN> -32.34659 -42.58821 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9348" Parameter: A <- "-74.9348" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3466" Parameter: B <- "-32.3466" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5882" Parameter: C <- "-42.5882" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2444 TOTAL ENERGY = -74.9348 RDTITL> * VAN DER WAALS = -32.3466 ELECTROSTATIC = -42.5882 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2444" Parameter: CONF_N -> "8002" Comparing "2444" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2445" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752000 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755839 ATOM PAIRS WERE FOUND FOR ATOM LIST 41729 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29242 from a total of 755839 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2445 -79.06980 4.13499 0.73188 INTE EXTERN> -26.33175 -52.73805 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0698" Parameter: A <- "-79.0698" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3318" Parameter: B <- "-26.3318" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.738" Parameter: C <- "-52.738" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2445 TOTAL ENERGY = -79.0698 RDTITL> * VAN DER WAALS = -26.3318 ELECTROSTATIC = -52.738 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2445" Parameter: CONF_N -> "8002" Comparing "2445" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2446" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755839 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756480 ATOM PAIRS WERE FOUND FOR ATOM LIST 41756 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29840 from a total of 756480 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2446 -77.16788 -1.90191 0.66680 INTE EXTERN> -30.35755 -46.81033 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1679" Parameter: A <- "-77.1679" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3576" Parameter: B <- "-30.3576" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8103" Parameter: C <- "-46.8103" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2446 TOTAL ENERGY = -77.1679 RDTITL> * VAN DER WAALS = -30.3576 ELECTROSTATIC = -46.8103 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2446" Parameter: CONF_N -> "8002" Comparing "2446" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2447" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756480 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755974 ATOM PAIRS WERE FOUND FOR ATOM LIST 41727 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29353 from a total of 755974 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2447 -74.73703 -2.43085 0.54927 INTE EXTERN> -32.48269 -42.25434 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.737" Parameter: A <- "-74.737" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4827" Parameter: B <- "-32.4827" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2543" Parameter: C <- "-42.2543" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2447 TOTAL ENERGY = -74.737 RDTITL> * VAN DER WAALS = -32.4827 ELECTROSTATIC = -42.2543 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2447" Parameter: CONF_N -> "8002" Comparing "2447" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2448" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755974 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755538 ATOM PAIRS WERE FOUND FOR ATOM LIST 41841 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29618 from a total of 755538 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2448 -72.34550 -2.39153 0.81230 INTE EXTERN> -23.64752 -48.69798 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3455" Parameter: A <- "-72.3455" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6475" Parameter: B <- "-23.6475" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.698" Parameter: C <- "-48.698" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2448 TOTAL ENERGY = -72.3455 RDTITL> * VAN DER WAALS = -23.6475 ELECTROSTATIC = -48.698 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2448" Parameter: CONF_N -> "8002" Comparing "2448" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2449" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755538 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760473 ATOM PAIRS WERE FOUND FOR ATOM LIST 41887 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29990 from a total of 760473 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2449 -76.04679 3.70129 0.68024 INTE EXTERN> -30.07707 -45.96972 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0468" Parameter: A <- "-76.0468" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0771" Parameter: B <- "-30.0771" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9697" Parameter: C <- "-45.9697" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2449 TOTAL ENERGY = -76.0468 RDTITL> * VAN DER WAALS = -30.0771 ELECTROSTATIC = -45.9697 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2449" Parameter: CONF_N -> "8002" Comparing "2449" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2450" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760473 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759881 ATOM PAIRS WERE FOUND FOR ATOM LIST 42091 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29997 from a total of 759881 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2450 -74.68085 -1.36594 0.71572 INTE EXTERN> -26.37821 -48.30264 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6809" Parameter: A <- "-74.6809" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3782" Parameter: B <- "-26.3782" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3026" Parameter: C <- "-48.3026" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2450 TOTAL ENERGY = -74.6809 RDTITL> * VAN DER WAALS = -26.3782 ELECTROSTATIC = -48.3026 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2450" Parameter: CONF_N -> "8002" Comparing "2450" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2451" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759881 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758279 ATOM PAIRS WERE FOUND FOR ATOM LIST 41653 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30127 from a total of 758279 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2451 -73.59247 -1.08839 0.56730 INTE EXTERN> -32.43900 -41.15346 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5925" Parameter: A <- "-73.5925" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.439" Parameter: B <- "-32.439" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1535" Parameter: C <- "-41.1535" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2451 TOTAL ENERGY = -73.5925 RDTITL> * VAN DER WAALS = -32.439 ELECTROSTATIC = -41.1535 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2451" Parameter: CONF_N -> "8002" Comparing "2451" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2452" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758279 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751253 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29166 from a total of 751253 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2452 -69.65575 -3.93671 0.55216 INTE EXTERN> -29.31291 -40.34285 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6558" Parameter: A <- "-69.6558" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3129" Parameter: B <- "-29.3129" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3428" Parameter: C <- "-40.3428" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2452 TOTAL ENERGY = -69.6558 RDTITL> * VAN DER WAALS = -29.3129 ELECTROSTATIC = -40.3428 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2452" Parameter: CONF_N -> "8002" Comparing "2452" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2453" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751253 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41849 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30293 from a total of 757586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2453 -73.31243 3.65668 0.67574 INTE EXTERN> -31.93992 -41.37251 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3124" Parameter: A <- "-73.3124" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9399" Parameter: B <- "-31.9399" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3725" Parameter: C <- "-41.3725" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2453 TOTAL ENERGY = -73.3124 RDTITL> * VAN DER WAALS = -31.9399 ELECTROSTATIC = -41.3725 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2453" Parameter: CONF_N -> "8002" Comparing "2453" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2454" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755655 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29896 from a total of 755655 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2454 -72.77459 -0.53783 0.69805 INTE EXTERN> -27.16330 -45.61129 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7746" Parameter: A <- "-72.7746" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1633" Parameter: B <- "-27.1633" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6113" Parameter: C <- "-45.6113" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2454 TOTAL ENERGY = -72.7746 RDTITL> * VAN DER WAALS = -27.1633 ELECTROSTATIC = -45.6113 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2454" Parameter: CONF_N -> "8002" Comparing "2454" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2455" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755655 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755648 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29632 from a total of 755648 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2455 -69.68164 -3.09295 0.66819 INTE EXTERN> -26.85673 -42.82492 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6816" Parameter: A <- "-69.6816" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8567" Parameter: B <- "-26.8567" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8249" Parameter: C <- "-42.8249" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2455 TOTAL ENERGY = -69.6816 RDTITL> * VAN DER WAALS = -26.8567 ELECTROSTATIC = -42.8249 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2455" Parameter: CONF_N -> "8002" Comparing "2455" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2456" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755648 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761665 ATOM PAIRS WERE FOUND FOR ATOM LIST 41935 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30357 from a total of 761665 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2456 -67.37298 -2.30866 0.65644 INTE EXTERN> -29.08008 -38.29291 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.373" Parameter: A <- "-67.373" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0801" Parameter: B <- "-29.0801" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2929" Parameter: C <- "-38.2929" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2456 TOTAL ENERGY = -67.373 RDTITL> * VAN DER WAALS = -29.0801 ELECTROSTATIC = -38.2929 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2456" Parameter: CONF_N -> "8002" Comparing "2456" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2457" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761665 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766758 ATOM PAIRS WERE FOUND FOR ATOM LIST 42257 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30339 from a total of 766758 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2457 -72.24328 4.87030 0.67626 INTE EXTERN> -31.82385 -40.41943 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2433" Parameter: A <- "-72.2433" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8238" Parameter: B <- "-31.8238" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4194" Parameter: C <- "-40.4194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2457 TOTAL ENERGY = -72.2433 RDTITL> * VAN DER WAALS = -31.8238 ELECTROSTATIC = -40.4194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2457" Parameter: CONF_N -> "8002" Comparing "2457" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2458" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766758 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763590 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30238 from a total of 763590 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2458 -65.23572 -7.00756 0.61306 INTE EXTERN> -30.82118 -34.41454 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2357" Parameter: A <- "-65.2357" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8212" Parameter: B <- "-30.8212" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4145" Parameter: C <- "-34.4145" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2458 TOTAL ENERGY = -65.2357 RDTITL> * VAN DER WAALS = -30.8212 ELECTROSTATIC = -34.4145 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2458" Parameter: CONF_N -> "8002" Comparing "2458" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2459" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763590 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761420 ATOM PAIRS WERE FOUND FOR ATOM LIST 41915 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29894 from a total of 761420 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2459 -71.12789 5.89217 0.56250 INTE EXTERN> -32.68589 -38.44199 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1279" Parameter: A <- "-71.1279" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6859" Parameter: B <- "-32.6859" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.442" Parameter: C <- "-38.442" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2459 TOTAL ENERGY = -71.1279 RDTITL> * VAN DER WAALS = -32.6859 ELECTROSTATIC = -38.442 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2459" Parameter: CONF_N -> "8002" Comparing "2459" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2460" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761420 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758164 ATOM PAIRS WERE FOUND FOR ATOM LIST 41793 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29914 from a total of 758164 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2460 -71.92522 0.79733 0.73891 INTE EXTERN> -25.28773 -46.63748 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9252" Parameter: A <- "-71.9252" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2877" Parameter: B <- "-25.2877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6375" Parameter: C <- "-46.6375" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2460 TOTAL ENERGY = -71.9252 RDTITL> * VAN DER WAALS = -25.2877 ELECTROSTATIC = -46.6375 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2460" Parameter: CONF_N -> "8002" Comparing "2460" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2461" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758164 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762003 ATOM PAIRS WERE FOUND FOR ATOM LIST 41927 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30030 from a total of 762003 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2461 -67.53106 -4.39416 0.77370 INTE EXTERN> -26.03645 -41.49461 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5311" Parameter: A <- "-67.5311" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0365" Parameter: B <- "-26.0365" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4946" Parameter: C <- "-41.4946" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2461 TOTAL ENERGY = -67.5311 RDTITL> * VAN DER WAALS = -26.0365 ELECTROSTATIC = -41.4946 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2461" Parameter: CONF_N -> "8002" Comparing "2461" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2462" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762003 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759676 ATOM PAIRS WERE FOUND FOR ATOM LIST 42005 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29344 from a total of 759676 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2462 -68.13572 0.60466 0.52429 INTE EXTERN> -31.35149 -36.78423 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1357" Parameter: A <- "-68.1357" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3515" Parameter: B <- "-31.3515" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7842" Parameter: C <- "-36.7842" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2462 TOTAL ENERGY = -68.1357 RDTITL> * VAN DER WAALS = -31.3515 ELECTROSTATIC = -36.7842 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2462" Parameter: CONF_N -> "8002" Comparing "2462" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2463" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759676 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765535 ATOM PAIRS WERE FOUND FOR ATOM LIST 42325 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29958 from a total of 765535 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2463 -66.97012 -1.16560 0.70396 INTE EXTERN> -24.93785 -42.03227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9701" Parameter: A <- "-66.9701" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9379" Parameter: B <- "-24.9379" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0323" Parameter: C <- "-42.0323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2463 TOTAL ENERGY = -66.9701 RDTITL> * VAN DER WAALS = -24.9379 ELECTROSTATIC = -42.0323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2463" Parameter: CONF_N -> "8002" Comparing "2463" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2464" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765535 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760198 ATOM PAIRS WERE FOUND FOR ATOM LIST 41946 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 760198 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2464 -59.33225 -7.63787 0.59950 INTE EXTERN> -29.81517 -29.51708 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.3322" Parameter: A <- "-59.3322" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8152" Parameter: B <- "-29.8152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.5171" Parameter: C <- "-29.5171" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2464 TOTAL ENERGY = -59.3322 RDTITL> * VAN DER WAALS = -29.8152 ELECTROSTATIC = -29.5171 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2464" Parameter: CONF_N -> "8002" Comparing "2464" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2465" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760198 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754604 ATOM PAIRS WERE FOUND FOR ATOM LIST 41642 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29472 from a total of 754604 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2465 -69.37120 10.03895 0.71276 INTE EXTERN> -28.05528 -41.31593 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3712" Parameter: A <- "-69.3712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0553" Parameter: B <- "-28.0553" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3159" Parameter: C <- "-41.3159" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2465 TOTAL ENERGY = -69.3712 RDTITL> * VAN DER WAALS = -28.0553 ELECTROSTATIC = -41.3159 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2465" Parameter: CONF_N -> "8002" Comparing "2465" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2466" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754604 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759193 ATOM PAIRS WERE FOUND FOR ATOM LIST 41687 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29921 from a total of 759193 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2466 -67.53691 -1.83430 0.64786 INTE EXTERN> -28.75511 -38.78180 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5369" Parameter: A <- "-67.5369" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7551" Parameter: B <- "-28.7551" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7818" Parameter: C <- "-38.7818" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2466 TOTAL ENERGY = -67.5369 RDTITL> * VAN DER WAALS = -28.7551 ELECTROSTATIC = -38.7818 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2466" Parameter: CONF_N -> "8002" Comparing "2466" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2467" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759193 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757754 ATOM PAIRS WERE FOUND FOR ATOM LIST 41792 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29979 from a total of 757754 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2467 -66.29134 -1.24557 0.55126 INTE EXTERN> -32.17726 -34.11408 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2913" Parameter: A <- "-66.2913" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1773" Parameter: B <- "-32.1773" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1141" Parameter: C <- "-34.1141" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2467 TOTAL ENERGY = -66.2913 RDTITL> * VAN DER WAALS = -32.1773 ELECTROSTATIC = -34.1141 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2467" Parameter: CONF_N -> "8002" Comparing "2467" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2468" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757754 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761056 ATOM PAIRS WERE FOUND FOR ATOM LIST 41886 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29312 from a total of 761056 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2468 -66.81743 0.52609 0.56202 INTE EXTERN> -31.40665 -35.41077 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8174" Parameter: A <- "-66.8174" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4067" Parameter: B <- "-31.4067" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4108" Parameter: C <- "-35.4108" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2468 TOTAL ENERGY = -66.8174 RDTITL> * VAN DER WAALS = -31.4067 ELECTROSTATIC = -35.4108 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2468" Parameter: CONF_N -> "8002" Comparing "2468" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2469" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761056 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760591 ATOM PAIRS WERE FOUND FOR ATOM LIST 42088 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29890 from a total of 760591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2469 -66.94945 0.13202 0.50011 INTE EXTERN> -32.85172 -34.09773 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9494" Parameter: A <- "-66.9494" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8517" Parameter: B <- "-32.8517" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.0977" Parameter: C <- "-34.0977" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2469 TOTAL ENERGY = -66.9494 RDTITL> * VAN DER WAALS = -32.8517 ELECTROSTATIC = -34.0977 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2469" Parameter: CONF_N -> "8002" Comparing "2469" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2470" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758866 ATOM PAIRS WERE FOUND FOR ATOM LIST 41912 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30182 from a total of 758866 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2470 -61.89143 -5.05801 0.66380 INTE EXTERN> -28.79417 -33.09726 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.8914" Parameter: A <- "-61.8914" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7942" Parameter: B <- "-28.7942" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.0973" Parameter: C <- "-33.0973" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2470 TOTAL ENERGY = -61.8914 RDTITL> * VAN DER WAALS = -28.7942 ELECTROSTATIC = -33.0973 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2470" Parameter: CONF_N -> "8002" Comparing "2470" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2471" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758866 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762887 ATOM PAIRS WERE FOUND FOR ATOM LIST 42027 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30029 from a total of 762887 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2471 -69.52436 7.63292 0.70345 INTE EXTERN> -27.19045 -42.33391 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5244" Parameter: A <- "-69.5244" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1905" Parameter: B <- "-27.1905" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3339" Parameter: C <- "-42.3339" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2471 TOTAL ENERGY = -69.5244 RDTITL> * VAN DER WAALS = -27.1905 ELECTROSTATIC = -42.3339 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2471" Parameter: CONF_N -> "8002" Comparing "2471" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2472" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762887 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757978 ATOM PAIRS WERE FOUND FOR ATOM LIST 41920 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29703 from a total of 757978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2472 -70.20315 0.67880 0.67418 INTE EXTERN> -27.97572 -42.22743 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2032" Parameter: A <- "-70.2032" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9757" Parameter: B <- "-27.9757" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2274" Parameter: C <- "-42.2274" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2472 TOTAL ENERGY = -70.2032 RDTITL> * VAN DER WAALS = -27.9757 ELECTROSTATIC = -42.2274 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2472" Parameter: CONF_N -> "8002" Comparing "2472" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2473" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761840 ATOM PAIRS WERE FOUND FOR ATOM LIST 42136 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30887 from a total of 761840 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2473 -63.42155 -6.78160 0.57479 INTE EXTERN> -31.14777 -32.27378 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4215" Parameter: A <- "-63.4215" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1478" Parameter: B <- "-31.1478" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2738" Parameter: C <- "-32.2738" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2473 TOTAL ENERGY = -63.4215 RDTITL> * VAN DER WAALS = -31.1478 ELECTROSTATIC = -32.2738 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2473" Parameter: CONF_N -> "8002" Comparing "2473" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2474" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761840 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760588 ATOM PAIRS WERE FOUND FOR ATOM LIST 42090 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30373 from a total of 760588 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2474 -71.20453 7.78298 0.61133 INTE EXTERN> -31.34126 -39.86327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2045" Parameter: A <- "-71.2045" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3413" Parameter: B <- "-31.3413" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8633" Parameter: C <- "-39.8633" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2474 TOTAL ENERGY = -71.2045 RDTITL> * VAN DER WAALS = -31.3413 ELECTROSTATIC = -39.8633 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2474" Parameter: CONF_N -> "8002" Comparing "2474" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2475" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760588 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761237 ATOM PAIRS WERE FOUND FOR ATOM LIST 41872 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29825 from a total of 761237 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2475 -75.03515 3.83063 0.61185 INTE EXTERN> -32.00976 -43.02540 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0352" Parameter: A <- "-75.0352" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0098" Parameter: B <- "-32.0098" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0254" Parameter: C <- "-43.0254" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2475 TOTAL ENERGY = -75.0352 RDTITL> * VAN DER WAALS = -32.0098 ELECTROSTATIC = -43.0254 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2475" Parameter: CONF_N -> "8002" Comparing "2475" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2476" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761237 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761658 ATOM PAIRS WERE FOUND FOR ATOM LIST 41853 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30256 from a total of 761658 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2476 -65.50508 -9.53008 0.67117 INTE EXTERN> -27.29010 -38.21498 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5051" Parameter: A <- "-65.5051" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2901" Parameter: B <- "-27.2901" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.215" Parameter: C <- "-38.215" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2476 TOTAL ENERGY = -65.5051 RDTITL> * VAN DER WAALS = -27.2901 ELECTROSTATIC = -38.215 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2476" Parameter: CONF_N -> "8002" Comparing "2476" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2477" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761658 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758845 ATOM PAIRS WERE FOUND FOR ATOM LIST 41809 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29572 from a total of 758845 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2477 -73.44901 7.94393 0.63307 INTE EXTERN> -32.66998 -40.77902 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.449" Parameter: A <- "-73.449" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.67" Parameter: B <- "-32.67" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.779" Parameter: C <- "-40.779" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2477 TOTAL ENERGY = -73.449 RDTITL> * VAN DER WAALS = -32.67 ELECTROSTATIC = -40.779 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2477" Parameter: CONF_N -> "8002" Comparing "2477" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2478" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758845 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764608 ATOM PAIRS WERE FOUND FOR ATOM LIST 42089 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30427 from a total of 764608 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2478 -70.09782 -3.35118 0.74906 INTE EXTERN> -24.55216 -45.54566 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0978" Parameter: A <- "-70.0978" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5522" Parameter: B <- "-24.5522" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5457" Parameter: C <- "-45.5457" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2478 TOTAL ENERGY = -70.0978 RDTITL> * VAN DER WAALS = -24.5522 ELECTROSTATIC = -45.5457 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2478" Parameter: CONF_N -> "8002" Comparing "2478" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2479" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764608 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757072 ATOM PAIRS WERE FOUND FOR ATOM LIST 41825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29686 from a total of 757072 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2479 -72.86123 2.76341 0.57612 INTE EXTERN> -32.97739 -39.88384 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8612" Parameter: A <- "-72.8612" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9774" Parameter: B <- "-32.9774" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8838" Parameter: C <- "-39.8838" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2479 TOTAL ENERGY = -72.8612 RDTITL> * VAN DER WAALS = -32.9774 ELECTROSTATIC = -39.8838 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2479" Parameter: CONF_N -> "8002" Comparing "2479" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2480" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757072 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758061 ATOM PAIRS WERE FOUND FOR ATOM LIST 41808 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30008 from a total of 758061 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2480 -71.74105 -1.12018 0.62532 INTE EXTERN> -31.20773 -40.53332 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.741" Parameter: A <- "-71.741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2077" Parameter: B <- "-31.2077" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5333" Parameter: C <- "-40.5333" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2480 TOTAL ENERGY = -71.741 RDTITL> * VAN DER WAALS = -31.2077 ELECTROSTATIC = -40.5333 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2480" Parameter: CONF_N -> "8002" Comparing "2480" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2481" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758061 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757255 ATOM PAIRS WERE FOUND FOR ATOM LIST 41678 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29192 from a total of 757255 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2481 -63.74524 -7.99580 0.57263 INTE EXTERN> -31.83756 -31.90769 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7452" Parameter: A <- "-63.7452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8376" Parameter: B <- "-31.8376" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.9077" Parameter: C <- "-31.9077" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2481 TOTAL ENERGY = -63.7452 RDTITL> * VAN DER WAALS = -31.8376 ELECTROSTATIC = -31.9077 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2481" Parameter: CONF_N -> "8002" Comparing "2481" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2482" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757255 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759963 ATOM PAIRS WERE FOUND FOR ATOM LIST 41875 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29499 from a total of 759963 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2482 -69.20391 5.45866 0.52487 INTE EXTERN> -34.06338 -35.14053 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2039" Parameter: A <- "-69.2039" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0634" Parameter: B <- "-34.0634" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1405" Parameter: C <- "-35.1405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2482 TOTAL ENERGY = -69.2039 RDTITL> * VAN DER WAALS = -34.0634 ELECTROSTATIC = -35.1405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2482" Parameter: CONF_N -> "8002" Comparing "2482" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2483" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759963 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756417 ATOM PAIRS WERE FOUND FOR ATOM LIST 41472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29811 from a total of 756417 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2483 -64.75622 -4.44769 0.74136 INTE EXTERN> -28.11634 -36.63988 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7562" Parameter: A <- "-64.7562" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1163" Parameter: B <- "-28.1163" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6399" Parameter: C <- "-36.6399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2483 TOTAL ENERGY = -64.7562 RDTITL> * VAN DER WAALS = -28.1163 ELECTROSTATIC = -36.6399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2483" Parameter: CONF_N -> "8002" Comparing "2483" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2484" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756417 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756711 ATOM PAIRS WERE FOUND FOR ATOM LIST 41817 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29921 from a total of 756711 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2484 -63.25308 -1.50314 0.53021 INTE EXTERN> -33.39753 -29.85555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.2531" Parameter: A <- "-63.2531" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3975" Parameter: B <- "-33.3975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.8555" Parameter: C <- "-29.8555" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2484 TOTAL ENERGY = -63.2531 RDTITL> * VAN DER WAALS = -33.3975 ELECTROSTATIC = -29.8555 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2484" Parameter: CONF_N -> "8002" Comparing "2484" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2485" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756711 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760068 ATOM PAIRS WERE FOUND FOR ATOM LIST 42014 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29658 from a total of 760068 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2485 -70.36994 7.11686 0.56889 INTE EXTERN> -34.06278 -36.30717 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3699" Parameter: A <- "-70.3699" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0628" Parameter: B <- "-34.0628" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3072" Parameter: C <- "-36.3072" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2485 TOTAL ENERGY = -70.3699 RDTITL> * VAN DER WAALS = -34.0628 ELECTROSTATIC = -36.3072 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2485" Parameter: CONF_N -> "8002" Comparing "2485" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2486" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760068 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756270 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29441 from a total of 756270 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2486 -62.63974 -7.73020 0.55066 INTE EXTERN> -31.71576 -30.92399 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.6397" Parameter: A <- "-62.6397" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7158" Parameter: B <- "-31.7158" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.924" Parameter: C <- "-30.924" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2486 TOTAL ENERGY = -62.6397 RDTITL> * VAN DER WAALS = -31.7158 ELECTROSTATIC = -30.924 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2486" Parameter: CONF_N -> "8002" Comparing "2486" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2487" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756270 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759101 ATOM PAIRS WERE FOUND FOR ATOM LIST 41848 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30284 from a total of 759101 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2487 -63.69896 1.05921 0.55432 INTE EXTERN> -31.58986 -32.10909 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.699" Parameter: A <- "-63.699" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5899" Parameter: B <- "-31.5899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.1091" Parameter: C <- "-32.1091" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2487 TOTAL ENERGY = -63.699 RDTITL> * VAN DER WAALS = -31.5899 ELECTROSTATIC = -32.1091 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2487" Parameter: CONF_N -> "8002" Comparing "2487" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2488" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759101 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761763 ATOM PAIRS WERE FOUND FOR ATOM LIST 42212 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29253 from a total of 761763 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2488 -68.26650 4.56755 0.58023 INTE EXTERN> -32.32712 -35.93938 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2665" Parameter: A <- "-68.2665" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3271" Parameter: B <- "-32.3271" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9394" Parameter: C <- "-35.9394" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2488 TOTAL ENERGY = -68.2665 RDTITL> * VAN DER WAALS = -32.3271 ELECTROSTATIC = -35.9394 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2488" Parameter: CONF_N -> "8002" Comparing "2488" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2489" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761763 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760578 ATOM PAIRS WERE FOUND FOR ATOM LIST 41964 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30271 from a total of 760578 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2489 -69.21964 0.95314 0.76500 INTE EXTERN> -28.85607 -40.36357 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2196" Parameter: A <- "-69.2196" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8561" Parameter: B <- "-28.8561" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3636" Parameter: C <- "-40.3636" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2489 TOTAL ENERGY = -69.2196 RDTITL> * VAN DER WAALS = -28.8561 ELECTROSTATIC = -40.3636 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2489" Parameter: CONF_N -> "8002" Comparing "2489" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2490" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760578 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758032 ATOM PAIRS WERE FOUND FOR ATOM LIST 41763 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29796 from a total of 758032 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2490 -65.86516 -3.35448 0.62876 INTE EXTERN> -30.88446 -34.98070 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8652" Parameter: A <- "-65.8652" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8845" Parameter: B <- "-30.8845" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9807" Parameter: C <- "-34.9807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2490 TOTAL ENERGY = -65.8652 RDTITL> * VAN DER WAALS = -30.8845 ELECTROSTATIC = -34.9807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2490" Parameter: CONF_N -> "8002" Comparing "2490" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2491" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758032 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763515 ATOM PAIRS WERE FOUND FOR ATOM LIST 42102 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30657 from a total of 763515 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2491 -64.19574 -1.66942 0.63691 INTE EXTERN> -27.13063 -37.06511 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1957" Parameter: A <- "-64.1957" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1306" Parameter: B <- "-27.1306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0651" Parameter: C <- "-37.0651" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2491 TOTAL ENERGY = -64.1957 RDTITL> * VAN DER WAALS = -27.1306 ELECTROSTATIC = -37.0651 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2491" Parameter: CONF_N -> "8002" Comparing "2491" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2492" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763515 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755754 ATOM PAIRS WERE FOUND FOR ATOM LIST 41624 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29663 from a total of 755754 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2492 -66.42024 2.22451 0.53188 INTE EXTERN> -31.32733 -35.09292 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4202" Parameter: A <- "-66.4202" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3273" Parameter: B <- "-31.3273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0929" Parameter: C <- "-35.0929" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2492 TOTAL ENERGY = -66.4202 RDTITL> * VAN DER WAALS = -31.3273 ELECTROSTATIC = -35.0929 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2492" Parameter: CONF_N -> "8002" Comparing "2492" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2493" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755754 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760567 ATOM PAIRS WERE FOUND FOR ATOM LIST 42024 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29718 from a total of 760567 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2493 -63.21826 -3.20198 0.70840 INTE EXTERN> -28.66135 -34.55691 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.2183" Parameter: A <- "-63.2183" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6614" Parameter: B <- "-28.6614" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5569" Parameter: C <- "-34.5569" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2493 TOTAL ENERGY = -63.2183 RDTITL> * VAN DER WAALS = -28.6614 ELECTROSTATIC = -34.5569 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2493" Parameter: CONF_N -> "8002" Comparing "2493" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2494" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760567 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761753 ATOM PAIRS WERE FOUND FOR ATOM LIST 42206 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29658 from a total of 761753 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2494 -65.54065 2.32239 0.60675 INTE EXTERN> -31.83963 -33.70103 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5407" Parameter: A <- "-65.5407" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8396" Parameter: B <- "-31.8396" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.701" Parameter: C <- "-33.701" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2494 TOTAL ENERGY = -65.5407 RDTITL> * VAN DER WAALS = -31.8396 ELECTROSTATIC = -33.701 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2494" Parameter: CONF_N -> "8002" Comparing "2494" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2495" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761753 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758234 ATOM PAIRS WERE FOUND FOR ATOM LIST 41914 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29885 from a total of 758234 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2495 -63.00800 -2.53266 0.52616 INTE EXTERN> -33.50146 -29.50653 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.008" Parameter: A <- "-63.008" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5015" Parameter: B <- "-33.5015" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.5065" Parameter: C <- "-29.5065" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2495 TOTAL ENERGY = -63.008 RDTITL> * VAN DER WAALS = -33.5015 ELECTROSTATIC = -29.5065 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2495" Parameter: CONF_N -> "8002" Comparing "2495" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2496" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758234 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754271 ATOM PAIRS WERE FOUND FOR ATOM LIST 41671 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29435 from a total of 754271 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2496 -62.06796 -0.94004 0.63370 INTE EXTERN> -28.36017 -33.70779 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.068" Parameter: A <- "-62.068" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3602" Parameter: B <- "-28.3602" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7078" Parameter: C <- "-33.7078" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2496 TOTAL ENERGY = -62.068 RDTITL> * VAN DER WAALS = -28.3602 ELECTROSTATIC = -33.7078 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2496" Parameter: CONF_N -> "8002" Comparing "2496" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2497" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754271 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755516 ATOM PAIRS WERE FOUND FOR ATOM LIST 41833 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29736 from a total of 755516 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2497 -66.66279 4.59483 0.63872 INTE EXTERN> -27.55065 -39.11214 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6628" Parameter: A <- "-66.6628" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5507" Parameter: B <- "-27.5507" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1121" Parameter: C <- "-39.1121" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2497 TOTAL ENERGY = -66.6628 RDTITL> * VAN DER WAALS = -27.5507 ELECTROSTATIC = -39.1121 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2497" Parameter: CONF_N -> "8002" Comparing "2497" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2498" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755516 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751818 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30278 from a total of 751818 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2498 -66.22744 -0.43535 0.64124 INTE EXTERN> -31.16950 -35.05793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2274" Parameter: A <- "-66.2274" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1695" Parameter: B <- "-31.1695" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0579" Parameter: C <- "-35.0579" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2498 TOTAL ENERGY = -66.2274 RDTITL> * VAN DER WAALS = -31.1695 ELECTROSTATIC = -35.0579 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2498" Parameter: CONF_N -> "8002" Comparing "2498" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2499" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751818 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753490 ATOM PAIRS WERE FOUND FOR ATOM LIST 41615 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29864 from a total of 753490 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2499 -64.41298 -1.81445 0.51998 INTE EXTERN> -30.54619 -33.86679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.413" Parameter: A <- "-64.413" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5462" Parameter: B <- "-30.5462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8668" Parameter: C <- "-33.8668" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2499 TOTAL ENERGY = -64.413 RDTITL> * VAN DER WAALS = -30.5462 ELECTROSTATIC = -33.8668 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2499" Parameter: CONF_N -> "8002" Comparing "2499" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2500" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753490 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760417 ATOM PAIRS WERE FOUND FOR ATOM LIST 42135 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29581 from a total of 760417 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2500 -66.94670 2.53372 0.67005 INTE EXTERN> -28.88442 -38.06228 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9467" Parameter: A <- "-66.9467" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8844" Parameter: B <- "-28.8844" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0623" Parameter: C <- "-38.0623" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2500 TOTAL ENERGY = -66.9467 RDTITL> * VAN DER WAALS = -28.8844 ELECTROSTATIC = -38.0623 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2500" Parameter: CONF_N -> "8002" Comparing "2500" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2501" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760417 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754508 ATOM PAIRS WERE FOUND FOR ATOM LIST 41614 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29553 from a total of 754508 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2501 -61.12371 -5.82299 0.60032 INTE EXTERN> -29.31091 -31.81280 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.1237" Parameter: A <- "-61.1237" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3109" Parameter: B <- "-29.3109" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.8128" Parameter: C <- "-31.8128" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2501 TOTAL ENERGY = -61.1237 RDTITL> * VAN DER WAALS = -29.3109 ELECTROSTATIC = -31.8128 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2501" Parameter: CONF_N -> "8002" Comparing "2501" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2502" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754508 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755599 ATOM PAIRS WERE FOUND FOR ATOM LIST 41567 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29681 from a total of 755599 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2502 -65.24022 4.11651 0.61265 INTE EXTERN> -32.02692 -33.21330 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2402" Parameter: A <- "-65.2402" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0269" Parameter: B <- "-32.0269" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2133" Parameter: C <- "-33.2133" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2502 TOTAL ENERGY = -65.2402 RDTITL> * VAN DER WAALS = -32.0269 ELECTROSTATIC = -33.2133 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2502" Parameter: CONF_N -> "8002" Comparing "2502" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2503" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755599 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762351 ATOM PAIRS WERE FOUND FOR ATOM LIST 42032 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29784 from a total of 762351 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2503 -60.57389 -4.66633 0.84817 INTE EXTERN> -22.86932 -37.70457 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.5739" Parameter: A <- "-60.5739" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.8693" Parameter: B <- "-22.8693" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7046" Parameter: C <- "-37.7046" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2503 TOTAL ENERGY = -60.5739 RDTITL> * VAN DER WAALS = -22.8693 ELECTROSTATIC = -37.7046 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2503" Parameter: CONF_N -> "8002" Comparing "2503" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2504" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762351 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758208 ATOM PAIRS WERE FOUND FOR ATOM LIST 41869 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29390 from a total of 758208 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2504 -67.00746 6.43356 0.59634 INTE EXTERN> -28.94674 -38.06071 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0075" Parameter: A <- "-67.0075" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9467" Parameter: B <- "-28.9467" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0607" Parameter: C <- "-38.0607" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2504 TOTAL ENERGY = -67.0075 RDTITL> * VAN DER WAALS = -28.9467 ELECTROSTATIC = -38.0607 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2504" Parameter: CONF_N -> "8002" Comparing "2504" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2505" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758208 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758612 ATOM PAIRS WERE FOUND FOR ATOM LIST 41976 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29329 from a total of 758612 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2505 -63.64245 -3.36501 0.58340 INTE EXTERN> -30.00591 -33.63653 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6424" Parameter: A <- "-63.6424" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0059" Parameter: B <- "-30.0059" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6365" Parameter: C <- "-33.6365" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2505 TOTAL ENERGY = -63.6424 RDTITL> * VAN DER WAALS = -30.0059 ELECTROSTATIC = -33.6365 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2505" Parameter: CONF_N -> "8002" Comparing "2505" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2506" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758612 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763768 ATOM PAIRS WERE FOUND FOR ATOM LIST 42107 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30446 from a total of 763768 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2506 -62.40021 -1.24224 0.79845 INTE EXTERN> -26.62192 -35.77829 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.4002" Parameter: A <- "-62.4002" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6219" Parameter: B <- "-26.6219" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7783" Parameter: C <- "-35.7783" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2506 TOTAL ENERGY = -62.4002 RDTITL> * VAN DER WAALS = -26.6219 ELECTROSTATIC = -35.7783 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2506" Parameter: CONF_N -> "8002" Comparing "2506" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2507" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763768 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760953 ATOM PAIRS WERE FOUND FOR ATOM LIST 42091 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30217 from a total of 760953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2507 -67.96453 5.56433 0.61064 INTE EXTERN> -29.16346 -38.80107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9645" Parameter: A <- "-67.9645" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1635" Parameter: B <- "-29.1635" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8011" Parameter: C <- "-38.8011" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2507 TOTAL ENERGY = -67.9645 RDTITL> * VAN DER WAALS = -29.1635 ELECTROSTATIC = -38.8011 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2507" Parameter: CONF_N -> "8002" Comparing "2507" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2508" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760021 ATOM PAIRS WERE FOUND FOR ATOM LIST 41962 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29839 from a total of 760021 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2508 -66.15983 -1.80470 0.48211 INTE EXTERN> -31.19364 -34.96619 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1598" Parameter: A <- "-66.1598" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1936" Parameter: B <- "-31.1936" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9662" Parameter: C <- "-34.9662" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2508 TOTAL ENERGY = -66.1598 RDTITL> * VAN DER WAALS = -31.1936 ELECTROSTATIC = -34.9662 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2508" Parameter: CONF_N -> "8002" Comparing "2508" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2509" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760021 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756359 ATOM PAIRS WERE FOUND FOR ATOM LIST 41754 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29717 from a total of 756359 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2509 -66.44436 0.28453 0.61985 INTE EXTERN> -28.20910 -38.23526 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4444" Parameter: A <- "-66.4444" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2091" Parameter: B <- "-28.2091" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2353" Parameter: C <- "-38.2353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2509 TOTAL ENERGY = -66.4444 RDTITL> * VAN DER WAALS = -28.2091 ELECTROSTATIC = -38.2353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2509" Parameter: CONF_N -> "8002" Comparing "2509" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2510" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756359 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753819 ATOM PAIRS WERE FOUND FOR ATOM LIST 41550 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29381 from a total of 753819 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2510 -66.56163 0.11728 0.57567 INTE EXTERN> -30.44192 -36.11971 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5616" Parameter: A <- "-66.5616" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4419" Parameter: B <- "-30.4419" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1197" Parameter: C <- "-36.1197" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2510 TOTAL ENERGY = -66.5616 RDTITL> * VAN DER WAALS = -30.4419 ELECTROSTATIC = -36.1197 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2510" Parameter: CONF_N -> "8002" Comparing "2510" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2511" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753819 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761603 ATOM PAIRS WERE FOUND FOR ATOM LIST 42042 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30026 from a total of 761603 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2511 -73.56121 6.99958 0.65331 INTE EXTERN> -31.89220 -41.66901 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5612" Parameter: A <- "-73.5612" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8922" Parameter: B <- "-31.8922" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.669" Parameter: C <- "-41.669" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2511 TOTAL ENERGY = -73.5612 RDTITL> * VAN DER WAALS = -31.8922 ELECTROSTATIC = -41.669 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2511" Parameter: CONF_N -> "8002" Comparing "2511" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2512" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761603 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761415 ATOM PAIRS WERE FOUND FOR ATOM LIST 42234 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30308 from a total of 761415 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2512 -72.17140 -1.38981 0.58270 INTE EXTERN> -32.89593 -39.27548 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1714" Parameter: A <- "-72.1714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8959" Parameter: B <- "-32.8959" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2755" Parameter: C <- "-39.2755" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2512 TOTAL ENERGY = -72.1714 RDTITL> * VAN DER WAALS = -32.8959 ELECTROSTATIC = -39.2755 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2512" Parameter: CONF_N -> "8002" Comparing "2512" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2513" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761415 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762466 ATOM PAIRS WERE FOUND FOR ATOM LIST 42094 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30534 from a total of 762466 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2513 -69.64374 -2.52766 0.55067 INTE EXTERN> -35.91176 -33.73198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6437" Parameter: A <- "-69.6437" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.9118" Parameter: B <- "-35.9118" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.732" Parameter: C <- "-33.732" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2513 TOTAL ENERGY = -69.6437 RDTITL> * VAN DER WAALS = -35.9118 ELECTROSTATIC = -33.732 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2513" Parameter: CONF_N -> "8002" Comparing "2513" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2514" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762466 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755454 ATOM PAIRS WERE FOUND FOR ATOM LIST 41505 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29266 from a total of 755454 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2514 -66.76494 -2.87880 0.49178 INTE EXTERN> -34.50197 -32.26297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7649" Parameter: A <- "-66.7649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.502" Parameter: B <- "-34.502" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.263" Parameter: C <- "-32.263" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2514 TOTAL ENERGY = -66.7649 RDTITL> * VAN DER WAALS = -34.502 ELECTROSTATIC = -32.263 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2514" Parameter: CONF_N -> "8002" Comparing "2514" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2515" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755454 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751202 ATOM PAIRS WERE FOUND FOR ATOM LIST 41503 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28892 from a total of 751202 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2515 -67.61451 0.84957 0.55059 INTE EXTERN> -31.85200 -35.76251 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6145" Parameter: A <- "-67.6145" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.852" Parameter: B <- "-31.852" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7625" Parameter: C <- "-35.7625" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2515 TOTAL ENERGY = -67.6145 RDTITL> * VAN DER WAALS = -31.852 ELECTROSTATIC = -35.7625 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2515" Parameter: CONF_N -> "8002" Comparing "2515" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2516" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751202 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757020 ATOM PAIRS WERE FOUND FOR ATOM LIST 41994 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29995 from a total of 757020 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2516 -72.76635 5.15184 0.62544 INTE EXTERN> -30.37931 -42.38703 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7663" Parameter: A <- "-72.7663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3793" Parameter: B <- "-30.3793" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.387" Parameter: C <- "-42.387" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2516 TOTAL ENERGY = -72.7663 RDTITL> * VAN DER WAALS = -30.3793 ELECTROSTATIC = -42.387 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2516" Parameter: CONF_N -> "8002" Comparing "2516" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2517" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757020 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755631 ATOM PAIRS WERE FOUND FOR ATOM LIST 41748 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29943 from a total of 755631 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2517 -64.67730 -8.08905 0.52810 INTE EXTERN> -33.78593 -30.89137 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6773" Parameter: A <- "-64.6773" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7859" Parameter: B <- "-33.7859" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.8914" Parameter: C <- "-30.8914" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2517 TOTAL ENERGY = -64.6773 RDTITL> * VAN DER WAALS = -33.7859 ELECTROSTATIC = -30.8914 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2517" Parameter: CONF_N -> "8002" Comparing "2517" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2518" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755631 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753029 ATOM PAIRS WERE FOUND FOR ATOM LIST 41365 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29903 from a total of 753029 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2518 -60.14659 -4.53071 0.55850 INTE EXTERN> -29.47636 -30.67023 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.1466" Parameter: A <- "-60.1466" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4764" Parameter: B <- "-29.4764" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.6702" Parameter: C <- "-30.6702" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2518 TOTAL ENERGY = -60.1466 RDTITL> * VAN DER WAALS = -29.4764 ELECTROSTATIC = -30.6702 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2518" Parameter: CONF_N -> "8002" Comparing "2518" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2519" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753029 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757989 ATOM PAIRS WERE FOUND FOR ATOM LIST 41731 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29755 from a total of 757989 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2519 -72.92665 12.78006 0.72691 INTE EXTERN> -27.33061 -45.59603 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9266" Parameter: A <- "-72.9266" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3306" Parameter: B <- "-27.3306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.596" Parameter: C <- "-45.596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2519 TOTAL ENERGY = -72.9266 RDTITL> * VAN DER WAALS = -27.3306 ELECTROSTATIC = -45.596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2519" Parameter: CONF_N -> "8002" Comparing "2519" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2520" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757989 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758297 ATOM PAIRS WERE FOUND FOR ATOM LIST 41594 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30197 from a total of 758297 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2520 -58.00658 -14.92007 0.65679 INTE EXTERN> -27.68094 -30.32564 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.0066" Parameter: A <- "-58.0066" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6809" Parameter: B <- "-27.6809" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.3256" Parameter: C <- "-30.3256" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2520 TOTAL ENERGY = -58.0066 RDTITL> * VAN DER WAALS = -27.6809 ELECTROSTATIC = -30.3256 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2520" Parameter: CONF_N -> "8002" Comparing "2520" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2521" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758297 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761684 ATOM PAIRS WERE FOUND FOR ATOM LIST 41799 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30675 from a total of 761684 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2521 -73.49786 15.49128 0.68463 INTE EXTERN> -31.12930 -42.36856 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4979" Parameter: A <- "-73.4979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1293" Parameter: B <- "-31.1293" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3686" Parameter: C <- "-42.3686" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2521 TOTAL ENERGY = -73.4979 RDTITL> * VAN DER WAALS = -31.1293 ELECTROSTATIC = -42.3686 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2521" Parameter: CONF_N -> "8002" Comparing "2521" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2522" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761684 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757085 ATOM PAIRS WERE FOUND FOR ATOM LIST 41662 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29800 from a total of 757085 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2522 -74.62695 1.12910 0.61498 INTE EXTERN> -32.23065 -42.39630 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.627" Parameter: A <- "-74.627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2306" Parameter: B <- "-32.2306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3963" Parameter: C <- "-42.3963" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2522 TOTAL ENERGY = -74.627 RDTITL> * VAN DER WAALS = -32.2306 ELECTROSTATIC = -42.3963 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2522" Parameter: CONF_N -> "8002" Comparing "2522" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2523" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757085 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756194 ATOM PAIRS WERE FOUND FOR ATOM LIST 41420 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30514 from a total of 756194 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2523 -70.86914 -3.75781 0.61698 INTE EXTERN> -32.57220 -38.29694 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8691" Parameter: A <- "-70.8691" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5722" Parameter: B <- "-32.5722" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2969" Parameter: C <- "-38.2969" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2523 TOTAL ENERGY = -70.8691 RDTITL> * VAN DER WAALS = -32.5722 ELECTROSTATIC = -38.2969 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2523" Parameter: CONF_N -> "8002" Comparing "2523" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2524" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756194 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756746 ATOM PAIRS WERE FOUND FOR ATOM LIST 41442 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30346 from a total of 756746 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2524 -72.91997 2.05083 0.67011 INTE EXTERN> -29.62149 -43.29848 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.92" Parameter: A <- "-72.92" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6215" Parameter: B <- "-29.6215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2985" Parameter: C <- "-43.2985" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2524 TOTAL ENERGY = -72.92 RDTITL> * VAN DER WAALS = -29.6215 ELECTROSTATIC = -43.2985 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2524" Parameter: CONF_N -> "8002" Comparing "2524" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2525" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756746 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759729 ATOM PAIRS WERE FOUND FOR ATOM LIST 41742 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30561 from a total of 759729 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2525 -66.72493 -6.19503 0.72341 INTE EXTERN> -26.75493 -39.97001 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7249" Parameter: A <- "-66.7249" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7549" Parameter: B <- "-26.7549" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.97" Parameter: C <- "-39.97" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2525 TOTAL ENERGY = -66.7249 RDTITL> * VAN DER WAALS = -26.7549 ELECTROSTATIC = -39.97 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2525" Parameter: CONF_N -> "8002" Comparing "2525" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2526" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759729 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757102 ATOM PAIRS WERE FOUND FOR ATOM LIST 41777 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30259 from a total of 757102 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2526 -64.26932 -2.45561 0.56468 INTE EXTERN> -32.41199 -31.85733 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2693" Parameter: A <- "-64.2693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.412" Parameter: B <- "-32.412" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.8573" Parameter: C <- "-31.8573" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2526 TOTAL ENERGY = -64.2693 RDTITL> * VAN DER WAALS = -32.412 ELECTROSTATIC = -31.8573 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2526" Parameter: CONF_N -> "8002" Comparing "2526" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2527" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757102 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754955 ATOM PAIRS WERE FOUND FOR ATOM LIST 41561 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30364 from a total of 754955 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2527 -69.95447 5.68515 0.63604 INTE EXTERN> -30.84040 -39.11407 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9545" Parameter: A <- "-69.9545" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8404" Parameter: B <- "-30.8404" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1141" Parameter: C <- "-39.1141" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2527 TOTAL ENERGY = -69.9545 RDTITL> * VAN DER WAALS = -30.8404 ELECTROSTATIC = -39.1141 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2527" Parameter: CONF_N -> "8002" Comparing "2527" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2528" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754955 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757306 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30308 from a total of 757306 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2528 -70.81989 0.86542 0.65736 INTE EXTERN> -30.06804 -40.75186 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8199" Parameter: A <- "-70.8199" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.068" Parameter: B <- "-30.068" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7519" Parameter: C <- "-40.7519" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2528 TOTAL ENERGY = -70.8199 RDTITL> * VAN DER WAALS = -30.068 ELECTROSTATIC = -40.7519 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2528" Parameter: CONF_N -> "8002" Comparing "2528" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2529" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757306 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755749 ATOM PAIRS WERE FOUND FOR ATOM LIST 41665 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30283 from a total of 755749 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2529 -83.78913 12.96924 0.74876 INTE EXTERN> -29.58816 -54.20097 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.7891" Parameter: A <- "-83.7891" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5882" Parameter: B <- "-29.5882" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.201" Parameter: C <- "-54.201" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2529 TOTAL ENERGY = -83.7891 RDTITL> * VAN DER WAALS = -29.5882 ELECTROSTATIC = -54.201 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2529" Parameter: CONF_N -> "8002" Comparing "2529" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2530" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755749 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41864 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30493 from a total of 765009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2530 -78.12749 -5.66165 0.77973 INTE EXTERN> -29.06153 -49.06595 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1275" Parameter: A <- "-78.1275" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0615" Parameter: B <- "-29.0615" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.066" Parameter: C <- "-49.066" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2530 TOTAL ENERGY = -78.1275 RDTITL> * VAN DER WAALS = -29.0615 ELECTROSTATIC = -49.066 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2530" Parameter: CONF_N -> "8002" Comparing "2530" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2531" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760954 ATOM PAIRS WERE FOUND FOR ATOM LIST 42045 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29748 from a total of 760954 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2531 -65.62737 -12.50011 0.56596 INTE EXTERN> -31.06497 -34.56240 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6274" Parameter: A <- "-65.6274" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.065" Parameter: B <- "-31.065" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5624" Parameter: C <- "-34.5624" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2531 TOTAL ENERGY = -65.6274 RDTITL> * VAN DER WAALS = -31.065 ELECTROSTATIC = -34.5624 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2531" Parameter: CONF_N -> "8002" Comparing "2531" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2532" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760954 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755884 ATOM PAIRS WERE FOUND FOR ATOM LIST 41563 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29954 from a total of 755884 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2532 -61.57959 -4.04778 0.67705 INTE EXTERN> -28.50299 -33.07659 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.5796" Parameter: A <- "-61.5796" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.503" Parameter: B <- "-28.503" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.0766" Parameter: C <- "-33.0766" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2532 TOTAL ENERGY = -61.5796 RDTITL> * VAN DER WAALS = -28.503 ELECTROSTATIC = -33.0766 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2532" Parameter: CONF_N -> "8002" Comparing "2532" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2533" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755884 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756374 ATOM PAIRS WERE FOUND FOR ATOM LIST 41720 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30238 from a total of 756374 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2533 -76.82083 15.24124 0.57928 INTE EXTERN> -34.40827 -42.41256 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8208" Parameter: A <- "-76.8208" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.4083" Parameter: B <- "-34.4083" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4126" Parameter: C <- "-42.4126" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2533 TOTAL ENERGY = -76.8208 RDTITL> * VAN DER WAALS = -34.4083 ELECTROSTATIC = -42.4126 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2533" Parameter: CONF_N -> "8002" Comparing "2533" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2534" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756374 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759940 ATOM PAIRS WERE FOUND FOR ATOM LIST 41801 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29673 from a total of 759940 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2534 -67.16712 -9.65371 0.58450 INTE EXTERN> -32.90558 -34.26155 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1671" Parameter: A <- "-67.1671" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9056" Parameter: B <- "-32.9056" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2615" Parameter: C <- "-34.2615" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2534 TOTAL ENERGY = -67.1671 RDTITL> * VAN DER WAALS = -32.9056 ELECTROSTATIC = -34.2615 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2534" Parameter: CONF_N -> "8002" Comparing "2534" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2535" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759940 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751693 ATOM PAIRS WERE FOUND FOR ATOM LIST 41353 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29237 from a total of 751693 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2535 -67.13114 -0.03598 0.48226 INTE EXTERN> -33.95055 -33.18059 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1311" Parameter: A <- "-67.1311" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9505" Parameter: B <- "-33.9505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1806" Parameter: C <- "-33.1806" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2535 TOTAL ENERGY = -67.1311 RDTITL> * VAN DER WAALS = -33.9505 ELECTROSTATIC = -33.1806 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2535" Parameter: CONF_N -> "8002" Comparing "2535" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2536" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751693 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760370 ATOM PAIRS WERE FOUND FOR ATOM LIST 41852 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29984 from a total of 760370 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2536 -70.18412 3.05298 0.63885 INTE EXTERN> -28.84979 -41.33433 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1841" Parameter: A <- "-70.1841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8498" Parameter: B <- "-28.8498" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3343" Parameter: C <- "-41.3343" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2536 TOTAL ENERGY = -70.1841 RDTITL> * VAN DER WAALS = -28.8498 ELECTROSTATIC = -41.3343 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2536" Parameter: CONF_N -> "8002" Comparing "2536" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2537" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760370 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765407 ATOM PAIRS WERE FOUND FOR ATOM LIST 42119 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29810 from a total of 765407 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2537 -69.74130 -0.44283 0.68578 INTE EXTERN> -26.72182 -43.01947 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7413" Parameter: A <- "-69.7413" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7218" Parameter: B <- "-26.7218" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0195" Parameter: C <- "-43.0195" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2537 TOTAL ENERGY = -69.7413 RDTITL> * VAN DER WAALS = -26.7218 ELECTROSTATIC = -43.0195 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2537" Parameter: CONF_N -> "8002" Comparing "2537" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2538" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765407 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760306 ATOM PAIRS WERE FOUND FOR ATOM LIST 41946 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29799 from a total of 760306 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2538 -72.55046 2.80917 0.58216 INTE EXTERN> -30.97378 -41.57668 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5505" Parameter: A <- "-72.5505" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9738" Parameter: B <- "-30.9738" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5767" Parameter: C <- "-41.5767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2538 TOTAL ENERGY = -72.5505 RDTITL> * VAN DER WAALS = -30.9738 ELECTROSTATIC = -41.5767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2538" Parameter: CONF_N -> "8002" Comparing "2538" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2539" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760306 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29073 from a total of 754958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2539 -69.28007 -3.27039 0.61389 INTE EXTERN> -30.45650 -38.82358 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2801" Parameter: A <- "-69.2801" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4565" Parameter: B <- "-30.4565" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8236" Parameter: C <- "-38.8236" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2539 TOTAL ENERGY = -69.2801 RDTITL> * VAN DER WAALS = -30.4565 ELECTROSTATIC = -38.8236 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2539" Parameter: CONF_N -> "8002" Comparing "2539" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2540" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766355 ATOM PAIRS WERE FOUND FOR ATOM LIST 42142 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29417 from a total of 766355 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2540 -66.87974 -2.40034 0.67347 INTE EXTERN> -28.28010 -38.59963 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8797" Parameter: A <- "-66.8797" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2801" Parameter: B <- "-28.2801" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5996" Parameter: C <- "-38.5996" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2540 TOTAL ENERGY = -66.8797 RDTITL> * VAN DER WAALS = -28.2801 ELECTROSTATIC = -38.5996 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2540" Parameter: CONF_N -> "8002" Comparing "2540" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2541" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766355 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758249 ATOM PAIRS WERE FOUND FOR ATOM LIST 41529 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28960 from a total of 758249 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2541 -74.14500 7.26526 0.58003 INTE EXTERN> -31.98568 -42.15931 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.145" Parameter: A <- "-74.145" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9857" Parameter: B <- "-31.9857" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1593" Parameter: C <- "-42.1593" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2541 TOTAL ENERGY = -74.145 RDTITL> * VAN DER WAALS = -31.9857 ELECTROSTATIC = -42.1593 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2541" Parameter: CONF_N -> "8002" Comparing "2541" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2542" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758249 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754050 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29186 from a total of 754050 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2542 -68.21043 -5.93457 0.69704 INTE EXTERN> -26.56859 -41.64184 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2104" Parameter: A <- "-68.2104" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5686" Parameter: B <- "-26.5686" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6418" Parameter: C <- "-41.6418" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2542 TOTAL ENERGY = -68.2104 RDTITL> * VAN DER WAALS = -26.5686 ELECTROSTATIC = -41.6418 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2542" Parameter: CONF_N -> "8002" Comparing "2542" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2543" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754050 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753206 ATOM PAIRS WERE FOUND FOR ATOM LIST 41404 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29408 from a total of 753206 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2543 -71.30374 3.09331 0.86387 INTE EXTERN> -23.78011 -47.52363 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3037" Parameter: A <- "-71.3037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7801" Parameter: B <- "-23.7801" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5236" Parameter: C <- "-47.5236" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2543 TOTAL ENERGY = -71.3037 RDTITL> * VAN DER WAALS = -23.7801 ELECTROSTATIC = -47.5236 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2543" Parameter: CONF_N -> "8002" Comparing "2543" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2544" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753206 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759468 ATOM PAIRS WERE FOUND FOR ATOM LIST 41657 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29454 from a total of 759468 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2544 -68.87208 -2.43166 0.86061 INTE EXTERN> -23.03844 -45.83363 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8721" Parameter: A <- "-68.8721" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.0384" Parameter: B <- "-23.0384" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8336" Parameter: C <- "-45.8336" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2544 TOTAL ENERGY = -68.8721 RDTITL> * VAN DER WAALS = -23.0384 ELECTROSTATIC = -45.8336 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2544" Parameter: CONF_N -> "8002" Comparing "2544" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2545" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759468 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757309 ATOM PAIRS WERE FOUND FOR ATOM LIST 41823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29418 from a total of 757309 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2545 -78.63219 9.76011 0.66321 INTE EXTERN> -30.83250 -47.79969 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6322" Parameter: A <- "-78.6322" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8325" Parameter: B <- "-30.8325" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7997" Parameter: C <- "-47.7997" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2545 TOTAL ENERGY = -78.6322 RDTITL> * VAN DER WAALS = -30.8325 ELECTROSTATIC = -47.7997 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2545" Parameter: CONF_N -> "8002" Comparing "2545" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2546" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757309 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756234 ATOM PAIRS WERE FOUND FOR ATOM LIST 41613 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29023 from a total of 756234 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2546 -63.36615 -15.26604 0.50663 INTE EXTERN> -33.13949 -30.22666 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3661" Parameter: A <- "-63.3661" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1395" Parameter: B <- "-33.1395" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.2267" Parameter: C <- "-30.2267" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2546 TOTAL ENERGY = -63.3661 RDTITL> * VAN DER WAALS = -33.1395 ELECTROSTATIC = -30.2267 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2546" Parameter: CONF_N -> "8002" Comparing "2546" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2547" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756234 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760964 ATOM PAIRS WERE FOUND FOR ATOM LIST 41720 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29671 from a total of 760964 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2547 -69.60224 6.23609 0.79787 INTE EXTERN> -23.14464 -46.45760 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6022" Parameter: A <- "-69.6022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.1446" Parameter: B <- "-23.1446" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4576" Parameter: C <- "-46.4576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2547 TOTAL ENERGY = -69.6022 RDTITL> * VAN DER WAALS = -23.1446 ELECTROSTATIC = -46.4576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2547" Parameter: CONF_N -> "8002" Comparing "2547" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2548" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760964 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752061 ATOM PAIRS WERE FOUND FOR ATOM LIST 41286 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29317 from a total of 752061 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2548 -67.92473 -1.67751 0.63553 INTE EXTERN> -27.14452 -40.78021 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9247" Parameter: A <- "-67.9247" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1445" Parameter: B <- "-27.1445" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7802" Parameter: C <- "-40.7802" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2548 TOTAL ENERGY = -67.9247 RDTITL> * VAN DER WAALS = -27.1445 ELECTROSTATIC = -40.7802 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2548" Parameter: CONF_N -> "8002" Comparing "2548" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2549" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752061 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757315 ATOM PAIRS WERE FOUND FOR ATOM LIST 41649 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29829 from a total of 757315 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2549 -71.87531 3.95058 0.64431 INTE EXTERN> -30.05567 -41.81964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8753" Parameter: A <- "-71.8753" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0557" Parameter: B <- "-30.0557" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8196" Parameter: C <- "-41.8196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2549 TOTAL ENERGY = -71.8753 RDTITL> * VAN DER WAALS = -30.0557 ELECTROSTATIC = -41.8196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2549" Parameter: CONF_N -> "8002" Comparing "2549" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2550" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757315 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753350 ATOM PAIRS WERE FOUND FOR ATOM LIST 41145 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29329 from a total of 753350 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2550 -70.06843 -1.80688 0.65381 INTE EXTERN> -30.60981 -39.45862 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0684" Parameter: A <- "-70.0684" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6098" Parameter: B <- "-30.6098" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4586" Parameter: C <- "-39.4586" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2550 TOTAL ENERGY = -70.0684 RDTITL> * VAN DER WAALS = -30.6098 ELECTROSTATIC = -39.4586 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2550" Parameter: CONF_N -> "8002" Comparing "2550" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2551" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753350 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751978 ATOM PAIRS WERE FOUND FOR ATOM LIST 41259 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28865 from a total of 751978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2551 -70.50186 0.43343 0.67019 INTE EXTERN> -26.00071 -44.50115 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5019" Parameter: A <- "-70.5019" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0007" Parameter: B <- "-26.0007" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5012" Parameter: C <- "-44.5012" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2551 TOTAL ENERGY = -70.5019 RDTITL> * VAN DER WAALS = -26.0007 ELECTROSTATIC = -44.5012 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2551" Parameter: CONF_N -> "8002" Comparing "2551" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2552" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756866 ATOM PAIRS WERE FOUND FOR ATOM LIST 41573 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28969 from a total of 756866 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2552 -71.59884 1.09698 0.69138 INTE EXTERN> -26.84820 -44.75064 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5988" Parameter: A <- "-71.5988" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8482" Parameter: B <- "-26.8482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7506" Parameter: C <- "-44.7506" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2552 TOTAL ENERGY = -71.5988 RDTITL> * VAN DER WAALS = -26.8482 ELECTROSTATIC = -44.7506 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2552" Parameter: CONF_N -> "8002" Comparing "2552" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2553" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756866 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751352 ATOM PAIRS WERE FOUND FOR ATOM LIST 41531 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28836 from a total of 751352 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2553 -80.52742 8.92858 0.71929 INTE EXTERN> -25.97167 -54.55575 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5274" Parameter: A <- "-80.5274" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9717" Parameter: B <- "-25.9717" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.5558" Parameter: C <- "-54.5558" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2553 TOTAL ENERGY = -80.5274 RDTITL> * VAN DER WAALS = -25.9717 ELECTROSTATIC = -54.5558 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2553" Parameter: CONF_N -> "8002" Comparing "2553" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2554" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751352 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753561 ATOM PAIRS WERE FOUND FOR ATOM LIST 41548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29025 from a total of 753561 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2554 -67.07909 -13.44833 0.60084 INTE EXTERN> -29.58502 -37.49407 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0791" Parameter: A <- "-67.0791" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.585" Parameter: B <- "-29.585" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4941" Parameter: C <- "-37.4941" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2554 TOTAL ENERGY = -67.0791 RDTITL> * VAN DER WAALS = -29.585 ELECTROSTATIC = -37.4941 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2554" Parameter: CONF_N -> "8002" Comparing "2554" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2555" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753561 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758938 ATOM PAIRS WERE FOUND FOR ATOM LIST 41754 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28744 from a total of 758938 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2555 -70.98985 3.91076 0.67087 INTE EXTERN> -26.17003 -44.81982 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9898" Parameter: A <- "-70.9898" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.17" Parameter: B <- "-26.17" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8198" Parameter: C <- "-44.8198" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2555 TOTAL ENERGY = -70.9898 RDTITL> * VAN DER WAALS = -26.17 ELECTROSTATIC = -44.8198 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2555" Parameter: CONF_N -> "8002" Comparing "2555" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2556" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758938 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758603 ATOM PAIRS WERE FOUND FOR ATOM LIST 41641 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28703 from a total of 758603 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2556 -66.58036 -4.40948 0.54737 INTE EXTERN> -31.71716 -34.86320 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5804" Parameter: A <- "-66.5804" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7172" Parameter: B <- "-31.7172" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8632" Parameter: C <- "-34.8632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2556 TOTAL ENERGY = -66.5804 RDTITL> * VAN DER WAALS = -31.7172 ELECTROSTATIC = -34.8632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2556" Parameter: CONF_N -> "8002" Comparing "2556" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2557" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758603 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757260 ATOM PAIRS WERE FOUND FOR ATOM LIST 41554 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28994 from a total of 757260 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2557 -61.96615 -4.61421 0.72738 INTE EXTERN> -23.54963 -38.41652 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.9661" Parameter: A <- "-61.9661" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.5496" Parameter: B <- "-23.5496" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4165" Parameter: C <- "-38.4165" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2557 TOTAL ENERGY = -61.9661 RDTITL> * VAN DER WAALS = -23.5496 ELECTROSTATIC = -38.4165 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2557" Parameter: CONF_N -> "8002" Comparing "2557" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2558" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757260 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754261 ATOM PAIRS WERE FOUND FOR ATOM LIST 41588 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29064 from a total of 754261 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2558 -69.53722 7.57108 0.66760 INTE EXTERN> -27.18616 -42.35107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5372" Parameter: A <- "-69.5372" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1862" Parameter: B <- "-27.1862" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3511" Parameter: C <- "-42.3511" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2558 TOTAL ENERGY = -69.5372 RDTITL> * VAN DER WAALS = -27.1862 ELECTROSTATIC = -42.3511 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2558" Parameter: CONF_N -> "8002" Comparing "2558" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2559" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754261 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752940 ATOM PAIRS WERE FOUND FOR ATOM LIST 41535 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29153 from a total of 752940 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2559 -67.16333 -2.37390 0.66134 INTE EXTERN> -26.77384 -40.38949 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1633" Parameter: A <- "-67.1633" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7738" Parameter: B <- "-26.7738" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3895" Parameter: C <- "-40.3895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2559 TOTAL ENERGY = -67.1633 RDTITL> * VAN DER WAALS = -26.7738 ELECTROSTATIC = -40.3895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2559" Parameter: CONF_N -> "8002" Comparing "2559" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2560" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752940 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753974 ATOM PAIRS WERE FOUND FOR ATOM LIST 41363 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29116 from a total of 753974 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2560 -69.87281 2.70949 0.67423 INTE EXTERN> -28.62656 -41.24625 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8728" Parameter: A <- "-69.8728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6266" Parameter: B <- "-28.6266" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2462" Parameter: C <- "-41.2462" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2560 TOTAL ENERGY = -69.8728 RDTITL> * VAN DER WAALS = -28.6266 ELECTROSTATIC = -41.2462 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2560" Parameter: CONF_N -> "8002" Comparing "2560" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2561" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753974 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757080 ATOM PAIRS WERE FOUND FOR ATOM LIST 41606 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28635 from a total of 757080 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2561 -69.61618 -0.25664 0.55015 INTE EXTERN> -31.14885 -38.46733 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6162" Parameter: A <- "-69.6162" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1488" Parameter: B <- "-31.1488" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4673" Parameter: C <- "-38.4673" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2561 TOTAL ENERGY = -69.6162 RDTITL> * VAN DER WAALS = -31.1488 ELECTROSTATIC = -38.4673 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2561" Parameter: CONF_N -> "8002" Comparing "2561" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2562" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757080 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762017 ATOM PAIRS WERE FOUND FOR ATOM LIST 41618 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29263 from a total of 762017 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2562 -67.87179 -1.74439 0.54218 INTE EXTERN> -32.47694 -35.39485 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8718" Parameter: A <- "-67.8718" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4769" Parameter: B <- "-32.4769" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3948" Parameter: C <- "-35.3948" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2562 TOTAL ENERGY = -67.8718 RDTITL> * VAN DER WAALS = -32.4769 ELECTROSTATIC = -35.3948 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2562" Parameter: CONF_N -> "8002" Comparing "2562" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2563" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762017 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757221 ATOM PAIRS WERE FOUND FOR ATOM LIST 41848 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29369 from a total of 757221 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2563 -64.99177 -2.88002 0.63311 INTE EXTERN> -28.46102 -36.53075 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9918" Parameter: A <- "-64.9918" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.461" Parameter: B <- "-28.461" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5308" Parameter: C <- "-36.5308" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2563 TOTAL ENERGY = -64.9918 RDTITL> * VAN DER WAALS = -28.461 ELECTROSTATIC = -36.5308 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2563" Parameter: CONF_N -> "8002" Comparing "2563" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2564" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757221 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752440 ATOM PAIRS WERE FOUND FOR ATOM LIST 41357 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29030 from a total of 752440 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2564 -71.83954 6.84777 0.69490 INTE EXTERN> -28.19757 -43.64197 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8395" Parameter: A <- "-71.8395" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1976" Parameter: B <- "-28.1976" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.642" Parameter: C <- "-43.642" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2564 TOTAL ENERGY = -71.8395 RDTITL> * VAN DER WAALS = -28.1976 ELECTROSTATIC = -43.642 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2564" Parameter: CONF_N -> "8002" Comparing "2564" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2565" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752440 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751605 ATOM PAIRS WERE FOUND FOR ATOM LIST 41315 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29247 from a total of 751605 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2565 -69.47596 -2.36357 0.63182 INTE EXTERN> -29.37394 -40.10203 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.476" Parameter: A <- "-69.476" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3739" Parameter: B <- "-29.3739" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.102" Parameter: C <- "-40.102" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2565 TOTAL ENERGY = -69.476 RDTITL> * VAN DER WAALS = -29.3739 ELECTROSTATIC = -40.102 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2565" Parameter: CONF_N -> "8002" Comparing "2565" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2566" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751605 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755423 ATOM PAIRS WERE FOUND FOR ATOM LIST 41603 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29320 from a total of 755423 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2566 -65.74256 -3.73340 0.50634 INTE EXTERN> -33.78932 -31.95324 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7426" Parameter: A <- "-65.7426" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7893" Parameter: B <- "-33.7893" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.9532" Parameter: C <- "-31.9532" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2566 TOTAL ENERGY = -65.7426 RDTITL> * VAN DER WAALS = -33.7893 ELECTROSTATIC = -31.9532 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2566" Parameter: CONF_N -> "8002" Comparing "2566" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2567" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755423 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757188 ATOM PAIRS WERE FOUND FOR ATOM LIST 41662 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30039 from a total of 757188 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2567 -68.18959 2.44703 0.59271 INTE EXTERN> -31.04777 -37.14182 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1896" Parameter: A <- "-68.1896" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0478" Parameter: B <- "-31.0478" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1418" Parameter: C <- "-37.1418" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2567 TOTAL ENERGY = -68.1896 RDTITL> * VAN DER WAALS = -31.0478 ELECTROSTATIC = -37.1418 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2567" Parameter: CONF_N -> "8002" Comparing "2567" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2568" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757188 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751922 ATOM PAIRS WERE FOUND FOR ATOM LIST 41582 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28892 from a total of 751922 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2568 -73.21607 5.02648 0.57543 INTE EXTERN> -31.31237 -41.90370 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2161" Parameter: A <- "-73.2161" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3124" Parameter: B <- "-31.3124" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9037" Parameter: C <- "-41.9037" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2568 TOTAL ENERGY = -73.2161 RDTITL> * VAN DER WAALS = -31.3124 ELECTROSTATIC = -41.9037 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2568" Parameter: CONF_N -> "8002" Comparing "2568" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2569" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751922 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752575 ATOM PAIRS WERE FOUND FOR ATOM LIST 41593 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30160 from a total of 752575 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2569 -67.52477 -5.69131 0.62734 INTE EXTERN> -30.59160 -36.93317 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5248" Parameter: A <- "-67.5248" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5916" Parameter: B <- "-30.5916" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9332" Parameter: C <- "-36.9332" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2569 TOTAL ENERGY = -67.5248 RDTITL> * VAN DER WAALS = -30.5916 ELECTROSTATIC = -36.9332 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2569" Parameter: CONF_N -> "8002" Comparing "2569" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2570" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752575 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752397 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29680 from a total of 752397 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2570 -73.78114 6.25637 0.62445 INTE EXTERN> -29.06641 -44.71472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7811" Parameter: A <- "-73.7811" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0664" Parameter: B <- "-29.0664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7147" Parameter: C <- "-44.7147" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2570 TOTAL ENERGY = -73.7811 RDTITL> * VAN DER WAALS = -29.0664 ELECTROSTATIC = -44.7147 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2570" Parameter: CONF_N -> "8002" Comparing "2570" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2571" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752397 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755765 ATOM PAIRS WERE FOUND FOR ATOM LIST 41987 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30051 from a total of 755765 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2571 -62.27365 -11.50749 0.58195 INTE EXTERN> -30.02513 -32.24852 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.2736" Parameter: A <- "-62.2736" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0251" Parameter: B <- "-30.0251" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2485" Parameter: C <- "-32.2485" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2571 TOTAL ENERGY = -62.2736 RDTITL> * VAN DER WAALS = -30.0251 ELECTROSTATIC = -32.2485 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2571" Parameter: CONF_N -> "8002" Comparing "2571" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2572" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755765 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759930 ATOM PAIRS WERE FOUND FOR ATOM LIST 42013 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29930 from a total of 759930 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2572 -69.03490 6.76125 0.85400 INTE EXTERN> -22.42732 -46.60758 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0349" Parameter: A <- "-69.0349" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.4273" Parameter: B <- "-22.4273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6076" Parameter: C <- "-46.6076" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2572 TOTAL ENERGY = -69.0349 RDTITL> * VAN DER WAALS = -22.4273 ELECTROSTATIC = -46.6076 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2572" Parameter: CONF_N -> "8002" Comparing "2572" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2573" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759930 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762196 ATOM PAIRS WERE FOUND FOR ATOM LIST 41750 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30004 from a total of 762196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2573 -66.32216 -2.71273 0.61017 INTE EXTERN> -30.86437 -35.45779 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3222" Parameter: A <- "-66.3222" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8644" Parameter: B <- "-30.8644" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4578" Parameter: C <- "-35.4578" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2573 TOTAL ENERGY = -66.3222 RDTITL> * VAN DER WAALS = -30.8644 ELECTROSTATIC = -35.4578 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2573" Parameter: CONF_N -> "8002" Comparing "2573" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2574" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762960 ATOM PAIRS WERE FOUND FOR ATOM LIST 41956 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29383 from a total of 762960 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2574 -67.67479 1.35262 0.61891 INTE EXTERN> -31.62974 -36.04505 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6748" Parameter: A <- "-67.6748" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6297" Parameter: B <- "-31.6297" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.045" Parameter: C <- "-36.045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2574 TOTAL ENERGY = -67.6748 RDTITL> * VAN DER WAALS = -31.6297 ELECTROSTATIC = -36.045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2574" Parameter: CONF_N -> "8002" Comparing "2574" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2575" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762960 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759546 ATOM PAIRS WERE FOUND FOR ATOM LIST 41837 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29987 from a total of 759546 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2575 -71.48459 3.80980 0.71573 INTE EXTERN> -26.83332 -44.65127 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4846" Parameter: A <- "-71.4846" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8333" Parameter: B <- "-26.8333" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6513" Parameter: C <- "-44.6513" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2575 TOTAL ENERGY = -71.4846 RDTITL> * VAN DER WAALS = -26.8333 ELECTROSTATIC = -44.6513 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2575" Parameter: CONF_N -> "8002" Comparing "2575" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2576" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759546 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757846 ATOM PAIRS WERE FOUND FOR ATOM LIST 41724 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29499 from a total of 757846 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2576 -73.48764 2.00305 0.66022 INTE EXTERN> -29.77366 -43.71398 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4876" Parameter: A <- "-73.4876" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7737" Parameter: B <- "-29.7737" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.714" Parameter: C <- "-43.714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2576 TOTAL ENERGY = -73.4876 RDTITL> * VAN DER WAALS = -29.7737 ELECTROSTATIC = -43.714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2576" Parameter: CONF_N -> "8002" Comparing "2576" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2577" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757846 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758423 ATOM PAIRS WERE FOUND FOR ATOM LIST 41728 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29818 from a total of 758423 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2577 -77.11306 3.62542 0.72230 INTE EXTERN> -29.77233 -47.34073 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1131" Parameter: A <- "-77.1131" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7723" Parameter: B <- "-29.7723" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3407" Parameter: C <- "-47.3407" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2577 TOTAL ENERGY = -77.1131 RDTITL> * VAN DER WAALS = -29.7723 ELECTROSTATIC = -47.3407 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2577" Parameter: CONF_N -> "8002" Comparing "2577" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2578" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758423 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757553 ATOM PAIRS WERE FOUND FOR ATOM LIST 41612 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29982 from a total of 757553 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2578 -72.62304 -4.49002 0.63218 INTE EXTERN> -30.23552 -42.38752 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.623" Parameter: A <- "-72.623" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2355" Parameter: B <- "-30.2355" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3875" Parameter: C <- "-42.3875" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2578 TOTAL ENERGY = -72.623 RDTITL> * VAN DER WAALS = -30.2355 ELECTROSTATIC = -42.3875 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2578" Parameter: CONF_N -> "8002" Comparing "2578" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2579" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757553 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755878 ATOM PAIRS WERE FOUND FOR ATOM LIST 41452 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29073 from a total of 755878 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2579 -70.78416 -1.83887 0.57514 INTE EXTERN> -29.04994 -41.73423 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7842" Parameter: A <- "-70.7842" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0499" Parameter: B <- "-29.0499" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7342" Parameter: C <- "-41.7342" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2579 TOTAL ENERGY = -70.7842 RDTITL> * VAN DER WAALS = -29.0499 ELECTROSTATIC = -41.7342 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2579" Parameter: CONF_N -> "8002" Comparing "2579" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2580" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755878 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752913 ATOM PAIRS WERE FOUND FOR ATOM LIST 41406 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29154 from a total of 752913 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2580 -70.55907 -0.22509 0.72386 INTE EXTERN> -25.89978 -44.65929 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5591" Parameter: A <- "-70.5591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8998" Parameter: B <- "-25.8998" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6593" Parameter: C <- "-44.6593" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2580 TOTAL ENERGY = -70.5591 RDTITL> * VAN DER WAALS = -25.8998 ELECTROSTATIC = -44.6593 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2580" Parameter: CONF_N -> "8002" Comparing "2580" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2581" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752913 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753408 ATOM PAIRS WERE FOUND FOR ATOM LIST 41492 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29660 from a total of 753408 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2581 -67.95645 -2.60262 0.51898 INTE EXTERN> -32.91014 -35.04631 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9564" Parameter: A <- "-67.9564" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9101" Parameter: B <- "-32.9101" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0463" Parameter: C <- "-35.0463" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2581 TOTAL ENERGY = -67.9564 RDTITL> * VAN DER WAALS = -32.9101 ELECTROSTATIC = -35.0463 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2581" Parameter: CONF_N -> "8002" Comparing "2581" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2582" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753408 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756017 ATOM PAIRS WERE FOUND FOR ATOM LIST 41436 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29675 from a total of 756017 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2582 -68.07818 0.12174 0.53841 INTE EXTERN> -31.92517 -36.15301 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0782" Parameter: A <- "-68.0782" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9252" Parameter: B <- "-31.9252" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.153" Parameter: C <- "-36.153" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2582 TOTAL ENERGY = -68.0782 RDTITL> * VAN DER WAALS = -31.9252 ELECTROSTATIC = -36.153 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2582" Parameter: CONF_N -> "8002" Comparing "2582" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2583" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756017 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751104 ATOM PAIRS WERE FOUND FOR ATOM LIST 41277 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28852 from a total of 751104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2583 -75.99330 7.91511 0.64141 INTE EXTERN> -27.37272 -48.62058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9933" Parameter: A <- "-75.9933" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3727" Parameter: B <- "-27.3727" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6206" Parameter: C <- "-48.6206" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2583 TOTAL ENERGY = -75.9933 RDTITL> * VAN DER WAALS = -27.3727 ELECTROSTATIC = -48.6206 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2583" Parameter: CONF_N -> "8002" Comparing "2583" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2584" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757354 ATOM PAIRS WERE FOUND FOR ATOM LIST 41659 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29481 from a total of 757354 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2584 -68.32489 -7.66841 0.70969 INTE EXTERN> -26.40451 -41.92037 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3249" Parameter: A <- "-68.3249" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4045" Parameter: B <- "-26.4045" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9204" Parameter: C <- "-41.9204" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2584 TOTAL ENERGY = -68.3249 RDTITL> * VAN DER WAALS = -26.4045 ELECTROSTATIC = -41.9204 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2584" Parameter: CONF_N -> "8002" Comparing "2584" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2585" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757354 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759169 ATOM PAIRS WERE FOUND FOR ATOM LIST 41600 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30031 from a total of 759169 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2585 -73.09386 4.76897 0.62017 INTE EXTERN> -27.58313 -45.51073 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0939" Parameter: A <- "-73.0939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5831" Parameter: B <- "-27.5831" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5107" Parameter: C <- "-45.5107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2585 TOTAL ENERGY = -73.0939 RDTITL> * VAN DER WAALS = -27.5831 ELECTROSTATIC = -45.5107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2585" Parameter: CONF_N -> "8002" Comparing "2585" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2586" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759169 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760605 ATOM PAIRS WERE FOUND FOR ATOM LIST 41818 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29506 from a total of 760605 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2586 -71.03788 -2.05597 0.54707 INTE EXTERN> -32.76108 -38.27680 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0379" Parameter: A <- "-71.0379" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7611" Parameter: B <- "-32.7611" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2768" Parameter: C <- "-38.2768" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2586 TOTAL ENERGY = -71.0379 RDTITL> * VAN DER WAALS = -32.7611 ELECTROSTATIC = -38.2768 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2586" Parameter: CONF_N -> "8002" Comparing "2586" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2587" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760605 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759390 ATOM PAIRS WERE FOUND FOR ATOM LIST 41648 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29479 from a total of 759390 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2587 -73.00473 1.96685 0.57715 INTE EXTERN> -31.03599 -41.96874 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0047" Parameter: A <- "-73.0047" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.036" Parameter: B <- "-31.036" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9687" Parameter: C <- "-41.9687" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2587 TOTAL ENERGY = -73.0047 RDTITL> * VAN DER WAALS = -31.036 ELECTROSTATIC = -41.9687 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2587" Parameter: CONF_N -> "8002" Comparing "2587" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2588" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759390 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759072 ATOM PAIRS WERE FOUND FOR ATOM LIST 41760 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29678 from a total of 759072 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2588 -69.82002 -3.18471 0.66433 INTE EXTERN> -30.68379 -39.13622 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.82" Parameter: A <- "-69.82" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6838" Parameter: B <- "-30.6838" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1362" Parameter: C <- "-39.1362" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2588 TOTAL ENERGY = -69.82 RDTITL> * VAN DER WAALS = -30.6838 ELECTROSTATIC = -39.1362 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2588" Parameter: CONF_N -> "8002" Comparing "2588" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2589" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759072 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763188 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29598 from a total of 763188 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2589 -66.93530 -2.88472 0.68076 INTE EXTERN> -28.66850 -38.26680 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9353" Parameter: A <- "-66.9353" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6685" Parameter: B <- "-28.6685" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2668" Parameter: C <- "-38.2668" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2589 TOTAL ENERGY = -66.9353 RDTITL> * VAN DER WAALS = -28.6685 ELECTROSTATIC = -38.2668 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2589" Parameter: CONF_N -> "8002" Comparing "2589" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2590" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763188 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758644 ATOM PAIRS WERE FOUND FOR ATOM LIST 41548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30139 from a total of 758644 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2590 -68.41807 1.48277 0.59754 INTE EXTERN> -29.64714 -38.77093 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4181" Parameter: A <- "-68.4181" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6471" Parameter: B <- "-29.6471" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7709" Parameter: C <- "-38.7709" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2590 TOTAL ENERGY = -68.4181 RDTITL> * VAN DER WAALS = -29.6471 ELECTROSTATIC = -38.7709 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2590" Parameter: CONF_N -> "8002" Comparing "2590" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2591" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758644 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759953 ATOM PAIRS WERE FOUND FOR ATOM LIST 41692 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29989 from a total of 759953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2591 -73.71723 5.29917 0.60751 INTE EXTERN> -30.09106 -43.62617 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7172" Parameter: A <- "-73.7172" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0911" Parameter: B <- "-30.0911" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6262" Parameter: C <- "-43.6262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2591 TOTAL ENERGY = -73.7172 RDTITL> * VAN DER WAALS = -30.0911 ELECTROSTATIC = -43.6262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2591" Parameter: CONF_N -> "8002" Comparing "2591" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2592" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759193 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29844 from a total of 759193 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2592 -69.65972 -4.05752 0.66139 INTE EXTERN> -28.43247 -41.22725 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6597" Parameter: A <- "-69.6597" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4325" Parameter: B <- "-28.4325" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2272" Parameter: C <- "-41.2272" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2592 TOTAL ENERGY = -69.6597 RDTITL> * VAN DER WAALS = -28.4325 ELECTROSTATIC = -41.2272 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2592" Parameter: CONF_N -> "8002" Comparing "2592" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2593" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759193 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41496 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30123 from a total of 753601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2593 -69.44865 -0.21107 0.55196 INTE EXTERN> -33.50868 -35.93997 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4487" Parameter: A <- "-69.4487" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5087" Parameter: B <- "-33.5087" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.94" Parameter: C <- "-35.94" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2593 TOTAL ENERGY = -69.4487 RDTITL> * VAN DER WAALS = -33.5087 ELECTROSTATIC = -35.94 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2593" Parameter: CONF_N -> "8002" Comparing "2593" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2594" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756588 ATOM PAIRS WERE FOUND FOR ATOM LIST 41479 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29806 from a total of 756588 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2594 -57.38602 -12.06263 0.47576 INTE EXTERN> -33.75581 -23.63021 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.386" Parameter: A <- "-57.386" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7558" Parameter: B <- "-33.7558" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-23.6302" Parameter: C <- "-23.6302" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2594 TOTAL ENERGY = -57.386 RDTITL> * VAN DER WAALS = -33.7558 ELECTROSTATIC = -23.6302 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2594" Parameter: CONF_N -> "8002" Comparing "2594" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2595" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756588 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755401 ATOM PAIRS WERE FOUND FOR ATOM LIST 41504 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29480 from a total of 755401 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2595 -69.95313 12.56711 0.50298 INTE EXTERN> -33.23638 -36.71675 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9531" Parameter: A <- "-69.9531" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2364" Parameter: B <- "-33.2364" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7168" Parameter: C <- "-36.7168" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2595 TOTAL ENERGY = -69.9531 RDTITL> * VAN DER WAALS = -33.2364 ELECTROSTATIC = -36.7168 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2595" Parameter: CONF_N -> "8002" Comparing "2595" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2596" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755401 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759004 ATOM PAIRS WERE FOUND FOR ATOM LIST 41622 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29849 from a total of 759004 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2596 -71.17874 1.22561 0.60539 INTE EXTERN> -32.82439 -38.35435 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1787" Parameter: A <- "-71.1787" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8244" Parameter: B <- "-32.8244" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3544" Parameter: C <- "-38.3544" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2596 TOTAL ENERGY = -71.1787 RDTITL> * VAN DER WAALS = -32.8244 ELECTROSTATIC = -38.3544 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2596" Parameter: CONF_N -> "8002" Comparing "2596" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2597" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759004 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764217 ATOM PAIRS WERE FOUND FOR ATOM LIST 41910 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29393 from a total of 764217 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2597 -70.74542 -0.43332 0.67386 INTE EXTERN> -28.92028 -41.82513 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7454" Parameter: A <- "-70.7454" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9203" Parameter: B <- "-28.9203" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8251" Parameter: C <- "-41.8251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2597 TOTAL ENERGY = -70.7454 RDTITL> * VAN DER WAALS = -28.9203 ELECTROSTATIC = -41.8251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2597" Parameter: CONF_N -> "8002" Comparing "2597" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2598" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764217 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765967 ATOM PAIRS WERE FOUND FOR ATOM LIST 41951 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30163 from a total of 765967 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2598 -71.10328 0.35786 0.63849 INTE EXTERN> -29.72012 -41.38316 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1033" Parameter: A <- "-71.1033" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7201" Parameter: B <- "-29.7201" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3832" Parameter: C <- "-41.3832" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2598 TOTAL ENERGY = -71.1033 RDTITL> * VAN DER WAALS = -29.7201 ELECTROSTATIC = -41.3832 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2598" Parameter: CONF_N -> "8002" Comparing "2598" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2599" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765967 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759628 ATOM PAIRS WERE FOUND FOR ATOM LIST 41772 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30091 from a total of 759628 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2599 -68.74298 -2.36030 0.61897 INTE EXTERN> -29.05873 -39.68425 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.743" Parameter: A <- "-68.743" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0587" Parameter: B <- "-29.0587" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6842" Parameter: C <- "-39.6842" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2599 TOTAL ENERGY = -68.743 RDTITL> * VAN DER WAALS = -29.0587 ELECTROSTATIC = -39.6842 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2599" Parameter: CONF_N -> "8002" Comparing "2599" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2600" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759628 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762069 ATOM PAIRS WERE FOUND FOR ATOM LIST 41861 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29815 from a total of 762069 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2600 -63.68774 -5.05524 0.71031 INTE EXTERN> -26.64538 -37.04237 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6877" Parameter: A <- "-63.6877" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6454" Parameter: B <- "-26.6454" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0424" Parameter: C <- "-37.0424" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2600 TOTAL ENERGY = -63.6877 RDTITL> * VAN DER WAALS = -26.6454 ELECTROSTATIC = -37.0424 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2600" Parameter: CONF_N -> "8002" Comparing "2600" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2601" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762069 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763300 ATOM PAIRS WERE FOUND FOR ATOM LIST 41976 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29790 from a total of 763300 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2601 -69.68117 5.99342 0.54171 INTE EXTERN> -34.90026 -34.78090 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6812" Parameter: A <- "-69.6812" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9003" Parameter: B <- "-34.9003" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7809" Parameter: C <- "-34.7809" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2601 TOTAL ENERGY = -69.6812 RDTITL> * VAN DER WAALS = -34.9003 ELECTROSTATIC = -34.7809 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2601" Parameter: CONF_N -> "8002" Comparing "2601" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2602" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763300 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754634 ATOM PAIRS WERE FOUND FOR ATOM LIST 41583 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29698 from a total of 754634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2602 -63.77450 -5.90667 0.56774 INTE EXTERN> -31.21970 -32.55480 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7745" Parameter: A <- "-63.7745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2197" Parameter: B <- "-31.2197" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5548" Parameter: C <- "-32.5548" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2602 TOTAL ENERGY = -63.7745 RDTITL> * VAN DER WAALS = -31.2197 ELECTROSTATIC = -32.5548 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2602" Parameter: CONF_N -> "8002" Comparing "2602" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2603" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760607 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29508 from a total of 760607 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2603 -63.51106 -0.26344 0.52732 INTE EXTERN> -32.43411 -31.07695 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5111" Parameter: A <- "-63.5111" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4341" Parameter: B <- "-32.4341" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.0769" Parameter: C <- "-31.0769" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2603 TOTAL ENERGY = -63.5111 RDTITL> * VAN DER WAALS = -32.4341 ELECTROSTATIC = -31.0769 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2603" Parameter: CONF_N -> "8002" Comparing "2603" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2604" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760607 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762863 ATOM PAIRS WERE FOUND FOR ATOM LIST 42051 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29549 from a total of 762863 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2604 -65.47211 1.96105 0.64109 INTE EXTERN> -26.99901 -38.47310 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4721" Parameter: A <- "-65.4721" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.999" Parameter: B <- "-26.999" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4731" Parameter: C <- "-38.4731" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2604 TOTAL ENERGY = -65.4721 RDTITL> * VAN DER WAALS = -26.999 ELECTROSTATIC = -38.4731 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2604" Parameter: CONF_N -> "8002" Comparing "2604" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2605" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762863 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753790 ATOM PAIRS WERE FOUND FOR ATOM LIST 41477 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29128 from a total of 753790 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2605 -72.35961 6.88749 0.68546 INTE EXTERN> -25.93714 -46.42247 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3596" Parameter: A <- "-72.3596" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9371" Parameter: B <- "-25.9371" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4225" Parameter: C <- "-46.4225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2605 TOTAL ENERGY = -72.3596 RDTITL> * VAN DER WAALS = -25.9371 ELECTROSTATIC = -46.4225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2605" Parameter: CONF_N -> "8002" Comparing "2605" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2606" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753790 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758142 ATOM PAIRS WERE FOUND FOR ATOM LIST 41525 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29738 from a total of 758142 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2606 -66.33068 -6.02893 0.56912 INTE EXTERN> -29.76891 -36.56178 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3307" Parameter: A <- "-66.3307" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7689" Parameter: B <- "-29.7689" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5618" Parameter: C <- "-36.5618" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2606 TOTAL ENERGY = -66.3307 RDTITL> * VAN DER WAALS = -29.7689 ELECTROSTATIC = -36.5618 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2606" Parameter: CONF_N -> "8002" Comparing "2606" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2607" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758142 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753676 ATOM PAIRS WERE FOUND FOR ATOM LIST 41318 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29457 from a total of 753676 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2607 -67.36338 1.03270 0.57292 INTE EXTERN> -30.21758 -37.14580 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3634" Parameter: A <- "-67.3634" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2176" Parameter: B <- "-30.2176" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1458" Parameter: C <- "-37.1458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2607 TOTAL ENERGY = -67.3634 RDTITL> * VAN DER WAALS = -30.2176 ELECTROSTATIC = -37.1458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2607" Parameter: CONF_N -> "8002" Comparing "2607" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2608" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753676 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762077 ATOM PAIRS WERE FOUND FOR ATOM LIST 41973 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29855 from a total of 762077 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2608 -62.22193 -5.14145 0.56609 INTE EXTERN> -29.59402 -32.62791 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.2219" Parameter: A <- "-62.2219" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.594" Parameter: B <- "-29.594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.6279" Parameter: C <- "-32.6279" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2608 TOTAL ENERGY = -62.2219 RDTITL> * VAN DER WAALS = -29.594 ELECTROSTATIC = -32.6279 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2608" Parameter: CONF_N -> "8002" Comparing "2608" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2609" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762077 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761467 ATOM PAIRS WERE FOUND FOR ATOM LIST 42155 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30323 from a total of 761467 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2609 -74.24777 12.02584 0.71931 INTE EXTERN> -24.87221 -49.37557 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2478" Parameter: A <- "-74.2478" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8722" Parameter: B <- "-24.8722" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3756" Parameter: C <- "-49.3756" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2609 TOTAL ENERGY = -74.2478 RDTITL> * VAN DER WAALS = -24.8722 ELECTROSTATIC = -49.3756 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2609" Parameter: CONF_N -> "8002" Comparing "2609" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2610" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761467 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757578 ATOM PAIRS WERE FOUND FOR ATOM LIST 41732 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29019 from a total of 757578 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2610 -64.71669 -9.53109 0.62805 INTE EXTERN> -24.49388 -40.22281 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7167" Parameter: A <- "-64.7167" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4939" Parameter: B <- "-24.4939" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2228" Parameter: C <- "-40.2228" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2610 TOTAL ENERGY = -64.7167 RDTITL> * VAN DER WAALS = -24.4939 ELECTROSTATIC = -40.2228 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2610" Parameter: CONF_N -> "8002" Comparing "2610" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2611" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757578 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759366 ATOM PAIRS WERE FOUND FOR ATOM LIST 41929 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29543 from a total of 759366 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2611 -68.05257 3.33589 0.66681 INTE EXTERN> -26.46639 -41.58619 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0526" Parameter: A <- "-68.0526" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4664" Parameter: B <- "-26.4664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5862" Parameter: C <- "-41.5862" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2611 TOTAL ENERGY = -68.0526 RDTITL> * VAN DER WAALS = -26.4664 ELECTROSTATIC = -41.5862 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2611" Parameter: CONF_N -> "8002" Comparing "2611" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2612" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759366 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766107 ATOM PAIRS WERE FOUND FOR ATOM LIST 42015 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29665 from a total of 766107 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2612 -63.41491 -4.63766 0.58105 INTE EXTERN> -30.35974 -33.05517 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4149" Parameter: A <- "-63.4149" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3597" Parameter: B <- "-30.3597" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.0552" Parameter: C <- "-33.0552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2612 TOTAL ENERGY = -63.4149 RDTITL> * VAN DER WAALS = -30.3597 ELECTROSTATIC = -33.0552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2612" Parameter: CONF_N -> "8002" Comparing "2612" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2613" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766107 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761424 ATOM PAIRS WERE FOUND FOR ATOM LIST 41827 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29427 from a total of 761424 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2613 -70.79042 7.37551 0.66729 INTE EXTERN> -29.28524 -41.50518 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7904" Parameter: A <- "-70.7904" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2852" Parameter: B <- "-29.2852" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5052" Parameter: C <- "-41.5052" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2613 TOTAL ENERGY = -70.7904 RDTITL> * VAN DER WAALS = -29.2852 ELECTROSTATIC = -41.5052 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2613" Parameter: CONF_N -> "8002" Comparing "2613" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2614" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761424 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761803 ATOM PAIRS WERE FOUND FOR ATOM LIST 41705 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29646 from a total of 761803 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2614 -69.35205 -1.43837 0.63819 INTE EXTERN> -28.97982 -40.37223 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3521" Parameter: A <- "-69.3521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9798" Parameter: B <- "-28.9798" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3722" Parameter: C <- "-40.3722" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2614 TOTAL ENERGY = -69.3521 RDTITL> * VAN DER WAALS = -28.9798 ELECTROSTATIC = -40.3722 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2614" Parameter: CONF_N -> "8002" Comparing "2614" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2615" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761803 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761534 ATOM PAIRS WERE FOUND FOR ATOM LIST 42107 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29045 from a total of 761534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2615 -70.05347 0.70142 0.62865 INTE EXTERN> -30.28107 -39.77240 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0535" Parameter: A <- "-70.0535" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2811" Parameter: B <- "-30.2811" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7724" Parameter: C <- "-39.7724" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2615 TOTAL ENERGY = -70.0535 RDTITL> * VAN DER WAALS = -30.2811 ELECTROSTATIC = -39.7724 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2615" Parameter: CONF_N -> "8002" Comparing "2615" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2616" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764976 ATOM PAIRS WERE FOUND FOR ATOM LIST 42062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30611 from a total of 764976 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2616 -74.47487 4.42140 0.72988 INTE EXTERN> -26.63440 -47.84048 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4749" Parameter: A <- "-74.4749" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6344" Parameter: B <- "-26.6344" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8405" Parameter: C <- "-47.8405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2616 TOTAL ENERGY = -74.4749 RDTITL> * VAN DER WAALS = -26.6344 ELECTROSTATIC = -47.8405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2616" Parameter: CONF_N -> "8002" Comparing "2616" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2617" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764976 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766431 ATOM PAIRS WERE FOUND FOR ATOM LIST 42256 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30010 from a total of 766431 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2617 -69.09161 -5.38326 0.59423 INTE EXTERN> -31.86969 -37.22192 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0916" Parameter: A <- "-69.0916" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8697" Parameter: B <- "-31.8697" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2219" Parameter: C <- "-37.2219" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2617 TOTAL ENERGY = -69.0916 RDTITL> * VAN DER WAALS = -31.8697 ELECTROSTATIC = -37.2219 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2617" Parameter: CONF_N -> "8002" Comparing "2617" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2618" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766431 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760235 ATOM PAIRS WERE FOUND FOR ATOM LIST 41611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29493 from a total of 760235 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2618 -65.94017 -3.15144 0.58505 INTE EXTERN> -31.69156 -34.24861 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9402" Parameter: A <- "-65.9402" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6916" Parameter: B <- "-31.6916" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2486" Parameter: C <- "-34.2486" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2618 TOTAL ENERGY = -65.9402 RDTITL> * VAN DER WAALS = -31.6916 ELECTROSTATIC = -34.2486 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2618" Parameter: CONF_N -> "8002" Comparing "2618" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2619" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760235 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761795 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29886 from a total of 761795 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2619 -70.79912 4.85895 0.55427 INTE EXTERN> -34.60065 -36.19847 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7991" Parameter: A <- "-70.7991" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6006" Parameter: B <- "-34.6006" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1985" Parameter: C <- "-36.1985" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2619 TOTAL ENERGY = -70.7991 RDTITL> * VAN DER WAALS = -34.6006 ELECTROSTATIC = -36.1985 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2619" Parameter: CONF_N -> "8002" Comparing "2619" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2620" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761795 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770070 ATOM PAIRS WERE FOUND FOR ATOM LIST 42132 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29778 from a total of 770070 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2620 -64.41272 -6.38640 0.67472 INTE EXTERN> -28.60717 -35.80555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.4127" Parameter: A <- "-64.4127" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6072" Parameter: B <- "-28.6072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8055" Parameter: C <- "-35.8055" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2620 TOTAL ENERGY = -64.4127 RDTITL> * VAN DER WAALS = -28.6072 ELECTROSTATIC = -35.8055 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2620" Parameter: CONF_N -> "8002" Comparing "2620" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2621" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770070 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761610 ATOM PAIRS WERE FOUND FOR ATOM LIST 41754 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29289 from a total of 761610 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2621 -64.66211 0.24939 0.76741 INTE EXTERN> -22.72211 -41.94000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6621" Parameter: A <- "-64.6621" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.7221" Parameter: B <- "-22.7221" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.94" Parameter: C <- "-41.94" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2621 TOTAL ENERGY = -64.6621 RDTITL> * VAN DER WAALS = -22.7221 ELECTROSTATIC = -41.94 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2621" Parameter: CONF_N -> "8002" Comparing "2621" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2622" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761610 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760872 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29933 from a total of 760872 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2622 -68.19302 3.53091 0.65375 INTE EXTERN> -30.24002 -37.95300 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.193" Parameter: A <- "-68.193" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.24" Parameter: B <- "-30.24" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.953" Parameter: C <- "-37.953" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2622 TOTAL ENERGY = -68.193 RDTITL> * VAN DER WAALS = -30.24 ELECTROSTATIC = -37.953 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2622" Parameter: CONF_N -> "8002" Comparing "2622" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2623" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760872 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759546 ATOM PAIRS WERE FOUND FOR ATOM LIST 41659 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29361 from a total of 759546 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2623 -70.35277 2.15975 0.74284 INTE EXTERN> -24.98568 -45.36709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3528" Parameter: A <- "-70.3528" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9857" Parameter: B <- "-24.9857" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3671" Parameter: C <- "-45.3671" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2623 TOTAL ENERGY = -70.3528 RDTITL> * VAN DER WAALS = -24.9857 ELECTROSTATIC = -45.3671 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2623" Parameter: CONF_N -> "8002" Comparing "2623" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2624" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759546 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765225 ATOM PAIRS WERE FOUND FOR ATOM LIST 41902 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29711 from a total of 765225 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2624 -73.72122 3.36845 0.65160 INTE EXTERN> -30.55651 -43.16472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7212" Parameter: A <- "-73.7212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5565" Parameter: B <- "-30.5565" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1647" Parameter: C <- "-43.1647" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2624 TOTAL ENERGY = -73.7212 RDTITL> * VAN DER WAALS = -30.5565 ELECTROSTATIC = -43.1647 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2624" Parameter: CONF_N -> "8002" Comparing "2624" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2625" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765225 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756428 ATOM PAIRS WERE FOUND FOR ATOM LIST 41815 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29761 from a total of 756428 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2625 -71.73929 -1.98193 0.71746 INTE EXTERN> -26.20579 -45.53350 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7393" Parameter: A <- "-71.7393" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2058" Parameter: B <- "-26.2058" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5335" Parameter: C <- "-45.5335" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2625 TOTAL ENERGY = -71.7393 RDTITL> * VAN DER WAALS = -26.2058 ELECTROSTATIC = -45.5335 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2625" Parameter: CONF_N -> "8002" Comparing "2625" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2626" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756428 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764185 ATOM PAIRS WERE FOUND FOR ATOM LIST 41983 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29734 from a total of 764185 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2626 -73.25226 1.51297 0.72751 INTE EXTERN> -26.82936 -46.42290 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2523" Parameter: A <- "-73.2523" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8294" Parameter: B <- "-26.8294" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4229" Parameter: C <- "-46.4229" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2626 TOTAL ENERGY = -73.2523 RDTITL> * VAN DER WAALS = -26.8294 ELECTROSTATIC = -46.4229 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2626" Parameter: CONF_N -> "8002" Comparing "2626" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2627" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764185 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761981 ATOM PAIRS WERE FOUND FOR ATOM LIST 42026 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29524 from a total of 761981 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2627 -66.93631 -6.31595 0.55025 INTE EXTERN> -31.07399 -35.86232 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9363" Parameter: A <- "-66.9363" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.074" Parameter: B <- "-31.074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8623" Parameter: C <- "-35.8623" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2627 TOTAL ENERGY = -66.9363 RDTITL> * VAN DER WAALS = -31.074 ELECTROSTATIC = -35.8623 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2627" Parameter: CONF_N -> "8002" Comparing "2627" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2628" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761981 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759377 ATOM PAIRS WERE FOUND FOR ATOM LIST 41697 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29695 from a total of 759377 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2628 -73.00439 6.06808 0.59339 INTE EXTERN> -31.15762 -41.84677 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0044" Parameter: A <- "-73.0044" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1576" Parameter: B <- "-31.1576" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8468" Parameter: C <- "-41.8468" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2628 TOTAL ENERGY = -73.0044 RDTITL> * VAN DER WAALS = -31.1576 ELECTROSTATIC = -41.8468 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2628" Parameter: CONF_N -> "8002" Comparing "2628" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2629" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759377 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754758 ATOM PAIRS WERE FOUND FOR ATOM LIST 41429 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29562 from a total of 754758 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2629 -69.11159 -3.89281 0.52273 INTE EXTERN> -31.11222 -37.99937 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1116" Parameter: A <- "-69.1116" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1122" Parameter: B <- "-31.1122" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9994" Parameter: C <- "-37.9994" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2629 TOTAL ENERGY = -69.1116 RDTITL> * VAN DER WAALS = -31.1122 ELECTROSTATIC = -37.9994 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2629" Parameter: CONF_N -> "8002" Comparing "2629" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2630" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754758 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760924 ATOM PAIRS WERE FOUND FOR ATOM LIST 41842 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29765 from a total of 760924 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2630 -72.86573 3.75414 0.55696 INTE EXTERN> -32.79774 -40.06799 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8657" Parameter: A <- "-72.8657" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7977" Parameter: B <- "-32.7977" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.068" Parameter: C <- "-40.068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2630 TOTAL ENERGY = -72.8657 RDTITL> * VAN DER WAALS = -32.7977 ELECTROSTATIC = -40.068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2630" Parameter: CONF_N -> "8002" Comparing "2630" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2631" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760924 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762451 ATOM PAIRS WERE FOUND FOR ATOM LIST 41831 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29970 from a total of 762451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2631 -81.92837 9.06264 0.80950 INTE EXTERN> -27.60725 -54.32113 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9284" Parameter: A <- "-81.9284" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6072" Parameter: B <- "-27.6072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.3211" Parameter: C <- "-54.3211" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2631 TOTAL ENERGY = -81.9284 RDTITL> * VAN DER WAALS = -27.6072 ELECTROSTATIC = -54.3211 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2631" Parameter: CONF_N -> "8002" Comparing "2631" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2632" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760142 ATOM PAIRS WERE FOUND FOR ATOM LIST 41580 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29774 from a total of 760142 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2632 -77.14019 -4.78818 0.73672 INTE EXTERN> -28.11520 -49.02499 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1402" Parameter: A <- "-77.1402" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1152" Parameter: B <- "-28.1152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.025" Parameter: C <- "-49.025" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2632 TOTAL ENERGY = -77.1402 RDTITL> * VAN DER WAALS = -28.1152 ELECTROSTATIC = -49.025 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2632" Parameter: CONF_N -> "8002" Comparing "2632" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2633" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760142 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761387 ATOM PAIRS WERE FOUND FOR ATOM LIST 41851 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29414 from a total of 761387 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2633 -68.89228 -8.24791 0.61415 INTE EXTERN> -32.24635 -36.64593 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8923" Parameter: A <- "-68.8923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2463" Parameter: B <- "-32.2463" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6459" Parameter: C <- "-36.6459" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2633 TOTAL ENERGY = -68.8923 RDTITL> * VAN DER WAALS = -32.2463 ELECTROSTATIC = -36.6459 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2633" Parameter: CONF_N -> "8002" Comparing "2633" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2634" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761387 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761574 ATOM PAIRS WERE FOUND FOR ATOM LIST 41627 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29627 from a total of 761574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2634 -67.36456 -1.52772 0.61014 INTE EXTERN> -32.76134 -34.60322 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3646" Parameter: A <- "-67.3646" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7613" Parameter: B <- "-32.7613" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.6032" Parameter: C <- "-34.6032" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2634 TOTAL ENERGY = -67.3646 RDTITL> * VAN DER WAALS = -32.7613 ELECTROSTATIC = -34.6032 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2634" Parameter: CONF_N -> "8002" Comparing "2634" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2635" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755592 ATOM PAIRS WERE FOUND FOR ATOM LIST 41396 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29585 from a total of 755592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2635 -73.96626 6.60170 0.70197 INTE EXTERN> -30.67375 -43.29252 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9663" Parameter: A <- "-73.9663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6737" Parameter: B <- "-30.6737" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2925" Parameter: C <- "-43.2925" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2635 TOTAL ENERGY = -73.9663 RDTITL> * VAN DER WAALS = -30.6737 ELECTROSTATIC = -43.2925 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2635" Parameter: CONF_N -> "8002" Comparing "2635" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2636" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759961 ATOM PAIRS WERE FOUND FOR ATOM LIST 41760 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29389 from a total of 759961 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2636 -70.09239 -3.87387 0.63678 INTE EXTERN> -28.84574 -41.24664 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0924" Parameter: A <- "-70.0924" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8457" Parameter: B <- "-28.8457" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2466" Parameter: C <- "-41.2466" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2636 TOTAL ENERGY = -70.0924 RDTITL> * VAN DER WAALS = -28.8457 ELECTROSTATIC = -41.2466 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2636" Parameter: CONF_N -> "8002" Comparing "2636" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2637" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759961 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756179 ATOM PAIRS WERE FOUND FOR ATOM LIST 41558 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29659 from a total of 756179 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2637 -68.31991 -1.77248 0.65125 INTE EXTERN> -28.65641 -39.66351 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3199" Parameter: A <- "-68.3199" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6564" Parameter: B <- "-28.6564" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6635" Parameter: C <- "-39.6635" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2637 TOTAL ENERGY = -68.3199 RDTITL> * VAN DER WAALS = -28.6564 ELECTROSTATIC = -39.6635 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2637" Parameter: CONF_N -> "8002" Comparing "2637" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2638" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756179 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757783 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29493 from a total of 757783 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2638 -65.92985 -2.39007 0.63600 INTE EXTERN> -28.92721 -37.00264 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9298" Parameter: A <- "-65.9298" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9272" Parameter: B <- "-28.9272" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0026" Parameter: C <- "-37.0026" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2638 TOTAL ENERGY = -65.9298 RDTITL> * VAN DER WAALS = -28.9272 ELECTROSTATIC = -37.0026 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2638" Parameter: CONF_N -> "8002" Comparing "2638" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2639" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757783 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757852 ATOM PAIRS WERE FOUND FOR ATOM LIST 41701 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29199 from a total of 757852 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2639 -67.55237 1.62253 0.61345 INTE EXTERN> -28.00385 -39.54852 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5524" Parameter: A <- "-67.5524" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0039" Parameter: B <- "-28.0039" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5485" Parameter: C <- "-39.5485" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2639 TOTAL ENERGY = -67.5524 RDTITL> * VAN DER WAALS = -28.0039 ELECTROSTATIC = -39.5485 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2639" Parameter: CONF_N -> "8002" Comparing "2639" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2640" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757852 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759253 ATOM PAIRS WERE FOUND FOR ATOM LIST 41780 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29019 from a total of 759253 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2640 -63.84113 -3.71124 0.60500 INTE EXTERN> -27.40719 -36.43394 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.8411" Parameter: A <- "-63.8411" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4072" Parameter: B <- "-27.4072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4339" Parameter: C <- "-36.4339" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2640 TOTAL ENERGY = -63.8411 RDTITL> * VAN DER WAALS = -27.4072 ELECTROSTATIC = -36.4339 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2640" Parameter: CONF_N -> "8002" Comparing "2640" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2641" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759253 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761712 ATOM PAIRS WERE FOUND FOR ATOM LIST 42031 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29919 from a total of 761712 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2641 -69.02808 5.18695 0.52108 INTE EXTERN> -33.58295 -35.44513 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0281" Parameter: A <- "-69.0281" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.583" Parameter: B <- "-33.583" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4451" Parameter: C <- "-35.4451" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2641 TOTAL ENERGY = -69.0281 RDTITL> * VAN DER WAALS = -33.583 ELECTROSTATIC = -35.4451 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2641" Parameter: CONF_N -> "8002" Comparing "2641" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2642" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761712 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759197 ATOM PAIRS WERE FOUND FOR ATOM LIST 41748 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29634 from a total of 759197 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2642 -71.25509 2.22701 0.62324 INTE EXTERN> -29.50125 -41.75384 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2551" Parameter: A <- "-71.2551" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5013" Parameter: B <- "-29.5013" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7538" Parameter: C <- "-41.7538" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2642 TOTAL ENERGY = -71.2551 RDTITL> * VAN DER WAALS = -29.5013 ELECTROSTATIC = -41.7538 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2642" Parameter: CONF_N -> "8002" Comparing "2642" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2643" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759197 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758589 ATOM PAIRS WERE FOUND FOR ATOM LIST 41705 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28943 from a total of 758589 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2643 -69.09640 -2.15869 0.56183 INTE EXTERN> -31.90862 -37.18778 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0964" Parameter: A <- "-69.0964" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9086" Parameter: B <- "-31.9086" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1878" Parameter: C <- "-37.1878" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2643 TOTAL ENERGY = -69.0964 RDTITL> * VAN DER WAALS = -31.9086 ELECTROSTATIC = -37.1878 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2643" Parameter: CONF_N -> "8002" Comparing "2643" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2644" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758589 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764056 ATOM PAIRS WERE FOUND FOR ATOM LIST 42083 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29994 from a total of 764056 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2644 -70.64348 1.54708 0.66383 INTE EXTERN> -30.29670 -40.34678 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6435" Parameter: A <- "-70.6435" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2967" Parameter: B <- "-30.2967" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3468" Parameter: C <- "-40.3468" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2644 TOTAL ENERGY = -70.6435 RDTITL> * VAN DER WAALS = -30.2967 ELECTROSTATIC = -40.3468 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2644" Parameter: CONF_N -> "8002" Comparing "2644" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2645" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764056 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759030 ATOM PAIRS WERE FOUND FOR ATOM LIST 41543 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29434 from a total of 759030 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2645 -76.11352 5.47004 0.65155 INTE EXTERN> -30.42075 -45.69277 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1135" Parameter: A <- "-76.1135" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4208" Parameter: B <- "-30.4208" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6928" Parameter: C <- "-45.6928" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2645 TOTAL ENERGY = -76.1135 RDTITL> * VAN DER WAALS = -30.4208 ELECTROSTATIC = -45.6928 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2645" Parameter: CONF_N -> "8002" Comparing "2645" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2646" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759030 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758834 ATOM PAIRS WERE FOUND FOR ATOM LIST 41648 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29684 from a total of 758834 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2646 -72.81399 -3.29953 0.64578 INTE EXTERN> -28.56444 -44.24955 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.814" Parameter: A <- "-72.814" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5644" Parameter: B <- "-28.5644" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2495" Parameter: C <- "-44.2495" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2646 TOTAL ENERGY = -72.814 RDTITL> * VAN DER WAALS = -28.5644 ELECTROSTATIC = -44.2495 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2646" Parameter: CONF_N -> "8002" Comparing "2646" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2647" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758834 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761515 ATOM PAIRS WERE FOUND FOR ATOM LIST 41656 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30022 from a total of 761515 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2647 -68.63200 -4.18199 0.67893 INTE EXTERN> -27.58956 -41.04244 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.632" Parameter: A <- "-68.632" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5896" Parameter: B <- "-27.5896" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0424" Parameter: C <- "-41.0424" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2647 TOTAL ENERGY = -68.632 RDTITL> * VAN DER WAALS = -27.5896 ELECTROSTATIC = -41.0424 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2647" Parameter: CONF_N -> "8002" Comparing "2647" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2648" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761515 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761686 ATOM PAIRS WERE FOUND FOR ATOM LIST 41672 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29183 from a total of 761686 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2648 -65.57817 -3.05383 0.57658 INTE EXTERN> -28.44934 -37.12883 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5782" Parameter: A <- "-65.5782" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4493" Parameter: B <- "-28.4493" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1288" Parameter: C <- "-37.1288" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2648 TOTAL ENERGY = -65.5782 RDTITL> * VAN DER WAALS = -28.4493 ELECTROSTATIC = -37.1288 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2648" Parameter: CONF_N -> "8002" Comparing "2648" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2649" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761686 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761703 ATOM PAIRS WERE FOUND FOR ATOM LIST 41758 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29107 from a total of 761703 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2649 -69.84901 4.27084 0.59081 INTE EXTERN> -30.79340 -39.05561 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.849" Parameter: A <- "-69.849" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7934" Parameter: B <- "-30.7934" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0556" Parameter: C <- "-39.0556" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2649 TOTAL ENERGY = -69.849 RDTITL> * VAN DER WAALS = -30.7934 ELECTROSTATIC = -39.0556 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2649" Parameter: CONF_N -> "8002" Comparing "2649" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2650" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761703 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759777 ATOM PAIRS WERE FOUND FOR ATOM LIST 41654 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29362 from a total of 759777 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2650 -74.78474 4.93573 0.61335 INTE EXTERN> -32.29420 -42.49055 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7847" Parameter: A <- "-74.7847" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2942" Parameter: B <- "-32.2942" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4905" Parameter: C <- "-42.4905" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2650 TOTAL ENERGY = -74.7847 RDTITL> * VAN DER WAALS = -32.2942 ELECTROSTATIC = -42.4905 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2650" Parameter: CONF_N -> "8002" Comparing "2650" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2651" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759777 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768124 ATOM PAIRS WERE FOUND FOR ATOM LIST 42153 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29857 from a total of 768124 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2651 -74.33383 -0.45091 0.70607 INTE EXTERN> -27.93463 -46.39921 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3338" Parameter: A <- "-74.3338" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9346" Parameter: B <- "-27.9346" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3992" Parameter: C <- "-46.3992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2651 TOTAL ENERGY = -74.3338 RDTITL> * VAN DER WAALS = -27.9346 ELECTROSTATIC = -46.3992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2651" Parameter: CONF_N -> "8002" Comparing "2651" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2652" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768124 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764177 ATOM PAIRS WERE FOUND FOR ATOM LIST 41976 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29618 from a total of 764177 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2652 -71.69596 -2.63788 0.75350 INTE EXTERN> -26.31585 -45.38011 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.696" Parameter: A <- "-71.696" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3158" Parameter: B <- "-26.3158" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3801" Parameter: C <- "-45.3801" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2652 TOTAL ENERGY = -71.696 RDTITL> * VAN DER WAALS = -26.3158 ELECTROSTATIC = -45.3801 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2652" Parameter: CONF_N -> "8002" Comparing "2652" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2653" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764177 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757184 ATOM PAIRS WERE FOUND FOR ATOM LIST 41608 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29412 from a total of 757184 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2653 -75.07683 3.38087 0.66794 INTE EXTERN> -29.96430 -45.11253 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0768" Parameter: A <- "-75.0768" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9643" Parameter: B <- "-29.9643" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1125" Parameter: C <- "-45.1125" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2653 TOTAL ENERGY = -75.0768 RDTITL> * VAN DER WAALS = -29.9643 ELECTROSTATIC = -45.1125 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2653" Parameter: CONF_N -> "8002" Comparing "2653" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2654" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757184 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759417 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30069 from a total of 759417 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2654 -78.08116 3.00433 0.69295 INTE EXTERN> -31.03366 -47.04750 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0812" Parameter: A <- "-78.0812" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0337" Parameter: B <- "-31.0337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0475" Parameter: C <- "-47.0475" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2654 TOTAL ENERGY = -78.0812 RDTITL> * VAN DER WAALS = -31.0337 ELECTROSTATIC = -47.0475 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2654" Parameter: CONF_N -> "8002" Comparing "2654" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2655" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759417 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758538 ATOM PAIRS WERE FOUND FOR ATOM LIST 41801 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29964 from a total of 758538 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2655 -76.69662 -1.38454 0.75635 INTE EXTERN> -26.70029 -49.99633 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6966" Parameter: A <- "-76.6966" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7003" Parameter: B <- "-26.7003" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9963" Parameter: C <- "-49.9963" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2655 TOTAL ENERGY = -76.6966 RDTITL> * VAN DER WAALS = -26.7003 ELECTROSTATIC = -49.9963 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2655" Parameter: CONF_N -> "8002" Comparing "2655" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2656" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758538 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758262 ATOM PAIRS WERE FOUND FOR ATOM LIST 41677 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29994 from a total of 758262 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2656 -71.43962 -5.25701 0.62126 INTE EXTERN> -30.57669 -40.86293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4396" Parameter: A <- "-71.4396" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5767" Parameter: B <- "-30.5767" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8629" Parameter: C <- "-40.8629" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2656 TOTAL ENERGY = -71.4396 RDTITL> * VAN DER WAALS = -30.5767 ELECTROSTATIC = -40.8629 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2656" Parameter: CONF_N -> "8002" Comparing "2656" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2657" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758262 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762147 ATOM PAIRS WERE FOUND FOR ATOM LIST 41876 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29485 from a total of 762147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2657 -70.82319 -0.61643 0.64815 INTE EXTERN> -30.86301 -39.96017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8232" Parameter: A <- "-70.8232" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.863" Parameter: B <- "-30.863" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9602" Parameter: C <- "-39.9602" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2657 TOTAL ENERGY = -70.8232 RDTITL> * VAN DER WAALS = -30.863 ELECTROSTATIC = -39.9602 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2657" Parameter: CONF_N -> "8002" Comparing "2657" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2658" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760505 ATOM PAIRS WERE FOUND FOR ATOM LIST 41780 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29674 from a total of 760505 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2658 -77.22216 6.39898 0.67351 INTE EXTERN> -31.14624 -46.07592 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2222" Parameter: A <- "-77.2222" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1462" Parameter: B <- "-31.1462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0759" Parameter: C <- "-46.0759" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2658 TOTAL ENERGY = -77.2222 RDTITL> * VAN DER WAALS = -31.1462 ELECTROSTATIC = -46.0759 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2658" Parameter: CONF_N -> "8002" Comparing "2658" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2659" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760505 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758594 ATOM PAIRS WERE FOUND FOR ATOM LIST 41654 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29441 from a total of 758594 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2659 -70.53879 -6.68338 0.69147 INTE EXTERN> -27.71184 -42.82695 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5388" Parameter: A <- "-70.5388" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7118" Parameter: B <- "-27.7118" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.827" Parameter: C <- "-42.827" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2659 TOTAL ENERGY = -70.5388 RDTITL> * VAN DER WAALS = -27.7118 ELECTROSTATIC = -42.827 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2659" Parameter: CONF_N -> "8002" Comparing "2659" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2660" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758594 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758729 ATOM PAIRS WERE FOUND FOR ATOM LIST 41833 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29697 from a total of 758729 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2660 -70.57609 0.03730 0.63807 INTE EXTERN> -30.72253 -39.85356 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5761" Parameter: A <- "-70.5761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7225" Parameter: B <- "-30.7225" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8536" Parameter: C <- "-39.8536" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2660 TOTAL ENERGY = -70.5761 RDTITL> * VAN DER WAALS = -30.7225 ELECTROSTATIC = -39.8536 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2660" Parameter: CONF_N -> "8002" Comparing "2660" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2661" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758729 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762083 ATOM PAIRS WERE FOUND FOR ATOM LIST 41815 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29445 from a total of 762083 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2661 -67.01732 -3.55877 0.71827 INTE EXTERN> -24.66537 -42.35195 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0173" Parameter: A <- "-67.0173" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6654" Parameter: B <- "-24.6654" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.352" Parameter: C <- "-42.352" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2661 TOTAL ENERGY = -67.0173 RDTITL> * VAN DER WAALS = -24.6654 ELECTROSTATIC = -42.352 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2661" Parameter: CONF_N -> "8002" Comparing "2661" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2662" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762083 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764008 ATOM PAIRS WERE FOUND FOR ATOM LIST 42010 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29552 from a total of 764008 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2662 -67.83794 0.82062 0.64694 INTE EXTERN> -29.80199 -38.03595 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8379" Parameter: A <- "-67.8379" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.802" Parameter: B <- "-29.802" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0359" Parameter: C <- "-38.0359" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2662 TOTAL ENERGY = -67.8379 RDTITL> * VAN DER WAALS = -29.802 ELECTROSTATIC = -38.0359 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2662" Parameter: CONF_N -> "8002" Comparing "2662" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2663" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764008 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760947 ATOM PAIRS WERE FOUND FOR ATOM LIST 41702 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29378 from a total of 760947 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2663 -62.19683 -5.64111 0.53005 INTE EXTERN> -30.60678 -31.59005 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.1968" Parameter: A <- "-62.1968" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6068" Parameter: B <- "-30.6068" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.59" Parameter: C <- "-31.59" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2663 TOTAL ENERGY = -62.1968 RDTITL> * VAN DER WAALS = -30.6068 ELECTROSTATIC = -31.59 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2663" Parameter: CONF_N -> "8002" Comparing "2663" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2664" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760947 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760103 ATOM PAIRS WERE FOUND FOR ATOM LIST 41619 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29432 from a total of 760103 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2664 -77.23469 15.03787 0.78343 INTE EXTERN> -28.20599 -49.02870 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2347" Parameter: A <- "-77.2347" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.206" Parameter: B <- "-28.206" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0287" Parameter: C <- "-49.0287" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2664 TOTAL ENERGY = -77.2347 RDTITL> * VAN DER WAALS = -28.206 ELECTROSTATIC = -49.0287 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2664" Parameter: CONF_N -> "8002" Comparing "2664" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2665" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760103 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757579 ATOM PAIRS WERE FOUND FOR ATOM LIST 41525 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28703 from a total of 757579 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2665 -60.91595 -16.31875 0.69479 INTE EXTERN> -22.50699 -38.40896 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.9159" Parameter: A <- "-60.9159" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.507" Parameter: B <- "-22.507" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.409" Parameter: C <- "-38.409" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2665 TOTAL ENERGY = -60.9159 RDTITL> * VAN DER WAALS = -22.507 ELECTROSTATIC = -38.409 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2665" Parameter: CONF_N -> "8002" Comparing "2665" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2666" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757579 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758738 ATOM PAIRS WERE FOUND FOR ATOM LIST 41662 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29039 from a total of 758738 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2666 -67.89664 6.98069 0.61826 INTE EXTERN> -29.27150 -38.62514 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8966" Parameter: A <- "-67.8966" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2715" Parameter: B <- "-29.2715" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6251" Parameter: C <- "-38.6251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2666 TOTAL ENERGY = -67.8966 RDTITL> * VAN DER WAALS = -29.2715 ELECTROSTATIC = -38.6251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2666" Parameter: CONF_N -> "8002" Comparing "2666" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2667" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758738 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760216 ATOM PAIRS WERE FOUND FOR ATOM LIST 41532 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29155 from a total of 760216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2667 -64.80974 -3.08690 0.57833 INTE EXTERN> -31.55653 -33.25322 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8097" Parameter: A <- "-64.8097" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5565" Parameter: B <- "-31.5565" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2532" Parameter: C <- "-33.2532" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2667 TOTAL ENERGY = -64.8097 RDTITL> * VAN DER WAALS = -31.5565 ELECTROSTATIC = -33.2532 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2667" Parameter: CONF_N -> "8002" Comparing "2667" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2668" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761115 ATOM PAIRS WERE FOUND FOR ATOM LIST 41773 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29499 from a total of 761115 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2668 -61.19453 -3.61521 0.67180 INTE EXTERN> -28.27870 -32.91583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.1945" Parameter: A <- "-61.1945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2787" Parameter: B <- "-28.2787" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.9158" Parameter: C <- "-32.9158" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2668 TOTAL ENERGY = -61.1945 RDTITL> * VAN DER WAALS = -28.2787 ELECTROSTATIC = -32.9158 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2668" Parameter: CONF_N -> "8002" Comparing "2668" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2669" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761115 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768216 ATOM PAIRS WERE FOUND FOR ATOM LIST 42013 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29350 from a total of 768216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2669 -70.05765 8.86312 0.67299 INTE EXTERN> -30.91487 -39.14278 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0576" Parameter: A <- "-70.0576" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9149" Parameter: B <- "-30.9149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1428" Parameter: C <- "-39.1428" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2669 TOTAL ENERGY = -70.0576 RDTITL> * VAN DER WAALS = -30.9149 ELECTROSTATIC = -39.1428 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2669" Parameter: CONF_N -> "8002" Comparing "2669" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2670" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767415 ATOM PAIRS WERE FOUND FOR ATOM LIST 41959 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29383 from a total of 767415 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2670 -64.79334 -5.26431 0.56922 INTE EXTERN> -31.60402 -33.18931 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7933" Parameter: A <- "-64.7933" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.604" Parameter: B <- "-31.604" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1893" Parameter: C <- "-33.1893" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2670 TOTAL ENERGY = -64.7933 RDTITL> * VAN DER WAALS = -31.604 ELECTROSTATIC = -33.1893 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2670" Parameter: CONF_N -> "8002" Comparing "2670" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2671" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767415 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760862 ATOM PAIRS WERE FOUND FOR ATOM LIST 41914 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28771 from a total of 760862 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2671 -66.31542 1.52209 0.69010 INTE EXTERN> -26.22827 -40.08715 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3154" Parameter: A <- "-66.3154" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2283" Parameter: B <- "-26.2283" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0872" Parameter: C <- "-40.0872" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2671 TOTAL ENERGY = -66.3154 RDTITL> * VAN DER WAALS = -26.2283 ELECTROSTATIC = -40.0872 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2671" Parameter: CONF_N -> "8002" Comparing "2671" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2672" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760862 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763762 ATOM PAIRS WERE FOUND FOR ATOM LIST 41942 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29082 from a total of 763762 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2672 -69.81962 3.50420 0.59248 INTE EXTERN> -30.15729 -39.66234 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8196" Parameter: A <- "-69.8196" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1573" Parameter: B <- "-30.1573" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6623" Parameter: C <- "-39.6623" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2672 TOTAL ENERGY = -69.8196 RDTITL> * VAN DER WAALS = -30.1573 ELECTROSTATIC = -39.6623 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2672" Parameter: CONF_N -> "8002" Comparing "2672" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2673" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763762 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759013 ATOM PAIRS WERE FOUND FOR ATOM LIST 41452 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28792 from a total of 759013 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2673 -65.85579 -3.96384 0.60193 INTE EXTERN> -27.79814 -38.05765 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8558" Parameter: A <- "-65.8558" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7981" Parameter: B <- "-27.7981" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0576" Parameter: C <- "-38.0576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2673 TOTAL ENERGY = -65.8558 RDTITL> * VAN DER WAALS = -27.7981 ELECTROSTATIC = -38.0576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2673" Parameter: CONF_N -> "8002" Comparing "2673" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2674" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759013 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762985 ATOM PAIRS WERE FOUND FOR ATOM LIST 41737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29161 from a total of 762985 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2674 -66.58757 0.73178 0.59783 INTE EXTERN> -29.62197 -36.96560 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5876" Parameter: A <- "-66.5876" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.622" Parameter: B <- "-29.622" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9656" Parameter: C <- "-36.9656" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2674 TOTAL ENERGY = -66.5876 RDTITL> * VAN DER WAALS = -29.622 ELECTROSTATIC = -36.9656 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2674" Parameter: CONF_N -> "8002" Comparing "2674" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2675" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762985 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759618 ATOM PAIRS WERE FOUND FOR ATOM LIST 41689 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29317 from a total of 759618 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2675 -72.05440 5.46684 0.61263 INTE EXTERN> -30.64028 -41.41412 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0544" Parameter: A <- "-72.0544" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6403" Parameter: B <- "-30.6403" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4141" Parameter: C <- "-41.4141" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2675 TOTAL ENERGY = -72.0544 RDTITL> * VAN DER WAALS = -30.6403 ELECTROSTATIC = -41.4141 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2675" Parameter: CONF_N -> "8002" Comparing "2675" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2676" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759618 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763982 ATOM PAIRS WERE FOUND FOR ATOM LIST 42046 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28550 from a total of 763982 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2676 -68.91268 -3.14172 0.64148 INTE EXTERN> -30.10179 -38.81089 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9127" Parameter: A <- "-68.9127" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1018" Parameter: B <- "-30.1018" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8109" Parameter: C <- "-38.8109" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2676 TOTAL ENERGY = -68.9127 RDTITL> * VAN DER WAALS = -30.1018 ELECTROSTATIC = -38.8109 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2676" Parameter: CONF_N -> "8002" Comparing "2676" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2677" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763982 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762309 ATOM PAIRS WERE FOUND FOR ATOM LIST 42064 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28854 from a total of 762309 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2677 -58.54014 -10.37254 0.59711 INTE EXTERN> -26.75940 -31.78073 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.5401" Parameter: A <- "-58.5401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7594" Parameter: B <- "-26.7594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.7807" Parameter: C <- "-31.7807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2677 TOTAL ENERGY = -58.5401 RDTITL> * VAN DER WAALS = -26.7594 ELECTROSTATIC = -31.7807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2677" Parameter: CONF_N -> "8002" Comparing "2677" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2678" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762309 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767166 ATOM PAIRS WERE FOUND FOR ATOM LIST 42082 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29706 from a total of 767166 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2678 -72.75903 14.21889 0.73204 INTE EXTERN> -29.21135 -43.54768 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.759" Parameter: A <- "-72.759" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2113" Parameter: B <- "-29.2113" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5477" Parameter: C <- "-43.5477" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2678 TOTAL ENERGY = -72.759 RDTITL> * VAN DER WAALS = -29.2113 ELECTROSTATIC = -43.5477 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2678" Parameter: CONF_N -> "8002" Comparing "2678" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2679" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767166 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768473 ATOM PAIRS WERE FOUND FOR ATOM LIST 42354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29837 from a total of 768473 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2679 -64.90260 -7.85643 0.59964 INTE EXTERN> -32.90250 -32.00010 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9026" Parameter: A <- "-64.9026" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9025" Parameter: B <- "-32.9025" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.0001" Parameter: C <- "-32.0001" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2679 TOTAL ENERGY = -64.9026 RDTITL> * VAN DER WAALS = -32.9025 ELECTROSTATIC = -32.0001 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2679" Parameter: CONF_N -> "8002" Comparing "2679" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2680" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768473 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763591 ATOM PAIRS WERE FOUND FOR ATOM LIST 41922 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29714 from a total of 763591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2680 -68.43461 3.53201 0.64290 INTE EXTERN> -28.18389 -40.25072 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4346" Parameter: A <- "-68.4346" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1839" Parameter: B <- "-28.1839" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2507" Parameter: C <- "-40.2507" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2680 TOTAL ENERGY = -68.4346 RDTITL> * VAN DER WAALS = -28.1839 ELECTROSTATIC = -40.2507 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2680" Parameter: CONF_N -> "8002" Comparing "2680" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2681" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759237 ATOM PAIRS WERE FOUND FOR ATOM LIST 41788 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29586 from a total of 759237 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2681 -73.50330 5.06869 0.61179 INTE EXTERN> -33.15128 -40.35202 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5033" Parameter: A <- "-73.5033" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1513" Parameter: B <- "-33.1513" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.352" Parameter: C <- "-40.352" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2681 TOTAL ENERGY = -73.5033 RDTITL> * VAN DER WAALS = -33.1513 ELECTROSTATIC = -40.352 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2681" Parameter: CONF_N -> "8002" Comparing "2681" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2682" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759237 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764276 ATOM PAIRS WERE FOUND FOR ATOM LIST 42005 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29659 from a total of 764276 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2682 -69.78383 -3.71947 0.69123 INTE EXTERN> -26.22340 -43.56043 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7838" Parameter: A <- "-69.7838" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2234" Parameter: B <- "-26.2234" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5604" Parameter: C <- "-43.5604" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2682 TOTAL ENERGY = -69.7838 RDTITL> * VAN DER WAALS = -26.2234 ELECTROSTATIC = -43.5604 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2682" Parameter: CONF_N -> "8002" Comparing "2682" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2683" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764276 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765260 ATOM PAIRS WERE FOUND FOR ATOM LIST 42150 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30534 from a total of 765260 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2683 -65.77907 -4.00476 0.67014 INTE EXTERN> -28.08075 -37.69833 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7791" Parameter: A <- "-65.7791" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0807" Parameter: B <- "-28.0807" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6983" Parameter: C <- "-37.6983" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2683 TOTAL ENERGY = -65.7791 RDTITL> * VAN DER WAALS = -28.0807 ELECTROSTATIC = -37.6983 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2683" Parameter: CONF_N -> "8002" Comparing "2683" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2684" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765260 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767534 ATOM PAIRS WERE FOUND FOR ATOM LIST 41983 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29544 from a total of 767534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2684 -73.45013 7.67106 0.83097 INTE EXTERN> -21.23132 -52.21881 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4501" Parameter: A <- "-73.4501" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.2313" Parameter: B <- "-21.2313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2188" Parameter: C <- "-52.2188" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2684 TOTAL ENERGY = -73.4501 RDTITL> * VAN DER WAALS = -21.2313 ELECTROSTATIC = -52.2188 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2684" Parameter: CONF_N -> "8002" Comparing "2684" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2685" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757924 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29018 from a total of 757924 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2685 -65.55568 -7.89445 0.65260 INTE EXTERN> -27.36781 -38.18787 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5557" Parameter: A <- "-65.5557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3678" Parameter: B <- "-27.3678" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1879" Parameter: C <- "-38.1879" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2685 TOTAL ENERGY = -65.5557 RDTITL> * VAN DER WAALS = -27.3678 ELECTROSTATIC = -38.1879 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2685" Parameter: CONF_N -> "8002" Comparing "2685" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2686" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757924 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756595 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29920 from a total of 756595 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2686 -80.47813 14.92245 0.61593 INTE EXTERN> -33.63613 -46.84200 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4781" Parameter: A <- "-80.4781" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6361" Parameter: B <- "-33.6361" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.842" Parameter: C <- "-46.842" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2686 TOTAL ENERGY = -80.4781 RDTITL> * VAN DER WAALS = -33.6361 ELECTROSTATIC = -46.842 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2686" Parameter: CONF_N -> "8002" Comparing "2686" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2687" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756595 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758610 ATOM PAIRS WERE FOUND FOR ATOM LIST 41695 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30342 from a total of 758610 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2687 -72.46926 -8.00887 0.69614 INTE EXTERN> -27.75391 -44.71535 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4693" Parameter: A <- "-72.4693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7539" Parameter: B <- "-27.7539" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7154" Parameter: C <- "-44.7154" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2687 TOTAL ENERGY = -72.4693 RDTITL> * VAN DER WAALS = -27.7539 ELECTROSTATIC = -44.7154 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2687" Parameter: CONF_N -> "8002" Comparing "2687" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2688" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758610 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756087 ATOM PAIRS WERE FOUND FOR ATOM LIST 41434 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29855 from a total of 756087 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2688 -66.22839 -6.24088 0.65571 INTE EXTERN> -30.62790 -35.60049 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2284" Parameter: A <- "-66.2284" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6279" Parameter: B <- "-30.6279" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6005" Parameter: C <- "-35.6005" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2688 TOTAL ENERGY = -66.2284 RDTITL> * VAN DER WAALS = -30.6279 ELECTROSTATIC = -35.6005 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2688" Parameter: CONF_N -> "8002" Comparing "2688" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2689" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756087 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754411 ATOM PAIRS WERE FOUND FOR ATOM LIST 41411 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29545 from a total of 754411 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2689 -72.75192 6.52353 0.63801 INTE EXTERN> -30.52552 -42.22640 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7519" Parameter: A <- "-72.7519" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5255" Parameter: B <- "-30.5255" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2264" Parameter: C <- "-42.2264" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2689 TOTAL ENERGY = -72.7519 RDTITL> * VAN DER WAALS = -30.5255 ELECTROSTATIC = -42.2264 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2689" Parameter: CONF_N -> "8002" Comparing "2689" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2690" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754411 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762038 ATOM PAIRS WERE FOUND FOR ATOM LIST 41910 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29593 from a total of 762038 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2690 -75.89853 3.14661 0.79644 INTE EXTERN> -26.38017 -49.51836 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8985" Parameter: A <- "-75.8985" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3802" Parameter: B <- "-26.3802" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5184" Parameter: C <- "-49.5184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2690 TOTAL ENERGY = -75.8985 RDTITL> * VAN DER WAALS = -26.3802 ELECTROSTATIC = -49.5184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2690" Parameter: CONF_N -> "8002" Comparing "2690" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2691" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762038 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760302 ATOM PAIRS WERE FOUND FOR ATOM LIST 41539 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29399 from a total of 760302 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2691 -72.42254 -3.47599 0.70884 INTE EXTERN> -27.84265 -44.57988 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4225" Parameter: A <- "-72.4225" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8427" Parameter: B <- "-27.8427" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5799" Parameter: C <- "-44.5799" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2691 TOTAL ENERGY = -72.4225 RDTITL> * VAN DER WAALS = -27.8427 ELECTROSTATIC = -44.5799 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2691" Parameter: CONF_N -> "8002" Comparing "2691" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2692" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760302 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761642 ATOM PAIRS WERE FOUND FOR ATOM LIST 41895 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30100 from a total of 761642 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2692 -73.43466 1.01213 0.77759 INTE EXTERN> -26.99681 -46.43785 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4347" Parameter: A <- "-73.4347" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9968" Parameter: B <- "-26.9968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4379" Parameter: C <- "-46.4379" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2692 TOTAL ENERGY = -73.4347 RDTITL> * VAN DER WAALS = -26.9968 ELECTROSTATIC = -46.4379 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2692" Parameter: CONF_N -> "8002" Comparing "2692" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2693" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761642 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761205 ATOM PAIRS WERE FOUND FOR ATOM LIST 41914 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29805 from a total of 761205 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2693 -67.37895 -6.05571 0.63073 INTE EXTERN> -28.61500 -38.76395 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.379" Parameter: A <- "-67.379" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.615" Parameter: B <- "-28.615" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.764" Parameter: C <- "-38.764" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2693 TOTAL ENERGY = -67.379 RDTITL> * VAN DER WAALS = -28.615 ELECTROSTATIC = -38.764 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2693" Parameter: CONF_N -> "8002" Comparing "2693" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2694" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761205 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756688 ATOM PAIRS WERE FOUND FOR ATOM LIST 41532 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29120 from a total of 756688 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2694 -74.88612 7.50717 0.73332 INTE EXTERN> -25.21551 -49.67061 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8861" Parameter: A <- "-74.8861" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2155" Parameter: B <- "-25.2155" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6706" Parameter: C <- "-49.6706" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2694 TOTAL ENERGY = -74.8861 RDTITL> * VAN DER WAALS = -25.2155 ELECTROSTATIC = -49.6706 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2694" Parameter: CONF_N -> "8002" Comparing "2694" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2695" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756688 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757756 ATOM PAIRS WERE FOUND FOR ATOM LIST 41750 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30072 from a total of 757756 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2695 -73.38274 -1.50338 0.69824 INTE EXTERN> -28.34090 -45.04184 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3827" Parameter: A <- "-73.3827" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3409" Parameter: B <- "-28.3409" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0418" Parameter: C <- "-45.0418" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2695 TOTAL ENERGY = -73.3827 RDTITL> * VAN DER WAALS = -28.3409 ELECTROSTATIC = -45.0418 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2695" Parameter: CONF_N -> "8002" Comparing "2695" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2696" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757756 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757296 ATOM PAIRS WERE FOUND FOR ATOM LIST 41608 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29532 from a total of 757296 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2696 -74.64320 1.26046 0.67229 INTE EXTERN> -30.77523 -43.86797 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6432" Parameter: A <- "-74.6432" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7752" Parameter: B <- "-30.7752" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.868" Parameter: C <- "-43.868" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2696 TOTAL ENERGY = -74.6432 RDTITL> * VAN DER WAALS = -30.7752 ELECTROSTATIC = -43.868 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2696" Parameter: CONF_N -> "8002" Comparing "2696" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2697" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757296 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749371 ATOM PAIRS WERE FOUND FOR ATOM LIST 41126 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29375 from a total of 749371 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2697 -77.72093 3.07774 0.74852 INTE EXTERN> -30.06654 -47.65440 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7209" Parameter: A <- "-77.7209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0665" Parameter: B <- "-30.0665" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6544" Parameter: C <- "-47.6544" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2697 TOTAL ENERGY = -77.7209 RDTITL> * VAN DER WAALS = -30.0665 ELECTROSTATIC = -47.6544 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2697" Parameter: CONF_N -> "8002" Comparing "2697" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2698" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749371 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759451 ATOM PAIRS WERE FOUND FOR ATOM LIST 41748 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29832 from a total of 759451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2698 -66.58716 -11.13377 0.79828 INTE EXTERN> -25.08080 -41.50636 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5872" Parameter: A <- "-66.5872" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0808" Parameter: B <- "-25.0808" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5064" Parameter: C <- "-41.5064" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2698 TOTAL ENERGY = -66.5872 RDTITL> * VAN DER WAALS = -25.0808 ELECTROSTATIC = -41.5064 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2698" Parameter: CONF_N -> "8002" Comparing "2698" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2699" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753737 ATOM PAIRS WERE FOUND FOR ATOM LIST 41702 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29498 from a total of 753737 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2699 -69.76526 3.17810 0.71511 INTE EXTERN> -27.36982 -42.39545 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7653" Parameter: A <- "-69.7653" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3698" Parameter: B <- "-27.3698" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3954" Parameter: C <- "-42.3954" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2699 TOTAL ENERGY = -69.7653 RDTITL> * VAN DER WAALS = -27.3698 ELECTROSTATIC = -42.3954 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2699" Parameter: CONF_N -> "8002" Comparing "2699" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2700" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753737 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751410 ATOM PAIRS WERE FOUND FOR ATOM LIST 41322 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29777 from a total of 751410 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2700 -60.98204 -8.78322 0.58880 INTE EXTERN> -28.93246 -32.04957 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.982" Parameter: A <- "-60.982" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9325" Parameter: B <- "-28.9325" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.0496" Parameter: C <- "-32.0496" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2700 TOTAL ENERGY = -60.982 RDTITL> * VAN DER WAALS = -28.9325 ELECTROSTATIC = -32.0496 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2700" Parameter: CONF_N -> "8002" Comparing "2700" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2701" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751410 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755474 ATOM PAIRS WERE FOUND FOR ATOM LIST 41527 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30201 from a total of 755474 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2701 -68.42784 7.44580 0.60036 INTE EXTERN> -30.04976 -38.37808 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4278" Parameter: A <- "-68.4278" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0498" Parameter: B <- "-30.0498" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3781" Parameter: C <- "-38.3781" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2701 TOTAL ENERGY = -68.4278 RDTITL> * VAN DER WAALS = -30.0498 ELECTROSTATIC = -38.3781 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2701" Parameter: CONF_N -> "8002" Comparing "2701" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2702" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755474 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758108 ATOM PAIRS WERE FOUND FOR ATOM LIST 41713 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30287 from a total of 758108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2702 -73.25378 4.82594 0.64134 INTE EXTERN> -29.99379 -43.26000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2538" Parameter: A <- "-73.2538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9938" Parameter: B <- "-29.9938" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.26" Parameter: C <- "-43.26" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2702 TOTAL ENERGY = -73.2538 RDTITL> * VAN DER WAALS = -29.9938 ELECTROSTATIC = -43.26 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2702" Parameter: CONF_N -> "8002" Comparing "2702" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2703" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755336 ATOM PAIRS WERE FOUND FOR ATOM LIST 41557 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30373 from a total of 755336 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2703 -72.99424 -0.25954 0.61866 INTE EXTERN> -32.32280 -40.67144 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9942" Parameter: A <- "-72.9942" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3228" Parameter: B <- "-32.3228" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6714" Parameter: C <- "-40.6714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2703 TOTAL ENERGY = -72.9942 RDTITL> * VAN DER WAALS = -32.3228 ELECTROSTATIC = -40.6714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2703" Parameter: CONF_N -> "8002" Comparing "2703" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2704" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755336 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760508 ATOM PAIRS WERE FOUND FOR ATOM LIST 41653 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29983 from a total of 760508 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2704 -76.87191 3.87767 0.60002 INTE EXTERN> -31.87957 -44.99234 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8719" Parameter: A <- "-76.8719" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8796" Parameter: B <- "-31.8796" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9923" Parameter: C <- "-44.9923" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2704 TOTAL ENERGY = -76.8719 RDTITL> * VAN DER WAALS = -31.8796 ELECTROSTATIC = -44.9923 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2704" Parameter: CONF_N -> "8002" Comparing "2704" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2705" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760508 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753916 ATOM PAIRS WERE FOUND FOR ATOM LIST 41329 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29688 from a total of 753916 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2705 -76.08410 -0.78781 0.60231 INTE EXTERN> -32.20636 -43.87774 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0841" Parameter: A <- "-76.0841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2064" Parameter: B <- "-32.2064" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8777" Parameter: C <- "-43.8777" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2705 TOTAL ENERGY = -76.0841 RDTITL> * VAN DER WAALS = -32.2064 ELECTROSTATIC = -43.8777 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2705" Parameter: CONF_N -> "8002" Comparing "2705" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2706" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753916 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760180 ATOM PAIRS WERE FOUND FOR ATOM LIST 41810 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29652 from a total of 760180 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2706 -76.90129 0.81720 0.60921 INTE EXTERN> -31.78297 -45.11832 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9013" Parameter: A <- "-76.9013" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.783" Parameter: B <- "-31.783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1183" Parameter: C <- "-45.1183" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2706 TOTAL ENERGY = -76.9013 RDTITL> * VAN DER WAALS = -31.783 ELECTROSTATIC = -45.1183 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2706" Parameter: CONF_N -> "8002" Comparing "2706" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2707" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760180 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755278 ATOM PAIRS WERE FOUND FOR ATOM LIST 41557 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29878 from a total of 755278 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2707 -67.66766 -9.23363 0.57502 INTE EXTERN> -31.85757 -35.81009 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6677" Parameter: A <- "-67.6677" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8576" Parameter: B <- "-31.8576" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8101" Parameter: C <- "-35.8101" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2707 TOTAL ENERGY = -67.6677 RDTITL> * VAN DER WAALS = -31.8576 ELECTROSTATIC = -35.8101 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2707" Parameter: CONF_N -> "8002" Comparing "2707" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2708" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755278 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756390 ATOM PAIRS WERE FOUND FOR ATOM LIST 41604 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30030 from a total of 756390 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2708 -67.73145 0.06379 0.62302 INTE EXTERN> -29.44447 -38.28698 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7315" Parameter: A <- "-67.7315" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4445" Parameter: B <- "-29.4445" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.287" Parameter: C <- "-38.287" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2708 TOTAL ENERGY = -67.7315 RDTITL> * VAN DER WAALS = -29.4445 ELECTROSTATIC = -38.287 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2708" Parameter: CONF_N -> "8002" Comparing "2708" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2709" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756390 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755669 ATOM PAIRS WERE FOUND FOR ATOM LIST 41733 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30047 from a total of 755669 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2709 -70.96075 3.22930 0.60549 INTE EXTERN> -30.01750 -40.94326 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9608" Parameter: A <- "-70.9608" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0175" Parameter: B <- "-30.0175" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9433" Parameter: C <- "-40.9433" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2709 TOTAL ENERGY = -70.9608 RDTITL> * VAN DER WAALS = -30.0175 ELECTROSTATIC = -40.9433 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2709" Parameter: CONF_N -> "8002" Comparing "2709" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2710" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755669 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755924 ATOM PAIRS WERE FOUND FOR ATOM LIST 41418 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30260 from a total of 755924 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2710 -73.94738 2.98663 0.64204 INTE EXTERN> -29.90587 -44.04151 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9474" Parameter: A <- "-73.9474" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9059" Parameter: B <- "-29.9059" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0415" Parameter: C <- "-44.0415" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2710 TOTAL ENERGY = -73.9474 RDTITL> * VAN DER WAALS = -29.9059 ELECTROSTATIC = -44.0415 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2710" Parameter: CONF_N -> "8002" Comparing "2710" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2711" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755924 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755942 ATOM PAIRS WERE FOUND FOR ATOM LIST 41663 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29579 from a total of 755942 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2711 -70.43092 -3.51646 0.58985 INTE EXTERN> -31.61413 -38.81679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4309" Parameter: A <- "-70.4309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6141" Parameter: B <- "-31.6141" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8168" Parameter: C <- "-38.8168" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2711 TOTAL ENERGY = -70.4309 RDTITL> * VAN DER WAALS = -31.6141 ELECTROSTATIC = -38.8168 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2711" Parameter: CONF_N -> "8002" Comparing "2711" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2712" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755942 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755844 ATOM PAIRS WERE FOUND FOR ATOM LIST 41478 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29929 from a total of 755844 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2712 -65.80450 -4.62642 0.65801 INTE EXTERN> -27.41689 -38.38761 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8045" Parameter: A <- "-65.8045" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4169" Parameter: B <- "-27.4169" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3876" Parameter: C <- "-38.3876" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2712 TOTAL ENERGY = -65.8045 RDTITL> * VAN DER WAALS = -27.4169 ELECTROSTATIC = -38.3876 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2712" Parameter: CONF_N -> "8002" Comparing "2712" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2713" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755844 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756533 ATOM PAIRS WERE FOUND FOR ATOM LIST 41471 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29906 from a total of 756533 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2713 -64.06547 -1.73903 0.58603 INTE EXTERN> -30.96420 -33.10127 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0655" Parameter: A <- "-64.0655" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9642" Parameter: B <- "-30.9642" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1013" Parameter: C <- "-33.1013" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2713 TOTAL ENERGY = -64.0655 RDTITL> * VAN DER WAALS = -30.9642 ELECTROSTATIC = -33.1013 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2713" Parameter: CONF_N -> "8002" Comparing "2713" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2714" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756533 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752218 ATOM PAIRS WERE FOUND FOR ATOM LIST 41294 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30021 from a total of 752218 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2714 -62.60380 -1.46167 0.58302 INTE EXTERN> -28.80117 -33.80264 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.6038" Parameter: A <- "-62.6038" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8012" Parameter: B <- "-28.8012" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8026" Parameter: C <- "-33.8026" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2714 TOTAL ENERGY = -62.6038 RDTITL> * VAN DER WAALS = -28.8012 ELECTROSTATIC = -33.8026 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2714" Parameter: CONF_N -> "8002" Comparing "2714" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2715" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752218 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753167 ATOM PAIRS WERE FOUND FOR ATOM LIST 41420 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30163 from a total of 753167 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2715 -62.30907 -0.29473 0.51938 INTE EXTERN> -30.93809 -31.37098 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3091" Parameter: A <- "-62.3091" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9381" Parameter: B <- "-30.9381" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.371" Parameter: C <- "-31.371" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2715 TOTAL ENERGY = -62.3091 RDTITL> * VAN DER WAALS = -30.9381 ELECTROSTATIC = -31.371 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2715" Parameter: CONF_N -> "8002" Comparing "2715" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2716" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753167 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762429 ATOM PAIRS WERE FOUND FOR ATOM LIST 41865 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29906 from a total of 762429 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2716 -68.67146 6.36239 0.60704 INTE EXTERN> -31.00725 -37.66421 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6715" Parameter: A <- "-68.6715" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0073" Parameter: B <- "-31.0073" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6642" Parameter: C <- "-37.6642" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2716 TOTAL ENERGY = -68.6715 RDTITL> * VAN DER WAALS = -31.0073 ELECTROSTATIC = -37.6642 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2716" Parameter: CONF_N -> "8002" Comparing "2716" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2717" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762429 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755831 ATOM PAIRS WERE FOUND FOR ATOM LIST 41630 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30004 from a total of 755831 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2717 -63.58155 -5.08991 0.63073 INTE EXTERN> -29.55586 -34.02568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5815" Parameter: A <- "-63.5815" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5559" Parameter: B <- "-29.5559" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.0257" Parameter: C <- "-34.0257" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2717 TOTAL ENERGY = -63.5815 RDTITL> * VAN DER WAALS = -29.5559 ELECTROSTATIC = -34.0257 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2717" Parameter: CONF_N -> "8002" Comparing "2717" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2718" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755831 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758401 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29909 from a total of 758401 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2718 -66.92039 3.33884 0.64583 INTE EXTERN> -28.70237 -38.21801 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9204" Parameter: A <- "-66.9204" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7024" Parameter: B <- "-28.7024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.218" Parameter: C <- "-38.218" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2718 TOTAL ENERGY = -66.9204 RDTITL> * VAN DER WAALS = -28.7024 ELECTROSTATIC = -38.218 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2718" Parameter: CONF_N -> "8002" Comparing "2718" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2719" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758401 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763443 ATOM PAIRS WERE FOUND FOR ATOM LIST 41986 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30432 from a total of 763443 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2719 -69.32661 2.40622 0.61962 INTE EXTERN> -29.97786 -39.34875 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3266" Parameter: A <- "-69.3266" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9779" Parameter: B <- "-29.9779" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3487" Parameter: C <- "-39.3487" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2719 TOTAL ENERGY = -69.3266 RDTITL> * VAN DER WAALS = -29.9779 ELECTROSTATIC = -39.3487 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2719" Parameter: CONF_N -> "8002" Comparing "2719" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2720" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763443 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763537 ATOM PAIRS WERE FOUND FOR ATOM LIST 42146 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30487 from a total of 763537 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2720 -61.75410 -7.57251 0.79820 INTE EXTERN> -21.11695 -40.63715 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.7541" Parameter: A <- "-61.7541" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.117" Parameter: B <- "-21.117" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6371" Parameter: C <- "-40.6371" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2720 TOTAL ENERGY = -61.7541 RDTITL> * VAN DER WAALS = -21.117 ELECTROSTATIC = -40.6371 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2720" Parameter: CONF_N -> "8002" Comparing "2720" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2721" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763537 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758262 ATOM PAIRS WERE FOUND FOR ATOM LIST 41754 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29920 from a total of 758262 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2721 -66.93864 5.18454 0.70814 INTE EXTERN> -28.28429 -38.65435 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9386" Parameter: A <- "-66.9386" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2843" Parameter: B <- "-28.2843" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6544" Parameter: C <- "-38.6544" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2721 TOTAL ENERGY = -66.9386 RDTITL> * VAN DER WAALS = -28.2843 ELECTROSTATIC = -38.6544 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2721" Parameter: CONF_N -> "8002" Comparing "2721" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2722" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758262 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755262 ATOM PAIRS WERE FOUND FOR ATOM LIST 41589 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29504 from a total of 755262 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2722 -58.37502 -8.56362 0.45503 INTE EXTERN> -33.64013 -24.73488 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.375" Parameter: A <- "-58.375" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6401" Parameter: B <- "-33.6401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-24.7349" Parameter: C <- "-24.7349" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2722 TOTAL ENERGY = -58.375 RDTITL> * VAN DER WAALS = -33.6401 ELECTROSTATIC = -24.7349 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2722" Parameter: CONF_N -> "8002" Comparing "2722" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2723" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755262 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755925 ATOM PAIRS WERE FOUND FOR ATOM LIST 41657 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30200 from a total of 755925 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2723 -62.64881 4.27379 0.62080 INTE EXTERN> -28.73577 -33.91304 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.6488" Parameter: A <- "-62.6488" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7358" Parameter: B <- "-28.7358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.913" Parameter: C <- "-33.913" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2723 TOTAL ENERGY = -62.6488 RDTITL> * VAN DER WAALS = -28.7358 ELECTROSTATIC = -33.913 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2723" Parameter: CONF_N -> "8002" Comparing "2723" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2724" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755925 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761379 ATOM PAIRS WERE FOUND FOR ATOM LIST 41613 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30266 from a total of 761379 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2724 -66.46832 3.81951 0.71761 INTE EXTERN> -24.73389 -41.73443 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4683" Parameter: A <- "-66.4683" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7339" Parameter: B <- "-24.7339" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7344" Parameter: C <- "-41.7344" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2724 TOTAL ENERGY = -66.4683 RDTITL> * VAN DER WAALS = -24.7339 ELECTROSTATIC = -41.7344 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2724" Parameter: CONF_N -> "8002" Comparing "2724" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2725" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761379 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761572 ATOM PAIRS WERE FOUND FOR ATOM LIST 41869 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30359 from a total of 761572 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2725 -62.02985 -4.43847 0.72750 INTE EXTERN> -24.47996 -37.54989 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.0299" Parameter: A <- "-62.0299" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.48" Parameter: B <- "-24.48" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5499" Parameter: C <- "-37.5499" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2725 TOTAL ENERGY = -62.0299 RDTITL> * VAN DER WAALS = -24.48 ELECTROSTATIC = -37.5499 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2725" Parameter: CONF_N -> "8002" Comparing "2725" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2726" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761572 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754640 ATOM PAIRS WERE FOUND FOR ATOM LIST 41742 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29743 from a total of 754640 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2726 -69.65323 7.62338 0.78545 INTE EXTERN> -25.92866 -43.72458 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6532" Parameter: A <- "-69.6532" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9287" Parameter: B <- "-25.9287" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7246" Parameter: C <- "-43.7246" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2726 TOTAL ENERGY = -69.6532 RDTITL> * VAN DER WAALS = -25.9287 ELECTROSTATIC = -43.7246 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2726" Parameter: CONF_N -> "8002" Comparing "2726" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2727" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754640 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760097 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30447 from a total of 760097 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2727 -68.69132 -0.96191 0.64068 INTE EXTERN> -29.11574 -39.57558 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6913" Parameter: A <- "-68.6913" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1157" Parameter: B <- "-29.1157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5756" Parameter: C <- "-39.5756" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2727 TOTAL ENERGY = -68.6913 RDTITL> * VAN DER WAALS = -29.1157 ELECTROSTATIC = -39.5756 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2727" Parameter: CONF_N -> "8002" Comparing "2727" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2728" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760097 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758426 ATOM PAIRS WERE FOUND FOR ATOM LIST 41834 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30022 from a total of 758426 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2728 -66.70886 -1.98246 0.60300 INTE EXTERN> -28.76965 -37.93921 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7089" Parameter: A <- "-66.7089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7696" Parameter: B <- "-28.7696" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9392" Parameter: C <- "-37.9392" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2728 TOTAL ENERGY = -66.7089 RDTITL> * VAN DER WAALS = -28.7696 ELECTROSTATIC = -37.9392 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2728" Parameter: CONF_N -> "8002" Comparing "2728" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2729" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758426 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759863 ATOM PAIRS WERE FOUND FOR ATOM LIST 41839 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30429 from a total of 759863 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2729 -67.69877 0.98992 0.79360 INTE EXTERN> -24.53305 -43.16573 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6988" Parameter: A <- "-67.6988" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.533" Parameter: B <- "-24.533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1657" Parameter: C <- "-43.1657" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2729 TOTAL ENERGY = -67.6988 RDTITL> * VAN DER WAALS = -24.533 ELECTROSTATIC = -43.1657 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2729" Parameter: CONF_N -> "8002" Comparing "2729" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2730" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759863 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763269 ATOM PAIRS WERE FOUND FOR ATOM LIST 41875 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30065 from a total of 763269 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2730 -65.29626 -2.40251 0.55508 INTE EXTERN> -31.22270 -34.07356 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2963" Parameter: A <- "-65.2963" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2227" Parameter: B <- "-31.2227" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.0736" Parameter: C <- "-34.0736" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2730 TOTAL ENERGY = -65.2963 RDTITL> * VAN DER WAALS = -31.2227 ELECTROSTATIC = -34.0736 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2730" Parameter: CONF_N -> "8002" Comparing "2730" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2731" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763269 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759453 ATOM PAIRS WERE FOUND FOR ATOM LIST 41734 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 759453 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2731 -62.44773 -2.84853 0.63467 INTE EXTERN> -31.51664 -30.93110 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.4477" Parameter: A <- "-62.4477" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5166" Parameter: B <- "-31.5166" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.9311" Parameter: C <- "-30.9311" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2731 TOTAL ENERGY = -62.4477 RDTITL> * VAN DER WAALS = -31.5166 ELECTROSTATIC = -30.9311 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2731" Parameter: CONF_N -> "8002" Comparing "2731" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2732" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759453 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761444 ATOM PAIRS WERE FOUND FOR ATOM LIST 41622 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30169 from a total of 761444 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2732 -66.53667 4.08893 0.64017 INTE EXTERN> -31.93676 -34.59991 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5367" Parameter: A <- "-66.5367" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9368" Parameter: B <- "-31.9368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5999" Parameter: C <- "-34.5999" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2732 TOTAL ENERGY = -66.5367 RDTITL> * VAN DER WAALS = -31.9368 ELECTROSTATIC = -34.5999 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2732" Parameter: CONF_N -> "8002" Comparing "2732" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2733" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761444 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41883 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29981 from a total of 760958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2733 -73.32245 6.78579 0.72047 INTE EXTERN> -28.28173 -45.04072 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3225" Parameter: A <- "-73.3225" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2817" Parameter: B <- "-28.2817" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0407" Parameter: C <- "-45.0407" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2733 TOTAL ENERGY = -73.3225 RDTITL> * VAN DER WAALS = -28.2817 ELECTROSTATIC = -45.0407 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2733" Parameter: CONF_N -> "8002" Comparing "2733" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2734" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757139 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29948 from a total of 757139 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2734 -65.51494 -7.80751 0.68763 INTE EXTERN> -24.92021 -40.59473 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5149" Parameter: A <- "-65.5149" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9202" Parameter: B <- "-24.9202" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5947" Parameter: C <- "-40.5947" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2734 TOTAL ENERGY = -65.5149 RDTITL> * VAN DER WAALS = -24.9202 ELECTROSTATIC = -40.5947 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2734" Parameter: CONF_N -> "8002" Comparing "2734" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2735" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757139 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762681 ATOM PAIRS WERE FOUND FOR ATOM LIST 41852 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30172 from a total of 762681 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2735 -62.52044 -2.99450 0.70625 INTE EXTERN> -24.61335 -37.90709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5204" Parameter: A <- "-62.5204" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6134" Parameter: B <- "-24.6134" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9071" Parameter: C <- "-37.9071" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2735 TOTAL ENERGY = -62.5204 RDTITL> * VAN DER WAALS = -24.6134 ELECTROSTATIC = -37.9071 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2735" Parameter: CONF_N -> "8002" Comparing "2735" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2736" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762681 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755712 ATOM PAIRS WERE FOUND FOR ATOM LIST 41744 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29842 from a total of 755712 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2736 -67.52016 4.99972 0.59241 INTE EXTERN> -30.16749 -37.35267 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5202" Parameter: A <- "-67.5202" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1675" Parameter: B <- "-30.1675" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3527" Parameter: C <- "-37.3527" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2736 TOTAL ENERGY = -67.5202 RDTITL> * VAN DER WAALS = -30.1675 ELECTROSTATIC = -37.3527 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2736" Parameter: CONF_N -> "8002" Comparing "2736" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2737" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755712 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762528 ATOM PAIRS WERE FOUND FOR ATOM LIST 41925 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30200 from a total of 762528 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2737 -69.58282 2.06266 0.72190 INTE EXTERN> -25.04246 -44.54037 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5828" Parameter: A <- "-69.5828" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0425" Parameter: B <- "-25.0425" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5404" Parameter: C <- "-44.5404" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2737 TOTAL ENERGY = -69.5828 RDTITL> * VAN DER WAALS = -25.0425 ELECTROSTATIC = -44.5404 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2737" Parameter: CONF_N -> "8002" Comparing "2737" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2738" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762528 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762939 ATOM PAIRS WERE FOUND FOR ATOM LIST 41830 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30663 from a total of 762939 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2738 -65.37986 -4.20296 0.61161 INTE EXTERN> -29.95758 -35.42228 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3799" Parameter: A <- "-65.3799" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9576" Parameter: B <- "-29.9576" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4223" Parameter: C <- "-35.4223" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2738 TOTAL ENERGY = -65.3799 RDTITL> * VAN DER WAALS = -29.9576 ELECTROSTATIC = -35.4223 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2738" Parameter: CONF_N -> "8002" Comparing "2738" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2739" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762939 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762774 ATOM PAIRS WERE FOUND FOR ATOM LIST 41934 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30537 from a total of 762774 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2739 -63.95600 -1.42387 0.73231 INTE EXTERN> -27.25846 -36.69753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.956" Parameter: A <- "-63.956" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2585" Parameter: B <- "-27.2585" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6975" Parameter: C <- "-36.6975" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2739 TOTAL ENERGY = -63.956 RDTITL> * VAN DER WAALS = -27.2585 ELECTROSTATIC = -36.6975 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2739" Parameter: CONF_N -> "8002" Comparing "2739" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2740" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762774 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765650 ATOM PAIRS WERE FOUND FOR ATOM LIST 42081 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30654 from a total of 765650 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2740 -58.13991 -5.81609 0.54004 INTE EXTERN> -30.81637 -27.32354 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.1399" Parameter: A <- "-58.1399" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8164" Parameter: B <- "-30.8164" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.3235" Parameter: C <- "-27.3235" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2740 TOTAL ENERGY = -58.1399 RDTITL> * VAN DER WAALS = -30.8164 ELECTROSTATIC = -27.3235 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2740" Parameter: CONF_N -> "8002" Comparing "2740" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2741" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765650 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760696 ATOM PAIRS WERE FOUND FOR ATOM LIST 41944 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30616 from a total of 760696 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2741 -63.37874 5.23882 0.58160 INTE EXTERN> -31.97393 -31.40481 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3787" Parameter: A <- "-63.3787" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9739" Parameter: B <- "-31.9739" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4048" Parameter: C <- "-31.4048" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2741 TOTAL ENERGY = -63.3787 RDTITL> * VAN DER WAALS = -31.9739 ELECTROSTATIC = -31.4048 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2741" Parameter: CONF_N -> "8002" Comparing "2741" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2742" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760696 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762228 ATOM PAIRS WERE FOUND FOR ATOM LIST 41945 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30546 from a total of 762228 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2742 -69.86640 6.48766 0.69392 INTE EXTERN> -28.88219 -40.98421 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8664" Parameter: A <- "-69.8664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8822" Parameter: B <- "-28.8822" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9842" Parameter: C <- "-40.9842" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2742 TOTAL ENERGY = -69.8664 RDTITL> * VAN DER WAALS = -28.8822 ELECTROSTATIC = -40.9842 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2742" Parameter: CONF_N -> "8002" Comparing "2742" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2743" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762228 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770064 ATOM PAIRS WERE FOUND FOR ATOM LIST 42235 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30893 from a total of 770064 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2743 -68.15639 -1.71001 0.78869 INTE EXTERN> -24.60953 -43.54686 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1564" Parameter: A <- "-68.1564" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6095" Parameter: B <- "-24.6095" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5469" Parameter: C <- "-43.5469" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2743 TOTAL ENERGY = -68.1564 RDTITL> * VAN DER WAALS = -24.6095 ELECTROSTATIC = -43.5469 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2743" Parameter: CONF_N -> "8002" Comparing "2743" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2744" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770064 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753684 ATOM PAIRS WERE FOUND FOR ATOM LIST 41632 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30422 from a total of 753684 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2744 -64.94583 -3.21056 0.76735 INTE EXTERN> -25.09118 -39.85464 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9458" Parameter: A <- "-64.9458" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0912" Parameter: B <- "-25.0912" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8546" Parameter: C <- "-39.8546" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2744 TOTAL ENERGY = -64.9458 RDTITL> * VAN DER WAALS = -25.0912 ELECTROSTATIC = -39.8546 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2744" Parameter: CONF_N -> "8002" Comparing "2744" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2745" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753684 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758918 ATOM PAIRS WERE FOUND FOR ATOM LIST 41809 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30567 from a total of 758918 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2745 -59.59794 -5.34789 0.56996 INTE EXTERN> -30.28919 -29.30876 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.5979" Parameter: A <- "-59.5979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2892" Parameter: B <- "-30.2892" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.3088" Parameter: C <- "-29.3088" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2745 TOTAL ENERGY = -59.5979 RDTITL> * VAN DER WAALS = -30.2892 ELECTROSTATIC = -29.3088 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2745" Parameter: CONF_N -> "8002" Comparing "2745" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2746" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758918 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762949 ATOM PAIRS WERE FOUND FOR ATOM LIST 41879 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30316 from a total of 762949 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2746 -66.60330 7.00536 0.66972 INTE EXTERN> -31.88553 -34.71777 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6033" Parameter: A <- "-66.6033" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8855" Parameter: B <- "-31.8855" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7178" Parameter: C <- "-34.7178" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2746 TOTAL ENERGY = -66.6033 RDTITL> * VAN DER WAALS = -31.8855 ELECTROSTATIC = -34.7178 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2746" Parameter: CONF_N -> "8002" Comparing "2746" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2747" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762949 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763961 ATOM PAIRS WERE FOUND FOR ATOM LIST 42003 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30278 from a total of 763961 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2747 -67.91024 1.30694 0.67327 INTE EXTERN> -30.13728 -37.77296 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9102" Parameter: A <- "-67.9102" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1373" Parameter: B <- "-30.1373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.773" Parameter: C <- "-37.773" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2747 TOTAL ENERGY = -67.9102 RDTITL> * VAN DER WAALS = -30.1373 ELECTROSTATIC = -37.773 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2747" Parameter: CONF_N -> "8002" Comparing "2747" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2748" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763961 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758199 ATOM PAIRS WERE FOUND FOR ATOM LIST 41600 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29627 from a total of 758199 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2748 -60.67273 -7.23752 0.53033 INTE EXTERN> -29.33511 -31.33761 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.6727" Parameter: A <- "-60.6727" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3351" Parameter: B <- "-29.3351" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.3376" Parameter: C <- "-31.3376" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2748 TOTAL ENERGY = -60.6727 RDTITL> * VAN DER WAALS = -29.3351 ELECTROSTATIC = -31.3376 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2748" Parameter: CONF_N -> "8002" Comparing "2748" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2749" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758199 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760791 ATOM PAIRS WERE FOUND FOR ATOM LIST 41689 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29532 from a total of 760791 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2749 -68.49464 7.82191 0.52850 INTE EXTERN> -34.03285 -34.46178 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4946" Parameter: A <- "-68.4946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0329" Parameter: B <- "-34.0329" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4618" Parameter: C <- "-34.4618" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2749 TOTAL ENERGY = -68.4946 RDTITL> * VAN DER WAALS = -34.0329 ELECTROSTATIC = -34.4618 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2749" Parameter: CONF_N -> "8002" Comparing "2749" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2750" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760791 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763365 ATOM PAIRS WERE FOUND FOR ATOM LIST 41952 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30599 from a total of 763365 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2750 -59.93446 -8.56018 0.65308 INTE EXTERN> -25.09686 -34.83760 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.9345" Parameter: A <- "-59.9345" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0969" Parameter: B <- "-25.0969" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8376" Parameter: C <- "-34.8376" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2750 TOTAL ENERGY = -59.9345 RDTITL> * VAN DER WAALS = -25.0969 ELECTROSTATIC = -34.8376 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2750" Parameter: CONF_N -> "8002" Comparing "2750" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2751" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763365 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763182 ATOM PAIRS WERE FOUND FOR ATOM LIST 41982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30638 from a total of 763182 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2751 -65.02156 5.08711 0.59465 INTE EXTERN> -30.87156 -34.15000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0216" Parameter: A <- "-65.0216" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8716" Parameter: B <- "-30.8716" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.15" Parameter: C <- "-34.15" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2751 TOTAL ENERGY = -65.0216 RDTITL> * VAN DER WAALS = -30.8716 ELECTROSTATIC = -34.15 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2751" Parameter: CONF_N -> "8002" Comparing "2751" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2752" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763182 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755813 ATOM PAIRS WERE FOUND FOR ATOM LIST 41611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30148 from a total of 755813 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2752 -71.70195 6.68039 0.66472 INTE EXTERN> -29.80984 -41.89211 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.702" Parameter: A <- "-71.702" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8098" Parameter: B <- "-29.8098" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8921" Parameter: C <- "-41.8921" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2752 TOTAL ENERGY = -71.702 RDTITL> * VAN DER WAALS = -29.8098 ELECTROSTATIC = -41.8921 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2752" Parameter: CONF_N -> "8002" Comparing "2752" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2753" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755813 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757930 ATOM PAIRS WERE FOUND FOR ATOM LIST 41633 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30502 from a total of 757930 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2753 -65.44200 -6.25995 0.55459 INTE EXTERN> -30.31795 -35.12405 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.442" Parameter: A <- "-65.442" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.318" Parameter: B <- "-30.318" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1241" Parameter: C <- "-35.1241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2753 TOTAL ENERGY = -65.442 RDTITL> * VAN DER WAALS = -30.318 ELECTROSTATIC = -35.1241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2753" Parameter: CONF_N -> "8002" Comparing "2753" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2754" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757930 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754103 ATOM PAIRS WERE FOUND FOR ATOM LIST 41228 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29657 from a total of 754103 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2754 -65.30988 -0.13213 0.55915 INTE EXTERN> -32.84665 -32.46323 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3099" Parameter: A <- "-65.3099" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8466" Parameter: B <- "-32.8466" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.4632" Parameter: C <- "-32.4632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2754 TOTAL ENERGY = -65.3099 RDTITL> * VAN DER WAALS = -32.8466 ELECTROSTATIC = -32.4632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2754" Parameter: CONF_N -> "8002" Comparing "2754" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2755" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754103 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759914 ATOM PAIRS WERE FOUND FOR ATOM LIST 41804 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30111 from a total of 759914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2755 -68.11554 2.80566 0.65949 INTE EXTERN> -29.41213 -38.70341 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1155" Parameter: A <- "-68.1155" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4121" Parameter: B <- "-29.4121" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7034" Parameter: C <- "-38.7034" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2755 TOTAL ENERGY = -68.1155 RDTITL> * VAN DER WAALS = -29.4121 ELECTROSTATIC = -38.7034 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2755" Parameter: CONF_N -> "8002" Comparing "2755" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2756" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758820 ATOM PAIRS WERE FOUND FOR ATOM LIST 41780 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30053 from a total of 758820 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2756 -76.43189 8.31635 0.61568 INTE EXTERN> -34.04791 -42.38398 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4319" Parameter: A <- "-76.4319" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0479" Parameter: B <- "-34.0479" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.384" Parameter: C <- "-42.384" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2756 TOTAL ENERGY = -76.4319 RDTITL> * VAN DER WAALS = -34.0479 ELECTROSTATIC = -42.384 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2756" Parameter: CONF_N -> "8002" Comparing "2756" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2757" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758820 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763104 ATOM PAIRS WERE FOUND FOR ATOM LIST 41952 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30280 from a total of 763104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2757 -60.59230 -15.83959 0.50341 INTE EXTERN> -31.91681 -28.67550 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.5923" Parameter: A <- "-60.5923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9168" Parameter: B <- "-31.9168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.6755" Parameter: C <- "-28.6755" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2757 TOTAL ENERGY = -60.5923 RDTITL> * VAN DER WAALS = -31.9168 ELECTROSTATIC = -28.6755 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2757" Parameter: CONF_N -> "8002" Comparing "2757" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2758" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756202 ATOM PAIRS WERE FOUND FOR ATOM LIST 41458 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29882 from a total of 756202 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2758 -62.96091 2.36860 0.56586 INTE EXTERN> -30.87181 -32.08910 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9609" Parameter: A <- "-62.9609" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8718" Parameter: B <- "-30.8718" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.0891" Parameter: C <- "-32.0891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2758 TOTAL ENERGY = -62.9609 RDTITL> * VAN DER WAALS = -30.8718 ELECTROSTATIC = -32.0891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2758" Parameter: CONF_N -> "8002" Comparing "2758" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2759" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756202 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757798 ATOM PAIRS WERE FOUND FOR ATOM LIST 41405 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30205 from a total of 757798 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2759 -61.78259 -1.17832 0.61357 INTE EXTERN> -27.92788 -33.85471 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.7826" Parameter: A <- "-61.7826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9279" Parameter: B <- "-27.9279" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8547" Parameter: C <- "-33.8547" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2759 TOTAL ENERGY = -61.7826 RDTITL> * VAN DER WAALS = -27.9279 ELECTROSTATIC = -33.8547 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2759" Parameter: CONF_N -> "8002" Comparing "2759" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2760" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757798 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759471 ATOM PAIRS WERE FOUND FOR ATOM LIST 41685 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30170 from a total of 759471 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2760 -73.16015 11.37756 0.63796 INTE EXTERN> -31.94419 -41.21596 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1601" Parameter: A <- "-73.1601" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9442" Parameter: B <- "-31.9442" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.216" Parameter: C <- "-41.216" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2760 TOTAL ENERGY = -73.1601 RDTITL> * VAN DER WAALS = -31.9442 ELECTROSTATIC = -41.216 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2760" Parameter: CONF_N -> "8002" Comparing "2760" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2761" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759471 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761385 ATOM PAIRS WERE FOUND FOR ATOM LIST 41653 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30160 from a total of 761385 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2761 -62.71625 -10.44390 0.49395 INTE EXTERN> -33.59313 -29.12312 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7163" Parameter: A <- "-62.7163" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5931" Parameter: B <- "-33.5931" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.1231" Parameter: C <- "-29.1231" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2761 TOTAL ENERGY = -62.7163 RDTITL> * VAN DER WAALS = -33.5931 ELECTROSTATIC = -29.1231 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2761" Parameter: CONF_N -> "8002" Comparing "2761" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2762" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761385 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761967 ATOM PAIRS WERE FOUND FOR ATOM LIST 41690 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30247 from a total of 761967 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2762 -62.75605 0.03980 0.44158 INTE EXTERN> -35.96209 -26.79397 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7561" Parameter: A <- "-62.7561" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.9621" Parameter: B <- "-35.9621" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-26.794" Parameter: C <- "-26.794" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2762 TOTAL ENERGY = -62.7561 RDTITL> * VAN DER WAALS = -35.9621 ELECTROSTATIC = -26.794 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2762" Parameter: CONF_N -> "8002" Comparing "2762" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2763" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761967 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758579 ATOM PAIRS WERE FOUND FOR ATOM LIST 41367 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30174 from a total of 758579 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2763 -72.76670 10.01065 0.62964 INTE EXTERN> -30.91516 -41.85154 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7667" Parameter: A <- "-72.7667" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9152" Parameter: B <- "-30.9152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8515" Parameter: C <- "-41.8515" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2763 TOTAL ENERGY = -72.7667 RDTITL> * VAN DER WAALS = -30.9152 ELECTROSTATIC = -41.8515 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2763" Parameter: CONF_N -> "8002" Comparing "2763" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2764" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758579 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756593 ATOM PAIRS WERE FOUND FOR ATOM LIST 41433 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30438 from a total of 756593 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2764 -59.94678 -12.81992 0.58108 INTE EXTERN> -28.93129 -31.01549 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.9468" Parameter: A <- "-59.9468" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9313" Parameter: B <- "-28.9313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.0155" Parameter: C <- "-31.0155" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2764 TOTAL ENERGY = -59.9468 RDTITL> * VAN DER WAALS = -28.9313 ELECTROSTATIC = -31.0155 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2764" Parameter: CONF_N -> "8002" Comparing "2764" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2765" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756593 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762130 ATOM PAIRS WERE FOUND FOR ATOM LIST 41636 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30387 from a total of 762130 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2765 -65.69217 5.74539 0.60414 INTE EXTERN> -30.80078 -34.89139 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6922" Parameter: A <- "-65.6922" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8008" Parameter: B <- "-30.8008" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8914" Parameter: C <- "-34.8914" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2765 TOTAL ENERGY = -65.6922 RDTITL> * VAN DER WAALS = -30.8008 ELECTROSTATIC = -34.8914 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2765" Parameter: CONF_N -> "8002" Comparing "2765" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2766" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762130 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762943 ATOM PAIRS WERE FOUND FOR ATOM LIST 41906 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30249 from a total of 762943 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2766 -73.94013 8.24795 0.68615 INTE EXTERN> -28.73222 -45.20791 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9401" Parameter: A <- "-73.9401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7322" Parameter: B <- "-28.7322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2079" Parameter: C <- "-45.2079" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2766 TOTAL ENERGY = -73.9401 RDTITL> * VAN DER WAALS = -28.7322 ELECTROSTATIC = -45.2079 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2766" Parameter: CONF_N -> "8002" Comparing "2766" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2767" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762943 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761566 ATOM PAIRS WERE FOUND FOR ATOM LIST 41667 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30329 from a total of 761566 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2767 -70.80415 -3.13598 0.56968 INTE EXTERN> -32.44633 -38.35782 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8041" Parameter: A <- "-70.8041" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4463" Parameter: B <- "-32.4463" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3578" Parameter: C <- "-38.3578" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2767 TOTAL ENERGY = -70.8041 RDTITL> * VAN DER WAALS = -32.4463 ELECTROSTATIC = -38.3578 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2767" Parameter: CONF_N -> "8002" Comparing "2767" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2768" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761566 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758451 ATOM PAIRS WERE FOUND FOR ATOM LIST 41486 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29772 from a total of 758451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2768 -67.34809 -3.45605 0.70373 INTE EXTERN> -28.44717 -38.90092 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3481" Parameter: A <- "-67.3481" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4472" Parameter: B <- "-28.4472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9009" Parameter: C <- "-38.9009" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2768 TOTAL ENERGY = -67.3481 RDTITL> * VAN DER WAALS = -28.4472 ELECTROSTATIC = -38.9009 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2768" Parameter: CONF_N -> "8002" Comparing "2768" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2769" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758649 ATOM PAIRS WERE FOUND FOR ATOM LIST 41537 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29954 from a total of 758649 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2769 -64.12371 -3.22438 0.63658 INTE EXTERN> -27.69684 -36.42687 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1237" Parameter: A <- "-64.1237" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6968" Parameter: B <- "-27.6968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4269" Parameter: C <- "-36.4269" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2769 TOTAL ENERGY = -64.1237 RDTITL> * VAN DER WAALS = -27.6968 ELECTROSTATIC = -36.4269 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2769" Parameter: CONF_N -> "8002" Comparing "2769" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2770" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758649 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763232 ATOM PAIRS WERE FOUND FOR ATOM LIST 42002 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30464 from a total of 763232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2770 -73.64572 9.52201 0.71621 INTE EXTERN> -28.44282 -45.20290 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6457" Parameter: A <- "-73.6457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4428" Parameter: B <- "-28.4428" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2029" Parameter: C <- "-45.2029" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2770 TOTAL ENERGY = -73.6457 RDTITL> * VAN DER WAALS = -28.4428 ELECTROSTATIC = -45.2029 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2770" Parameter: CONF_N -> "8002" Comparing "2770" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2771" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758109 ATOM PAIRS WERE FOUND FOR ATOM LIST 41586 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29723 from a total of 758109 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2771 -64.54728 -9.09844 0.58682 INTE EXTERN> -29.97631 -34.57098 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5473" Parameter: A <- "-64.5473" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9763" Parameter: B <- "-29.9763" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.571" Parameter: C <- "-34.571" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2771 TOTAL ENERGY = -64.5473 RDTITL> * VAN DER WAALS = -29.9763 ELECTROSTATIC = -34.571 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2771" Parameter: CONF_N -> "8002" Comparing "2771" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2772" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758109 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760602 ATOM PAIRS WERE FOUND FOR ATOM LIST 41716 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30483 from a total of 760602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2772 -71.54338 6.99609 0.70251 INTE EXTERN> -28.35905 -43.18433 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5434" Parameter: A <- "-71.5434" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.359" Parameter: B <- "-28.359" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1843" Parameter: C <- "-43.1843" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2772 TOTAL ENERGY = -71.5434 RDTITL> * VAN DER WAALS = -28.359 ELECTROSTATIC = -43.1843 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2772" Parameter: CONF_N -> "8002" Comparing "2772" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2773" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760077 ATOM PAIRS WERE FOUND FOR ATOM LIST 41763 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30577 from a total of 760077 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2773 -68.06704 -3.47634 0.59609 INTE EXTERN> -29.37522 -38.69181 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.067" Parameter: A <- "-68.067" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3752" Parameter: B <- "-29.3752" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6918" Parameter: C <- "-38.6918" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2773 TOTAL ENERGY = -68.067 RDTITL> * VAN DER WAALS = -29.3752 ELECTROSTATIC = -38.6918 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2773" Parameter: CONF_N -> "8002" Comparing "2773" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2774" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760077 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765471 ATOM PAIRS WERE FOUND FOR ATOM LIST 42010 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30861 from a total of 765471 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2774 -66.30427 -1.76276 0.68305 INTE EXTERN> -26.81139 -39.49289 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3043" Parameter: A <- "-66.3043" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8114" Parameter: B <- "-26.8114" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4929" Parameter: C <- "-39.4929" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2774 TOTAL ENERGY = -66.3043 RDTITL> * VAN DER WAALS = -26.8114 ELECTROSTATIC = -39.4929 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2774" Parameter: CONF_N -> "8002" Comparing "2774" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2775" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765471 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765027 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30466 from a total of 765027 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2775 -68.79810 2.49382 0.66071 INTE EXTERN> -26.98227 -41.81583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7981" Parameter: A <- "-68.7981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9823" Parameter: B <- "-26.9823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8158" Parameter: C <- "-41.8158" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2775 TOTAL ENERGY = -68.7981 RDTITL> * VAN DER WAALS = -26.9823 ELECTROSTATIC = -41.8158 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2775" Parameter: CONF_N -> "8002" Comparing "2775" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2776" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765027 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764618 ATOM PAIRS WERE FOUND FOR ATOM LIST 42062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30549 from a total of 764618 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2776 -77.92155 9.12345 0.72402 INTE EXTERN> -28.83274 -49.08881 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9215" Parameter: A <- "-77.9215" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8327" Parameter: B <- "-28.8327" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0888" Parameter: C <- "-49.0888" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2776 TOTAL ENERGY = -77.9215 RDTITL> * VAN DER WAALS = -28.8327 ELECTROSTATIC = -49.0888 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2776" Parameter: CONF_N -> "8002" Comparing "2776" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2777" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764618 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41788 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30235 from a total of 760958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2777 -68.36281 -9.55873 0.64138 INTE EXTERN> -30.06602 -38.29679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3628" Parameter: A <- "-68.3628" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.066" Parameter: B <- "-30.066" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2968" Parameter: C <- "-38.2968" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2777 TOTAL ENERGY = -68.3628 RDTITL> * VAN DER WAALS = -30.066 ELECTROSTATIC = -38.2968 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2777" Parameter: CONF_N -> "8002" Comparing "2777" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2778" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759132 ATOM PAIRS WERE FOUND FOR ATOM LIST 41732 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29956 from a total of 759132 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2778 -68.66824 0.30542 0.76946 INTE EXTERN> -26.86109 -41.80715 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6682" Parameter: A <- "-68.6682" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8611" Parameter: B <- "-26.8611" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8071" Parameter: C <- "-41.8071" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2778 TOTAL ENERGY = -68.6682 RDTITL> * VAN DER WAALS = -26.8611 ELECTROSTATIC = -41.8071 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2778" Parameter: CONF_N -> "8002" Comparing "2778" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2779" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759132 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765204 ATOM PAIRS WERE FOUND FOR ATOM LIST 42125 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30670 from a total of 765204 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2779 -61.82088 -6.84736 0.60135 INTE EXTERN> -30.86273 -30.95815 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.8209" Parameter: A <- "-61.8209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8627" Parameter: B <- "-30.8627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.9581" Parameter: C <- "-30.9581" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2779 TOTAL ENERGY = -61.8209 RDTITL> * VAN DER WAALS = -30.8627 ELECTROSTATIC = -30.9581 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2779" Parameter: CONF_N -> "8002" Comparing "2779" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2780" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765204 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761521 ATOM PAIRS WERE FOUND FOR ATOM LIST 41962 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30545 from a total of 761521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2780 -69.14199 7.32111 0.83284 INTE EXTERN> -24.56472 -44.57726 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.142" Parameter: A <- "-69.142" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5647" Parameter: B <- "-24.5647" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5773" Parameter: C <- "-44.5773" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2780 TOTAL ENERGY = -69.142 RDTITL> * VAN DER WAALS = -24.5647 ELECTROSTATIC = -44.5773 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2780" Parameter: CONF_N -> "8002" Comparing "2780" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2781" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763485 ATOM PAIRS WERE FOUND FOR ATOM LIST 41945 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30322 from a total of 763485 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2781 -64.65903 -4.48296 0.68220 INTE EXTERN> -29.64816 -35.01087 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.659" Parameter: A <- "-64.659" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6482" Parameter: B <- "-29.6482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0109" Parameter: C <- "-35.0109" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2781 TOTAL ENERGY = -64.659 RDTITL> * VAN DER WAALS = -29.6482 ELECTROSTATIC = -35.0109 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2781" Parameter: CONF_N -> "8002" Comparing "2781" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2782" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763485 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758918 ATOM PAIRS WERE FOUND FOR ATOM LIST 41810 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30178 from a total of 758918 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2782 -61.29490 -3.36413 0.44386 INTE EXTERN> -35.54146 -25.75344 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.2949" Parameter: A <- "-61.2949" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.5415" Parameter: B <- "-35.5415" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-25.7534" Parameter: C <- "-25.7534" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2782 TOTAL ENERGY = -61.2949 RDTITL> * VAN DER WAALS = -35.5415 ELECTROSTATIC = -25.7534 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2782" Parameter: CONF_N -> "8002" Comparing "2782" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2783" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758918 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765209 ATOM PAIRS WERE FOUND FOR ATOM LIST 41850 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30192 from a total of 765209 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2783 -72.11416 10.81927 0.62037 INTE EXTERN> -29.25698 -42.85718 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1142" Parameter: A <- "-72.1142" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.257" Parameter: B <- "-29.257" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8572" Parameter: C <- "-42.8572" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2783 TOTAL ENERGY = -72.1142 RDTITL> * VAN DER WAALS = -29.257 ELECTROSTATIC = -42.8572 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2783" Parameter: CONF_N -> "8002" Comparing "2783" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2784" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765209 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763728 ATOM PAIRS WERE FOUND FOR ATOM LIST 42104 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30998 from a total of 763728 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2784 -70.76114 -1.35302 0.64268 INTE EXTERN> -30.98669 -39.77445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7611" Parameter: A <- "-70.7611" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9867" Parameter: B <- "-30.9867" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7744" Parameter: C <- "-39.7744" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2784 TOTAL ENERGY = -70.7611 RDTITL> * VAN DER WAALS = -30.9867 ELECTROSTATIC = -39.7744 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2784" Parameter: CONF_N -> "8002" Comparing "2784" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2785" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763728 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761989 ATOM PAIRS WERE FOUND FOR ATOM LIST 41831 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29685 from a total of 761989 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2785 -68.86775 -1.89339 0.69080 INTE EXTERN> -25.98258 -42.88517 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8677" Parameter: A <- "-68.8677" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9826" Parameter: B <- "-25.9826" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8852" Parameter: C <- "-42.8852" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2785 TOTAL ENERGY = -68.8677 RDTITL> * VAN DER WAALS = -25.9826 ELECTROSTATIC = -42.8852 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2785" Parameter: CONF_N -> "8002" Comparing "2785" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2786" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761989 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762046 ATOM PAIRS WERE FOUND FOR ATOM LIST 41722 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30143 from a total of 762046 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2786 -69.90585 1.03810 0.62020 INTE EXTERN> -28.88561 -41.02024 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9059" Parameter: A <- "-69.9059" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8856" Parameter: B <- "-28.8856" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0202" Parameter: C <- "-41.0202" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2786 TOTAL ENERGY = -69.9059 RDTITL> * VAN DER WAALS = -28.8856 ELECTROSTATIC = -41.0202 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2786" Parameter: CONF_N -> "8002" Comparing "2786" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2787" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762046 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761500 ATOM PAIRS WERE FOUND FOR ATOM LIST 41858 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29489 from a total of 761500 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2787 -68.89890 -1.00695 0.51917 INTE EXTERN> -31.72105 -37.17786 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8989" Parameter: A <- "-68.8989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.721" Parameter: B <- "-31.721" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1779" Parameter: C <- "-37.1779" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2787 TOTAL ENERGY = -68.8989 RDTITL> * VAN DER WAALS = -31.721 ELECTROSTATIC = -37.1779 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2787" Parameter: CONF_N -> "8002" Comparing "2787" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2788" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761500 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759496 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29691 from a total of 759496 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2788 -67.47507 -1.42383 0.58578 INTE EXTERN> -31.72895 -35.74612 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4751" Parameter: A <- "-67.4751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.729" Parameter: B <- "-31.729" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7461" Parameter: C <- "-35.7461" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2788 TOTAL ENERGY = -67.4751 RDTITL> * VAN DER WAALS = -31.729 ELECTROSTATIC = -35.7461 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2788" Parameter: CONF_N -> "8002" Comparing "2788" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2789" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759496 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752869 ATOM PAIRS WERE FOUND FOR ATOM LIST 41300 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29124 from a total of 752869 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2789 -64.69281 -2.78227 0.60075 INTE EXTERN> -29.37546 -35.31734 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6928" Parameter: A <- "-64.6928" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3755" Parameter: B <- "-29.3755" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3173" Parameter: C <- "-35.3173" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2789 TOTAL ENERGY = -64.6928 RDTITL> * VAN DER WAALS = -29.3755 ELECTROSTATIC = -35.3173 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2789" Parameter: CONF_N -> "8002" Comparing "2789" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2790" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752869 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760313 ATOM PAIRS WERE FOUND FOR ATOM LIST 41764 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30172 from a total of 760313 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2790 -69.11899 4.42619 0.66050 INTE EXTERN> -28.77922 -40.33977 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.119" Parameter: A <- "-69.119" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7792" Parameter: B <- "-28.7792" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3398" Parameter: C <- "-40.3398" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2790 TOTAL ENERGY = -69.119 RDTITL> * VAN DER WAALS = -28.7792 ELECTROSTATIC = -40.3398 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2790" Parameter: CONF_N -> "8002" Comparing "2790" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2791" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760313 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758484 ATOM PAIRS WERE FOUND FOR ATOM LIST 41587 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30126 from a total of 758484 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2791 -69.04512 -0.07387 0.62471 INTE EXTERN> -30.58983 -38.45530 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0451" Parameter: A <- "-69.0451" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5898" Parameter: B <- "-30.5898" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4553" Parameter: C <- "-38.4553" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2791 TOTAL ENERGY = -69.0451 RDTITL> * VAN DER WAALS = -30.5898 ELECTROSTATIC = -38.4553 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2791" Parameter: CONF_N -> "8002" Comparing "2791" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2792" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758484 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756035 ATOM PAIRS WERE FOUND FOR ATOM LIST 41506 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30207 from a total of 756035 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2792 -67.06181 -1.98331 0.67672 INTE EXTERN> -29.74090 -37.32091 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0618" Parameter: A <- "-67.0618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7409" Parameter: B <- "-29.7409" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3209" Parameter: C <- "-37.3209" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2792 TOTAL ENERGY = -67.0618 RDTITL> * VAN DER WAALS = -29.7409 ELECTROSTATIC = -37.3209 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2792" Parameter: CONF_N -> "8002" Comparing "2792" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2793" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756035 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763649 ATOM PAIRS WERE FOUND FOR ATOM LIST 41844 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30547 from a total of 763649 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2793 -65.59100 -1.47082 0.80599 INTE EXTERN> -23.41332 -42.17768 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.591" Parameter: A <- "-65.591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4133" Parameter: B <- "-23.4133" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1777" Parameter: C <- "-42.1777" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2793 TOTAL ENERGY = -65.591 RDTITL> * VAN DER WAALS = -23.4133 ELECTROSTATIC = -42.1777 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2793" Parameter: CONF_N -> "8002" Comparing "2793" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2794" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763649 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760774 ATOM PAIRS WERE FOUND FOR ATOM LIST 41752 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30396 from a total of 760774 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2794 -72.77372 7.18273 0.63512 INTE EXTERN> -31.94380 -40.82993 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7737" Parameter: A <- "-72.7737" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9438" Parameter: B <- "-31.9438" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8299" Parameter: C <- "-40.8299" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2794 TOTAL ENERGY = -72.7737 RDTITL> * VAN DER WAALS = -31.9438 ELECTROSTATIC = -40.8299 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2794" Parameter: CONF_N -> "8002" Comparing "2794" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2795" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760774 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761251 ATOM PAIRS WERE FOUND FOR ATOM LIST 41843 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30182 from a total of 761251 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2795 -73.79355 1.01983 0.56584 INTE EXTERN> -32.61541 -41.17814 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7935" Parameter: A <- "-73.7935" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6154" Parameter: B <- "-32.6154" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1781" Parameter: C <- "-41.1781" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2795 TOTAL ENERGY = -73.7935 RDTITL> * VAN DER WAALS = -32.6154 ELECTROSTATIC = -41.1781 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2795" Parameter: CONF_N -> "8002" Comparing "2795" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2796" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761251 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759845 ATOM PAIRS WERE FOUND FOR ATOM LIST 41783 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29983 from a total of 759845 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2796 -67.53132 -6.26223 0.60085 INTE EXTERN> -32.21096 -35.32036 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5313" Parameter: A <- "-67.5313" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.211" Parameter: B <- "-32.211" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3204" Parameter: C <- "-35.3204" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2796 TOTAL ENERGY = -67.5313 RDTITL> * VAN DER WAALS = -32.211 ELECTROSTATIC = -35.3204 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2796" Parameter: CONF_N -> "8002" Comparing "2796" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2797" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759845 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763480 ATOM PAIRS WERE FOUND FOR ATOM LIST 41958 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29648 from a total of 763480 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2797 -71.85338 4.32206 0.63923 INTE EXTERN> -30.61035 -41.24303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8534" Parameter: A <- "-71.8534" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6104" Parameter: B <- "-30.6104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.243" Parameter: C <- "-41.243" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2797 TOTAL ENERGY = -71.8534 RDTITL> * VAN DER WAALS = -30.6104 ELECTROSTATIC = -41.243 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2797" Parameter: CONF_N -> "8002" Comparing "2797" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2798" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763480 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762904 ATOM PAIRS WERE FOUND FOR ATOM LIST 41811 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29741 from a total of 762904 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2798 -68.25154 -3.60184 0.59595 INTE EXTERN> -32.79496 -35.45657 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2515" Parameter: A <- "-68.2515" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.795" Parameter: B <- "-32.795" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4566" Parameter: C <- "-35.4566" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2798 TOTAL ENERGY = -68.2515 RDTITL> * VAN DER WAALS = -32.795 ELECTROSTATIC = -35.4566 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2798" Parameter: CONF_N -> "8002" Comparing "2798" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2799" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762904 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757917 ATOM PAIRS WERE FOUND FOR ATOM LIST 41777 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30016 from a total of 757917 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2799 -73.11765 4.86611 0.67076 INTE EXTERN> -27.39923 -45.71842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1176" Parameter: A <- "-73.1176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3992" Parameter: B <- "-27.3992" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7184" Parameter: C <- "-45.7184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2799 TOTAL ENERGY = -73.1176 RDTITL> * VAN DER WAALS = -27.3992 ELECTROSTATIC = -45.7184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2799" Parameter: CONF_N -> "8002" Comparing "2799" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2800" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757917 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766091 ATOM PAIRS WERE FOUND FOR ATOM LIST 42038 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30122 from a total of 766091 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2800 -72.82985 -0.28780 0.66471 INTE EXTERN> -28.72996 -44.09988 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8298" Parameter: A <- "-72.8298" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.73" Parameter: B <- "-28.73" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0999" Parameter: C <- "-44.0999" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2800 TOTAL ENERGY = -72.8298 RDTITL> * VAN DER WAALS = -28.73 ELECTROSTATIC = -44.0999 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2800" Parameter: CONF_N -> "8002" Comparing "2800" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2801" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766091 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768617 ATOM PAIRS WERE FOUND FOR ATOM LIST 42162 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30177 from a total of 768617 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2801 -65.17792 -7.65193 0.61387 INTE EXTERN> -32.04542 -33.13249 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1779" Parameter: A <- "-65.1779" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0454" Parameter: B <- "-32.0454" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1325" Parameter: C <- "-33.1325" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2801 TOTAL ENERGY = -65.1779 RDTITL> * VAN DER WAALS = -32.0454 ELECTROSTATIC = -33.1325 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2801" Parameter: CONF_N -> "8002" Comparing "2801" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2802" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768617 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767318 ATOM PAIRS WERE FOUND FOR ATOM LIST 41986 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29891 from a total of 767318 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2802 -72.84361 7.66569 0.53286 INTE EXTERN> -33.76396 -39.07965 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8436" Parameter: A <- "-72.8436" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.764" Parameter: B <- "-33.764" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0796" Parameter: C <- "-39.0796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2802 TOTAL ENERGY = -72.8436 RDTITL> * VAN DER WAALS = -33.764 ELECTROSTATIC = -39.0796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2802" Parameter: CONF_N -> "8002" Comparing "2802" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2803" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767318 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768854 ATOM PAIRS WERE FOUND FOR ATOM LIST 42096 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30146 from a total of 768854 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2803 -70.42907 -2.41454 0.63386 INTE EXTERN> -31.10542 -39.32365 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4291" Parameter: A <- "-70.4291" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1054" Parameter: B <- "-31.1054" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3236" Parameter: C <- "-39.3236" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2803 TOTAL ENERGY = -70.4291 RDTITL> * VAN DER WAALS = -31.1054 ELECTROSTATIC = -39.3236 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2803" Parameter: CONF_N -> "8002" Comparing "2803" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2804" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768854 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764898 ATOM PAIRS WERE FOUND FOR ATOM LIST 41945 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29872 from a total of 764898 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2804 -68.36585 -2.06322 0.55193 INTE EXTERN> -32.18053 -36.18533 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3659" Parameter: A <- "-68.3659" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1805" Parameter: B <- "-32.1805" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1853" Parameter: C <- "-36.1853" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2804 TOTAL ENERGY = -68.3659 RDTITL> * VAN DER WAALS = -32.1805 ELECTROSTATIC = -36.1853 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2804" Parameter: CONF_N -> "8002" Comparing "2804" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2805" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764898 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767909 ATOM PAIRS WERE FOUND FOR ATOM LIST 42075 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30281 from a total of 767909 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2805 -62.98777 -5.37808 0.71324 INTE EXTERN> -28.08288 -34.90489 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9878" Parameter: A <- "-62.9878" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0829" Parameter: B <- "-28.0829" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9049" Parameter: C <- "-34.9049" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2805 TOTAL ENERGY = -62.9878 RDTITL> * VAN DER WAALS = -28.0829 ELECTROSTATIC = -34.9049 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2805" Parameter: CONF_N -> "8002" Comparing "2805" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2806" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767909 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761406 ATOM PAIRS WERE FOUND FOR ATOM LIST 41738 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30030 from a total of 761406 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2806 -74.70834 11.72057 0.63067 INTE EXTERN> -30.32663 -44.38171 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7083" Parameter: A <- "-74.7083" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3266" Parameter: B <- "-30.3266" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3817" Parameter: C <- "-44.3817" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2806 TOTAL ENERGY = -74.7083 RDTITL> * VAN DER WAALS = -30.3266 ELECTROSTATIC = -44.3817 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2806" Parameter: CONF_N -> "8002" Comparing "2806" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2807" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761406 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764730 ATOM PAIRS WERE FOUND FOR ATOM LIST 41892 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29943 from a total of 764730 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2807 -66.96344 -7.74490 0.70216 INTE EXTERN> -21.47262 -45.49081 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9634" Parameter: A <- "-66.9634" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.4726" Parameter: B <- "-21.4726" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4908" Parameter: C <- "-45.4908" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2807 TOTAL ENERGY = -66.9634 RDTITL> * VAN DER WAALS = -21.4726 ELECTROSTATIC = -45.4908 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2807" Parameter: CONF_N -> "8002" Comparing "2807" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2808" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764730 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756073 ATOM PAIRS WERE FOUND FOR ATOM LIST 41701 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30037 from a total of 756073 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2808 -67.56491 0.60147 0.65373 INTE EXTERN> -27.57122 -39.99369 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5649" Parameter: A <- "-67.5649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5712" Parameter: B <- "-27.5712" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9937" Parameter: C <- "-39.9937" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2808 TOTAL ENERGY = -67.5649 RDTITL> * VAN DER WAALS = -27.5712 ELECTROSTATIC = -39.9937 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2808" Parameter: CONF_N -> "8002" Comparing "2808" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2809" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756073 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760799 ATOM PAIRS WERE FOUND FOR ATOM LIST 41811 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29889 from a total of 760799 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2809 -68.70922 1.14431 0.64683 INTE EXTERN> -27.50930 -41.19991 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7092" Parameter: A <- "-68.7092" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5093" Parameter: B <- "-27.5093" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1999" Parameter: C <- "-41.1999" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2809 TOTAL ENERGY = -68.7092 RDTITL> * VAN DER WAALS = -27.5093 ELECTROSTATIC = -41.1999 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2809" Parameter: CONF_N -> "8002" Comparing "2809" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2810" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760799 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764777 ATOM PAIRS WERE FOUND FOR ATOM LIST 41946 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30278 from a total of 764777 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2810 -71.26795 2.55873 0.60954 INTE EXTERN> -29.38459 -41.88336 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.268" Parameter: A <- "-71.268" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3846" Parameter: B <- "-29.3846" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8834" Parameter: C <- "-41.8834" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2810 TOTAL ENERGY = -71.268 RDTITL> * VAN DER WAALS = -29.3846 ELECTROSTATIC = -41.8834 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2810" Parameter: CONF_N -> "8002" Comparing "2810" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2811" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764777 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768761 ATOM PAIRS WERE FOUND FOR ATOM LIST 42143 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30209 from a total of 768761 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2811 -67.44573 -3.82222 0.66548 INTE EXTERN> -26.19982 -41.24591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4457" Parameter: A <- "-67.4457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1998" Parameter: B <- "-26.1998" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2459" Parameter: C <- "-41.2459" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2811 TOTAL ENERGY = -67.4457 RDTITL> * VAN DER WAALS = -26.1998 ELECTROSTATIC = -41.2459 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2811" Parameter: CONF_N -> "8002" Comparing "2811" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2812" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768761 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758598 ATOM PAIRS WERE FOUND FOR ATOM LIST 41842 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29780 from a total of 758598 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2812 -73.05741 5.61167 0.63776 INTE EXTERN> -30.22221 -42.83520 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0574" Parameter: A <- "-73.0574" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2222" Parameter: B <- "-30.2222" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8352" Parameter: C <- "-42.8352" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2812 TOTAL ENERGY = -73.0574 RDTITL> * VAN DER WAALS = -30.2222 ELECTROSTATIC = -42.8352 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2812" Parameter: CONF_N -> "8002" Comparing "2812" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2813" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758598 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767264 ATOM PAIRS WERE FOUND FOR ATOM LIST 42211 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30169 from a total of 767264 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2813 -70.28661 -2.77080 0.59050 INTE EXTERN> -30.70744 -39.57917 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2866" Parameter: A <- "-70.2866" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7074" Parameter: B <- "-30.7074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5792" Parameter: C <- "-39.5792" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2813 TOTAL ENERGY = -70.2866 RDTITL> * VAN DER WAALS = -30.7074 ELECTROSTATIC = -39.5792 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2813" Parameter: CONF_N -> "8002" Comparing "2813" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2814" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767264 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765940 ATOM PAIRS WERE FOUND FOR ATOM LIST 41824 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30360 from a total of 765940 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2814 -67.55682 -2.72979 0.54470 INTE EXTERN> -33.03409 -34.52273 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5568" Parameter: A <- "-67.5568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0341" Parameter: B <- "-33.0341" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5227" Parameter: C <- "-34.5227" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2814 TOTAL ENERGY = -67.5568 RDTITL> * VAN DER WAALS = -33.0341 ELECTROSTATIC = -34.5227 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2814" Parameter: CONF_N -> "8002" Comparing "2814" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2815" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765940 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767772 ATOM PAIRS WERE FOUND FOR ATOM LIST 42092 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30588 from a total of 767772 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2815 -69.81556 2.25873 0.65736 INTE EXTERN> -29.48606 -40.32950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8156" Parameter: A <- "-69.8156" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4861" Parameter: B <- "-29.4861" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3295" Parameter: C <- "-40.3295" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2815 TOTAL ENERGY = -69.8156 RDTITL> * VAN DER WAALS = -29.4861 ELECTROSTATIC = -40.3295 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2815" Parameter: CONF_N -> "8002" Comparing "2815" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2816" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767772 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766624 ATOM PAIRS WERE FOUND FOR ATOM LIST 42232 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30537 from a total of 766624 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2816 -71.06583 1.25028 0.62369 INTE EXTERN> -30.04800 -41.01784 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0658" Parameter: A <- "-71.0658" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.048" Parameter: B <- "-30.048" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0178" Parameter: C <- "-41.0178" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2816 TOTAL ENERGY = -71.0658 RDTITL> * VAN DER WAALS = -30.048 ELECTROSTATIC = -41.0178 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2816" Parameter: CONF_N -> "8002" Comparing "2816" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2817" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766624 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771365 ATOM PAIRS WERE FOUND FOR ATOM LIST 42290 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30212 from a total of 771365 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2817 -69.05372 -2.01212 0.55973 INTE EXTERN> -30.29135 -38.76236 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0537" Parameter: A <- "-69.0537" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2914" Parameter: B <- "-30.2914" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7624" Parameter: C <- "-38.7624" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2817 TOTAL ENERGY = -69.0537 RDTITL> * VAN DER WAALS = -30.2914 ELECTROSTATIC = -38.7624 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2817" Parameter: CONF_N -> "8002" Comparing "2817" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2818" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771365 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771037 ATOM PAIRS WERE FOUND FOR ATOM LIST 42236 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30721 from a total of 771037 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2818 -77.42387 8.37015 0.66888 INTE EXTERN> -31.18649 -46.23737 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4239" Parameter: A <- "-77.4239" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1865" Parameter: B <- "-31.1865" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2374" Parameter: C <- "-46.2374" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2818 TOTAL ENERGY = -77.4239 RDTITL> * VAN DER WAALS = -31.1865 ELECTROSTATIC = -46.2374 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2818" Parameter: CONF_N -> "8002" Comparing "2818" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2819" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771037 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764373 ATOM PAIRS WERE FOUND FOR ATOM LIST 42182 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30446 from a total of 764373 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2819 -72.33216 -5.09170 0.71343 INTE EXTERN> -26.48982 -45.84235 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3322" Parameter: A <- "-72.3322" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4898" Parameter: B <- "-26.4898" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8423" Parameter: C <- "-45.8423" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2819 TOTAL ENERGY = -72.3322 RDTITL> * VAN DER WAALS = -26.4898 ELECTROSTATIC = -45.8423 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2819" Parameter: CONF_N -> "8002" Comparing "2819" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2820" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764373 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760997 ATOM PAIRS WERE FOUND FOR ATOM LIST 41952 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30474 from a total of 760997 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2820 -75.12897 2.79681 0.65323 INTE EXTERN> -30.21543 -44.91354 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.129" Parameter: A <- "-75.129" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2154" Parameter: B <- "-30.2154" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9135" Parameter: C <- "-44.9135" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2820 TOTAL ENERGY = -75.129 RDTITL> * VAN DER WAALS = -30.2154 ELECTROSTATIC = -44.9135 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2820" Parameter: CONF_N -> "8002" Comparing "2820" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2821" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760997 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765222 ATOM PAIRS WERE FOUND FOR ATOM LIST 42056 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30383 from a total of 765222 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2821 -61.12879 -14.00018 0.59740 INTE EXTERN> -28.91903 -32.20976 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.1288" Parameter: A <- "-61.1288" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.919" Parameter: B <- "-28.919" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2098" Parameter: C <- "-32.2098" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2821 TOTAL ENERGY = -61.1288 RDTITL> * VAN DER WAALS = -28.919 ELECTROSTATIC = -32.2098 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2821" Parameter: CONF_N -> "8002" Comparing "2821" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2822" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765222 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766439 ATOM PAIRS WERE FOUND FOR ATOM LIST 42117 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30541 from a total of 766439 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2822 -70.47241 9.34362 0.69633 INTE EXTERN> -28.03222 -42.44019 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4724" Parameter: A <- "-70.4724" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0322" Parameter: B <- "-28.0322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4402" Parameter: C <- "-42.4402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2822 TOTAL ENERGY = -70.4724 RDTITL> * VAN DER WAALS = -28.0322 ELECTROSTATIC = -42.4402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2822" Parameter: CONF_N -> "8002" Comparing "2822" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2823" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766439 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763446 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30398 from a total of 763446 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2823 -70.41407 -0.05835 0.57315 INTE EXTERN> -30.21280 -40.20126 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4141" Parameter: A <- "-70.4141" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2128" Parameter: B <- "-30.2128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2013" Parameter: C <- "-40.2013" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2823 TOTAL ENERGY = -70.4141 RDTITL> * VAN DER WAALS = -30.2128 ELECTROSTATIC = -40.2013 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2823" Parameter: CONF_N -> "8002" Comparing "2823" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2824" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763446 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768636 ATOM PAIRS WERE FOUND FOR ATOM LIST 42207 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30702 from a total of 768636 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2824 -66.63314 -3.78093 0.59162 INTE EXTERN> -31.35147 -35.28167 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6331" Parameter: A <- "-66.6331" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3515" Parameter: B <- "-31.3515" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2817" Parameter: C <- "-35.2817" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2824 TOTAL ENERGY = -66.6331 RDTITL> * VAN DER WAALS = -31.3515 ELECTROSTATIC = -35.2817 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2824" Parameter: CONF_N -> "8002" Comparing "2824" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2825" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768636 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771471 ATOM PAIRS WERE FOUND FOR ATOM LIST 42394 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 31207 from a total of 771471 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2825 -64.32950 -2.30364 0.73180 INTE EXTERN> -25.31409 -39.01542 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3295" Parameter: A <- "-64.3295" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3141" Parameter: B <- "-25.3141" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0154" Parameter: C <- "-39.0154" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2825 TOTAL ENERGY = -64.3295 RDTITL> * VAN DER WAALS = -25.3141 ELECTROSTATIC = -39.0154 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2825" Parameter: CONF_N -> "8002" Comparing "2825" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2826" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771471 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765996 ATOM PAIRS WERE FOUND FOR ATOM LIST 42078 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30575 from a total of 765996 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2826 -74.03283 9.70333 0.58361 INTE EXTERN> -29.95176 -44.08107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0328" Parameter: A <- "-74.0328" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9518" Parameter: B <- "-29.9518" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0811" Parameter: C <- "-44.0811" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2826 TOTAL ENERGY = -74.0328 RDTITL> * VAN DER WAALS = -29.9518 ELECTROSTATIC = -44.0811 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2826" Parameter: CONF_N -> "8002" Comparing "2826" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2827" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765996 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768564 ATOM PAIRS WERE FOUND FOR ATOM LIST 42144 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30669 from a total of 768564 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2827 -74.07724 0.04441 0.62542 INTE EXTERN> -30.00062 -44.07662 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0772" Parameter: A <- "-74.0772" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0006" Parameter: B <- "-30.0006" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0766" Parameter: C <- "-44.0766" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2827 TOTAL ENERGY = -74.0772 RDTITL> * VAN DER WAALS = -30.0006 ELECTROSTATIC = -44.0766 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2827" Parameter: CONF_N -> "8002" Comparing "2827" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2828" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768564 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765942 ATOM PAIRS WERE FOUND FOR ATOM LIST 41890 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30265 from a total of 765942 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2828 -68.34213 -5.73510 0.67499 INTE EXTERN> -27.15663 -41.18550 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3421" Parameter: A <- "-68.3421" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1566" Parameter: B <- "-27.1566" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1855" Parameter: C <- "-41.1855" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2828 TOTAL ENERGY = -68.3421 RDTITL> * VAN DER WAALS = -27.1566 ELECTROSTATIC = -41.1855 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2828" Parameter: CONF_N -> "8002" Comparing "2828" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2829" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765942 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765871 ATOM PAIRS WERE FOUND FOR ATOM LIST 41964 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29583 from a total of 765871 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2829 -78.55788 10.21575 0.63142 INTE EXTERN> -30.89301 -47.66488 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5579" Parameter: A <- "-78.5579" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.893" Parameter: B <- "-30.893" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6649" Parameter: C <- "-47.6649" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2829 TOTAL ENERGY = -78.5579 RDTITL> * VAN DER WAALS = -30.893 ELECTROSTATIC = -47.6649 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2829" Parameter: CONF_N -> "8002" Comparing "2829" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2830" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765871 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768785 ATOM PAIRS WERE FOUND FOR ATOM LIST 42151 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30365 from a total of 768785 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2830 -76.51487 -2.04301 0.65098 INTE EXTERN> -29.96423 -46.55064 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5149" Parameter: A <- "-76.5149" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9642" Parameter: B <- "-29.9642" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5506" Parameter: C <- "-46.5506" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2830 TOTAL ENERGY = -76.5149 RDTITL> * VAN DER WAALS = -29.9642 ELECTROSTATIC = -46.5506 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2830" Parameter: CONF_N -> "8002" Comparing "2830" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2831" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768785 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761813 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29948 from a total of 761813 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2831 -74.18446 -2.33041 0.61884 INTE EXTERN> -29.35797 -44.82649 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1845" Parameter: A <- "-74.1845" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.358" Parameter: B <- "-29.358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8265" Parameter: C <- "-44.8265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2831 TOTAL ENERGY = -74.1845 RDTITL> * VAN DER WAALS = -29.358 ELECTROSTATIC = -44.8265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2831" Parameter: CONF_N -> "8002" Comparing "2831" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2832" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761813 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765548 ATOM PAIRS WERE FOUND FOR ATOM LIST 41887 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29767 from a total of 765548 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2832 -75.11762 0.93317 0.58629 INTE EXTERN> -30.79078 -44.32685 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1176" Parameter: A <- "-75.1176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7908" Parameter: B <- "-30.7908" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3268" Parameter: C <- "-44.3268" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2832 TOTAL ENERGY = -75.1176 RDTITL> * VAN DER WAALS = -30.7908 ELECTROSTATIC = -44.3268 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2832" Parameter: CONF_N -> "8002" Comparing "2832" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2833" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765548 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758279 ATOM PAIRS WERE FOUND FOR ATOM LIST 41669 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29667 from a total of 758279 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2833 -74.17948 -0.93814 0.58847 INTE EXTERN> -31.48267 -42.69681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1795" Parameter: A <- "-74.1795" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4827" Parameter: B <- "-31.4827" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6968" Parameter: C <- "-42.6968" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2833 TOTAL ENERGY = -74.1795 RDTITL> * VAN DER WAALS = -31.4827 ELECTROSTATIC = -42.6968 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2833" Parameter: CONF_N -> "8002" Comparing "2833" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2834" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758279 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41589 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30139 from a total of 758794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2834 -70.65085 -3.52863 0.60585 INTE EXTERN> -32.41941 -38.23144 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6508" Parameter: A <- "-70.6508" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4194" Parameter: B <- "-32.4194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2314" Parameter: C <- "-38.2314" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2834 TOTAL ENERGY = -70.6508 RDTITL> * VAN DER WAALS = -32.4194 ELECTROSTATIC = -38.2314 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2834" Parameter: CONF_N -> "8002" Comparing "2834" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2835" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760726 ATOM PAIRS WERE FOUND FOR ATOM LIST 41877 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29928 from a total of 760726 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2835 -63.04729 -7.60356 0.61409 INTE EXTERN> -27.94674 -35.10054 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.0473" Parameter: A <- "-63.0473" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9467" Parameter: B <- "-27.9467" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1005" Parameter: C <- "-35.1005" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2835 TOTAL ENERGY = -63.0473 RDTITL> * VAN DER WAALS = -27.9467 ELECTROSTATIC = -35.1005 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2835" Parameter: CONF_N -> "8002" Comparing "2835" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2836" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760726 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765636 ATOM PAIRS WERE FOUND FOR ATOM LIST 41942 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29861 from a total of 765636 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2836 -75.49681 12.44952 0.65813 INTE EXTERN> -27.92953 -47.56728 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4968" Parameter: A <- "-75.4968" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9295" Parameter: B <- "-27.9295" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5673" Parameter: C <- "-47.5673" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2836 TOTAL ENERGY = -75.4968 RDTITL> * VAN DER WAALS = -27.9295 ELECTROSTATIC = -47.5673 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2836" Parameter: CONF_N -> "8002" Comparing "2836" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2837" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765636 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764336 ATOM PAIRS WERE FOUND FOR ATOM LIST 42044 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30084 from a total of 764336 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2837 -83.80864 8.31184 0.77042 INTE EXTERN> -24.64859 -59.16005 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.8086" Parameter: A <- "-83.8086" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6486" Parameter: B <- "-24.6486" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.1601" Parameter: C <- "-59.1601" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2837 TOTAL ENERGY = -83.8086 RDTITL> * VAN DER WAALS = -24.6486 ELECTROSTATIC = -59.1601 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2837" Parameter: CONF_N -> "8002" Comparing "2837" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2838" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764336 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762211 ATOM PAIRS WERE FOUND FOR ATOM LIST 41962 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30152 from a total of 762211 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2838 -76.95555 -6.85309 0.71258 INTE EXTERN> -28.43620 -48.51935 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9556" Parameter: A <- "-76.9556" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4362" Parameter: B <- "-28.4362" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5194" Parameter: C <- "-48.5194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2838 TOTAL ENERGY = -76.9556 RDTITL> * VAN DER WAALS = -28.4362 ELECTROSTATIC = -48.5194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2838" Parameter: CONF_N -> "8002" Comparing "2838" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2839" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762211 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765604 ATOM PAIRS WERE FOUND FOR ATOM LIST 42196 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29659 from a total of 765604 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2839 -74.59541 -2.36014 0.59185 INTE EXTERN> -30.48662 -44.10879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5954" Parameter: A <- "-74.5954" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4866" Parameter: B <- "-30.4866" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1088" Parameter: C <- "-44.1088" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2839 TOTAL ENERGY = -74.5954 RDTITL> * VAN DER WAALS = -30.4866 ELECTROSTATIC = -44.1088 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2839" Parameter: CONF_N -> "8002" Comparing "2839" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2840" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765604 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768069 ATOM PAIRS WERE FOUND FOR ATOM LIST 42302 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30322 from a total of 768069 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2840 -75.06546 0.47005 0.68859 INTE EXTERN> -26.68089 -48.38457 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0655" Parameter: A <- "-75.0655" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6809" Parameter: B <- "-26.6809" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3846" Parameter: C <- "-48.3846" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2840 TOTAL ENERGY = -75.0655 RDTITL> * VAN DER WAALS = -26.6809 ELECTROSTATIC = -48.3846 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2840" Parameter: CONF_N -> "8002" Comparing "2840" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2841" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768069 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763053 ATOM PAIRS WERE FOUND FOR ATOM LIST 42069 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29416 from a total of 763053 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2841 -74.31601 -0.74945 0.56929 INTE EXTERN> -29.88486 -44.43115 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.316" Parameter: A <- "-74.316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8849" Parameter: B <- "-29.8849" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4312" Parameter: C <- "-44.4312" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2841 TOTAL ENERGY = -74.316 RDTITL> * VAN DER WAALS = -29.8849 ELECTROSTATIC = -44.4312 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2841" Parameter: CONF_N -> "8002" Comparing "2841" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2842" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763053 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771400 ATOM PAIRS WERE FOUND FOR ATOM LIST 42247 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29831 from a total of 771400 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2842 -75.28010 0.96409 0.65928 INTE EXTERN> -29.66915 -45.61095 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2801" Parameter: A <- "-75.2801" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6691" Parameter: B <- "-29.6691" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6109" Parameter: C <- "-45.6109" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2842 TOTAL ENERGY = -75.2801 RDTITL> * VAN DER WAALS = -29.6691 ELECTROSTATIC = -45.6109 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2842" Parameter: CONF_N -> "8002" Comparing "2842" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2843" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771400 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761196 ATOM PAIRS WERE FOUND FOR ATOM LIST 42079 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29363 from a total of 761196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2843 -65.76102 -9.51908 0.70366 INTE EXTERN> -23.88751 -41.87351 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.761" Parameter: A <- "-65.761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8875" Parameter: B <- "-23.8875" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8735" Parameter: C <- "-41.8735" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2843 TOTAL ENERGY = -65.761 RDTITL> * VAN DER WAALS = -23.8875 ELECTROSTATIC = -41.8735 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2843" Parameter: CONF_N -> "8002" Comparing "2843" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2844" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769990 ATOM PAIRS WERE FOUND FOR ATOM LIST 42286 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29931 from a total of 769990 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2844 -59.85428 -5.90674 0.62854 INTE EXTERN> -26.47937 -33.37491 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.8543" Parameter: A <- "-59.8543" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4794" Parameter: B <- "-26.4794" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.3749" Parameter: C <- "-33.3749" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2844 TOTAL ENERGY = -59.8543 RDTITL> * VAN DER WAALS = -26.4794 ELECTROSTATIC = -33.3749 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2844" Parameter: CONF_N -> "8002" Comparing "2844" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2845" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769990 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768688 ATOM PAIRS WERE FOUND FOR ATOM LIST 42422 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30210 from a total of 768688 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2845 -63.73537 3.88109 0.65319 INTE EXTERN> -25.58675 -38.14862 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7354" Parameter: A <- "-63.7354" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5868" Parameter: B <- "-25.5868" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1486" Parameter: C <- "-38.1486" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2845 TOTAL ENERGY = -63.7354 RDTITL> * VAN DER WAALS = -25.5868 ELECTROSTATIC = -38.1486 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2845" Parameter: CONF_N -> "8002" Comparing "2845" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2846" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768688 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768510 ATOM PAIRS WERE FOUND FOR ATOM LIST 42437 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30142 from a total of 768510 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2846 -69.16777 5.43239 0.54071 INTE EXTERN> -31.61002 -37.55775 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1678" Parameter: A <- "-69.1678" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.61" Parameter: B <- "-31.61" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5578" Parameter: C <- "-37.5578" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2846 TOTAL ENERGY = -69.1678 RDTITL> * VAN DER WAALS = -31.61 ELECTROSTATIC = -37.5578 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2846" Parameter: CONF_N -> "8002" Comparing "2846" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2847" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768510 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771171 ATOM PAIRS WERE FOUND FOR ATOM LIST 42477 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30184 from a total of 771171 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2847 -61.84852 -7.31925 0.50776 INTE EXTERN> -31.13435 -30.71417 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.8485" Parameter: A <- "-61.8485" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1343" Parameter: B <- "-31.1343" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.7142" Parameter: C <- "-30.7142" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2847 TOTAL ENERGY = -61.8485 RDTITL> * VAN DER WAALS = -31.1343 ELECTROSTATIC = -30.7142 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2847" Parameter: CONF_N -> "8002" Comparing "2847" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2848" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771171 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768402 ATOM PAIRS WERE FOUND FOR ATOM LIST 42227 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30397 from a total of 768402 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2848 -58.27914 -3.56937 0.58851 INTE EXTERN> -29.69041 -28.58873 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.2791" Parameter: A <- "-58.2791" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6904" Parameter: B <- "-29.6904" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.5887" Parameter: C <- "-28.5887" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2848 TOTAL ENERGY = -58.2791 RDTITL> * VAN DER WAALS = -29.6904 ELECTROSTATIC = -28.5887 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2848" Parameter: CONF_N -> "8002" Comparing "2848" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2849" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768402 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764301 ATOM PAIRS WERE FOUND FOR ATOM LIST 42121 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29120 from a total of 764301 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2849 -53.93074 -4.34840 0.61393 INTE EXTERN> -29.11361 -24.81713 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-53.9307" Parameter: A <- "-53.9307" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1136" Parameter: B <- "-29.1136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-24.8171" Parameter: C <- "-24.8171" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2849 TOTAL ENERGY = -53.9307 RDTITL> * VAN DER WAALS = -29.1136 ELECTROSTATIC = -24.8171 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2849" Parameter: CONF_N -> "8002" Comparing "2849" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2850" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764301 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768312 ATOM PAIRS WERE FOUND FOR ATOM LIST 42369 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29123 from a total of 768312 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2850 -69.39995 15.46921 0.62597 INTE EXTERN> -28.69745 -40.70249 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3999" Parameter: A <- "-69.3999" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6975" Parameter: B <- "-28.6975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7025" Parameter: C <- "-40.7025" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2850 TOTAL ENERGY = -69.3999 RDTITL> * VAN DER WAALS = -28.6975 ELECTROSTATIC = -40.7025 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2850" Parameter: CONF_N -> "8002" Comparing "2850" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2851" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768312 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766506 ATOM PAIRS WERE FOUND FOR ATOM LIST 42227 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29803 from a total of 766506 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2851 -66.11954 -3.28041 0.68662 INTE EXTERN> -25.02415 -41.09539 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1195" Parameter: A <- "-66.1195" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0241" Parameter: B <- "-25.0241" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0954" Parameter: C <- "-41.0954" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2851 TOTAL ENERGY = -66.1195 RDTITL> * VAN DER WAALS = -25.0241 ELECTROSTATIC = -41.0954 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2851" Parameter: CONF_N -> "8002" Comparing "2851" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2852" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766506 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766450 ATOM PAIRS WERE FOUND FOR ATOM LIST 42050 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29658 from a total of 766450 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2852 -61.18545 -4.93409 0.50561 INTE EXTERN> -33.15704 -28.02841 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.1854" Parameter: A <- "-61.1854" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.157" Parameter: B <- "-33.157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.0284" Parameter: C <- "-28.0284" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2852 TOTAL ENERGY = -61.1854 RDTITL> * VAN DER WAALS = -33.157 ELECTROSTATIC = -28.0284 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2852" Parameter: CONF_N -> "8002" Comparing "2852" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2853" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766450 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770388 ATOM PAIRS WERE FOUND FOR ATOM LIST 42422 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29946 from a total of 770388 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2853 -65.94302 4.75757 0.57129 INTE EXTERN> -31.81585 -34.12717 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.943" Parameter: A <- "-65.943" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8159" Parameter: B <- "-31.8159" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1272" Parameter: C <- "-34.1272" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2853 TOTAL ENERGY = -65.943 RDTITL> * VAN DER WAALS = -31.8159 ELECTROSTATIC = -34.1272 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2853" Parameter: CONF_N -> "8002" Comparing "2853" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2854" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770388 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771039 ATOM PAIRS WERE FOUND FOR ATOM LIST 42341 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30208 from a total of 771039 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2854 -63.49316 -2.44986 0.59073 INTE EXTERN> -32.73089 -30.76227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4932" Parameter: A <- "-63.4932" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7309" Parameter: B <- "-32.7309" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.7623" Parameter: C <- "-30.7623" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2854 TOTAL ENERGY = -63.4932 RDTITL> * VAN DER WAALS = -32.7309 ELECTROSTATIC = -30.7623 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2854" Parameter: CONF_N -> "8002" Comparing "2854" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2855" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771039 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768529 ATOM PAIRS WERE FOUND FOR ATOM LIST 42231 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29223 from a total of 768529 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2855 -58.22817 -5.26500 0.50775 INTE EXTERN> -32.62669 -25.60147 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.2282" Parameter: A <- "-58.2282" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6267" Parameter: B <- "-32.6267" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-25.6015" Parameter: C <- "-25.6015" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2855 TOTAL ENERGY = -58.2282 RDTITL> * VAN DER WAALS = -32.6267 ELECTROSTATIC = -25.6015 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2855" Parameter: CONF_N -> "8002" Comparing "2855" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2856" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768529 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 774978 ATOM PAIRS WERE FOUND FOR ATOM LIST 42318 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30146 from a total of 774978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2856 -54.41408 -3.81408 0.64675 INTE EXTERN> -27.19028 -27.22380 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-54.4141" Parameter: A <- "-54.4141" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1903" Parameter: B <- "-27.1903" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.2238" Parameter: C <- "-27.2238" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2856 TOTAL ENERGY = -54.4141 RDTITL> * VAN DER WAALS = -27.1903 ELECTROSTATIC = -27.2238 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2856" Parameter: CONF_N -> "8002" Comparing "2856" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2857" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 774978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 773948 ATOM PAIRS WERE FOUND FOR ATOM LIST 42548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29762 from a total of 773948 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2857 -62.88455 8.47047 0.54009 INTE EXTERN> -29.10516 -33.77940 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.8846" Parameter: A <- "-62.8846" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1052" Parameter: B <- "-29.1052" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7794" Parameter: C <- "-33.7794" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2857 TOTAL ENERGY = -62.8846 RDTITL> * VAN DER WAALS = -29.1052 ELECTROSTATIC = -33.7794 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2857" Parameter: CONF_N -> "8002" Comparing "2857" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2858" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 773948 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771587 ATOM PAIRS WERE FOUND FOR ATOM LIST 42339 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29387 from a total of 771587 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2858 -60.49469 -2.38986 0.59348 INTE EXTERN> -29.07166 -31.42303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.4947" Parameter: A <- "-60.4947" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0717" Parameter: B <- "-29.0717" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.423" Parameter: C <- "-31.423" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2858 TOTAL ENERGY = -60.4947 RDTITL> * VAN DER WAALS = -29.0717 ELECTROSTATIC = -31.423 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2858" Parameter: CONF_N -> "8002" Comparing "2858" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2859" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771587 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762904 ATOM PAIRS WERE FOUND FOR ATOM LIST 41835 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28697 from a total of 762904 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2859 -61.28255 0.78786 0.63576 INTE EXTERN> -29.13672 -32.14583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.2826" Parameter: A <- "-61.2826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1367" Parameter: B <- "-29.1367" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.1458" Parameter: C <- "-32.1458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2859 TOTAL ENERGY = -61.2826 RDTITL> * VAN DER WAALS = -29.1367 ELECTROSTATIC = -32.1458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2859" Parameter: CONF_N -> "8002" Comparing "2859" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2860" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762904 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765136 ATOM PAIRS WERE FOUND FOR ATOM LIST 42178 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29763 from a total of 765136 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2860 -66.79855 5.51600 0.61884 INTE EXTERN> -28.92888 -37.86967 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7985" Parameter: A <- "-66.7985" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9289" Parameter: B <- "-28.9289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8697" Parameter: C <- "-37.8697" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2860 TOTAL ENERGY = -66.7985 RDTITL> * VAN DER WAALS = -28.9289 ELECTROSTATIC = -37.8697 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2860" Parameter: CONF_N -> "8002" Comparing "2860" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2861" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765136 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768082 ATOM PAIRS WERE FOUND FOR ATOM LIST 42444 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29423 from a total of 768082 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2861 -53.51782 -13.28073 0.58012 INTE EXTERN> -28.87244 -24.64538 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-53.5178" Parameter: A <- "-53.5178" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8724" Parameter: B <- "-28.8724" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-24.6454" Parameter: C <- "-24.6454" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2861 TOTAL ENERGY = -53.5178 RDTITL> * VAN DER WAALS = -28.8724 ELECTROSTATIC = -24.6454 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2861" Parameter: CONF_N -> "8002" Comparing "2861" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2862" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768082 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768432 ATOM PAIRS WERE FOUND FOR ATOM LIST 42268 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29600 from a total of 768432 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2862 -60.87859 7.36077 0.61824 INTE EXTERN> -29.47245 -31.40614 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.8786" Parameter: A <- "-60.8786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4725" Parameter: B <- "-29.4725" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4061" Parameter: C <- "-31.4061" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2862 TOTAL ENERGY = -60.8786 RDTITL> * VAN DER WAALS = -29.4725 ELECTROSTATIC = -31.4061 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2862" Parameter: CONF_N -> "8002" Comparing "2862" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2863" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768432 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767502 ATOM PAIRS WERE FOUND FOR ATOM LIST 42125 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28752 from a total of 767502 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2863 -52.16627 -8.71232 0.58583 INTE EXTERN> -25.79869 -26.36758 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-52.1663" Parameter: A <- "-52.1663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7987" Parameter: B <- "-25.7987" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-26.3676" Parameter: C <- "-26.3676" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2863 TOTAL ENERGY = -52.1663 RDTITL> * VAN DER WAALS = -25.7987 ELECTROSTATIC = -26.3676 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2863" Parameter: CONF_N -> "8002" Comparing "2863" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2864" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767502 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766774 ATOM PAIRS WERE FOUND FOR ATOM LIST 42128 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29206 from a total of 766774 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2864 -59.12565 6.95938 0.58827 INTE EXTERN> -29.71006 -29.41559 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.1257" Parameter: A <- "-59.1257" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7101" Parameter: B <- "-29.7101" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.4156" Parameter: C <- "-29.4156" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2864 TOTAL ENERGY = -59.1257 RDTITL> * VAN DER WAALS = -29.7101 ELECTROSTATIC = -29.4156 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2864" Parameter: CONF_N -> "8002" Comparing "2864" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2865" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766774 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767147 ATOM PAIRS WERE FOUND FOR ATOM LIST 42108 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29665 from a total of 767147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2865 -62.85175 3.72610 0.55553 INTE EXTERN> -29.74410 -33.10765 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.8517" Parameter: A <- "-62.8517" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7441" Parameter: B <- "-29.7441" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1076" Parameter: C <- "-33.1076" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2865 TOTAL ENERGY = -62.8517 RDTITL> * VAN DER WAALS = -29.7441 ELECTROSTATIC = -33.1076 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2865" Parameter: CONF_N -> "8002" Comparing "2865" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2866" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769549 ATOM PAIRS WERE FOUND FOR ATOM LIST 42182 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29873 from a total of 769549 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2866 -64.22548 1.37373 0.57591 INTE EXTERN> -31.61724 -32.60824 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2255" Parameter: A <- "-64.2255" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6172" Parameter: B <- "-31.6172" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.6082" Parameter: C <- "-32.6082" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2866 TOTAL ENERGY = -64.2255 RDTITL> * VAN DER WAALS = -31.6172 ELECTROSTATIC = -32.6082 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2866" Parameter: CONF_N -> "8002" Comparing "2866" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2867" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769549 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762969 ATOM PAIRS WERE FOUND FOR ATOM LIST 41981 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30324 from a total of 762969 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2867 -60.30159 -3.92389 0.53104 INTE EXTERN> -28.99853 -31.30306 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.3016" Parameter: A <- "-60.3016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9985" Parameter: B <- "-28.9985" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.3031" Parameter: C <- "-31.3031" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2867 TOTAL ENERGY = -60.3016 RDTITL> * VAN DER WAALS = -28.9985 ELECTROSTATIC = -31.3031 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2867" Parameter: CONF_N -> "8002" Comparing "2867" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2868" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762969 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768128 ATOM PAIRS WERE FOUND FOR ATOM LIST 42192 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29578 from a total of 768128 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2868 -66.00074 5.69915 0.59314 INTE EXTERN> -28.81951 -37.18124 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0007" Parameter: A <- "-66.0007" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8195" Parameter: B <- "-28.8195" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1812" Parameter: C <- "-37.1812" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2868 TOTAL ENERGY = -66.0007 RDTITL> * VAN DER WAALS = -28.8195 ELECTROSTATIC = -37.1812 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2868" Parameter: CONF_N -> "8002" Comparing "2868" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2869" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768128 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768768 ATOM PAIRS WERE FOUND FOR ATOM LIST 42252 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29406 from a total of 768768 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2869 -66.97319 0.97245 0.61706 INTE EXTERN> -28.57653 -38.39666 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9732" Parameter: A <- "-66.9732" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5765" Parameter: B <- "-28.5765" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3967" Parameter: C <- "-38.3967" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2869 TOTAL ENERGY = -66.9732 RDTITL> * VAN DER WAALS = -28.5765 ELECTROSTATIC = -38.3967 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2869" Parameter: CONF_N -> "8002" Comparing "2869" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2870" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768768 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767234 ATOM PAIRS WERE FOUND FOR ATOM LIST 42346 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29245 from a total of 767234 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2870 -67.37870 0.40550 0.60453 INTE EXTERN> -28.77424 -38.60446 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3787" Parameter: A <- "-67.3787" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7742" Parameter: B <- "-28.7742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6045" Parameter: C <- "-38.6045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2870 TOTAL ENERGY = -67.3787 RDTITL> * VAN DER WAALS = -28.7742 ELECTROSTATIC = -38.6045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2870" Parameter: CONF_N -> "8002" Comparing "2870" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2871" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767234 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771979 ATOM PAIRS WERE FOUND FOR ATOM LIST 42483 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29580 from a total of 771979 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2871 -62.54984 -4.82885 0.58869 INTE EXTERN> -29.12121 -33.42863 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5498" Parameter: A <- "-62.5498" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1212" Parameter: B <- "-29.1212" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.4286" Parameter: C <- "-33.4286" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2871 TOTAL ENERGY = -62.5498 RDTITL> * VAN DER WAALS = -29.1212 ELECTROSTATIC = -33.4286 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2871" Parameter: CONF_N -> "8002" Comparing "2871" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2872" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771979 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767233 ATOM PAIRS WERE FOUND FOR ATOM LIST 42379 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29243 from a total of 767233 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2872 -62.36539 -0.18445 0.60495 INTE EXTERN> -28.75903 -33.60637 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3654" Parameter: A <- "-62.3654" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.759" Parameter: B <- "-28.759" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6064" Parameter: C <- "-33.6064" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2872 TOTAL ENERGY = -62.3654 RDTITL> * VAN DER WAALS = -28.759 ELECTROSTATIC = -33.6064 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2872" Parameter: CONF_N -> "8002" Comparing "2872" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2873" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767233 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765394 ATOM PAIRS WERE FOUND FOR ATOM LIST 42165 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29339 from a total of 765394 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2873 -54.99351 -7.37189 0.59163 INTE EXTERN> -26.83471 -28.15880 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-54.9935" Parameter: A <- "-54.9935" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8347" Parameter: B <- "-26.8347" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.1588" Parameter: C <- "-28.1588" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2873 TOTAL ENERGY = -54.9935 RDTITL> * VAN DER WAALS = -26.8347 ELECTROSTATIC = -28.1588 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2873" Parameter: CONF_N -> "8002" Comparing "2873" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2874" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765394 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758329 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29038 from a total of 758329 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2874 -60.17236 5.17885 0.63076 INTE EXTERN> -27.30848 -32.86388 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.1724" Parameter: A <- "-60.1724" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3085" Parameter: B <- "-27.3085" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.8639" Parameter: C <- "-32.8639" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2874 TOTAL ENERGY = -60.1724 RDTITL> * VAN DER WAALS = -27.3085 ELECTROSTATIC = -32.8639 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2874" Parameter: CONF_N -> "8002" Comparing "2874" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2875" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758329 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767720 ATOM PAIRS WERE FOUND FOR ATOM LIST 42085 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29524 from a total of 767720 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2875 -57.81606 -2.35630 0.66014 INTE EXTERN> -25.86577 -31.95028 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.8161" Parameter: A <- "-57.8161" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8658" Parameter: B <- "-25.8658" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.9503" Parameter: C <- "-31.9503" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2875 TOTAL ENERGY = -57.8161 RDTITL> * VAN DER WAALS = -25.8658 ELECTROSTATIC = -31.9503 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2875" Parameter: CONF_N -> "8002" Comparing "2875" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2876" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767720 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769824 ATOM PAIRS WERE FOUND FOR ATOM LIST 42472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30130 from a total of 769824 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2876 -57.39808 -0.41797 0.53941 INTE EXTERN> -30.34336 -27.05472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.3981" Parameter: A <- "-57.3981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3434" Parameter: B <- "-30.3434" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.0547" Parameter: C <- "-27.0547" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2876 TOTAL ENERGY = -57.3981 RDTITL> * VAN DER WAALS = -30.3434 ELECTROSTATIC = -27.0547 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2876" Parameter: CONF_N -> "8002" Comparing "2876" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2877" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769824 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764337 ATOM PAIRS WERE FOUND FOR ATOM LIST 42095 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29694 from a total of 764337 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2877 -63.11676 5.71867 0.66739 INTE EXTERN> -28.58988 -34.52688 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1168" Parameter: A <- "-63.1168" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5899" Parameter: B <- "-28.5899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5269" Parameter: C <- "-34.5269" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2877 TOTAL ENERGY = -63.1168 RDTITL> * VAN DER WAALS = -28.5899 ELECTROSTATIC = -34.5269 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2877" Parameter: CONF_N -> "8002" Comparing "2877" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2878" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764337 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764353 ATOM PAIRS WERE FOUND FOR ATOM LIST 42075 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29869 from a total of 764353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2878 -62.90110 -0.21565 0.63922 INTE EXTERN> -27.09527 -35.80583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9011" Parameter: A <- "-62.9011" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0953" Parameter: B <- "-27.0953" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8058" Parameter: C <- "-35.8058" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2878 TOTAL ENERGY = -62.9011 RDTITL> * VAN DER WAALS = -27.0953 ELECTROSTATIC = -35.8058 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2878" Parameter: CONF_N -> "8002" Comparing "2878" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2879" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765653 ATOM PAIRS WERE FOUND FOR ATOM LIST 41978 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29494 from a total of 765653 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2879 -57.84515 -5.05595 0.54187 INTE EXTERN> -29.99514 -27.85002 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.8452" Parameter: A <- "-57.8452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9951" Parameter: B <- "-29.9951" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.85" Parameter: C <- "-27.85" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2879 TOTAL ENERGY = -57.8452 RDTITL> * VAN DER WAALS = -29.9951 ELECTROSTATIC = -27.85 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2879" Parameter: CONF_N -> "8002" Comparing "2879" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2880" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765653 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759542 ATOM PAIRS WERE FOUND FOR ATOM LIST 41824 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29124 from a total of 759542 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2880 -63.53192 5.68677 0.49086 INTE EXTERN> -32.57007 -30.96185 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5319" Parameter: A <- "-63.5319" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5701" Parameter: B <- "-32.5701" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.9619" Parameter: C <- "-30.9619" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2880 TOTAL ENERGY = -63.5319 RDTITL> * VAN DER WAALS = -32.5701 ELECTROSTATIC = -30.9619 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2880" Parameter: CONF_N -> "8002" Comparing "2880" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2881" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759542 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763548 ATOM PAIRS WERE FOUND FOR ATOM LIST 42088 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29136 from a total of 763548 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2881 -65.75679 2.22487 0.56241 INTE EXTERN> -30.49010 -35.26669 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7568" Parameter: A <- "-65.7568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4901" Parameter: B <- "-30.4901" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2667" Parameter: C <- "-35.2667" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2881 TOTAL ENERGY = -65.7568 RDTITL> * VAN DER WAALS = -30.4901 ELECTROSTATIC = -35.2667 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2881" Parameter: CONF_N -> "8002" Comparing "2881" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2882" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763548 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766410 ATOM PAIRS WERE FOUND FOR ATOM LIST 42275 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29658 from a total of 766410 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2882 -66.96778 1.21099 0.52264 INTE EXTERN> -30.92814 -36.03963 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9678" Parameter: A <- "-66.9678" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9281" Parameter: B <- "-30.9281" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0396" Parameter: C <- "-36.0396" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2882 TOTAL ENERGY = -66.9678 RDTITL> * VAN DER WAALS = -30.9281 ELECTROSTATIC = -36.0396 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2882" Parameter: CONF_N -> "8002" Comparing "2882" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2883" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766410 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760779 ATOM PAIRS WERE FOUND FOR ATOM LIST 41852 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29550 from a total of 760779 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2883 -63.37694 -3.59084 0.70602 INTE EXTERN> -26.27492 -37.10202 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3769" Parameter: A <- "-63.3769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2749" Parameter: B <- "-26.2749" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.102" Parameter: C <- "-37.102" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2883 TOTAL ENERGY = -63.3769 RDTITL> * VAN DER WAALS = -26.2749 ELECTROSTATIC = -37.102 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2883" Parameter: CONF_N -> "8002" Comparing "2883" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2884" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760779 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766408 ATOM PAIRS WERE FOUND FOR ATOM LIST 42197 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29055 from a total of 766408 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2884 -58.83232 -4.54461 0.64073 INTE EXTERN> -26.60008 -32.23225 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.8323" Parameter: A <- "-58.8323" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6001" Parameter: B <- "-26.6001" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2322" Parameter: C <- "-32.2322" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2884 TOTAL ENERGY = -58.8323 RDTITL> * VAN DER WAALS = -26.6001 ELECTROSTATIC = -32.2322 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2884" Parameter: CONF_N -> "8002" Comparing "2884" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2885" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766408 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769967 ATOM PAIRS WERE FOUND FOR ATOM LIST 42306 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29291 from a total of 769967 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2885 -61.36597 2.53365 0.55335 INTE EXTERN> -29.94446 -31.42151 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.366" Parameter: A <- "-61.366" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9445" Parameter: B <- "-29.9445" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4215" Parameter: C <- "-31.4215" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2885 TOTAL ENERGY = -61.366 RDTITL> * VAN DER WAALS = -29.9445 ELECTROSTATIC = -31.4215 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2885" Parameter: CONF_N -> "8002" Comparing "2885" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2886" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769967 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760258 ATOM PAIRS WERE FOUND FOR ATOM LIST 41644 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28889 from a total of 760258 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2886 -62.87015 1.50417 0.62840 INTE EXTERN> -26.99930 -35.87085 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.8701" Parameter: A <- "-62.8701" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9993" Parameter: B <- "-26.9993" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8708" Parameter: C <- "-35.8708" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2886 TOTAL ENERGY = -62.8701 RDTITL> * VAN DER WAALS = -26.9993 ELECTROSTATIC = -35.8708 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2886" Parameter: CONF_N -> "8002" Comparing "2886" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2887" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760258 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764108 ATOM PAIRS WERE FOUND FOR ATOM LIST 42092 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28523 from a total of 764108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2887 -70.18010 7.30996 0.56685 INTE EXTERN> -29.18174 -40.99836 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1801" Parameter: A <- "-70.1801" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1817" Parameter: B <- "-29.1817" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9984" Parameter: C <- "-40.9984" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2887 TOTAL ENERGY = -70.1801 RDTITL> * VAN DER WAALS = -29.1817 ELECTROSTATIC = -40.9984 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2887" Parameter: CONF_N -> "8002" Comparing "2887" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2888" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764742 ATOM PAIRS WERE FOUND FOR ATOM LIST 41953 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28981 from a total of 764742 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2888 -62.99865 -7.18145 0.80542 INTE EXTERN> -21.74487 -41.25378 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9986" Parameter: A <- "-62.9986" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.7449" Parameter: B <- "-21.7449" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2538" Parameter: C <- "-41.2538" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2888 TOTAL ENERGY = -62.9986 RDTITL> * VAN DER WAALS = -21.7449 ELECTROSTATIC = -41.2538 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2888" Parameter: CONF_N -> "8002" Comparing "2888" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2889" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764742 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765538 ATOM PAIRS WERE FOUND FOR ATOM LIST 42090 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29362 from a total of 765538 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2889 -68.54259 5.54394 0.57265 INTE EXTERN> -28.87298 -39.66961 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5426" Parameter: A <- "-68.5426" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.873" Parameter: B <- "-28.873" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6696" Parameter: C <- "-39.6696" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2889 TOTAL ENERGY = -68.5426 RDTITL> * VAN DER WAALS = -28.873 ELECTROSTATIC = -39.6696 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2889" Parameter: CONF_N -> "8002" Comparing "2889" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2890" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765538 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761550 ATOM PAIRS WERE FOUND FOR ATOM LIST 41695 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29390 from a total of 761550 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2890 -64.90300 -3.63959 0.65565 INTE EXTERN> -26.45514 -38.44786 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.903" Parameter: A <- "-64.903" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4551" Parameter: B <- "-26.4551" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4479" Parameter: C <- "-38.4479" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2890 TOTAL ENERGY = -64.903 RDTITL> * VAN DER WAALS = -26.4551 ELECTROSTATIC = -38.4479 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2890" Parameter: CONF_N -> "8002" Comparing "2890" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2891" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761550 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759260 ATOM PAIRS WERE FOUND FOR ATOM LIST 41885 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29076 from a total of 759260 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2891 -64.21814 -0.68486 0.54998 INTE EXTERN> -29.00938 -35.20876 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2181" Parameter: A <- "-64.2181" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0094" Parameter: B <- "-29.0094" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2088" Parameter: C <- "-35.2088" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2891 TOTAL ENERGY = -64.2181 RDTITL> * VAN DER WAALS = -29.0094 ELECTROSTATIC = -35.2088 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2891" Parameter: CONF_N -> "8002" Comparing "2891" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2892" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759260 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759150 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28671 from a total of 759150 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2892 -63.01226 -1.20588 0.61108 INTE EXTERN> -26.88766 -36.12460 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.0123" Parameter: A <- "-63.0123" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8877" Parameter: B <- "-26.8877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1246" Parameter: C <- "-36.1246" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2892 TOTAL ENERGY = -63.0123 RDTITL> * VAN DER WAALS = -26.8877 ELECTROSTATIC = -36.1246 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2892" Parameter: CONF_N -> "8002" Comparing "2892" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2893" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759150 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761649 ATOM PAIRS WERE FOUND FOR ATOM LIST 41689 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29240 from a total of 761649 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2893 -62.10711 -0.90515 0.56861 INTE EXTERN> -28.87655 -33.23056 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.1071" Parameter: A <- "-62.1071" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8766" Parameter: B <- "-28.8766" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2306" Parameter: C <- "-33.2306" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2893 TOTAL ENERGY = -62.1071 RDTITL> * VAN DER WAALS = -28.8766 ELECTROSTATIC = -33.2306 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2893" Parameter: CONF_N -> "8002" Comparing "2893" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2894" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761649 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759698 ATOM PAIRS WERE FOUND FOR ATOM LIST 41896 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28399 from a total of 759698 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2894 -61.41264 -0.69448 0.56648 INTE EXTERN> -28.59193 -32.82071 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.4126" Parameter: A <- "-61.4126" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5919" Parameter: B <- "-28.5919" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.8207" Parameter: C <- "-32.8207" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2894 TOTAL ENERGY = -61.4126 RDTITL> * VAN DER WAALS = -28.5919 ELECTROSTATIC = -32.8207 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2894" Parameter: CONF_N -> "8002" Comparing "2894" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2895" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759698 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760249 ATOM PAIRS WERE FOUND FOR ATOM LIST 41956 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29435 from a total of 760249 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2895 -67.93536 6.52272 0.65721 INTE EXTERN> -28.17794 -39.75742 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9354" Parameter: A <- "-67.9354" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1779" Parameter: B <- "-28.1779" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7574" Parameter: C <- "-39.7574" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2895 TOTAL ENERGY = -67.9354 RDTITL> * VAN DER WAALS = -28.1779 ELECTROSTATIC = -39.7574 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2895" Parameter: CONF_N -> "8002" Comparing "2895" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2896" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760249 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765736 ATOM PAIRS WERE FOUND FOR ATOM LIST 41910 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29262 from a total of 765736 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2896 -70.15176 2.21641 0.62742 INTE EXTERN> -28.36515 -41.78661 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1518" Parameter: A <- "-70.1518" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3652" Parameter: B <- "-28.3652" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7866" Parameter: C <- "-41.7866" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2896 TOTAL ENERGY = -70.1518 RDTITL> * VAN DER WAALS = -28.3652 ELECTROSTATIC = -41.7866 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2896" Parameter: CONF_N -> "8002" Comparing "2896" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2897" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765736 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763415 ATOM PAIRS WERE FOUND FOR ATOM LIST 41977 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29619 from a total of 763415 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2897 -67.86267 -2.28910 0.56233 INTE EXTERN> -29.44513 -38.41754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8627" Parameter: A <- "-67.8627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4451" Parameter: B <- "-29.4451" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4175" Parameter: C <- "-38.4175" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2897 TOTAL ENERGY = -67.8627 RDTITL> * VAN DER WAALS = -29.4451 ELECTROSTATIC = -38.4175 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2897" Parameter: CONF_N -> "8002" Comparing "2897" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2898" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763415 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763673 ATOM PAIRS WERE FOUND FOR ATOM LIST 41970 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29644 from a total of 763673 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2898 -67.78509 -0.07758 0.64965 INTE EXTERN> -27.86558 -39.91950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7851" Parameter: A <- "-67.7851" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8656" Parameter: B <- "-27.8656" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9195" Parameter: C <- "-39.9195" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2898 TOTAL ENERGY = -67.7851 RDTITL> * VAN DER WAALS = -27.8656 ELECTROSTATIC = -39.9195 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2898" Parameter: CONF_N -> "8002" Comparing "2898" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2899" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763673 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769482 ATOM PAIRS WERE FOUND FOR ATOM LIST 42477 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30130 from a total of 769482 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2899 -69.17127 1.38618 0.62066 INTE EXTERN> -28.44559 -40.72567 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1713" Parameter: A <- "-69.1713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4456" Parameter: B <- "-28.4456" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7257" Parameter: C <- "-40.7257" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2899 TOTAL ENERGY = -69.1713 RDTITL> * VAN DER WAALS = -28.4456 ELECTROSTATIC = -40.7257 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2899" Parameter: CONF_N -> "8002" Comparing "2899" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2900" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769482 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766516 ATOM PAIRS WERE FOUND FOR ATOM LIST 42247 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29534 from a total of 766516 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2900 -68.03312 -1.13814 0.78323 INTE EXTERN> -25.38386 -42.64927 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0331" Parameter: A <- "-68.0331" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3839" Parameter: B <- "-25.3839" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6493" Parameter: C <- "-42.6493" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2900 TOTAL ENERGY = -68.0331 RDTITL> * VAN DER WAALS = -25.3839 ELECTROSTATIC = -42.6493 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2900" Parameter: CONF_N -> "8002" Comparing "2900" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2901" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766516 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763415 ATOM PAIRS WERE FOUND FOR ATOM LIST 42174 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29379 from a total of 763415 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2901 -69.69812 1.66500 0.54963 INTE EXTERN> -30.83421 -38.86390 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6981" Parameter: A <- "-69.6981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8342" Parameter: B <- "-30.8342" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8639" Parameter: C <- "-38.8639" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2901 TOTAL ENERGY = -69.6981 RDTITL> * VAN DER WAALS = -30.8342 ELECTROSTATIC = -38.8639 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2901" Parameter: CONF_N -> "8002" Comparing "2901" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2902" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763415 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761913 ATOM PAIRS WERE FOUND FOR ATOM LIST 42005 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28831 from a total of 761913 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2902 -61.61453 -8.08359 0.63242 INTE EXTERN> -25.17872 -36.43580 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.6145" Parameter: A <- "-61.6145" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1787" Parameter: B <- "-25.1787" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4358" Parameter: C <- "-36.4358" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2902 TOTAL ENERGY = -61.6145 RDTITL> * VAN DER WAALS = -25.1787 ELECTROSTATIC = -36.4358 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2902" Parameter: CONF_N -> "8002" Comparing "2902" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2903" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761913 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768109 ATOM PAIRS WERE FOUND FOR ATOM LIST 42358 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29782 from a total of 768109 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2903 -67.76345 6.14893 0.68395 INTE EXTERN> -25.33381 -42.42965 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7635" Parameter: A <- "-67.7635" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3338" Parameter: B <- "-25.3338" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4296" Parameter: C <- "-42.4296" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2903 TOTAL ENERGY = -67.7635 RDTITL> * VAN DER WAALS = -25.3338 ELECTROSTATIC = -42.4296 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2903" Parameter: CONF_N -> "8002" Comparing "2903" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2904" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768109 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770576 ATOM PAIRS WERE FOUND FOR ATOM LIST 42374 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29853 from a total of 770576 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2904 -60.89434 -6.86911 0.69078 INTE EXTERN> -24.04088 -36.85346 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.8943" Parameter: A <- "-60.8943" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0409" Parameter: B <- "-24.0409" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8535" Parameter: C <- "-36.8535" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2904 TOTAL ENERGY = -60.8943 RDTITL> * VAN DER WAALS = -24.0409 ELECTROSTATIC = -36.8535 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2904" Parameter: CONF_N -> "8002" Comparing "2904" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2905" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770576 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762596 ATOM PAIRS WERE FOUND FOR ATOM LIST 41950 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29724 from a total of 762596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2905 -58.25762 -2.63673 0.53368 INTE EXTERN> -29.37476 -28.88285 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.2576" Parameter: A <- "-58.2576" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3748" Parameter: B <- "-29.3748" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.8829" Parameter: C <- "-28.8829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2905 TOTAL ENERGY = -58.2576 RDTITL> * VAN DER WAALS = -29.3748 ELECTROSTATIC = -28.8829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2905" Parameter: CONF_N -> "8002" Comparing "2905" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2906" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754857 ATOM PAIRS WERE FOUND FOR ATOM LIST 41792 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30314 from a total of 754857 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2906 -69.28080 11.02318 0.61727 INTE EXTERN> -30.46371 -38.81709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2808" Parameter: A <- "-69.2808" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4637" Parameter: B <- "-30.4637" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8171" Parameter: C <- "-38.8171" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2906 TOTAL ENERGY = -69.2808 RDTITL> * VAN DER WAALS = -30.4637 ELECTROSTATIC = -38.8171 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2906" Parameter: CONF_N -> "8002" Comparing "2906" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2907" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754857 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757232 ATOM PAIRS WERE FOUND FOR ATOM LIST 41748 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30034 from a total of 757232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2907 -65.16101 -4.11979 0.56147 INTE EXTERN> -30.30317 -34.85783 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.161" Parameter: A <- "-65.161" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3032" Parameter: B <- "-30.3032" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8578" Parameter: C <- "-34.8578" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2907 TOTAL ENERGY = -65.161 RDTITL> * VAN DER WAALS = -30.3032 ELECTROSTATIC = -34.8578 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2907" Parameter: CONF_N -> "8002" Comparing "2907" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2908" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757957 ATOM PAIRS WERE FOUND FOR ATOM LIST 41852 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29959 from a total of 757957 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2908 -65.82371 0.66270 0.58268 INTE EXTERN> -28.21335 -37.61036 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8237" Parameter: A <- "-65.8237" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2133" Parameter: B <- "-28.2133" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6104" Parameter: C <- "-37.6104" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2908 TOTAL ENERGY = -65.8237 RDTITL> * VAN DER WAALS = -28.2133 ELECTROSTATIC = -37.6104 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2908" Parameter: CONF_N -> "8002" Comparing "2908" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2909" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757957 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762767 ATOM PAIRS WERE FOUND FOR ATOM LIST 42169 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30009 from a total of 762767 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2909 -69.94518 4.12147 0.64667 INTE EXTERN> -30.51099 -39.43419 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9452" Parameter: A <- "-69.9452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.511" Parameter: B <- "-30.511" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4342" Parameter: C <- "-39.4342" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2909 TOTAL ENERGY = -69.9452 RDTITL> * VAN DER WAALS = -30.511 ELECTROSTATIC = -39.4342 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2909" Parameter: CONF_N -> "8002" Comparing "2909" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2910" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762767 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763096 ATOM PAIRS WERE FOUND FOR ATOM LIST 42342 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29687 from a total of 763096 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2910 -73.83254 3.88736 0.60611 INTE EXTERN> -31.79312 -42.03942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8325" Parameter: A <- "-73.8325" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7931" Parameter: B <- "-31.7931" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0394" Parameter: C <- "-42.0394" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2910 TOTAL ENERGY = -73.8325 RDTITL> * VAN DER WAALS = -31.7931 ELECTROSTATIC = -42.0394 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2910" Parameter: CONF_N -> "8002" Comparing "2910" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2911" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763096 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761957 ATOM PAIRS WERE FOUND FOR ATOM LIST 41977 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29278 from a total of 761957 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2911 -66.38074 -7.45179 0.55641 INTE EXTERN> -30.36241 -36.01833 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3807" Parameter: A <- "-66.3807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3624" Parameter: B <- "-30.3624" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0183" Parameter: C <- "-36.0183" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2911 TOTAL ENERGY = -66.3807 RDTITL> * VAN DER WAALS = -30.3624 ELECTROSTATIC = -36.0183 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2911" Parameter: CONF_N -> "8002" Comparing "2911" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2912" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761957 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758351 ATOM PAIRS WERE FOUND FOR ATOM LIST 41917 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29500 from a total of 758351 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2912 -62.22628 -4.15446 0.61791 INTE EXTERN> -29.07442 -33.15187 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.2263" Parameter: A <- "-62.2263" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0744" Parameter: B <- "-29.0744" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1519" Parameter: C <- "-33.1519" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2912 TOTAL ENERGY = -62.2263 RDTITL> * VAN DER WAALS = -29.0744 ELECTROSTATIC = -33.1519 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2912" Parameter: CONF_N -> "8002" Comparing "2912" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2913" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758351 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762197 ATOM PAIRS WERE FOUND FOR ATOM LIST 42037 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29177 from a total of 762197 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2913 -63.48364 1.25735 0.61637 INTE EXTERN> -28.63131 -34.85233 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4836" Parameter: A <- "-63.4836" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6313" Parameter: B <- "-28.6313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8523" Parameter: C <- "-34.8523" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2913 TOTAL ENERGY = -63.4836 RDTITL> * VAN DER WAALS = -28.6313 ELECTROSTATIC = -34.8523 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2913" Parameter: CONF_N -> "8002" Comparing "2913" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2914" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762197 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762636 ATOM PAIRS WERE FOUND FOR ATOM LIST 42143 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30030 from a total of 762636 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2914 -66.86201 3.37838 0.54115 INTE EXTERN> -31.26418 -35.59783 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.862" Parameter: A <- "-66.862" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2642" Parameter: B <- "-31.2642" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5978" Parameter: C <- "-35.5978" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2914 TOTAL ENERGY = -66.862 RDTITL> * VAN DER WAALS = -31.2642 ELECTROSTATIC = -35.5978 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2914" Parameter: CONF_N -> "8002" Comparing "2914" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2915" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762636 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766823 ATOM PAIRS WERE FOUND FOR ATOM LIST 42093 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29847 from a total of 766823 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2915 -53.02662 -13.83539 0.62861 INTE EXTERN> -25.36745 -27.65918 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-53.0266" Parameter: A <- "-53.0266" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3674" Parameter: B <- "-25.3674" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.6592" Parameter: C <- "-27.6592" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2915 TOTAL ENERGY = -53.0266 RDTITL> * VAN DER WAALS = -25.3674 ELECTROSTATIC = -27.6592 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2915" Parameter: CONF_N -> "8002" Comparing "2915" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2916" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766823 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757336 ATOM PAIRS WERE FOUND FOR ATOM LIST 41853 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29032 from a total of 757336 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2916 -59.99927 6.97264 0.64296 INTE EXTERN> -27.11922 -32.88004 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.9993" Parameter: A <- "-59.9993" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1192" Parameter: B <- "-27.1192" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.88" Parameter: C <- "-32.88" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2916 TOTAL ENERGY = -59.9993 RDTITL> * VAN DER WAALS = -27.1192 ELECTROSTATIC = -32.88 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2916" Parameter: CONF_N -> "8002" Comparing "2916" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2917" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757336 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765899 ATOM PAIRS WERE FOUND FOR ATOM LIST 42362 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29779 from a total of 765899 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2917 -62.71803 2.71876 0.63351 INTE EXTERN> -30.65549 -32.06254 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.718" Parameter: A <- "-62.718" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6555" Parameter: B <- "-30.6555" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.0625" Parameter: C <- "-32.0625" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2917 TOTAL ENERGY = -62.718 RDTITL> * VAN DER WAALS = -30.6555 ELECTROSTATIC = -32.0625 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2917" Parameter: CONF_N -> "8002" Comparing "2917" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2918" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765899 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766935 ATOM PAIRS WERE FOUND FOR ATOM LIST 42274 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29856 from a total of 766935 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2918 -67.92588 5.20785 0.60223 INTE EXTERN> -28.77488 -39.15100 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9259" Parameter: A <- "-67.9259" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7749" Parameter: B <- "-28.7749" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.151" Parameter: C <- "-39.151" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2918 TOTAL ENERGY = -67.9259 RDTITL> * VAN DER WAALS = -28.7749 ELECTROSTATIC = -39.151 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2918" Parameter: CONF_N -> "8002" Comparing "2918" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2919" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766935 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768109 ATOM PAIRS WERE FOUND FOR ATOM LIST 42397 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30401 from a total of 768109 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2919 -59.67404 -8.25184 0.66632 INTE EXTERN> -26.83159 -32.84245 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.674" Parameter: A <- "-59.674" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8316" Parameter: B <- "-26.8316" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.8424" Parameter: C <- "-32.8424" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2919 TOTAL ENERGY = -59.674 RDTITL> * VAN DER WAALS = -26.8316 ELECTROSTATIC = -32.8424 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2919" Parameter: CONF_N -> "8002" Comparing "2919" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2920" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768109 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769233 ATOM PAIRS WERE FOUND FOR ATOM LIST 42387 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30253 from a total of 769233 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2920 -66.00509 6.33105 0.62563 INTE EXTERN> -30.41693 -35.58816 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0051" Parameter: A <- "-66.0051" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4169" Parameter: B <- "-30.4169" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5882" Parameter: C <- "-35.5882" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2920 TOTAL ENERGY = -66.0051 RDTITL> * VAN DER WAALS = -30.4169 ELECTROSTATIC = -35.5882 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2920" Parameter: CONF_N -> "8002" Comparing "2920" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2921" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769233 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765913 ATOM PAIRS WERE FOUND FOR ATOM LIST 42244 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30729 from a total of 765913 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2921 -59.68080 -6.32429 0.63589 INTE EXTERN> -29.01928 -30.66153 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.6808" Parameter: A <- "-59.6808" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0193" Parameter: B <- "-29.0193" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.6615" Parameter: C <- "-30.6615" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2921 TOTAL ENERGY = -59.6808 RDTITL> * VAN DER WAALS = -29.0193 ELECTROSTATIC = -30.6615 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2921" Parameter: CONF_N -> "8002" Comparing "2921" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2922" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765913 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758401 ATOM PAIRS WERE FOUND FOR ATOM LIST 42010 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29564 from a total of 758401 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2922 -58.90366 -0.77714 0.51260 INTE EXTERN> -31.49108 -27.41258 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.9037" Parameter: A <- "-58.9037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4911" Parameter: B <- "-31.4911" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.4126" Parameter: C <- "-27.4126" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2922 TOTAL ENERGY = -58.9037 RDTITL> * VAN DER WAALS = -31.4911 ELECTROSTATIC = -27.4126 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2922" Parameter: CONF_N -> "8002" Comparing "2922" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2923" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758401 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763634 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29826 from a total of 763634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2923 -61.43137 2.52772 0.53418 INTE EXTERN> -32.91035 -28.52103 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.4314" Parameter: A <- "-61.4314" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9103" Parameter: B <- "-32.9103" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.521" Parameter: C <- "-28.521" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2923 TOTAL ENERGY = -61.4314 RDTITL> * VAN DER WAALS = -32.9103 ELECTROSTATIC = -28.521 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2923" Parameter: CONF_N -> "8002" Comparing "2923" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2924" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763035 ATOM PAIRS WERE FOUND FOR ATOM LIST 41969 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30238 from a total of 763035 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2924 -64.72498 3.29360 0.50800 INTE EXTERN> -31.66659 -33.05838 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.725" Parameter: A <- "-64.725" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6666" Parameter: B <- "-31.6666" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.0584" Parameter: C <- "-33.0584" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2924 TOTAL ENERGY = -64.725 RDTITL> * VAN DER WAALS = -31.6666 ELECTROSTATIC = -33.0584 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2924" Parameter: CONF_N -> "8002" Comparing "2924" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2925" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763035 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767729 ATOM PAIRS WERE FOUND FOR ATOM LIST 42207 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30043 from a total of 767729 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2925 -55.91864 -8.80634 0.40938 INTE EXTERN> -34.70410 -21.21454 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.9186" Parameter: A <- "-55.9186" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.7041" Parameter: B <- "-34.7041" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-21.2145" Parameter: C <- "-21.2145" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2925 TOTAL ENERGY = -55.9186 RDTITL> * VAN DER WAALS = -34.7041 ELECTROSTATIC = -21.2145 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2925" Parameter: CONF_N -> "8002" Comparing "2925" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2926" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767729 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753603 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29403 from a total of 753603 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2926 -64.23521 8.31657 0.59320 INTE EXTERN> -31.08380 -33.15141 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2352" Parameter: A <- "-64.2352" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0838" Parameter: B <- "-31.0838" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1514" Parameter: C <- "-33.1514" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2926 TOTAL ENERGY = -64.2352 RDTITL> * VAN DER WAALS = -31.0838 ELECTROSTATIC = -33.1514 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2926" Parameter: CONF_N -> "8002" Comparing "2926" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2927" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753603 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756117 ATOM PAIRS WERE FOUND FOR ATOM LIST 41647 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29092 from a total of 756117 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2927 -56.24800 -7.98722 0.56412 INTE EXTERN> -28.86549 -27.38251 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-56.248" Parameter: A <- "-56.248" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8655" Parameter: B <- "-28.8655" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.3825" Parameter: C <- "-27.3825" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2927 TOTAL ENERGY = -56.248 RDTITL> * VAN DER WAALS = -28.8655 ELECTROSTATIC = -27.3825 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2927" Parameter: CONF_N -> "8002" Comparing "2927" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2928" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756117 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754434 ATOM PAIRS WERE FOUND FOR ATOM LIST 41686 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29505 from a total of 754434 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2928 -56.83655 0.58856 0.54264 INTE EXTERN> -28.94642 -27.89014 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-56.8366" Parameter: A <- "-56.8366" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9464" Parameter: B <- "-28.9464" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.8901" Parameter: C <- "-27.8901" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2928 TOTAL ENERGY = -56.8366 RDTITL> * VAN DER WAALS = -28.9464 ELECTROSTATIC = -27.8901 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2928" Parameter: CONF_N -> "8002" Comparing "2928" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2929" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754434 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763151 ATOM PAIRS WERE FOUND FOR ATOM LIST 42073 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29425 from a total of 763151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2929 -64.25280 7.41625 0.58700 INTE EXTERN> -29.23701 -35.01579 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2528" Parameter: A <- "-64.2528" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.237" Parameter: B <- "-29.237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0158" Parameter: C <- "-35.0158" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2929 TOTAL ENERGY = -64.2528 RDTITL> * VAN DER WAALS = -29.237 ELECTROSTATIC = -35.0158 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2929" Parameter: CONF_N -> "8002" Comparing "2929" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2930" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767557 ATOM PAIRS WERE FOUND FOR ATOM LIST 42435 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30058 from a total of 767557 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2930 -60.92088 -3.33192 0.66388 INTE EXTERN> -26.73349 -34.18740 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.9209" Parameter: A <- "-60.9209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7335" Parameter: B <- "-26.7335" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1874" Parameter: C <- "-34.1874" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2930 TOTAL ENERGY = -60.9209 RDTITL> * VAN DER WAALS = -26.7335 ELECTROSTATIC = -34.1874 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2930" Parameter: CONF_N -> "8002" Comparing "2930" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2931" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767557 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763468 ATOM PAIRS WERE FOUND FOR ATOM LIST 42191 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28878 from a total of 763468 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2931 -58.50832 -2.41256 0.56510 INTE EXTERN> -29.34057 -29.16774 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.5083" Parameter: A <- "-58.5083" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3406" Parameter: B <- "-29.3406" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.1677" Parameter: C <- "-29.1677" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2931 TOTAL ENERGY = -58.5083 RDTITL> * VAN DER WAALS = -29.3406 ELECTROSTATIC = -29.1677 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2931" Parameter: CONF_N -> "8002" Comparing "2931" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2932" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763468 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758863 ATOM PAIRS WERE FOUND FOR ATOM LIST 41839 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29122 from a total of 758863 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2932 -59.95383 1.44552 0.65566 INTE EXTERN> -28.21971 -31.73412 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.9538" Parameter: A <- "-59.9538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2197" Parameter: B <- "-28.2197" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.7341" Parameter: C <- "-31.7341" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2932 TOTAL ENERGY = -59.9538 RDTITL> * VAN DER WAALS = -28.2197 ELECTROSTATIC = -31.7341 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2932" Parameter: CONF_N -> "8002" Comparing "2932" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2933" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758863 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756922 ATOM PAIRS WERE FOUND FOR ATOM LIST 41711 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29749 from a total of 756922 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2933 -61.02872 1.07489 0.48308 INTE EXTERN> -33.61552 -27.41321 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.0287" Parameter: A <- "-61.0287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6155" Parameter: B <- "-33.6155" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.4132" Parameter: C <- "-27.4132" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2933 TOTAL ENERGY = -61.0287 RDTITL> * VAN DER WAALS = -33.6155 ELECTROSTATIC = -27.4132 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2933" Parameter: CONF_N -> "8002" Comparing "2933" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2934" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756922 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759232 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29747 from a total of 759232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2934 -58.50972 -2.51900 0.60950 INTE EXTERN> -27.91343 -30.59629 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.5097" Parameter: A <- "-58.5097" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9134" Parameter: B <- "-27.9134" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.5963" Parameter: C <- "-30.5963" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2934 TOTAL ENERGY = -58.5097 RDTITL> * VAN DER WAALS = -27.9134 ELECTROSTATIC = -30.5963 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2934" Parameter: CONF_N -> "8002" Comparing "2934" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2935" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761633 ATOM PAIRS WERE FOUND FOR ATOM LIST 41790 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29505 from a total of 761633 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2935 -61.77491 3.26519 0.57670 INTE EXTERN> -29.31774 -32.45717 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.7749" Parameter: A <- "-61.7749" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3177" Parameter: B <- "-29.3177" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.4572" Parameter: C <- "-32.4572" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2935 TOTAL ENERGY = -61.7749 RDTITL> * VAN DER WAALS = -29.3177 ELECTROSTATIC = -32.4572 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2935" Parameter: CONF_N -> "8002" Comparing "2935" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2936" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761633 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760129 ATOM PAIRS WERE FOUND FOR ATOM LIST 41839 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29950 from a total of 760129 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2936 -58.99557 -2.77934 0.53013 INTE EXTERN> -31.60955 -27.38602 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.9956" Parameter: A <- "-58.9956" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6095" Parameter: B <- "-31.6095" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.386" Parameter: C <- "-27.386" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2936 TOTAL ENERGY = -58.9956 RDTITL> * VAN DER WAALS = -31.6095 ELECTROSTATIC = -27.386 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2936" Parameter: CONF_N -> "8002" Comparing "2936" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2937" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760129 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757984 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29364 from a total of 757984 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2937 -59.92736 0.93179 0.54247 INTE EXTERN> -32.36746 -27.55990 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.9274" Parameter: A <- "-59.9274" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3675" Parameter: B <- "-32.3675" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.5599" Parameter: C <- "-27.5599" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2937 TOTAL ENERGY = -59.9274 RDTITL> * VAN DER WAALS = -32.3675 ELECTROSTATIC = -27.5599 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2937" Parameter: CONF_N -> "8002" Comparing "2937" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2938" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757984 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758964 ATOM PAIRS WERE FOUND FOR ATOM LIST 41774 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29263 from a total of 758964 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2938 -54.10547 -5.82190 0.50261 INTE EXTERN> -30.35744 -23.74803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-54.1055" Parameter: A <- "-54.1055" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3574" Parameter: B <- "-30.3574" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-23.748" Parameter: C <- "-23.748" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2938 TOTAL ENERGY = -54.1055 RDTITL> * VAN DER WAALS = -30.3574 ELECTROSTATIC = -23.748 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2938" Parameter: CONF_N -> "8002" Comparing "2938" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2939" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758964 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760054 ATOM PAIRS WERE FOUND FOR ATOM LIST 41979 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29763 from a total of 760054 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2939 -53.37899 -0.72648 0.60839 INTE EXTERN> -28.05065 -25.32834 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-53.379" Parameter: A <- "-53.379" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0507" Parameter: B <- "-28.0507" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-25.3283" Parameter: C <- "-25.3283" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2939 TOTAL ENERGY = -53.379 RDTITL> * VAN DER WAALS = -28.0507 ELECTROSTATIC = -25.3283 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2939" Parameter: CONF_N -> "8002" Comparing "2939" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2940" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760054 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758496 ATOM PAIRS WERE FOUND FOR ATOM LIST 41795 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29366 from a total of 758496 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2940 -63.82433 10.44534 0.55330 INTE EXTERN> -32.06291 -31.76142 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.8243" Parameter: A <- "-63.8243" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0629" Parameter: B <- "-32.0629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.7614" Parameter: C <- "-31.7614" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2940 TOTAL ENERGY = -63.8243 RDTITL> * VAN DER WAALS = -32.0629 ELECTROSTATIC = -31.7614 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2940" Parameter: CONF_N -> "8002" Comparing "2940" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2941" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758496 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757800 ATOM PAIRS WERE FOUND FOR ATOM LIST 41878 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29104 from a total of 757800 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2941 -64.35838 0.53405 0.65163 INTE EXTERN> -28.77217 -35.58621 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3584" Parameter: A <- "-64.3584" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7722" Parameter: B <- "-28.7722" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5862" Parameter: C <- "-35.5862" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2941 TOTAL ENERGY = -64.3584 RDTITL> * VAN DER WAALS = -28.7722 ELECTROSTATIC = -35.5862 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2941" Parameter: CONF_N -> "8002" Comparing "2941" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2942" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757800 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763816 ATOM PAIRS WERE FOUND FOR ATOM LIST 42142 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29590 from a total of 763816 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2942 -62.48691 -1.87147 0.59210 INTE EXTERN> -30.24038 -32.24653 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.4869" Parameter: A <- "-62.4869" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2404" Parameter: B <- "-30.2404" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2465" Parameter: C <- "-32.2465" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2942 TOTAL ENERGY = -62.4869 RDTITL> * VAN DER WAALS = -30.2404 ELECTROSTATIC = -32.2465 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2942" Parameter: CONF_N -> "8002" Comparing "2942" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2943" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763816 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761928 ATOM PAIRS WERE FOUND FOR ATOM LIST 41931 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29726 from a total of 761928 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2943 -57.67129 -4.81562 0.46444 INTE EXTERN> -32.82910 -24.84219 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.6713" Parameter: A <- "-57.6713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8291" Parameter: B <- "-32.8291" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-24.8422" Parameter: C <- "-24.8422" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2943 TOTAL ENERGY = -57.6713 RDTITL> * VAN DER WAALS = -32.8291 ELECTROSTATIC = -24.8422 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2943" Parameter: CONF_N -> "8002" Comparing "2943" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2944" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761928 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757697 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29204 from a total of 757697 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2944 -58.55413 0.88284 0.52251 INTE EXTERN> -30.41249 -28.14164 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.5541" Parameter: A <- "-58.5541" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4125" Parameter: B <- "-30.4125" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.1416" Parameter: C <- "-28.1416" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2944 TOTAL ENERGY = -58.5541 RDTITL> * VAN DER WAALS = -30.4125 ELECTROSTATIC = -28.1416 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2944" Parameter: CONF_N -> "8002" Comparing "2944" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2945" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757697 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759999 ATOM PAIRS WERE FOUND FOR ATOM LIST 41826 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29514 from a total of 759999 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2945 -63.68280 5.12867 0.60460 INTE EXTERN> -28.91743 -34.76537 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6828" Parameter: A <- "-63.6828" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9174" Parameter: B <- "-28.9174" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7654" Parameter: C <- "-34.7654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2945 TOTAL ENERGY = -63.6828 RDTITL> * VAN DER WAALS = -28.9174 ELECTROSTATIC = -34.7654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2945" Parameter: CONF_N -> "8002" Comparing "2945" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2946" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759999 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762641 ATOM PAIRS WERE FOUND FOR ATOM LIST 42026 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29909 from a total of 762641 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2946 -63.41561 -0.26719 0.63360 INTE EXTERN> -28.14380 -35.27181 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4156" Parameter: A <- "-63.4156" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1438" Parameter: B <- "-28.1438" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2718" Parameter: C <- "-35.2718" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2946 TOTAL ENERGY = -63.4156 RDTITL> * VAN DER WAALS = -28.1438 ELECTROSTATIC = -35.2718 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2946" Parameter: CONF_N -> "8002" Comparing "2946" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2947" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762641 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760978 ATOM PAIRS WERE FOUND FOR ATOM LIST 41762 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29415 from a total of 760978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2947 -67.64585 4.23024 0.67911 INTE EXTERN> -27.02715 -40.61870 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6458" Parameter: A <- "-67.6458" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0272" Parameter: B <- "-27.0272" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6187" Parameter: C <- "-40.6187" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2947 TOTAL ENERGY = -67.6458 RDTITL> * VAN DER WAALS = -27.0272 ELECTROSTATIC = -40.6187 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2947" Parameter: CONF_N -> "8002" Comparing "2947" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2948" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757468 ATOM PAIRS WERE FOUND FOR ATOM LIST 41643 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29002 from a total of 757468 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2948 -59.55404 -8.09181 0.57884 INTE EXTERN> -30.43232 -29.12172 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.554" Parameter: A <- "-59.554" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4323" Parameter: B <- "-30.4323" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.1217" Parameter: C <- "-29.1217" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2948 TOTAL ENERGY = -59.554 RDTITL> * VAN DER WAALS = -30.4323 ELECTROSTATIC = -29.1217 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2948" Parameter: CONF_N -> "8002" Comparing "2948" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2949" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757468 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761800 ATOM PAIRS WERE FOUND FOR ATOM LIST 41921 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29464 from a total of 761800 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2949 -60.89231 1.33828 0.58954 INTE EXTERN> -29.35478 -31.53753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.8923" Parameter: A <- "-60.8923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3548" Parameter: B <- "-29.3548" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.5375" Parameter: C <- "-31.5375" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2949 TOTAL ENERGY = -60.8923 RDTITL> * VAN DER WAALS = -29.3548 ELECTROSTATIC = -31.5375 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2949" Parameter: CONF_N -> "8002" Comparing "2949" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2950" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761800 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758606 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29265 from a total of 758606 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2950 -58.99977 -1.89255 0.52972 INTE EXTERN> -30.43565 -28.56411 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.9998" Parameter: A <- "-58.9998" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4357" Parameter: B <- "-30.4357" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.5641" Parameter: C <- "-28.5641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2950 TOTAL ENERGY = -58.9998 RDTITL> * VAN DER WAALS = -30.4357 ELECTROSTATIC = -28.5641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2950" Parameter: CONF_N -> "8002" Comparing "2950" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2951" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758606 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761901 ATOM PAIRS WERE FOUND FOR ATOM LIST 41961 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29778 from a total of 761901 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2951 -56.15035 -2.84941 0.76751 INTE EXTERN> -23.14060 -33.00975 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-56.1504" Parameter: A <- "-56.1504" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.1406" Parameter: B <- "-23.1406" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.0097" Parameter: C <- "-33.0097" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2951 TOTAL ENERGY = -56.1504 RDTITL> * VAN DER WAALS = -23.1406 ELECTROSTATIC = -33.0097 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2951" Parameter: CONF_N -> "8002" Comparing "2951" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2952" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761901 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763021 ATOM PAIRS WERE FOUND FOR ATOM LIST 41899 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29271 from a total of 763021 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2952 -62.39772 6.24737 0.61592 INTE EXTERN> -27.98764 -34.41009 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3977" Parameter: A <- "-62.3977" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9876" Parameter: B <- "-27.9876" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4101" Parameter: C <- "-34.4101" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2952 TOTAL ENERGY = -62.3977 RDTITL> * VAN DER WAALS = -27.9876 ELECTROSTATIC = -34.4101 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2952" Parameter: CONF_N -> "8002" Comparing "2952" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2953" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763021 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763760 ATOM PAIRS WERE FOUND FOR ATOM LIST 42106 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29199 from a total of 763760 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2953 -59.52459 -2.87313 0.80076 INTE EXTERN> -22.19348 -37.33111 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.5246" Parameter: A <- "-59.5246" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.1935" Parameter: B <- "-22.1935" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3311" Parameter: C <- "-37.3311" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2953 TOTAL ENERGY = -59.5246 RDTITL> * VAN DER WAALS = -22.1935 ELECTROSTATIC = -37.3311 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2953" Parameter: CONF_N -> "8002" Comparing "2953" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2954" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763760 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762596 ATOM PAIRS WERE FOUND FOR ATOM LIST 41909 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29276 from a total of 762596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2954 -54.75029 -4.77430 0.68906 INTE EXTERN> -25.07576 -29.67453 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-54.7503" Parameter: A <- "-54.7503" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0758" Parameter: B <- "-25.0758" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.6745" Parameter: C <- "-29.6745" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2954 TOTAL ENERGY = -54.7503 RDTITL> * VAN DER WAALS = -25.0758 ELECTROSTATIC = -29.6745 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2954" Parameter: CONF_N -> "8002" Comparing "2954" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2955" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761506 ATOM PAIRS WERE FOUND FOR ATOM LIST 41986 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28584 from a total of 761506 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2955 -61.89301 7.14272 0.59208 INTE EXTERN> -27.44747 -34.44555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.893" Parameter: A <- "-61.893" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4475" Parameter: B <- "-27.4475" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4455" Parameter: C <- "-34.4455" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2955 TOTAL ENERGY = -61.893 RDTITL> * VAN DER WAALS = -27.4475 ELECTROSTATIC = -34.4455 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2955" Parameter: CONF_N -> "8002" Comparing "2955" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2956" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761506 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764472 ATOM PAIRS WERE FOUND FOR ATOM LIST 41945 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28598 from a total of 764472 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2956 -59.13298 -2.76004 0.64665 INTE EXTERN> -26.53690 -32.59607 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.133" Parameter: A <- "-59.133" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5369" Parameter: B <- "-26.5369" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5961" Parameter: C <- "-32.5961" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2956 TOTAL ENERGY = -59.133 RDTITL> * VAN DER WAALS = -26.5369 ELECTROSTATIC = -32.5961 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2956" Parameter: CONF_N -> "8002" Comparing "2956" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2957" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764472 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759808 ATOM PAIRS WERE FOUND FOR ATOM LIST 41826 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28090 from a total of 759808 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2957 -57.63008 -1.50290 0.52057 INTE EXTERN> -28.97139 -28.65870 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.6301" Parameter: A <- "-57.6301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9714" Parameter: B <- "-28.9714" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.6587" Parameter: C <- "-28.6587" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2957 TOTAL ENERGY = -57.6301 RDTITL> * VAN DER WAALS = -28.9714 ELECTROSTATIC = -28.6587 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2957" Parameter: CONF_N -> "8002" Comparing "2957" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2958" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759808 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754828 ATOM PAIRS WERE FOUND FOR ATOM LIST 41402 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27943 from a total of 754828 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2958 -51.39023 -6.23986 0.49534 INTE EXTERN> -31.61661 -19.77362 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-51.3902" Parameter: A <- "-51.3902" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6166" Parameter: B <- "-31.6166" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-19.7736" Parameter: C <- "-19.7736" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2958 TOTAL ENERGY = -51.3902 RDTITL> * VAN DER WAALS = -31.6166 ELECTROSTATIC = -19.7736 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2958" Parameter: CONF_N -> "8002" Comparing "2958" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2959" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754828 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756366 ATOM PAIRS WERE FOUND FOR ATOM LIST 41656 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28758 from a total of 756366 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2959 -57.28692 5.89670 0.69455 INTE EXTERN> -27.64784 -29.63908 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.2869" Parameter: A <- "-57.2869" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6478" Parameter: B <- "-27.6478" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.6391" Parameter: C <- "-29.6391" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2959 TOTAL ENERGY = -57.2869 RDTITL> * VAN DER WAALS = -27.6478 ELECTROSTATIC = -29.6391 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2959" Parameter: CONF_N -> "8002" Comparing "2959" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2960" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756366 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758956 ATOM PAIRS WERE FOUND FOR ATOM LIST 41863 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28925 from a total of 758956 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2960 -50.80727 -6.47965 0.51502 INTE EXTERN> -31.77371 -19.03356 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-50.8073" Parameter: A <- "-50.8073" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7737" Parameter: B <- "-31.7737" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-19.0336" Parameter: C <- "-19.0336" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2960 TOTAL ENERGY = -50.8073 RDTITL> * VAN DER WAALS = -31.7737 ELECTROSTATIC = -19.0336 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2960" Parameter: CONF_N -> "8002" Comparing "2960" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2961" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758956 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765340 ATOM PAIRS WERE FOUND FOR ATOM LIST 42217 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29014 from a total of 765340 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2961 -59.67053 8.86325 0.51146 INTE EXTERN> -31.62465 -28.04588 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.6705" Parameter: A <- "-59.6705" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6246" Parameter: B <- "-31.6246" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.0459" Parameter: C <- "-28.0459" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2961 TOTAL ENERGY = -59.6705 RDTITL> * VAN DER WAALS = -31.6246 ELECTROSTATIC = -28.0459 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2961" Parameter: CONF_N -> "8002" Comparing "2961" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2962" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765340 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765548 ATOM PAIRS WERE FOUND FOR ATOM LIST 42071 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29685 from a total of 765548 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2962 -61.10311 1.43258 0.57243 INTE EXTERN> -30.00202 -31.10108 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.1031" Parameter: A <- "-61.1031" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.002" Parameter: B <- "-30.002" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.1011" Parameter: C <- "-31.1011" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2962 TOTAL ENERGY = -61.1031 RDTITL> * VAN DER WAALS = -30.002 ELECTROSTATIC = -31.1011 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2962" Parameter: CONF_N -> "8002" Comparing "2962" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2963" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765548 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766065 ATOM PAIRS WERE FOUND FOR ATOM LIST 41895 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28830 from a total of 766065 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2963 -52.85843 -8.24468 0.47220 INTE EXTERN> -30.92885 -21.92958 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-52.8584" Parameter: A <- "-52.8584" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9289" Parameter: B <- "-30.9289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-21.9296" Parameter: C <- "-21.9296" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2963 TOTAL ENERGY = -52.8584 RDTITL> * VAN DER WAALS = -30.9289 ELECTROSTATIC = -21.9296 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2963" Parameter: CONF_N -> "8002" Comparing "2963" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2964" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766065 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759598 ATOM PAIRS WERE FOUND FOR ATOM LIST 41677 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28952 from a total of 759598 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2964 -54.47814 1.61971 0.54425 INTE EXTERN> -29.09157 -25.38657 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-54.4781" Parameter: A <- "-54.4781" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0916" Parameter: B <- "-29.0916" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-25.3866" Parameter: C <- "-25.3866" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2964 TOTAL ENERGY = -54.4781 RDTITL> * VAN DER WAALS = -29.0916 ELECTROSTATIC = -25.3866 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2964" Parameter: CONF_N -> "8002" Comparing "2964" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2965" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759598 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764197 ATOM PAIRS WERE FOUND FOR ATOM LIST 41915 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29105 from a total of 764197 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2965 -61.66927 7.19112 0.56251 INTE EXTERN> -31.55115 -30.11811 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.6693" Parameter: A <- "-61.6693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5512" Parameter: B <- "-31.5512" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.1181" Parameter: C <- "-30.1181" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2965 TOTAL ENERGY = -61.6693 RDTITL> * VAN DER WAALS = -31.5512 ELECTROSTATIC = -30.1181 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2965" Parameter: CONF_N -> "8002" Comparing "2965" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2966" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764197 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757937 ATOM PAIRS WERE FOUND FOR ATOM LIST 41817 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28970 from a total of 757937 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2966 -63.51702 1.84776 0.63304 INTE EXTERN> -27.93554 -35.58148 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.517" Parameter: A <- "-63.517" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9355" Parameter: B <- "-27.9355" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5815" Parameter: C <- "-35.5815" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2966 TOTAL ENERGY = -63.517 RDTITL> * VAN DER WAALS = -27.9355 ELECTROSTATIC = -35.5815 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2966" Parameter: CONF_N -> "8002" Comparing "2966" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2967" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757937 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770173 ATOM PAIRS WERE FOUND FOR ATOM LIST 42344 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29721 from a total of 770173 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2967 -63.50386 -0.01316 0.59441 INTE EXTERN> -30.35979 -33.14407 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5039" Parameter: A <- "-63.5039" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3598" Parameter: B <- "-30.3598" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1441" Parameter: C <- "-33.1441" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2967 TOTAL ENERGY = -63.5039 RDTITL> * VAN DER WAALS = -30.3598 ELECTROSTATIC = -33.1441 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2967" Parameter: CONF_N -> "8002" Comparing "2967" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2968" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770173 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762060 ATOM PAIRS WERE FOUND FOR ATOM LIST 41927 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29310 from a total of 762060 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2968 -64.98990 1.48604 0.62780 INTE EXTERN> -27.11316 -37.87674 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9899" Parameter: A <- "-64.9899" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1132" Parameter: B <- "-27.1132" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8767" Parameter: C <- "-37.8767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2968 TOTAL ENERGY = -64.9899 RDTITL> * VAN DER WAALS = -27.1132 ELECTROSTATIC = -37.8767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2968" Parameter: CONF_N -> "8002" Comparing "2968" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2969" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762060 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767824 ATOM PAIRS WERE FOUND FOR ATOM LIST 42082 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29724 from a total of 767824 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2969 -53.84304 -11.14685 0.62015 INTE EXTERN> -28.60716 -25.23589 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-53.843" Parameter: A <- "-53.843" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6072" Parameter: B <- "-28.6072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-25.2359" Parameter: C <- "-25.2359" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2969 TOTAL ENERGY = -53.843 RDTITL> * VAN DER WAALS = -28.6072 ELECTROSTATIC = -25.2359 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2969" Parameter: CONF_N -> "8002" Comparing "2969" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2970" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767824 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772944 ATOM PAIRS WERE FOUND FOR ATOM LIST 42488 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30165 from a total of 772944 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2970 -66.59377 12.75072 0.58694 INTE EXTERN> -31.97776 -34.61601 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5938" Parameter: A <- "-66.5938" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9778" Parameter: B <- "-31.9778" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.616" Parameter: C <- "-34.616" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2970 TOTAL ENERGY = -66.5938 RDTITL> * VAN DER WAALS = -31.9778 ELECTROSTATIC = -34.616 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2970" Parameter: CONF_N -> "8002" Comparing "2970" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2971" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772944 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768482 ATOM PAIRS WERE FOUND FOR ATOM LIST 42184 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29445 from a total of 768482 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2971 -65.07348 -1.52029 0.48722 INTE EXTERN> -33.18965 -31.88383 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0735" Parameter: A <- "-65.0735" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1896" Parameter: B <- "-33.1896" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.8838" Parameter: C <- "-31.8838" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2971 TOTAL ENERGY = -65.0735 RDTITL> * VAN DER WAALS = -33.1896 ELECTROSTATIC = -31.8838 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2971" Parameter: CONF_N -> "8002" Comparing "2971" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2972" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768482 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762718 ATOM PAIRS WERE FOUND FOR ATOM LIST 42090 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29529 from a total of 762718 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2972 -64.76497 -0.30851 0.58910 INTE EXTERN> -30.41497 -34.35000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.765" Parameter: A <- "-64.765" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.415" Parameter: B <- "-30.415" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.35" Parameter: C <- "-34.35" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2972 TOTAL ENERGY = -64.765 RDTITL> * VAN DER WAALS = -30.415 ELECTROSTATIC = -34.35 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2972" Parameter: CONF_N -> "8002" Comparing "2972" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2973" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762718 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761900 ATOM PAIRS WERE FOUND FOR ATOM LIST 41812 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29993 from a total of 761900 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2973 -62.23378 -2.53119 0.59177 INTE EXTERN> -29.85232 -32.38146 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.2338" Parameter: A <- "-62.2338" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8523" Parameter: B <- "-29.8523" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.3815" Parameter: C <- "-32.3815" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2973 TOTAL ENERGY = -62.2338 RDTITL> * VAN DER WAALS = -29.8523 ELECTROSTATIC = -32.3815 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2973" Parameter: CONF_N -> "8002" Comparing "2973" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2974" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761900 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756756 ATOM PAIRS WERE FOUND FOR ATOM LIST 41550 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28970 from a total of 756756 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2974 -60.12903 -2.10475 0.48532 INTE EXTERN> -33.06675 -27.06228 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.129" Parameter: A <- "-60.129" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0668" Parameter: B <- "-33.0668" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.0623" Parameter: C <- "-27.0623" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2974 TOTAL ENERGY = -60.129 RDTITL> * VAN DER WAALS = -33.0668 ELECTROSTATIC = -27.0623 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2974" Parameter: CONF_N -> "8002" Comparing "2974" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2975" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756756 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761390 ATOM PAIRS WERE FOUND FOR ATOM LIST 41875 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28876 from a total of 761390 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2975 -59.11248 -1.01655 0.57146 INTE EXTERN> -28.43130 -30.68119 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.1125" Parameter: A <- "-59.1125" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4313" Parameter: B <- "-28.4313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.6812" Parameter: C <- "-30.6812" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2975 TOTAL ENERGY = -59.1125 RDTITL> * VAN DER WAALS = -28.4313 ELECTROSTATIC = -30.6812 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2975" Parameter: CONF_N -> "8002" Comparing "2975" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2976" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761390 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 775225 ATOM PAIRS WERE FOUND FOR ATOM LIST 42524 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30386 from a total of 775225 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2976 -62.78150 3.66901 0.60765 INTE EXTERN> -28.93299 -33.84851 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7815" Parameter: A <- "-62.7815" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.933" Parameter: B <- "-28.933" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8485" Parameter: C <- "-33.8485" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2976 TOTAL ENERGY = -62.7815 RDTITL> * VAN DER WAALS = -28.933 ELECTROSTATIC = -33.8485 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2976" Parameter: CONF_N -> "8002" Comparing "2976" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2977" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 775225 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768955 ATOM PAIRS WERE FOUND FOR ATOM LIST 42397 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30212 from a total of 768955 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2977 -64.61814 1.83664 0.71736 INTE EXTERN> -24.62050 -39.99763 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6181" Parameter: A <- "-64.6181" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6205" Parameter: B <- "-24.6205" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9976" Parameter: C <- "-39.9976" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2977 TOTAL ENERGY = -64.6181 RDTITL> * VAN DER WAALS = -24.6205 ELECTROSTATIC = -39.9976 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2977" Parameter: CONF_N -> "8002" Comparing "2977" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2978" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768955 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760618 ATOM PAIRS WERE FOUND FOR ATOM LIST 41961 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29490 from a total of 760618 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2978 -61.57557 -3.04257 0.55515 INTE EXTERN> -30.97552 -30.60005 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.5756" Parameter: A <- "-61.5756" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9755" Parameter: B <- "-30.9755" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.6" Parameter: C <- "-30.6" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2978 TOTAL ENERGY = -61.5756 RDTITL> * VAN DER WAALS = -30.9755 ELECTROSTATIC = -30.6 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2978" Parameter: CONF_N -> "8002" Comparing "2978" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2979" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760618 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768287 ATOM PAIRS WERE FOUND FOR ATOM LIST 42217 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29915 from a total of 768287 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2979 -65.18143 3.60586 0.80591 INTE EXTERN> -25.52624 -39.65519 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1814" Parameter: A <- "-65.1814" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5262" Parameter: B <- "-25.5262" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6552" Parameter: C <- "-39.6552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2979 TOTAL ENERGY = -65.1814 RDTITL> * VAN DER WAALS = -25.5262 ELECTROSTATIC = -39.6552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2979" Parameter: CONF_N -> "8002" Comparing "2979" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2980" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768287 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766715 ATOM PAIRS WERE FOUND FOR ATOM LIST 42433 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29829 from a total of 766715 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2980 -70.17675 4.99532 0.62444 INTE EXTERN> -29.67317 -40.50358 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1768" Parameter: A <- "-70.1768" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6732" Parameter: B <- "-29.6732" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5036" Parameter: C <- "-40.5036" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2980 TOTAL ENERGY = -70.1768 RDTITL> * VAN DER WAALS = -29.6732 ELECTROSTATIC = -40.5036 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2980" Parameter: CONF_N -> "8002" Comparing "2980" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2981" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766715 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763696 ATOM PAIRS WERE FOUND FOR ATOM LIST 42045 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30112 from a total of 763696 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2981 -75.07968 4.90293 0.63372 INTE EXTERN> -32.71574 -42.36394 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0797" Parameter: A <- "-75.0797" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7157" Parameter: B <- "-32.7157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3639" Parameter: C <- "-42.3639" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2981 TOTAL ENERGY = -75.0797 RDTITL> * VAN DER WAALS = -32.7157 ELECTROSTATIC = -42.3639 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2981" Parameter: CONF_N -> "8002" Comparing "2981" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2982" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763696 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768871 ATOM PAIRS WERE FOUND FOR ATOM LIST 42426 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30866 from a total of 768871 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2982 -74.61981 -0.45987 0.68248 INTE EXTERN> -26.85206 -47.76775 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6198" Parameter: A <- "-74.6198" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8521" Parameter: B <- "-26.8521" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7677" Parameter: C <- "-47.7677" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2982 TOTAL ENERGY = -74.6198 RDTITL> * VAN DER WAALS = -26.8521 ELECTROSTATIC = -47.7677 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2982" Parameter: CONF_N -> "8002" Comparing "2982" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2983" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768871 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764827 ATOM PAIRS WERE FOUND FOR ATOM LIST 42117 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30734 from a total of 764827 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2983 -77.26985 2.65004 0.67267 INTE EXTERN> -28.10790 -49.16195 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2699" Parameter: A <- "-77.2699" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1079" Parameter: B <- "-28.1079" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.162" Parameter: C <- "-49.162" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2983 TOTAL ENERGY = -77.2699 RDTITL> * VAN DER WAALS = -28.1079 ELECTROSTATIC = -49.162 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2983" Parameter: CONF_N -> "8002" Comparing "2983" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2984" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764827 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768691 ATOM PAIRS WERE FOUND FOR ATOM LIST 42534 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30978 from a total of 768691 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2984 -74.82578 -2.44407 0.79006 INTE EXTERN> -25.53576 -49.29002 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8258" Parameter: A <- "-74.8258" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5358" Parameter: B <- "-25.5358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.29" Parameter: C <- "-49.29" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2984 TOTAL ENERGY = -74.8258 RDTITL> * VAN DER WAALS = -25.5358 ELECTROSTATIC = -49.29 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2984" Parameter: CONF_N -> "8002" Comparing "2984" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2985" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768691 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763710 ATOM PAIRS WERE FOUND FOR ATOM LIST 41917 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30310 from a total of 763710 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2985 -73.29080 -1.53499 0.64245 INTE EXTERN> -25.27057 -48.02023 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2908" Parameter: A <- "-73.2908" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2706" Parameter: B <- "-25.2706" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0202" Parameter: C <- "-48.0202" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2985 TOTAL ENERGY = -73.2908 RDTITL> * VAN DER WAALS = -25.2706 ELECTROSTATIC = -48.0202 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2985" Parameter: CONF_N -> "8002" Comparing "2985" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2986" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763710 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760478 ATOM PAIRS WERE FOUND FOR ATOM LIST 41729 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30097 from a total of 760478 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2986 -73.20643 -0.08437 0.64543 INTE EXTERN> -28.14558 -45.06086 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2064" Parameter: A <- "-73.2064" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1456" Parameter: B <- "-28.1456" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0609" Parameter: C <- "-45.0609" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2986 TOTAL ENERGY = -73.2064 RDTITL> * VAN DER WAALS = -28.1456 ELECTROSTATIC = -45.0609 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2986" Parameter: CONF_N -> "8002" Comparing "2986" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2987" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760478 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761131 ATOM PAIRS WERE FOUND FOR ATOM LIST 41780 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29419 from a total of 761131 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2987 -74.50513 1.29870 0.66503 INTE EXTERN> -28.80412 -45.70101 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5051" Parameter: A <- "-74.5051" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8041" Parameter: B <- "-28.8041" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.701" Parameter: C <- "-45.701" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2987 TOTAL ENERGY = -74.5051 RDTITL> * VAN DER WAALS = -28.8041 ELECTROSTATIC = -45.701 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2987" Parameter: CONF_N -> "8002" Comparing "2987" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2988" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761131 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763364 ATOM PAIRS WERE FOUND FOR ATOM LIST 42115 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30079 from a total of 763364 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2988 -64.34556 -10.15957 0.69618 INTE EXTERN> -26.62938 -37.71618 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3456" Parameter: A <- "-64.3456" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6294" Parameter: B <- "-26.6294" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7162" Parameter: C <- "-37.7162" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2988 TOTAL ENERGY = -64.3456 RDTITL> * VAN DER WAALS = -26.6294 ELECTROSTATIC = -37.7162 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2988" Parameter: CONF_N -> "8002" Comparing "2988" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2989" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763364 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761681 ATOM PAIRS WERE FOUND FOR ATOM LIST 41925 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29896 from a total of 761681 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2989 -78.54928 14.20372 0.70451 INTE EXTERN> -29.74456 -48.80472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5493" Parameter: A <- "-78.5493" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7446" Parameter: B <- "-29.7446" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8047" Parameter: C <- "-48.8047" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2989 TOTAL ENERGY = -78.5493 RDTITL> * VAN DER WAALS = -29.7446 ELECTROSTATIC = -48.8047 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2989" Parameter: CONF_N -> "8002" Comparing "2989" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2990" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761681 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763714 ATOM PAIRS WERE FOUND FOR ATOM LIST 42034 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29551 from a total of 763714 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2990 -79.96703 1.41775 0.71765 INTE EXTERN> -27.40829 -52.55874 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.967" Parameter: A <- "-79.967" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4083" Parameter: B <- "-27.4083" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5587" Parameter: C <- "-52.5587" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2990 TOTAL ENERGY = -79.967 RDTITL> * VAN DER WAALS = -27.4083 ELECTROSTATIC = -52.5587 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2990" Parameter: CONF_N -> "8002" Comparing "2990" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2991" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763714 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766362 ATOM PAIRS WERE FOUND FOR ATOM LIST 42298 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29961 from a total of 766362 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2991 -70.14541 -9.82163 0.70473 INTE EXTERN> -25.03634 -45.10906 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1454" Parameter: A <- "-70.1454" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0363" Parameter: B <- "-25.0363" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1091" Parameter: C <- "-45.1091" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2991 TOTAL ENERGY = -70.1454 RDTITL> * VAN DER WAALS = -25.0363 ELECTROSTATIC = -45.1091 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2991" Parameter: CONF_N -> "8002" Comparing "2991" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2992" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766362 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766632 ATOM PAIRS WERE FOUND FOR ATOM LIST 42112 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29907 from a total of 766632 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2992 -65.16497 -4.98044 0.73302 INTE EXTERN> -23.75828 -41.40668 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.165" Parameter: A <- "-65.165" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7583" Parameter: B <- "-23.7583" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4067" Parameter: C <- "-41.4067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2992 TOTAL ENERGY = -65.165 RDTITL> * VAN DER WAALS = -23.7583 ELECTROSTATIC = -41.4067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2992" Parameter: CONF_N -> "8002" Comparing "2992" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2993" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766632 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762527 ATOM PAIRS WERE FOUND FOR ATOM LIST 41787 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29423 from a total of 762527 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2993 -69.90678 4.74181 0.60949 INTE EXTERN> -29.96134 -39.94544 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9068" Parameter: A <- "-69.9068" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9613" Parameter: B <- "-29.9613" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9454" Parameter: C <- "-39.9454" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2993 TOTAL ENERGY = -69.9068 RDTITL> * VAN DER WAALS = -29.9613 ELECTROSTATIC = -39.9454 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2993" Parameter: CONF_N -> "8002" Comparing "2993" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2994" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762527 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755322 ATOM PAIRS WERE FOUND FOR ATOM LIST 41482 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28256 from a total of 755322 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2994 -74.01168 4.10490 0.66952 INTE EXTERN> -25.15352 -48.85816 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0117" Parameter: A <- "-74.0117" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1535" Parameter: B <- "-25.1535" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8582" Parameter: C <- "-48.8582" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2994 TOTAL ENERGY = -74.0117 RDTITL> * VAN DER WAALS = -25.1535 ELECTROSTATIC = -48.8582 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2994" Parameter: CONF_N -> "8002" Comparing "2994" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2995" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755322 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761743 ATOM PAIRS WERE FOUND FOR ATOM LIST 41747 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29155 from a total of 761743 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2995 -67.93070 -6.08097 0.59284 INTE EXTERN> -26.94500 -40.98571 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9307" Parameter: A <- "-67.9307" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.945" Parameter: B <- "-26.945" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9857" Parameter: C <- "-40.9857" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2995 TOTAL ENERGY = -67.9307 RDTITL> * VAN DER WAALS = -26.945 ELECTROSTATIC = -40.9857 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2995" Parameter: CONF_N -> "8002" Comparing "2995" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2996" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761743 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761656 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29015 from a total of 761656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2996 -74.39298 6.46228 0.62322 INTE EXTERN> -27.38996 -47.00302 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.393" Parameter: A <- "-74.393" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.39" Parameter: B <- "-27.39" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.003" Parameter: C <- "-47.003" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2996 TOTAL ENERGY = -74.393 RDTITL> * VAN DER WAALS = -27.39 ELECTROSTATIC = -47.003 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2996" Parameter: CONF_N -> "8002" Comparing "2996" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2997" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759854 ATOM PAIRS WERE FOUND FOR ATOM LIST 41531 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28603 from a total of 759854 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2997 -66.60310 -7.78989 0.59453 INTE EXTERN> -29.26579 -37.33731 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6031" Parameter: A <- "-66.6031" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2658" Parameter: B <- "-29.2658" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3373" Parameter: C <- "-37.3373" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2997 TOTAL ENERGY = -66.6031 RDTITL> * VAN DER WAALS = -29.2658 ELECTROSTATIC = -37.3373 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2997" Parameter: CONF_N -> "8002" Comparing "2997" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2998" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759854 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756554 ATOM PAIRS WERE FOUND FOR ATOM LIST 41658 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29214 from a total of 756554 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2998 -67.39423 0.79113 0.61785 INTE EXTERN> -28.34678 -39.04745 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3942" Parameter: A <- "-67.3942" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3468" Parameter: B <- "-28.3468" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0475" Parameter: C <- "-39.0475" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2998 TOTAL ENERGY = -67.3942 RDTITL> * VAN DER WAALS = -28.3468 ELECTROSTATIC = -39.0475 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2998" Parameter: CONF_N -> "8002" Comparing "2998" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "2999" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756554 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755661 ATOM PAIRS WERE FOUND FOR ATOM LIST 41557 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28804 from a total of 755661 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 2999 -70.41057 3.01634 0.70173 INTE EXTERN> -26.44397 -43.96660 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4106" Parameter: A <- "-70.4106" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.444" Parameter: B <- "-26.444" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9666" Parameter: C <- "-43.9666" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 2999 TOTAL ENERGY = -70.4106 RDTITL> * VAN DER WAALS = -26.444 ELECTROSTATIC = -43.9666 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "2999" Parameter: CONF_N -> "8002" Comparing "2999" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3000" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755661 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764743 ATOM PAIRS WERE FOUND FOR ATOM LIST 41927 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29326 from a total of 764743 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3000 -66.89784 -3.51273 0.64192 INTE EXTERN> -26.95580 -39.94203 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8978" Parameter: A <- "-66.8978" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9558" Parameter: B <- "-26.9558" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.942" Parameter: C <- "-39.942" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3000 TOTAL ENERGY = -66.8978 RDTITL> * VAN DER WAALS = -26.9558 ELECTROSTATIC = -39.942 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3000" Parameter: CONF_N -> "8002" Comparing "3000" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3001" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764743 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763294 ATOM PAIRS WERE FOUND FOR ATOM LIST 41774 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29583 from a total of 763294 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3001 -79.62882 12.73099 0.67273 INTE EXTERN> -29.02079 -50.60803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6288" Parameter: A <- "-79.6288" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0208" Parameter: B <- "-29.0208" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.608" Parameter: C <- "-50.608" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3001 TOTAL ENERGY = -79.6288 RDTITL> * VAN DER WAALS = -29.0208 ELECTROSTATIC = -50.608 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3001" Parameter: CONF_N -> "8002" Comparing "3001" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3002" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763294 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759569 ATOM PAIRS WERE FOUND FOR ATOM LIST 41749 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29491 from a total of 759569 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3002 -70.34371 -9.28511 0.73648 INTE EXTERN> -26.38589 -43.95783 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3437" Parameter: A <- "-70.3437" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3859" Parameter: B <- "-26.3859" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9578" Parameter: C <- "-43.9578" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3002 TOTAL ENERGY = -70.3437 RDTITL> * VAN DER WAALS = -26.3859 ELECTROSTATIC = -43.9578 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3002" Parameter: CONF_N -> "8002" Comparing "3002" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3003" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759569 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761773 ATOM PAIRS WERE FOUND FOR ATOM LIST 41926 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29228 from a total of 761773 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3003 -73.50440 3.16069 0.57055 INTE EXTERN> -29.93215 -43.57225 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5044" Parameter: A <- "-73.5044" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9322" Parameter: B <- "-29.9322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5722" Parameter: C <- "-43.5722" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3003 TOTAL ENERGY = -73.5044 RDTITL> * VAN DER WAALS = -29.9322 ELECTROSTATIC = -43.5722 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3003" Parameter: CONF_N -> "8002" Comparing "3003" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3004" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761773 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760368 ATOM PAIRS WERE FOUND FOR ATOM LIST 41808 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28958 from a total of 760368 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3004 -77.92909 4.42469 0.68903 INTE EXTERN> -27.11852 -50.81057 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9291" Parameter: A <- "-77.9291" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1185" Parameter: B <- "-27.1185" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8106" Parameter: C <- "-50.8106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3004 TOTAL ENERGY = -77.9291 RDTITL> * VAN DER WAALS = -27.1185 ELECTROSTATIC = -50.8106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3004" Parameter: CONF_N -> "8002" Comparing "3004" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3005" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760368 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769225 ATOM PAIRS WERE FOUND FOR ATOM LIST 42177 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29347 from a total of 769225 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3005 -78.18504 0.25595 0.66300 INTE EXTERN> -27.24713 -50.93791 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.185" Parameter: A <- "-78.185" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2471" Parameter: B <- "-27.2471" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9379" Parameter: C <- "-50.9379" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3005 TOTAL ENERGY = -78.185 RDTITL> * VAN DER WAALS = -27.2471 ELECTROSTATIC = -50.9379 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3005" Parameter: CONF_N -> "8002" Comparing "3005" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3006" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769225 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758430 ATOM PAIRS WERE FOUND FOR ATOM LIST 41710 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29280 from a total of 758430 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3006 -74.83751 -3.34754 0.72087 INTE EXTERN> -26.04516 -48.79234 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8375" Parameter: A <- "-74.8375" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0452" Parameter: B <- "-26.0452" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7923" Parameter: C <- "-48.7923" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3006 TOTAL ENERGY = -74.8375 RDTITL> * VAN DER WAALS = -26.0452 ELECTROSTATIC = -48.7923 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3006" Parameter: CONF_N -> "8002" Comparing "3006" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3007" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758430 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759833 ATOM PAIRS WERE FOUND FOR ATOM LIST 41702 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28513 from a total of 759833 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3007 -79.95707 5.11956 0.76168 INTE EXTERN> -25.40880 -54.54826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9571" Parameter: A <- "-79.9571" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4088" Parameter: B <- "-25.4088" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.5483" Parameter: C <- "-54.5483" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3007 TOTAL ENERGY = -79.9571 RDTITL> * VAN DER WAALS = -25.4088 ELECTROSTATIC = -54.5483 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3007" Parameter: CONF_N -> "8002" Comparing "3007" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3008" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759833 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761321 ATOM PAIRS WERE FOUND FOR ATOM LIST 41859 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29384 from a total of 761321 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3008 -79.91379 -0.04328 0.74486 INTE EXTERN> -26.09248 -53.82131 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9138" Parameter: A <- "-79.9138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0925" Parameter: B <- "-26.0925" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8213" Parameter: C <- "-53.8213" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3008 TOTAL ENERGY = -79.9138 RDTITL> * VAN DER WAALS = -26.0925 ELECTROSTATIC = -53.8213 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3008" Parameter: CONF_N -> "8002" Comparing "3008" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3009" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761321 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758688 ATOM PAIRS WERE FOUND FOR ATOM LIST 41559 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28712 from a total of 758688 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3009 -79.00961 -0.90418 0.63288 INTE EXTERN> -30.13446 -48.87515 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0096" Parameter: A <- "-79.0096" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1345" Parameter: B <- "-30.1345" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8752" Parameter: C <- "-48.8752" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3009 TOTAL ENERGY = -79.0096 RDTITL> * VAN DER WAALS = -30.1345 ELECTROSTATIC = -48.8752 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3009" Parameter: CONF_N -> "8002" Comparing "3009" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3010" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758688 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760783 ATOM PAIRS WERE FOUND FOR ATOM LIST 41717 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29556 from a total of 760783 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3010 -69.81239 -9.19722 0.73863 INTE EXTERN> -23.22282 -46.58957 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8124" Parameter: A <- "-69.8124" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.2228" Parameter: B <- "-23.2228" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5896" Parameter: C <- "-46.5896" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3010 TOTAL ENERGY = -69.8124 RDTITL> * VAN DER WAALS = -23.2228 ELECTROSTATIC = -46.5896 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3010" Parameter: CONF_N -> "8002" Comparing "3010" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3011" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760783 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759736 ATOM PAIRS WERE FOUND FOR ATOM LIST 41826 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28927 from a total of 759736 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3011 -72.70552 2.89313 0.58639 INTE EXTERN> -29.80002 -42.90550 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7055" Parameter: A <- "-72.7055" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8" Parameter: B <- "-29.8" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9055" Parameter: C <- "-42.9055" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3011 TOTAL ENERGY = -72.7055 RDTITL> * VAN DER WAALS = -29.8 ELECTROSTATIC = -42.9055 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3011" Parameter: CONF_N -> "8002" Comparing "3011" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3012" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759736 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761810 ATOM PAIRS WERE FOUND FOR ATOM LIST 41795 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28791 from a total of 761810 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3012 -70.42732 -2.27821 0.64243 INTE EXTERN> -28.64545 -41.78187 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4273" Parameter: A <- "-70.4273" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6454" Parameter: B <- "-28.6454" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7819" Parameter: C <- "-41.7819" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3012 TOTAL ENERGY = -70.4273 RDTITL> * VAN DER WAALS = -28.6454 ELECTROSTATIC = -41.7819 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3012" Parameter: CONF_N -> "8002" Comparing "3012" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3013" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761810 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761259 ATOM PAIRS WERE FOUND FOR ATOM LIST 41844 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28970 from a total of 761259 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3013 -72.39021 1.96289 0.66911 INTE EXTERN> -26.66787 -45.72234 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3902" Parameter: A <- "-72.3902" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6679" Parameter: B <- "-26.6679" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7223" Parameter: C <- "-45.7223" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3013 TOTAL ENERGY = -72.3902 RDTITL> * VAN DER WAALS = -26.6679 ELECTROSTATIC = -45.7223 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3013" Parameter: CONF_N -> "8002" Comparing "3013" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3014" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761259 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753517 ATOM PAIRS WERE FOUND FOR ATOM LIST 41508 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28761 from a total of 753517 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3014 -64.03575 -8.35445 0.58708 INTE EXTERN> -31.86400 -32.17175 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0358" Parameter: A <- "-64.0358" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.864" Parameter: B <- "-31.864" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.1717" Parameter: C <- "-32.1717" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3014 TOTAL ENERGY = -64.0358 RDTITL> * VAN DER WAALS = -31.864 ELECTROSTATIC = -32.1717 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3014" Parameter: CONF_N -> "8002" Comparing "3014" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3015" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753517 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757749 ATOM PAIRS WERE FOUND FOR ATOM LIST 41471 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29206 from a total of 757749 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3015 -64.78348 0.74773 0.71418 INTE EXTERN> -27.96424 -36.81925 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7835" Parameter: A <- "-64.7835" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9642" Parameter: B <- "-27.9642" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8192" Parameter: C <- "-36.8192" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3015 TOTAL ENERGY = -64.7835 RDTITL> * VAN DER WAALS = -27.9642 ELECTROSTATIC = -36.8192 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3015" Parameter: CONF_N -> "8002" Comparing "3015" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3016" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757749 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754812 ATOM PAIRS WERE FOUND FOR ATOM LIST 41550 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29151 from a total of 754812 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3016 -64.14046 -0.64302 0.61816 INTE EXTERN> -29.40744 -34.73303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1405" Parameter: A <- "-64.1405" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4074" Parameter: B <- "-29.4074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.733" Parameter: C <- "-34.733" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3016 TOTAL ENERGY = -64.1405 RDTITL> * VAN DER WAALS = -29.4074 ELECTROSTATIC = -34.733 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3016" Parameter: CONF_N -> "8002" Comparing "3016" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3017" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754812 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760171 ATOM PAIRS WERE FOUND FOR ATOM LIST 41748 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29280 from a total of 760171 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3017 -69.06504 4.92458 0.69578 INTE EXTERN> -28.64146 -40.42359 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.065" Parameter: A <- "-69.065" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6415" Parameter: B <- "-28.6415" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4236" Parameter: C <- "-40.4236" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3017 TOTAL ENERGY = -69.065 RDTITL> * VAN DER WAALS = -28.6415 ELECTROSTATIC = -40.4236 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3017" Parameter: CONF_N -> "8002" Comparing "3017" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3018" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760171 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763363 ATOM PAIRS WERE FOUND FOR ATOM LIST 41978 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29746 from a total of 763363 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3018 -75.14753 6.08248 0.75360 INTE EXTERN> -26.82051 -48.32702 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1475" Parameter: A <- "-75.1475" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8205" Parameter: B <- "-26.8205" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.327" Parameter: C <- "-48.327" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3018 TOTAL ENERGY = -75.1475 RDTITL> * VAN DER WAALS = -26.8205 ELECTROSTATIC = -48.327 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3018" Parameter: CONF_N -> "8002" Comparing "3018" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3019" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763363 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765775 ATOM PAIRS WERE FOUND FOR ATOM LIST 41837 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29353 from a total of 765775 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3019 -73.56037 -1.58716 0.69120 INTE EXTERN> -29.75614 -43.80423 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5604" Parameter: A <- "-73.5604" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7561" Parameter: B <- "-29.7561" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8042" Parameter: C <- "-43.8042" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3019 TOTAL ENERGY = -73.5604 RDTITL> * VAN DER WAALS = -29.7561 ELECTROSTATIC = -43.8042 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3019" Parameter: CONF_N -> "8002" Comparing "3019" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3020" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765775 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760240 ATOM PAIRS WERE FOUND FOR ATOM LIST 41717 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29078 from a total of 760240 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3020 -74.30446 0.74410 0.69030 INTE EXTERN> -28.39026 -45.91421 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3045" Parameter: A <- "-74.3045" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3903" Parameter: B <- "-28.3903" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9142" Parameter: C <- "-45.9142" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3020 TOTAL ENERGY = -74.3045 RDTITL> * VAN DER WAALS = -28.3903 ELECTROSTATIC = -45.9142 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3020" Parameter: CONF_N -> "8002" Comparing "3020" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3021" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760240 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759737 ATOM PAIRS WERE FOUND FOR ATOM LIST 41783 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29400 from a total of 759737 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3021 -65.53909 -8.76537 0.79745 INTE EXTERN> -26.40753 -39.13156 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5391" Parameter: A <- "-65.5391" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4075" Parameter: B <- "-26.4075" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1316" Parameter: C <- "-39.1316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3021 TOTAL ENERGY = -65.5391 RDTITL> * VAN DER WAALS = -26.4075 ELECTROSTATIC = -39.1316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3021" Parameter: CONF_N -> "8002" Comparing "3021" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3022" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759737 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761695 ATOM PAIRS WERE FOUND FOR ATOM LIST 41853 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29268 from a total of 761695 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3022 -71.66573 6.12664 0.61268 INTE EXTERN> -31.75558 -39.91016 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6657" Parameter: A <- "-71.6657" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7556" Parameter: B <- "-31.7556" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9102" Parameter: C <- "-39.9102" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3022 TOTAL ENERGY = -71.6657 RDTITL> * VAN DER WAALS = -31.7556 ELECTROSTATIC = -39.9102 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3022" Parameter: CONF_N -> "8002" Comparing "3022" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3023" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761695 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761298 ATOM PAIRS WERE FOUND FOR ATOM LIST 41804 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29400 from a total of 761298 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3023 -72.03095 0.36522 0.63851 INTE EXTERN> -31.80601 -40.22494 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.031" Parameter: A <- "-72.031" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.806" Parameter: B <- "-31.806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2249" Parameter: C <- "-40.2249" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3023 TOTAL ENERGY = -72.031 RDTITL> * VAN DER WAALS = -31.806 ELECTROSTATIC = -40.2249 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3023" Parameter: CONF_N -> "8002" Comparing "3023" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3024" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761298 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760217 ATOM PAIRS WERE FOUND FOR ATOM LIST 41954 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29203 from a total of 760217 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3024 -72.39919 0.36823 0.69094 INTE EXTERN> -28.08242 -44.31677 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3992" Parameter: A <- "-72.3992" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0824" Parameter: B <- "-28.0824" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3168" Parameter: C <- "-44.3168" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3024 TOTAL ENERGY = -72.3992 RDTITL> * VAN DER WAALS = -28.0824 ELECTROSTATIC = -44.3168 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3024" Parameter: CONF_N -> "8002" Comparing "3024" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3025" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760217 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759269 ATOM PAIRS WERE FOUND FOR ATOM LIST 41852 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28588 from a total of 759269 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3025 -70.53575 -1.86344 0.72343 INTE EXTERN> -24.64993 -45.88582 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5357" Parameter: A <- "-70.5357" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6499" Parameter: B <- "-24.6499" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8858" Parameter: C <- "-45.8858" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3025 TOTAL ENERGY = -70.5357 RDTITL> * VAN DER WAALS = -24.6499 ELECTROSTATIC = -45.8858 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3025" Parameter: CONF_N -> "8002" Comparing "3025" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3026" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759269 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759313 ATOM PAIRS WERE FOUND FOR ATOM LIST 41851 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29139 from a total of 759313 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3026 -78.97053 8.43478 0.68672 INTE EXTERN> -32.31197 -46.65856 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9705" Parameter: A <- "-78.9705" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.312" Parameter: B <- "-32.312" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6586" Parameter: C <- "-46.6586" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3026 TOTAL ENERGY = -78.9705 RDTITL> * VAN DER WAALS = -32.312 ELECTROSTATIC = -46.6586 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3026" Parameter: CONF_N -> "8002" Comparing "3026" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3027" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759313 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769163 ATOM PAIRS WERE FOUND FOR ATOM LIST 42222 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30002 from a total of 769163 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3027 -73.81748 -5.15306 0.72131 INTE EXTERN> -27.78186 -46.03561 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8175" Parameter: A <- "-73.8175" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7819" Parameter: B <- "-27.7819" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0356" Parameter: C <- "-46.0356" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3027 TOTAL ENERGY = -73.8175 RDTITL> * VAN DER WAALS = -27.7819 ELECTROSTATIC = -46.0356 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3027" Parameter: CONF_N -> "8002" Comparing "3027" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3028" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769163 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764737 ATOM PAIRS WERE FOUND FOR ATOM LIST 42073 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29491 from a total of 764737 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3028 -75.65920 1.84172 0.72676 INTE EXTERN> -23.99740 -51.66180 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6592" Parameter: A <- "-75.6592" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9974" Parameter: B <- "-23.9974" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6618" Parameter: C <- "-51.6618" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3028 TOTAL ENERGY = -75.6592 RDTITL> * VAN DER WAALS = -23.9974 ELECTROSTATIC = -51.6618 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3028" Parameter: CONF_N -> "8002" Comparing "3028" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3029" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764737 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765263 ATOM PAIRS WERE FOUND FOR ATOM LIST 42232 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29492 from a total of 765263 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3029 -74.64721 -1.01198 0.69595 INTE EXTERN> -27.87246 -46.77475 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6472" Parameter: A <- "-74.6472" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8725" Parameter: B <- "-27.8725" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7748" Parameter: C <- "-46.7748" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3029 TOTAL ENERGY = -74.6472 RDTITL> * VAN DER WAALS = -27.8725 ELECTROSTATIC = -46.7748 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3029" Parameter: CONF_N -> "8002" Comparing "3029" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3030" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765263 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763389 ATOM PAIRS WERE FOUND FOR ATOM LIST 42103 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29809 from a total of 763389 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3030 -70.56373 -4.08348 0.66326 INTE EXTERN> -27.60793 -42.95580 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5637" Parameter: A <- "-70.5637" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6079" Parameter: B <- "-27.6079" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9558" Parameter: C <- "-42.9558" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3030 TOTAL ENERGY = -70.5637 RDTITL> * VAN DER WAALS = -27.6079 ELECTROSTATIC = -42.9558 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3030" Parameter: CONF_N -> "8002" Comparing "3030" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3031" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763389 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771051 ATOM PAIRS WERE FOUND FOR ATOM LIST 42460 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29280 from a total of 771051 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3031 -73.99376 3.43003 0.71503 INTE EXTERN> -25.71083 -48.28292 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9938" Parameter: A <- "-73.9938" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7108" Parameter: B <- "-25.7108" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2829" Parameter: C <- "-48.2829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3031 TOTAL ENERGY = -73.9938 RDTITL> * VAN DER WAALS = -25.7108 ELECTROSTATIC = -48.2829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3031" Parameter: CONF_N -> "8002" Comparing "3031" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3032" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771051 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768280 ATOM PAIRS WERE FOUND FOR ATOM LIST 42235 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29514 from a total of 768280 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3032 -72.53998 -1.45378 0.72748 INTE EXTERN> -25.91058 -46.62940 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.54" Parameter: A <- "-72.54" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9106" Parameter: B <- "-25.9106" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6294" Parameter: C <- "-46.6294" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3032 TOTAL ENERGY = -72.54 RDTITL> * VAN DER WAALS = -25.9106 ELECTROSTATIC = -46.6294 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3032" Parameter: CONF_N -> "8002" Comparing "3032" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3033" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768280 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769221 ATOM PAIRS WERE FOUND FOR ATOM LIST 41930 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29505 from a total of 769221 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3033 -73.73519 1.19521 0.77119 INTE EXTERN> -22.79875 -50.93644 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7352" Parameter: A <- "-73.7352" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.7987" Parameter: B <- "-22.7987" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9364" Parameter: C <- "-50.9364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3033 TOTAL ENERGY = -73.7352 RDTITL> * VAN DER WAALS = -22.7987 ELECTROSTATIC = -50.9364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3033" Parameter: CONF_N -> "8002" Comparing "3033" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3034" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769221 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771581 ATOM PAIRS WERE FOUND FOR ATOM LIST 42536 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30341 from a total of 771581 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3034 -73.58378 -0.15141 0.74983 INTE EXTERN> -23.12645 -50.45733 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5838" Parameter: A <- "-73.5838" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.1265" Parameter: B <- "-23.1265" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4573" Parameter: C <- "-50.4573" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3034 TOTAL ENERGY = -73.5838 RDTITL> * VAN DER WAALS = -23.1265 ELECTROSTATIC = -50.4573 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3034" Parameter: CONF_N -> "8002" Comparing "3034" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3035" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771581 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761609 ATOM PAIRS WERE FOUND FOR ATOM LIST 42029 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28897 from a total of 761609 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3035 -77.72925 4.14547 0.60178 INTE EXTERN> -29.40496 -48.32429 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7292" Parameter: A <- "-77.7292" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.405" Parameter: B <- "-29.405" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3243" Parameter: C <- "-48.3243" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3035 TOTAL ENERGY = -77.7292 RDTITL> * VAN DER WAALS = -29.405 ELECTROSTATIC = -48.3243 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3035" Parameter: CONF_N -> "8002" Comparing "3035" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3036" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761609 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765151 ATOM PAIRS WERE FOUND FOR ATOM LIST 41901 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28952 from a total of 765151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3036 -71.03874 -6.69050 0.65218 INTE EXTERN> -27.28775 -43.75100 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0387" Parameter: A <- "-71.0387" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2877" Parameter: B <- "-27.2877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.751" Parameter: C <- "-43.751" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3036 TOTAL ENERGY = -71.0387 RDTITL> * VAN DER WAALS = -27.2877 ELECTROSTATIC = -43.751 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3036" Parameter: CONF_N -> "8002" Comparing "3036" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3037" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770103 ATOM PAIRS WERE FOUND FOR ATOM LIST 42229 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29868 from a total of 770103 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3037 -77.01117 5.97243 0.76327 INTE EXTERN> -24.64235 -52.36883 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0112" Parameter: A <- "-77.0112" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6423" Parameter: B <- "-24.6423" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3688" Parameter: C <- "-52.3688" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3037 TOTAL ENERGY = -77.0112 RDTITL> * VAN DER WAALS = -24.6423 ELECTROSTATIC = -52.3688 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3037" Parameter: CONF_N -> "8002" Comparing "3037" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3038" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770103 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769645 ATOM PAIRS WERE FOUND FOR ATOM LIST 42324 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29369 from a total of 769645 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3038 -82.02373 5.01256 0.71219 INTE EXTERN> -27.24607 -54.77767 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.0237" Parameter: A <- "-82.0237" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2461" Parameter: B <- "-27.2461" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.7777" Parameter: C <- "-54.7777" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3038 TOTAL ENERGY = -82.0237 RDTITL> * VAN DER WAALS = -27.2461 ELECTROSTATIC = -54.7777 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3038" Parameter: CONF_N -> "8002" Comparing "3038" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3039" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769645 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767842 ATOM PAIRS WERE FOUND FOR ATOM LIST 42244 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29651 from a total of 767842 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3039 -76.26168 -5.76206 0.72126 INTE EXTERN> -24.78126 -51.48042 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2617" Parameter: A <- "-76.2617" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7813" Parameter: B <- "-24.7813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4804" Parameter: C <- "-51.4804" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3039 TOTAL ENERGY = -76.2617 RDTITL> * VAN DER WAALS = -24.7813 ELECTROSTATIC = -51.4804 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3039" Parameter: CONF_N -> "8002" Comparing "3039" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3040" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767842 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768442 ATOM PAIRS WERE FOUND FOR ATOM LIST 42328 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30260 from a total of 768442 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3040 -78.12828 1.86660 0.64773 INTE EXTERN> -30.42941 -47.69887 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1283" Parameter: A <- "-78.1283" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4294" Parameter: B <- "-30.4294" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6989" Parameter: C <- "-47.6989" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3040 TOTAL ENERGY = -78.1283 RDTITL> * VAN DER WAALS = -30.4294 ELECTROSTATIC = -47.6989 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3040" Parameter: CONF_N -> "8002" Comparing "3040" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3041" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768442 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768683 ATOM PAIRS WERE FOUND FOR ATOM LIST 42324 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29152 from a total of 768683 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3041 -70.84555 -7.28273 0.59432 INTE EXTERN> -29.52159 -41.32396 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8456" Parameter: A <- "-70.8456" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5216" Parameter: B <- "-29.5216" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.324" Parameter: C <- "-41.324" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3041 TOTAL ENERGY = -70.8456 RDTITL> * VAN DER WAALS = -29.5216 ELECTROSTATIC = -41.324 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3041" Parameter: CONF_N -> "8002" Comparing "3041" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3042" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768683 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765424 ATOM PAIRS WERE FOUND FOR ATOM LIST 42314 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29818 from a total of 765424 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3042 -82.73951 11.89396 0.64162 INTE EXTERN> -31.82179 -50.91772 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7395" Parameter: A <- "-82.7395" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8218" Parameter: B <- "-31.8218" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9177" Parameter: C <- "-50.9177" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3042 TOTAL ENERGY = -82.7395 RDTITL> * VAN DER WAALS = -31.8218 ELECTROSTATIC = -50.9177 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3042" Parameter: CONF_N -> "8002" Comparing "3042" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3043" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765424 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765265 ATOM PAIRS WERE FOUND FOR ATOM LIST 41991 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29179 from a total of 765265 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3043 -71.40750 -11.33201 0.59684 INTE EXTERN> -31.49804 -39.90945 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4075" Parameter: A <- "-71.4075" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.498" Parameter: B <- "-31.498" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9095" Parameter: C <- "-39.9095" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3043 TOTAL ENERGY = -71.4075 RDTITL> * VAN DER WAALS = -31.498 ELECTROSTATIC = -39.9095 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3043" Parameter: CONF_N -> "8002" Comparing "3043" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3044" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765265 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768574 ATOM PAIRS WERE FOUND FOR ATOM LIST 42185 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29825 from a total of 768574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3044 -76.18341 4.77591 0.68587 INTE EXTERN> -29.06762 -47.11579 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1834" Parameter: A <- "-76.1834" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0676" Parameter: B <- "-29.0676" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1158" Parameter: C <- "-47.1158" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3044 TOTAL ENERGY = -76.1834 RDTITL> * VAN DER WAALS = -29.0676 ELECTROSTATIC = -47.1158 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3044" Parameter: CONF_N -> "8002" Comparing "3044" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3045" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764615 ATOM PAIRS WERE FOUND FOR ATOM LIST 42071 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29828 from a total of 764615 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3045 -79.26029 3.07688 0.69010 INTE EXTERN> -29.26431 -49.99598 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2603" Parameter: A <- "-79.2603" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2643" Parameter: B <- "-29.2643" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.996" Parameter: C <- "-49.996" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3045 TOTAL ENERGY = -79.2603 RDTITL> * VAN DER WAALS = -29.2643 ELECTROSTATIC = -49.996 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3045" Parameter: CONF_N -> "8002" Comparing "3045" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3046" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764615 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767983 ATOM PAIRS WERE FOUND FOR ATOM LIST 42265 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29807 from a total of 767983 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3046 -75.32963 -3.93066 0.69283 INTE EXTERN> -29.25784 -46.07179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3296" Parameter: A <- "-75.3296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2578" Parameter: B <- "-29.2578" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0718" Parameter: C <- "-46.0718" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3046 TOTAL ENERGY = -75.3296 RDTITL> * VAN DER WAALS = -29.2578 ELECTROSTATIC = -46.0718 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3046" Parameter: CONF_N -> "8002" Comparing "3046" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3047" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767983 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766151 ATOM PAIRS WERE FOUND FOR ATOM LIST 42108 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29645 from a total of 766151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3047 -81.99319 6.66357 0.73940 INTE EXTERN> -27.88077 -54.11242 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9932" Parameter: A <- "-81.9932" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8808" Parameter: B <- "-27.8808" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.1124" Parameter: C <- "-54.1124" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3047 TOTAL ENERGY = -81.9932 RDTITL> * VAN DER WAALS = -27.8808 ELECTROSTATIC = -54.1124 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3047" Parameter: CONF_N -> "8002" Comparing "3047" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3048" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767253 ATOM PAIRS WERE FOUND FOR ATOM LIST 42184 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29411 from a total of 767253 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3048 -74.39649 -7.59670 0.68373 INTE EXTERN> -27.07598 -47.32051 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3965" Parameter: A <- "-74.3965" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.076" Parameter: B <- "-27.076" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3205" Parameter: C <- "-47.3205" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3048 TOTAL ENERGY = -74.3965 RDTITL> * VAN DER WAALS = -27.076 ELECTROSTATIC = -47.3205 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3048" Parameter: CONF_N -> "8002" Comparing "3048" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3049" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767253 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769444 ATOM PAIRS WERE FOUND FOR ATOM LIST 42306 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29435 from a total of 769444 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3049 -72.64639 -1.75011 0.85139 INTE EXTERN> -23.14831 -49.49808 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6464" Parameter: A <- "-72.6464" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.1483" Parameter: B <- "-23.1483" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4981" Parameter: C <- "-49.4981" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3049 TOTAL ENERGY = -72.6464 RDTITL> * VAN DER WAALS = -23.1483 ELECTROSTATIC = -49.4981 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3049" Parameter: CONF_N -> "8002" Comparing "3049" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3050" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769444 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766761 ATOM PAIRS WERE FOUND FOR ATOM LIST 42279 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29675 from a total of 766761 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3050 -75.64895 3.00256 0.63561 INTE EXTERN> -29.35038 -46.29857 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.649" Parameter: A <- "-75.649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3504" Parameter: B <- "-29.3504" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2986" Parameter: C <- "-46.2986" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3050 TOTAL ENERGY = -75.649 RDTITL> * VAN DER WAALS = -29.3504 ELECTROSTATIC = -46.2986 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3050" Parameter: CONF_N -> "8002" Comparing "3050" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3051" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766761 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770930 ATOM PAIRS WERE FOUND FOR ATOM LIST 42242 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28702 from a total of 770930 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3051 -73.76321 -1.88574 0.78523 INTE EXTERN> -25.00962 -48.75359 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7632" Parameter: A <- "-73.7632" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0096" Parameter: B <- "-25.0096" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7536" Parameter: C <- "-48.7536" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3051 TOTAL ENERGY = -73.7632 RDTITL> * VAN DER WAALS = -25.0096 ELECTROSTATIC = -48.7536 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3051" Parameter: CONF_N -> "8002" Comparing "3051" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3052" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770930 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769195 ATOM PAIRS WERE FOUND FOR ATOM LIST 42014 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29819 from a total of 769195 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3052 -77.06999 3.30678 0.60087 INTE EXTERN> -31.89125 -45.17874 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.07" Parameter: A <- "-77.07" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8912" Parameter: B <- "-31.8912" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1787" Parameter: C <- "-45.1787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3052 TOTAL ENERGY = -77.07 RDTITL> * VAN DER WAALS = -31.8912 ELECTROSTATIC = -45.1787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3052" Parameter: CONF_N -> "8002" Comparing "3052" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3053" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769195 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766389 ATOM PAIRS WERE FOUND FOR ATOM LIST 42251 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29730 from a total of 766389 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3053 -80.32626 3.25627 0.78338 INTE EXTERN> -24.79443 -55.53183 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3263" Parameter: A <- "-80.3263" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7944" Parameter: B <- "-24.7944" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.5318" Parameter: C <- "-55.5318" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3053 TOTAL ENERGY = -80.3263 RDTITL> * VAN DER WAALS = -24.7944 ELECTROSTATIC = -55.5318 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3053" Parameter: CONF_N -> "8002" Comparing "3053" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3054" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766389 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772491 ATOM PAIRS WERE FOUND FOR ATOM LIST 42469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29488 from a total of 772491 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3054 -72.86185 -7.46441 0.80458 INTE EXTERN> -24.15844 -48.70341 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8618" Parameter: A <- "-72.8618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1584" Parameter: B <- "-24.1584" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7034" Parameter: C <- "-48.7034" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3054 TOTAL ENERGY = -72.8618 RDTITL> * VAN DER WAALS = -24.1584 ELECTROSTATIC = -48.7034 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3054" Parameter: CONF_N -> "8002" Comparing "3054" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3055" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772491 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771170 ATOM PAIRS WERE FOUND FOR ATOM LIST 42385 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30244 from a total of 771170 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3055 -73.05992 0.19807 0.62911 INTE EXTERN> -29.76499 -43.29493 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0599" Parameter: A <- "-73.0599" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.765" Parameter: B <- "-29.765" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2949" Parameter: C <- "-43.2949" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3055 TOTAL ENERGY = -73.0599 RDTITL> * VAN DER WAALS = -29.765 ELECTROSTATIC = -43.2949 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3055" Parameter: CONF_N -> "8002" Comparing "3055" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3056" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771170 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765863 ATOM PAIRS WERE FOUND FOR ATOM LIST 42179 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29425 from a total of 765863 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3056 -71.12237 -1.93755 0.62193 INTE EXTERN> -28.22601 -42.89636 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1224" Parameter: A <- "-71.1224" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.226" Parameter: B <- "-28.226" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8964" Parameter: C <- "-42.8964" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3056 TOTAL ENERGY = -71.1224 RDTITL> * VAN DER WAALS = -28.226 ELECTROSTATIC = -42.8964 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3056" Parameter: CONF_N -> "8002" Comparing "3056" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3057" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765863 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761446 ATOM PAIRS WERE FOUND FOR ATOM LIST 41877 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29470 from a total of 761446 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3057 -67.20827 -3.91410 0.70435 INTE EXTERN> -27.25307 -39.95520 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2083" Parameter: A <- "-67.2083" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2531" Parameter: B <- "-27.2531" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9552" Parameter: C <- "-39.9552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3057 TOTAL ENERGY = -67.2083 RDTITL> * VAN DER WAALS = -27.2531 ELECTROSTATIC = -39.9552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3057" Parameter: CONF_N -> "8002" Comparing "3057" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3058" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761446 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769485 ATOM PAIRS WERE FOUND FOR ATOM LIST 42251 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29679 from a total of 769485 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3058 -69.49283 2.28456 0.63556 INTE EXTERN> -29.59463 -39.89820 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4928" Parameter: A <- "-69.4928" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5946" Parameter: B <- "-29.5946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8982" Parameter: C <- "-39.8982" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3058 TOTAL ENERGY = -69.4928 RDTITL> * VAN DER WAALS = -29.5946 ELECTROSTATIC = -39.8982 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3058" Parameter: CONF_N -> "8002" Comparing "3058" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3059" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769485 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 775856 ATOM PAIRS WERE FOUND FOR ATOM LIST 42447 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29984 from a total of 775856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3059 -80.98844 11.49561 0.68363 INTE EXTERN> -30.29637 -50.69207 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9884" Parameter: A <- "-80.9884" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2964" Parameter: B <- "-30.2964" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6921" Parameter: C <- "-50.6921" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3059 TOTAL ENERGY = -80.9884 RDTITL> * VAN DER WAALS = -30.2964 ELECTROSTATIC = -50.6921 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3059" Parameter: CONF_N -> "8002" Comparing "3059" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3060" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 775856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766715 ATOM PAIRS WERE FOUND FOR ATOM LIST 42125 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29604 from a total of 766715 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3060 -76.26109 -4.72734 0.67676 INTE EXTERN> -27.40615 -48.85494 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2611" Parameter: A <- "-76.2611" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4062" Parameter: B <- "-27.4062" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8549" Parameter: C <- "-48.8549" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3060 TOTAL ENERGY = -76.2611 RDTITL> * VAN DER WAALS = -27.4062 ELECTROSTATIC = -48.8549 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3060" Parameter: CONF_N -> "8002" Comparing "3060" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3061" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766715 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766696 ATOM PAIRS WERE FOUND FOR ATOM LIST 41970 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28685 from a total of 766696 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3061 -65.25871 -11.00238 0.66767 INTE EXTERN> -25.46050 -39.79822 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2587" Parameter: A <- "-65.2587" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4605" Parameter: B <- "-25.4605" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7982" Parameter: C <- "-39.7982" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3061 TOTAL ENERGY = -65.2587 RDTITL> * VAN DER WAALS = -25.4605 ELECTROSTATIC = -39.7982 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3061" Parameter: CONF_N -> "8002" Comparing "3061" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3062" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766696 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772866 ATOM PAIRS WERE FOUND FOR ATOM LIST 42319 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29922 from a total of 772866 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3062 -71.95359 6.69488 0.61972 INTE EXTERN> -30.15289 -41.80070 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9536" Parameter: A <- "-71.9536" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1529" Parameter: B <- "-30.1529" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8007" Parameter: C <- "-41.8007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3062 TOTAL ENERGY = -71.9536 RDTITL> * VAN DER WAALS = -30.1529 ELECTROSTATIC = -41.8007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3062" Parameter: CONF_N -> "8002" Comparing "3062" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3063" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772866 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770653 ATOM PAIRS WERE FOUND FOR ATOM LIST 42260 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29418 from a total of 770653 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3063 -73.29570 1.34211 0.76040 INTE EXTERN> -24.98888 -48.30682 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2957" Parameter: A <- "-73.2957" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9889" Parameter: B <- "-24.9889" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3068" Parameter: C <- "-48.3068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3063 TOTAL ENERGY = -73.2957 RDTITL> * VAN DER WAALS = -24.9889 ELECTROSTATIC = -48.3068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3063" Parameter: CONF_N -> "8002" Comparing "3063" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3064" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770653 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767153 ATOM PAIRS WERE FOUND FOR ATOM LIST 42195 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30097 from a total of 767153 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3064 -83.16541 9.86971 0.72940 INTE EXTERN> -30.26268 -52.90273 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.1654" Parameter: A <- "-83.1654" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2627" Parameter: B <- "-30.2627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9027" Parameter: C <- "-52.9027" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3064 TOTAL ENERGY = -83.1654 RDTITL> * VAN DER WAALS = -30.2627 ELECTROSTATIC = -52.9027 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3064" Parameter: CONF_N -> "8002" Comparing "3064" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3065" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767153 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767124 ATOM PAIRS WERE FOUND FOR ATOM LIST 42062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29888 from a total of 767124 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3065 -83.19834 0.03293 0.73220 INTE EXTERN> -28.53670 -54.66165 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.1983" Parameter: A <- "-83.1983" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5367" Parameter: B <- "-28.5367" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.6616" Parameter: C <- "-54.6616" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3065 TOTAL ENERGY = -83.1983 RDTITL> * VAN DER WAALS = -28.5367 ELECTROSTATIC = -54.6616 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3065" Parameter: CONF_N -> "8002" Comparing "3065" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3066" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767124 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771015 ATOM PAIRS WERE FOUND FOR ATOM LIST 42346 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30586 from a total of 771015 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3066 -81.21637 -1.98197 0.80624 INTE EXTERN> -24.35687 -56.85950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.2164" Parameter: A <- "-81.2164" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3569" Parameter: B <- "-24.3569" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.8595" Parameter: C <- "-56.8595" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3066 TOTAL ENERGY = -81.2164 RDTITL> * VAN DER WAALS = -24.3569 ELECTROSTATIC = -56.8595 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3066" Parameter: CONF_N -> "8002" Comparing "3066" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3067" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771015 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767185 ATOM PAIRS WERE FOUND FOR ATOM LIST 42178 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29506 from a total of 767185 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3067 -71.14800 -10.06838 0.74017 INTE EXTERN> -26.25858 -44.88941 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.148" Parameter: A <- "-71.148" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2586" Parameter: B <- "-26.2586" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8894" Parameter: C <- "-44.8894" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3067 TOTAL ENERGY = -71.148 RDTITL> * VAN DER WAALS = -26.2586 ELECTROSTATIC = -44.8894 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3067" Parameter: CONF_N -> "8002" Comparing "3067" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3068" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767185 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771816 ATOM PAIRS WERE FOUND FOR ATOM LIST 42405 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29729 from a total of 771816 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3068 -76.56639 5.41839 0.69734 INTE EXTERN> -31.67528 -44.89111 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5664" Parameter: A <- "-76.5664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6753" Parameter: B <- "-31.6753" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8911" Parameter: C <- "-44.8911" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3068 TOTAL ENERGY = -76.5664 RDTITL> * VAN DER WAALS = -31.6753 ELECTROSTATIC = -44.8911 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3068" Parameter: CONF_N -> "8002" Comparing "3068" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3069" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771816 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769447 ATOM PAIRS WERE FOUND FOR ATOM LIST 42333 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30165 from a total of 769447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3069 -78.36965 1.80326 0.68669 INTE EXTERN> -28.56162 -49.80803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3697" Parameter: A <- "-78.3697" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5616" Parameter: B <- "-28.5616" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.808" Parameter: C <- "-49.808" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3069 TOTAL ENERGY = -78.3697 RDTITL> * VAN DER WAALS = -28.5616 ELECTROSTATIC = -49.808 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3069" Parameter: CONF_N -> "8002" Comparing "3069" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3070" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767521 ATOM PAIRS WERE FOUND FOR ATOM LIST 42021 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29858 from a total of 767521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3070 -79.43018 1.06053 0.71581 INTE EXTERN> -27.42051 -52.00967 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4302" Parameter: A <- "-79.4302" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4205" Parameter: B <- "-27.4205" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0097" Parameter: C <- "-52.0097" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3070 TOTAL ENERGY = -79.4302 RDTITL> * VAN DER WAALS = -27.4205 ELECTROSTATIC = -52.0097 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3070" Parameter: CONF_N -> "8002" Comparing "3070" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3071" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766408 ATOM PAIRS WERE FOUND FOR ATOM LIST 42088 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29612 from a total of 766408 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3071 -73.74707 -5.68312 0.59177 INTE EXTERN> -33.40124 -40.34583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7471" Parameter: A <- "-73.7471" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4012" Parameter: B <- "-33.4012" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3458" Parameter: C <- "-40.3458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3071 TOTAL ENERGY = -73.7471 RDTITL> * VAN DER WAALS = -33.4012 ELECTROSTATIC = -40.3458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3071" Parameter: CONF_N -> "8002" Comparing "3071" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3072" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766408 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763413 ATOM PAIRS WERE FOUND FOR ATOM LIST 41950 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29374 from a total of 763413 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3072 -78.09992 4.35285 0.67552 INTE EXTERN> -30.34036 -47.75956 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0999" Parameter: A <- "-78.0999" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3404" Parameter: B <- "-30.3404" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7596" Parameter: C <- "-47.7596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3072 TOTAL ENERGY = -78.0999 RDTITL> * VAN DER WAALS = -30.3404 ELECTROSTATIC = -47.7596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3072" Parameter: CONF_N -> "8002" Comparing "3072" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3073" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763413 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772089 ATOM PAIRS WERE FOUND FOR ATOM LIST 42370 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29925 from a total of 772089 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3073 -79.02035 0.92043 0.74616 INTE EXTERN> -26.72651 -52.29384 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0204" Parameter: A <- "-79.0204" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7265" Parameter: B <- "-26.7265" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2938" Parameter: C <- "-52.2938" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3073 TOTAL ENERGY = -79.0204 RDTITL> * VAN DER WAALS = -26.7265 ELECTROSTATIC = -52.2938 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3073" Parameter: CONF_N -> "8002" Comparing "3073" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3074" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772089 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771807 ATOM PAIRS WERE FOUND FOR ATOM LIST 42276 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29759 from a total of 771807 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3074 -82.37789 3.35754 0.66985 INTE EXTERN> -28.92252 -53.45537 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3779" Parameter: A <- "-82.3779" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9225" Parameter: B <- "-28.9225" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4554" Parameter: C <- "-53.4554" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3074 TOTAL ENERGY = -82.3779 RDTITL> * VAN DER WAALS = -28.9225 ELECTROSTATIC = -53.4554 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3074" Parameter: CONF_N -> "8002" Comparing "3074" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3075" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771807 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768627 ATOM PAIRS WERE FOUND FOR ATOM LIST 42310 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30038 from a total of 768627 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3075 -79.74897 -2.62892 0.62236 INTE EXTERN> -32.45667 -47.29230 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.749" Parameter: A <- "-79.749" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4567" Parameter: B <- "-32.4567" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2923" Parameter: C <- "-47.2923" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3075 TOTAL ENERGY = -79.749 RDTITL> * VAN DER WAALS = -32.4567 ELECTROSTATIC = -47.2923 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3075" Parameter: CONF_N -> "8002" Comparing "3075" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3076" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768627 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764870 ATOM PAIRS WERE FOUND FOR ATOM LIST 41899 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29856 from a total of 764870 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3076 -79.79368 0.04471 0.62103 INTE EXTERN> -32.51668 -47.27699 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7937" Parameter: A <- "-79.7937" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5167" Parameter: B <- "-32.5167" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.277" Parameter: C <- "-47.277" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3076 TOTAL ENERGY = -79.7937 RDTITL> * VAN DER WAALS = -32.5167 ELECTROSTATIC = -47.277 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3076" Parameter: CONF_N -> "8002" Comparing "3076" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3077" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764870 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767367 ATOM PAIRS WERE FOUND FOR ATOM LIST 42211 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30276 from a total of 767367 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3077 -76.46419 -3.32948 0.75001 INTE EXTERN> -24.84432 -51.61987 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4642" Parameter: A <- "-76.4642" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8443" Parameter: B <- "-24.8443" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6199" Parameter: C <- "-51.6199" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3077 TOTAL ENERGY = -76.4642 RDTITL> * VAN DER WAALS = -24.8443 ELECTROSTATIC = -51.6199 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3077" Parameter: CONF_N -> "8002" Comparing "3077" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3078" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767367 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762435 ATOM PAIRS WERE FOUND FOR ATOM LIST 41953 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29547 from a total of 762435 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3078 -79.66601 3.20181 0.74911 INTE EXTERN> -27.02970 -52.63631 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.666" Parameter: A <- "-79.666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0297" Parameter: B <- "-27.0297" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6363" Parameter: C <- "-52.6363" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3078 TOTAL ENERGY = -79.666 RDTITL> * VAN DER WAALS = -27.0297 ELECTROSTATIC = -52.6363 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3078" Parameter: CONF_N -> "8002" Comparing "3078" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3079" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762435 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760996 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29666 from a total of 760996 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3079 -81.55021 1.88420 0.70974 INTE EXTERN> -29.06977 -52.48044 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5502" Parameter: A <- "-81.5502" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0698" Parameter: B <- "-29.0698" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.4804" Parameter: C <- "-52.4804" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3079 TOTAL ENERGY = -81.5502 RDTITL> * VAN DER WAALS = -29.0698 ELECTROSTATIC = -52.4804 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3079" Parameter: CONF_N -> "8002" Comparing "3079" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3080" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760996 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765445 ATOM PAIRS WERE FOUND FOR ATOM LIST 42249 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29488 from a total of 765445 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3080 -80.67057 -0.87964 0.75236 INTE EXTERN> -27.09770 -53.57287 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6706" Parameter: A <- "-80.6706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0977" Parameter: B <- "-27.0977" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.5729" Parameter: C <- "-53.5729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3080 TOTAL ENERGY = -80.6706 RDTITL> * VAN DER WAALS = -27.0977 ELECTROSTATIC = -53.5729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3080" Parameter: CONF_N -> "8002" Comparing "3080" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3081" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765445 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768464 ATOM PAIRS WERE FOUND FOR ATOM LIST 42258 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30138 from a total of 768464 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3081 -70.56668 -10.10389 0.70069 INTE EXTERN> -28.79381 -41.77287 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5667" Parameter: A <- "-70.5667" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7938" Parameter: B <- "-28.7938" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7729" Parameter: C <- "-41.7729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3081 TOTAL ENERGY = -70.5667 RDTITL> * VAN DER WAALS = -28.7938 ELECTROSTATIC = -41.7729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3081" Parameter: CONF_N -> "8002" Comparing "3081" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3082" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768464 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764675 ATOM PAIRS WERE FOUND FOR ATOM LIST 42093 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 764675 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3082 -75.23169 4.66502 0.71696 INTE EXTERN> -26.39224 -48.83945 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2317" Parameter: A <- "-75.2317" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3922" Parameter: B <- "-26.3922" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8395" Parameter: C <- "-48.8395" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3082 TOTAL ENERGY = -75.2317 RDTITL> * VAN DER WAALS = -26.3922 ELECTROSTATIC = -48.8395 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3082" Parameter: CONF_N -> "8002" Comparing "3082" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3083" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764675 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766625 ATOM PAIRS WERE FOUND FOR ATOM LIST 42115 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29725 from a total of 766625 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3083 -80.74714 5.51545 0.67070 INTE EXTERN> -31.35715 -49.38999 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7471" Parameter: A <- "-80.7471" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3571" Parameter: B <- "-31.3571" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.39" Parameter: C <- "-49.39" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3083 TOTAL ENERGY = -80.7471 RDTITL> * VAN DER WAALS = -31.3571 ELECTROSTATIC = -49.39 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3083" Parameter: CONF_N -> "8002" Comparing "3083" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3084" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766625 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772538 ATOM PAIRS WERE FOUND FOR ATOM LIST 42247 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29757 from a total of 772538 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3084 -80.49349 -0.25365 0.58461 INTE EXTERN> -35.89351 -44.59997 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4935" Parameter: A <- "-80.4935" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.8935" Parameter: B <- "-35.8935" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6" Parameter: C <- "-44.6" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3084 TOTAL ENERGY = -80.4935 RDTITL> * VAN DER WAALS = -35.8935 ELECTROSTATIC = -44.6 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3084" Parameter: CONF_N -> "8002" Comparing "3084" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3085" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772538 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763308 ATOM PAIRS WERE FOUND FOR ATOM LIST 41942 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29562 from a total of 763308 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3085 -82.89430 2.40081 0.72927 INTE EXTERN> -27.75793 -55.13637 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.8943" Parameter: A <- "-82.8943" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7579" Parameter: B <- "-27.7579" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.1364" Parameter: C <- "-55.1364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3085 TOTAL ENERGY = -82.8943 RDTITL> * VAN DER WAALS = -27.7579 ELECTROSTATIC = -55.1364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3085" Parameter: CONF_N -> "8002" Comparing "3085" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3086" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763308 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760638 ATOM PAIRS WERE FOUND FOR ATOM LIST 41780 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29819 from a total of 760638 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3086 -81.46113 -1.43317 0.78992 INTE EXTERN> -26.99682 -54.46431 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4611" Parameter: A <- "-81.4611" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9968" Parameter: B <- "-26.9968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.4643" Parameter: C <- "-54.4643" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3086 TOTAL ENERGY = -81.4611 RDTITL> * VAN DER WAALS = -26.9968 ELECTROSTATIC = -54.4643 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3086" Parameter: CONF_N -> "8002" Comparing "3086" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3087" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760638 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766161 ATOM PAIRS WERE FOUND FOR ATOM LIST 42088 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29238 from a total of 766161 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3087 -73.04088 -8.42024 0.69972 INTE EXTERN> -27.61735 -45.42354 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0409" Parameter: A <- "-73.0409" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6173" Parameter: B <- "-27.6173" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4235" Parameter: C <- "-45.4235" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3087 TOTAL ENERGY = -73.0409 RDTITL> * VAN DER WAALS = -27.6173 ELECTROSTATIC = -45.4235 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3087" Parameter: CONF_N -> "8002" Comparing "3087" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3088" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766161 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764143 ATOM PAIRS WERE FOUND FOR ATOM LIST 42086 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29668 from a total of 764143 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3088 -76.85750 3.81661 0.66783 INTE EXTERN> -30.02403 -46.83346 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8575" Parameter: A <- "-76.8575" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.024" Parameter: B <- "-30.024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8335" Parameter: C <- "-46.8335" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3088 TOTAL ENERGY = -76.8575 RDTITL> * VAN DER WAALS = -30.024 ELECTROSTATIC = -46.8335 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3088" Parameter: CONF_N -> "8002" Comparing "3088" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3089" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764143 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761910 ATOM PAIRS WERE FOUND FOR ATOM LIST 41743 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29535 from a total of 761910 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3089 -78.88096 2.02346 0.76197 INTE EXTERN> -27.14646 -51.73450 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.881" Parameter: A <- "-78.881" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1465" Parameter: B <- "-27.1465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7345" Parameter: C <- "-51.7345" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3089 TOTAL ENERGY = -78.881 RDTITL> * VAN DER WAALS = -27.1465 ELECTROSTATIC = -51.7345 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3089" Parameter: CONF_N -> "8002" Comparing "3089" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3090" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761910 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760668 ATOM PAIRS WERE FOUND FOR ATOM LIST 41789 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29318 from a total of 760668 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3090 -78.04462 -0.83634 0.79184 INTE EXTERN> -27.20521 -50.83941 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0446" Parameter: A <- "-78.0446" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2052" Parameter: B <- "-27.2052" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8394" Parameter: C <- "-50.8394" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3090 TOTAL ENERGY = -78.0446 RDTITL> * VAN DER WAALS = -27.2052 ELECTROSTATIC = -50.8394 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3090" Parameter: CONF_N -> "8002" Comparing "3090" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3091" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760668 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764232 ATOM PAIRS WERE FOUND FOR ATOM LIST 41818 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30093 from a total of 764232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3091 -79.87782 1.83320 0.60506 INTE EXTERN> -32.64835 -47.22947 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8778" Parameter: A <- "-79.8778" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6484" Parameter: B <- "-32.6484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2295" Parameter: C <- "-47.2295" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3091 TOTAL ENERGY = -79.8778 RDTITL> * VAN DER WAALS = -32.6484 ELECTROSTATIC = -47.2295 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3091" Parameter: CONF_N -> "8002" Comparing "3091" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3092" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41859 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29785 from a total of 762118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3092 -83.87169 3.99387 0.77342 INTE EXTERN> -27.73289 -56.13880 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.8717" Parameter: A <- "-83.8717" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7329" Parameter: B <- "-27.7329" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.1388" Parameter: C <- "-56.1388" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3092 TOTAL ENERGY = -83.8717 RDTITL> * VAN DER WAALS = -27.7329 ELECTROSTATIC = -56.1388 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3092" Parameter: CONF_N -> "8002" Comparing "3092" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3093" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764240 ATOM PAIRS WERE FOUND FOR ATOM LIST 42097 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29944 from a total of 764240 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3093 -81.47119 -2.40050 0.78015 INTE EXTERN> -27.16397 -54.30722 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4712" Parameter: A <- "-81.4712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.164" Parameter: B <- "-27.164" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.3072" Parameter: C <- "-54.3072" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3093 TOTAL ENERGY = -81.4712 RDTITL> * VAN DER WAALS = -27.164 ELECTROSTATIC = -54.3072 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3093" Parameter: CONF_N -> "8002" Comparing "3093" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3094" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764240 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762594 ATOM PAIRS WERE FOUND FOR ATOM LIST 42044 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29583 from a total of 762594 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3094 -83.33648 1.86529 0.64000 INTE EXTERN> -32.06038 -51.27611 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.3365" Parameter: A <- "-83.3365" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0604" Parameter: B <- "-32.0604" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2761" Parameter: C <- "-51.2761" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3094 TOTAL ENERGY = -83.3365 RDTITL> * VAN DER WAALS = -32.0604 ELECTROSTATIC = -51.2761 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3094" Parameter: CONF_N -> "8002" Comparing "3094" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3095" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762594 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759313 ATOM PAIRS WERE FOUND FOR ATOM LIST 41643 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29443 from a total of 759313 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3095 -70.90089 -12.43559 0.70137 INTE EXTERN> -29.77787 -41.12302 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9009" Parameter: A <- "-70.9009" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7779" Parameter: B <- "-29.7779" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.123" Parameter: C <- "-41.123" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3095 TOTAL ENERGY = -70.9009 RDTITL> * VAN DER WAALS = -29.7779 ELECTROSTATIC = -41.123 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3095" Parameter: CONF_N -> "8002" Comparing "3095" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3096" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759313 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753841 ATOM PAIRS WERE FOUND FOR ATOM LIST 41497 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29347 from a total of 753841 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3096 -80.95770 10.05680 0.68366 INTE EXTERN> -29.80845 -51.14925 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9577" Parameter: A <- "-80.9577" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8084" Parameter: B <- "-29.8084" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1492" Parameter: C <- "-51.1492" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3096 TOTAL ENERGY = -80.9577 RDTITL> * VAN DER WAALS = -29.8084 ELECTROSTATIC = -51.1492 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3096" Parameter: CONF_N -> "8002" Comparing "3096" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3097" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753841 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760732 ATOM PAIRS WERE FOUND FOR ATOM LIST 41817 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29768 from a total of 760732 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3097 -81.42950 0.47180 0.62667 INTE EXTERN> -31.47554 -49.95396 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4295" Parameter: A <- "-81.4295" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4755" Parameter: B <- "-31.4755" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.954" Parameter: C <- "-49.954" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3097 TOTAL ENERGY = -81.4295 RDTITL> * VAN DER WAALS = -31.4755 ELECTROSTATIC = -49.954 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3097" Parameter: CONF_N -> "8002" Comparing "3097" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3098" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760732 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759761 ATOM PAIRS WERE FOUND FOR ATOM LIST 41569 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30241 from a total of 759761 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3098 -87.30897 5.87947 0.68722 INTE EXTERN> -32.07794 -55.23103 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.309" Parameter: A <- "-87.309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0779" Parameter: B <- "-32.0779" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.231" Parameter: C <- "-55.231" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3098 TOTAL ENERGY = -87.309 RDTITL> * VAN DER WAALS = -32.0779 ELECTROSTATIC = -55.231 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3098" Parameter: CONF_N -> "8002" Comparing "3098" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3099" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759761 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756687 ATOM PAIRS WERE FOUND FOR ATOM LIST 41733 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29393 from a total of 756687 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3099 -78.47775 -8.83123 0.75432 INTE EXTERN> -26.13055 -52.34720 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4777" Parameter: A <- "-78.4777" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1305" Parameter: B <- "-26.1305" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3472" Parameter: C <- "-52.3472" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3099 TOTAL ENERGY = -78.4777 RDTITL> * VAN DER WAALS = -26.1305 ELECTROSTATIC = -52.3472 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3099" Parameter: CONF_N -> "8002" Comparing "3099" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3100" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756687 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30270 from a total of 763118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3100 -76.68420 -1.79355 0.64379 INTE EXTERN> -30.86590 -45.81830 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6842" Parameter: A <- "-76.6842" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8659" Parameter: B <- "-30.8659" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8183" Parameter: C <- "-45.8183" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3100 TOTAL ENERGY = -76.6842 RDTITL> * VAN DER WAALS = -30.8659 ELECTROSTATIC = -45.8183 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3100" Parameter: CONF_N -> "8002" Comparing "3100" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3101" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766520 ATOM PAIRS WERE FOUND FOR ATOM LIST 42137 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30669 from a total of 766520 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3101 -82.75811 6.07391 0.86149 INTE EXTERN> -27.00488 -55.75323 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7581" Parameter: A <- "-82.7581" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0049" Parameter: B <- "-27.0049" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.7532" Parameter: C <- "-55.7532" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3101 TOTAL ENERGY = -82.7581 RDTITL> * VAN DER WAALS = -27.0049 ELECTROSTATIC = -55.7532 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3101" Parameter: CONF_N -> "8002" Comparing "3101" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3102" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766520 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769528 ATOM PAIRS WERE FOUND FOR ATOM LIST 42310 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29856 from a total of 769528 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3102 -76.72205 -6.03605 0.58444 INTE EXTERN> -33.49864 -43.22342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7221" Parameter: A <- "-76.7221" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4986" Parameter: B <- "-33.4986" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2234" Parameter: C <- "-43.2234" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3102 TOTAL ENERGY = -76.7221 RDTITL> * VAN DER WAALS = -33.4986 ELECTROSTATIC = -43.2234 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3102" Parameter: CONF_N -> "8002" Comparing "3102" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3103" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769528 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41956 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30279 from a total of 763118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3103 -82.93571 6.21366 0.73828 INTE EXTERN> -29.43013 -53.50559 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9357" Parameter: A <- "-82.9357" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4301" Parameter: B <- "-29.4301" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.5056" Parameter: C <- "-53.5056" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3103 TOTAL ENERGY = -82.9357 RDTITL> * VAN DER WAALS = -29.4301 ELECTROSTATIC = -53.5056 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3103" Parameter: CONF_N -> "8002" Comparing "3103" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3104" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765309 ATOM PAIRS WERE FOUND FOR ATOM LIST 41960 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30635 from a total of 765309 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3104 -82.30852 -0.62719 0.68628 INTE EXTERN> -31.77079 -50.53773 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3085" Parameter: A <- "-82.3085" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7708" Parameter: B <- "-31.7708" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5377" Parameter: C <- "-50.5377" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3104 TOTAL ENERGY = -82.3085 RDTITL> * VAN DER WAALS = -31.7708 ELECTROSTATIC = -50.5377 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3104" Parameter: CONF_N -> "8002" Comparing "3104" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3105" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765309 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758440 ATOM PAIRS WERE FOUND FOR ATOM LIST 41838 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30028 from a total of 758440 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3105 -82.16998 -0.13854 0.73297 INTE EXTERN> -31.78377 -50.38621 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.17" Parameter: A <- "-82.17" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7838" Parameter: B <- "-31.7838" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3862" Parameter: C <- "-50.3862" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3105 TOTAL ENERGY = -82.17 RDTITL> * VAN DER WAALS = -31.7838 ELECTROSTATIC = -50.3862 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3105" Parameter: CONF_N -> "8002" Comparing "3105" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3106" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758440 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760232 ATOM PAIRS WERE FOUND FOR ATOM LIST 41680 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30050 from a total of 760232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3106 -80.36905 -1.80093 0.68164 INTE EXTERN> -31.17730 -49.19175 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3691" Parameter: A <- "-80.3691" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1773" Parameter: B <- "-31.1773" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1918" Parameter: C <- "-49.1918" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3106 TOTAL ENERGY = -80.3691 RDTITL> * VAN DER WAALS = -31.1773 ELECTROSTATIC = -49.1918 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3106" Parameter: CONF_N -> "8002" Comparing "3106" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3107" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763766 ATOM PAIRS WERE FOUND FOR ATOM LIST 41976 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30311 from a total of 763766 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3107 -80.96414 0.59508 0.67012 INTE EXTERN> -31.23113 -49.73301 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9641" Parameter: A <- "-80.9641" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2311" Parameter: B <- "-31.2311" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.733" Parameter: C <- "-49.733" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3107 TOTAL ENERGY = -80.9641 RDTITL> * VAN DER WAALS = -31.2311 ELECTROSTATIC = -49.733 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3107" Parameter: CONF_N -> "8002" Comparing "3107" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3108" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763766 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767887 ATOM PAIRS WERE FOUND FOR ATOM LIST 42183 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30206 from a total of 767887 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3108 -76.56404 -4.40010 0.71106 INTE EXTERN> -29.68053 -46.88350 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.564" Parameter: A <- "-76.564" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6805" Parameter: B <- "-29.6805" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8835" Parameter: C <- "-46.8835" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3108 TOTAL ENERGY = -76.564 RDTITL> * VAN DER WAALS = -29.6805 ELECTROSTATIC = -46.8835 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3108" Parameter: CONF_N -> "8002" Comparing "3108" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3109" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767887 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765876 ATOM PAIRS WERE FOUND FOR ATOM LIST 42165 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30213 from a total of 765876 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3109 -80.11558 3.55154 0.70524 INTE EXTERN> -30.47624 -49.63934 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1156" Parameter: A <- "-80.1156" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4762" Parameter: B <- "-30.4762" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6393" Parameter: C <- "-49.6393" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3109 TOTAL ENERGY = -80.1156 RDTITL> * VAN DER WAALS = -30.4762 ELECTROSTATIC = -49.6393 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3109" Parameter: CONF_N -> "8002" Comparing "3109" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3110" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765876 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762813 ATOM PAIRS WERE FOUND FOR ATOM LIST 41887 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29858 from a total of 762813 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3110 -84.25995 4.14438 0.63786 INTE EXTERN> -33.94046 -50.31949 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.26" Parameter: A <- "-84.26" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9405" Parameter: B <- "-33.9405" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3195" Parameter: C <- "-50.3195" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3110 TOTAL ENERGY = -84.26 RDTITL> * VAN DER WAALS = -33.9405 ELECTROSTATIC = -50.3195 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3110" Parameter: CONF_N -> "8002" Comparing "3110" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3111" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762813 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761960 ATOM PAIRS WERE FOUND FOR ATOM LIST 42068 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30160 from a total of 761960 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3111 -69.10401 -15.15594 0.72274 INTE EXTERN> -27.17800 -41.92601 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.104" Parameter: A <- "-69.104" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.178" Parameter: B <- "-27.178" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.926" Parameter: C <- "-41.926" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3111 TOTAL ENERGY = -69.104 RDTITL> * VAN DER WAALS = -27.178 ELECTROSTATIC = -41.926 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3111" Parameter: CONF_N -> "8002" Comparing "3111" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3112" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761960 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41848 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29930 from a total of 761586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3112 -73.48180 4.37780 0.63310 INTE EXTERN> -30.74387 -42.73794 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4818" Parameter: A <- "-73.4818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7439" Parameter: B <- "-30.7439" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7379" Parameter: C <- "-42.7379" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3112 TOTAL ENERGY = -73.4818 RDTITL> * VAN DER WAALS = -30.7439 ELECTROSTATIC = -42.7379 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3112" Parameter: CONF_N -> "8002" Comparing "3112" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3113" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763466 ATOM PAIRS WERE FOUND FOR ATOM LIST 41918 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29404 from a total of 763466 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3113 -83.90211 10.42031 0.69075 INTE EXTERN> -31.03917 -52.86294 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.9021" Parameter: A <- "-83.9021" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0392" Parameter: B <- "-31.0392" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8629" Parameter: C <- "-52.8629" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3113 TOTAL ENERGY = -83.9021 RDTITL> * VAN DER WAALS = -31.0392 ELECTROSTATIC = -52.8629 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3113" Parameter: CONF_N -> "8002" Comparing "3113" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3114" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763466 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760245 ATOM PAIRS WERE FOUND FOR ATOM LIST 41827 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29843 from a total of 760245 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3114 -80.19688 -3.70524 0.73233 INTE EXTERN> -26.78845 -53.40843 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1969" Parameter: A <- "-80.1969" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7884" Parameter: B <- "-26.7884" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4084" Parameter: C <- "-53.4084" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3114 TOTAL ENERGY = -80.1969 RDTITL> * VAN DER WAALS = -26.7884 ELECTROSTATIC = -53.4084 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3114" Parameter: CONF_N -> "8002" Comparing "3114" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3115" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760245 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765385 ATOM PAIRS WERE FOUND FOR ATOM LIST 42008 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30158 from a total of 765385 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3115 -83.14673 2.94985 0.70199 INTE EXTERN> -30.61611 -52.53062 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.1467" Parameter: A <- "-83.1467" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6161" Parameter: B <- "-30.6161" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5306" Parameter: C <- "-52.5306" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3115 TOTAL ENERGY = -83.1467 RDTITL> * VAN DER WAALS = -30.6161 ELECTROSTATIC = -52.5306 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3115" Parameter: CONF_N -> "8002" Comparing "3115" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3116" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765385 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768629 ATOM PAIRS WERE FOUND FOR ATOM LIST 42334 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30513 from a total of 768629 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3116 -80.32596 -2.82077 0.75775 INTE EXTERN> -27.69365 -52.63231 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.326" Parameter: A <- "-80.326" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6937" Parameter: B <- "-27.6937" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6323" Parameter: C <- "-52.6323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3116 TOTAL ENERGY = -80.326 RDTITL> * VAN DER WAALS = -27.6937 ELECTROSTATIC = -52.6323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3116" Parameter: CONF_N -> "8002" Comparing "3116" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3117" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768629 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765246 ATOM PAIRS WERE FOUND FOR ATOM LIST 41748 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29975 from a total of 765246 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3117 -83.22273 2.89677 0.72810 INTE EXTERN> -30.98496 -52.23777 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.2227" Parameter: A <- "-83.2227" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.985" Parameter: B <- "-30.985" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2378" Parameter: C <- "-52.2378" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3117 TOTAL ENERGY = -83.2227 RDTITL> * VAN DER WAALS = -30.985 ELECTROSTATIC = -52.2378 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3117" Parameter: CONF_N -> "8002" Comparing "3117" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3118" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765246 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763441 ATOM PAIRS WERE FOUND FOR ATOM LIST 42063 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29612 from a total of 763441 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3118 -87.21854 3.99580 0.73923 INTE EXTERN> -28.41204 -58.80650 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.2185" Parameter: A <- "-87.2185" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.412" Parameter: B <- "-28.412" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.8065" Parameter: C <- "-58.8065" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3118 TOTAL ENERGY = -87.2185 RDTITL> * VAN DER WAALS = -28.412 ELECTROSTATIC = -58.8065 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3118" Parameter: CONF_N -> "8002" Comparing "3118" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3119" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763441 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765071 ATOM PAIRS WERE FOUND FOR ATOM LIST 41981 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29637 from a total of 765071 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3119 -76.95673 -10.26181 0.79760 INTE EXTERN> -25.40474 -51.55199 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9567" Parameter: A <- "-76.9567" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4047" Parameter: B <- "-25.4047" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.552" Parameter: C <- "-51.552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3119 TOTAL ENERGY = -76.9567 RDTITL> * VAN DER WAALS = -25.4047 ELECTROSTATIC = -51.552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3119" Parameter: CONF_N -> "8002" Comparing "3119" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3120" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765071 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763711 ATOM PAIRS WERE FOUND FOR ATOM LIST 42012 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29426 from a total of 763711 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3120 -80.55771 3.60098 0.72235 INTE EXTERN> -28.31247 -52.24524 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5577" Parameter: A <- "-80.5577" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3125" Parameter: B <- "-28.3125" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2452" Parameter: C <- "-52.2452" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3120 TOTAL ENERGY = -80.5577 RDTITL> * VAN DER WAALS = -28.3125 ELECTROSTATIC = -52.2452 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3120" Parameter: CONF_N -> "8002" Comparing "3120" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3121" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763711 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766455 ATOM PAIRS WERE FOUND FOR ATOM LIST 42342 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29500 from a total of 766455 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3121 -77.17270 -3.38501 0.79250 INTE EXTERN> -25.59980 -51.57290 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1727" Parameter: A <- "-77.1727" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5998" Parameter: B <- "-25.5998" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5729" Parameter: C <- "-51.5729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3121 TOTAL ENERGY = -77.1727 RDTITL> * VAN DER WAALS = -25.5998 ELECTROSTATIC = -51.5729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3121" Parameter: CONF_N -> "8002" Comparing "3121" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3122" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766455 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762955 ATOM PAIRS WERE FOUND FOR ATOM LIST 41978 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29323 from a total of 762955 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3122 -81.55807 4.38537 0.64840 INTE EXTERN> -32.85659 -48.70148 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5581" Parameter: A <- "-81.5581" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8566" Parameter: B <- "-32.8566" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7015" Parameter: C <- "-48.7015" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3122 TOTAL ENERGY = -81.5581 RDTITL> * VAN DER WAALS = -32.8566 ELECTROSTATIC = -48.7015 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3122" Parameter: CONF_N -> "8002" Comparing "3122" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3123" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762955 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766871 ATOM PAIRS WERE FOUND FOR ATOM LIST 42161 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29606 from a total of 766871 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3123 -75.40298 -6.15509 0.68910 INTE EXTERN> -27.70750 -47.69548 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.403" Parameter: A <- "-75.403" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7075" Parameter: B <- "-27.7075" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6955" Parameter: C <- "-47.6955" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3123 TOTAL ENERGY = -75.403 RDTITL> * VAN DER WAALS = -27.7075 ELECTROSTATIC = -47.6955 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3123" Parameter: CONF_N -> "8002" Comparing "3123" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3124" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766871 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763883 ATOM PAIRS WERE FOUND FOR ATOM LIST 42019 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30129 from a total of 763883 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3124 -79.68567 4.28269 0.74866 INTE EXTERN> -29.18355 -50.50212 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6857" Parameter: A <- "-79.6857" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1835" Parameter: B <- "-29.1835" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5021" Parameter: C <- "-50.5021" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3124 TOTAL ENERGY = -79.6857 RDTITL> * VAN DER WAALS = -29.1835 ELECTROSTATIC = -50.5021 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3124" Parameter: CONF_N -> "8002" Comparing "3124" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3125" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763883 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766773 ATOM PAIRS WERE FOUND FOR ATOM LIST 42068 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29835 from a total of 766773 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3125 -77.09316 -2.59251 0.68752 INTE EXTERN> -30.97359 -46.11957 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0932" Parameter: A <- "-77.0932" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9736" Parameter: B <- "-30.9736" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1196" Parameter: C <- "-46.1196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3125 TOTAL ENERGY = -77.0932 RDTITL> * VAN DER WAALS = -30.9736 ELECTROSTATIC = -46.1196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3125" Parameter: CONF_N -> "8002" Comparing "3125" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3126" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766773 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763801 ATOM PAIRS WERE FOUND FOR ATOM LIST 42215 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29866 from a total of 763801 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3126 -76.45080 -0.64236 0.70258 INTE EXTERN> -30.17036 -46.28043 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4508" Parameter: A <- "-76.4508" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1704" Parameter: B <- "-30.1704" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2804" Parameter: C <- "-46.2804" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3126 TOTAL ENERGY = -76.4508 RDTITL> * VAN DER WAALS = -30.1704 ELECTROSTATIC = -46.2804 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3126" Parameter: CONF_N -> "8002" Comparing "3126" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3127" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763801 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762953 ATOM PAIRS WERE FOUND FOR ATOM LIST 41896 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29205 from a total of 762953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3127 -81.00577 4.55497 0.73575 INTE EXTERN> -26.78318 -54.22259 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.0058" Parameter: A <- "-81.0058" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7832" Parameter: B <- "-26.7832" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2226" Parameter: C <- "-54.2226" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3127 TOTAL ENERGY = -81.0058 RDTITL> * VAN DER WAALS = -26.7832 ELECTROSTATIC = -54.2226 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3127" Parameter: CONF_N -> "8002" Comparing "3127" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3128" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760845 ATOM PAIRS WERE FOUND FOR ATOM LIST 41886 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30045 from a total of 760845 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3128 -77.69193 -3.31384 0.74531 INTE EXTERN> -26.31092 -51.38101 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6919" Parameter: A <- "-77.6919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3109" Parameter: B <- "-26.3109" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.381" Parameter: C <- "-51.381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3128 TOTAL ENERGY = -77.6919 RDTITL> * VAN DER WAALS = -26.3109 ELECTROSTATIC = -51.381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3128" Parameter: CONF_N -> "8002" Comparing "3128" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3129" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760845 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765255 ATOM PAIRS WERE FOUND FOR ATOM LIST 42063 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29751 from a total of 765255 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3129 -82.43476 4.74283 0.69940 INTE EXTERN> -28.56410 -53.87066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.4348" Parameter: A <- "-82.4348" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5641" Parameter: B <- "-28.5641" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8707" Parameter: C <- "-53.8707" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3129 TOTAL ENERGY = -82.4348 RDTITL> * VAN DER WAALS = -28.5641 ELECTROSTATIC = -53.8707 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3129" Parameter: CONF_N -> "8002" Comparing "3129" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3130" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765255 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41985 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30003 from a total of 764586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3130 -77.28700 -5.14776 0.75145 INTE EXTERN> -23.94967 -53.33733 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.287" Parameter: A <- "-77.287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9497" Parameter: B <- "-23.9497" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3373" Parameter: C <- "-53.3373" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3130 TOTAL ENERGY = -77.287 RDTITL> * VAN DER WAALS = -23.9497 ELECTROSTATIC = -53.3373 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3130" Parameter: CONF_N -> "8002" Comparing "3130" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3131" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769371 ATOM PAIRS WERE FOUND FOR ATOM LIST 42328 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29591 from a total of 769371 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3131 -70.38307 -6.90392 0.76858 INTE EXTERN> -22.48522 -47.89786 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3831" Parameter: A <- "-70.3831" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.4852" Parameter: B <- "-22.4852" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8979" Parameter: C <- "-47.8979" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3131 TOTAL ENERGY = -70.3831 RDTITL> * VAN DER WAALS = -22.4852 ELECTROSTATIC = -47.8979 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3131" Parameter: CONF_N -> "8002" Comparing "3131" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3132" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769371 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759883 ATOM PAIRS WERE FOUND FOR ATOM LIST 41786 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29627 from a total of 759883 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3132 -78.90860 8.52553 0.73640 INTE EXTERN> -26.22160 -52.68700 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9086" Parameter: A <- "-78.9086" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2216" Parameter: B <- "-26.2216" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.687" Parameter: C <- "-52.687" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3132 TOTAL ENERGY = -78.9086 RDTITL> * VAN DER WAALS = -26.2216 ELECTROSTATIC = -52.687 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3132" Parameter: CONF_N -> "8002" Comparing "3132" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3133" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759883 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766821 ATOM PAIRS WERE FOUND FOR ATOM LIST 41962 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30193 from a total of 766821 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3133 -78.14612 -0.76248 0.79379 INTE EXTERN> -24.64593 -53.50019 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1461" Parameter: A <- "-78.1461" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6459" Parameter: B <- "-24.6459" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.5002" Parameter: C <- "-53.5002" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3133 TOTAL ENERGY = -78.1461 RDTITL> * VAN DER WAALS = -24.6459 ELECTROSTATIC = -53.5002 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3133" Parameter: CONF_N -> "8002" Comparing "3133" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3134" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766821 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764406 ATOM PAIRS WERE FOUND FOR ATOM LIST 42094 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30140 from a total of 764406 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3134 -72.15092 -5.99520 0.64711 INTE EXTERN> -30.56161 -41.58931 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1509" Parameter: A <- "-72.1509" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5616" Parameter: B <- "-30.5616" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5893" Parameter: C <- "-41.5893" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3134 TOTAL ENERGY = -72.1509 RDTITL> * VAN DER WAALS = -30.5616 ELECTROSTATIC = -41.5893 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3134" Parameter: CONF_N -> "8002" Comparing "3134" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3135" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764406 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767470 ATOM PAIRS WERE FOUND FOR ATOM LIST 41994 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29882 from a total of 767470 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3135 -79.29893 7.14802 0.65643 INTE EXTERN> -31.50204 -47.79689 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2989" Parameter: A <- "-79.2989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.502" Parameter: B <- "-31.502" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7969" Parameter: C <- "-47.7969" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3135 TOTAL ENERGY = -79.2989 RDTITL> * VAN DER WAALS = -31.502 ELECTROSTATIC = -47.7969 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3135" Parameter: CONF_N -> "8002" Comparing "3135" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3136" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767470 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763705 ATOM PAIRS WERE FOUND FOR ATOM LIST 42070 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30235 from a total of 763705 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3136 -76.87662 -2.42231 0.66672 INTE EXTERN> -30.98834 -45.88828 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8766" Parameter: A <- "-76.8766" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9883" Parameter: B <- "-30.9883" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8883" Parameter: C <- "-45.8883" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3136 TOTAL ENERGY = -76.8766 RDTITL> * VAN DER WAALS = -30.9883 ELECTROSTATIC = -45.8883 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3136" Parameter: CONF_N -> "8002" Comparing "3136" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3137" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763705 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766922 ATOM PAIRS WERE FOUND FOR ATOM LIST 42035 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30285 from a total of 766922 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3137 -83.42316 6.54654 0.68941 INTE EXTERN> -30.37322 -53.04994 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.4232" Parameter: A <- "-83.4232" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3732" Parameter: B <- "-30.3732" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0499" Parameter: C <- "-53.0499" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3137 TOTAL ENERGY = -83.4232 RDTITL> * VAN DER WAALS = -30.3732 ELECTROSTATIC = -53.0499 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3137" Parameter: CONF_N -> "8002" Comparing "3137" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3138" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766922 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764589 ATOM PAIRS WERE FOUND FOR ATOM LIST 42081 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30222 from a total of 764589 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3138 -81.69451 -1.72865 0.67059 INTE EXTERN> -28.60216 -53.09235 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6945" Parameter: A <- "-81.6945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6022" Parameter: B <- "-28.6022" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0924" Parameter: C <- "-53.0924" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3138 TOTAL ENERGY = -81.6945 RDTITL> * VAN DER WAALS = -28.6022 ELECTROSTATIC = -53.0924 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3138" Parameter: CONF_N -> "8002" Comparing "3138" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3139" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764589 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765519 ATOM PAIRS WERE FOUND FOR ATOM LIST 42122 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30131 from a total of 765519 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3139 -82.10137 0.40686 0.63149 INTE EXTERN> -33.85405 -48.24733 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.1014" Parameter: A <- "-82.1014" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.854" Parameter: B <- "-33.854" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2473" Parameter: C <- "-48.2473" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3139 TOTAL ENERGY = -82.1014 RDTITL> * VAN DER WAALS = -33.854 ELECTROSTATIC = -48.2473 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3139" Parameter: CONF_N -> "8002" Comparing "3139" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3140" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765519 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762038 ATOM PAIRS WERE FOUND FOR ATOM LIST 42012 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30098 from a total of 762038 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3140 -82.43727 0.33590 0.63746 INTE EXTERN> -31.28192 -51.15535 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.4373" Parameter: A <- "-82.4373" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2819" Parameter: B <- "-31.2819" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1554" Parameter: C <- "-51.1554" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3140 TOTAL ENERGY = -82.4373 RDTITL> * VAN DER WAALS = -31.2819 ELECTROSTATIC = -51.1554 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3140" Parameter: CONF_N -> "8002" Comparing "3140" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3141" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762038 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766848 ATOM PAIRS WERE FOUND FOR ATOM LIST 42226 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30379 from a total of 766848 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3141 -80.91375 -1.52352 0.63535 INTE EXTERN> -34.39084 -46.52292 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9138" Parameter: A <- "-80.9138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3908" Parameter: B <- "-34.3908" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5229" Parameter: C <- "-46.5229" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3141 TOTAL ENERGY = -80.9138 RDTITL> * VAN DER WAALS = -34.3908 ELECTROSTATIC = -46.5229 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3141" Parameter: CONF_N -> "8002" Comparing "3141" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3142" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766848 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765467 ATOM PAIRS WERE FOUND FOR ATOM LIST 42160 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29682 from a total of 765467 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3142 -74.48919 -6.42457 0.63584 INTE EXTERN> -29.83490 -44.65428 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4892" Parameter: A <- "-74.4892" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8349" Parameter: B <- "-29.8349" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6543" Parameter: C <- "-44.6543" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3142 TOTAL ENERGY = -74.4892 RDTITL> * VAN DER WAALS = -29.8349 ELECTROSTATIC = -44.6543 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3142" Parameter: CONF_N -> "8002" Comparing "3142" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3143" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765467 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767589 ATOM PAIRS WERE FOUND FOR ATOM LIST 42260 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30351 from a total of 767589 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3143 -76.29415 1.80497 0.55423 INTE EXTERN> -35.08015 -41.21400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2942" Parameter: A <- "-76.2942" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.0801" Parameter: B <- "-35.0801" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.214" Parameter: C <- "-41.214" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3143 TOTAL ENERGY = -76.2942 RDTITL> * VAN DER WAALS = -35.0801 ELECTROSTATIC = -41.214 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3143" Parameter: CONF_N -> "8002" Comparing "3143" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3144" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767589 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765209 ATOM PAIRS WERE FOUND FOR ATOM LIST 42164 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29970 from a total of 765209 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3144 -71.75580 -4.53835 0.64929 INTE EXTERN> -31.55472 -40.20108 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7558" Parameter: A <- "-71.7558" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5547" Parameter: B <- "-31.5547" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2011" Parameter: C <- "-40.2011" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3144 TOTAL ENERGY = -71.7558 RDTITL> * VAN DER WAALS = -31.5547 ELECTROSTATIC = -40.2011 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3144" Parameter: CONF_N -> "8002" Comparing "3144" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3145" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765209 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764470 ATOM PAIRS WERE FOUND FOR ATOM LIST 41966 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29775 from a total of 764470 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3145 -80.62505 8.86925 0.74191 INTE EXTERN> -30.62377 -50.00128 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6251" Parameter: A <- "-80.6251" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6238" Parameter: B <- "-30.6238" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0013" Parameter: C <- "-50.0013" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3145 TOTAL ENERGY = -80.6251 RDTITL> * VAN DER WAALS = -30.6238 ELECTROSTATIC = -50.0013 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3145" Parameter: CONF_N -> "8002" Comparing "3145" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3146" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764470 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768601 ATOM PAIRS WERE FOUND FOR ATOM LIST 42330 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30285 from a total of 768601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3146 -81.51402 0.88897 0.62723 INTE EXTERN> -35.48566 -46.02837 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.514" Parameter: A <- "-81.514" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.4857" Parameter: B <- "-35.4857" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0284" Parameter: C <- "-46.0284" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3146 TOTAL ENERGY = -81.514 RDTITL> * VAN DER WAALS = -35.4857 ELECTROSTATIC = -46.0284 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3146" Parameter: CONF_N -> "8002" Comparing "3146" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3147" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764449 ATOM PAIRS WERE FOUND FOR ATOM LIST 41999 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30204 from a total of 764449 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3147 -75.32233 -6.19170 0.66267 INTE EXTERN> -30.90311 -44.41922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3223" Parameter: A <- "-75.3223" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9031" Parameter: B <- "-30.9031" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4192" Parameter: C <- "-44.4192" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3147 TOTAL ENERGY = -75.3223 RDTITL> * VAN DER WAALS = -30.9031 ELECTROSTATIC = -44.4192 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3147" Parameter: CONF_N -> "8002" Comparing "3147" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3148" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764449 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768671 ATOM PAIRS WERE FOUND FOR ATOM LIST 42352 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30224 from a total of 768671 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3148 -72.25913 -3.06320 0.63789 INTE EXTERN> -31.71859 -40.54054 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2591" Parameter: A <- "-72.2591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7186" Parameter: B <- "-31.7186" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5405" Parameter: C <- "-40.5405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3148 TOTAL ENERGY = -72.2591 RDTITL> * VAN DER WAALS = -31.7186 ELECTROSTATIC = -40.5405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3148" Parameter: CONF_N -> "8002" Comparing "3148" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3149" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768671 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759608 ATOM PAIRS WERE FOUND FOR ATOM LIST 42051 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30029 from a total of 759608 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3149 -72.09462 -0.16451 0.74792 INTE EXTERN> -25.26456 -46.83007 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0946" Parameter: A <- "-72.0946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2646" Parameter: B <- "-25.2646" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8301" Parameter: C <- "-46.8301" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3149 TOTAL ENERGY = -72.0946 RDTITL> * VAN DER WAALS = -25.2646 ELECTROSTATIC = -46.8301 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3149" Parameter: CONF_N -> "8002" Comparing "3149" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3150" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759608 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30452 from a total of 764586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3150 -72.59189 0.49727 0.67252 INTE EXTERN> -27.64326 -44.94863 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5919" Parameter: A <- "-72.5919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6433" Parameter: B <- "-27.6433" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9486" Parameter: C <- "-44.9486" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3150 TOTAL ENERGY = -72.5919 RDTITL> * VAN DER WAALS = -27.6433 ELECTROSTATIC = -44.9486 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3150" Parameter: CONF_N -> "8002" Comparing "3150" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3151" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767873 ATOM PAIRS WERE FOUND FOR ATOM LIST 42275 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30125 from a total of 767873 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3151 -72.87704 0.28515 0.71440 INTE EXTERN> -26.58326 -46.29378 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.877" Parameter: A <- "-72.877" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5833" Parameter: B <- "-26.5833" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2938" Parameter: C <- "-46.2938" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3151 TOTAL ENERGY = -72.877 RDTITL> * VAN DER WAALS = -26.5833 ELECTROSTATIC = -46.2938 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3151" Parameter: CONF_N -> "8002" Comparing "3151" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3152" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767873 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770758 ATOM PAIRS WERE FOUND FOR ATOM LIST 42397 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30022 from a total of 770758 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3152 -70.06167 -2.81538 0.70287 INTE EXTERN> -28.86098 -41.20069 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0617" Parameter: A <- "-70.0617" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.861" Parameter: B <- "-28.861" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2007" Parameter: C <- "-41.2007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3152 TOTAL ENERGY = -70.0617 RDTITL> * VAN DER WAALS = -28.861 ELECTROSTATIC = -41.2007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3152" Parameter: CONF_N -> "8002" Comparing "3152" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3153" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770758 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759479 ATOM PAIRS WERE FOUND FOR ATOM LIST 41846 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30070 from a total of 759479 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3153 -78.37883 8.31716 0.81681 INTE EXTERN> -25.46980 -52.90902 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3788" Parameter: A <- "-78.3788" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4698" Parameter: B <- "-25.4698" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.909" Parameter: C <- "-52.909" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3153 TOTAL ENERGY = -78.3788 RDTITL> * VAN DER WAALS = -25.4698 ELECTROSTATIC = -52.909 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3153" Parameter: CONF_N -> "8002" Comparing "3153" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3154" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759479 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766621 ATOM PAIRS WERE FOUND FOR ATOM LIST 42346 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30255 from a total of 766621 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3154 -79.68476 1.30593 0.66401 INTE EXTERN> -32.96263 -46.72213 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6848" Parameter: A <- "-79.6848" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9626" Parameter: B <- "-32.9626" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7221" Parameter: C <- "-46.7221" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3154 TOTAL ENERGY = -79.6848 RDTITL> * VAN DER WAALS = -32.9626 ELECTROSTATIC = -46.7221 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3154" Parameter: CONF_N -> "8002" Comparing "3154" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3155" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766621 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767393 ATOM PAIRS WERE FOUND FOR ATOM LIST 42232 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30282 from a total of 767393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3155 -79.88194 0.19718 0.80107 INTE EXTERN> -28.11458 -51.76737 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8819" Parameter: A <- "-79.8819" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1146" Parameter: B <- "-28.1146" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7674" Parameter: C <- "-51.7674" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3155 TOTAL ENERGY = -79.8819 RDTITL> * VAN DER WAALS = -28.1146 ELECTROSTATIC = -51.7674 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3155" Parameter: CONF_N -> "8002" Comparing "3155" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3156" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767881 ATOM PAIRS WERE FOUND FOR ATOM LIST 42377 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30525 from a total of 767881 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3156 -71.20535 -8.67660 0.60076 INTE EXTERN> -30.74811 -40.45724 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2053" Parameter: A <- "-71.2053" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7481" Parameter: B <- "-30.7481" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4572" Parameter: C <- "-40.4572" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3156 TOTAL ENERGY = -71.2053 RDTITL> * VAN DER WAALS = -30.7481 ELECTROSTATIC = -40.4572 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3156" Parameter: CONF_N -> "8002" Comparing "3156" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3157" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767881 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767177 ATOM PAIRS WERE FOUND FOR ATOM LIST 42298 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29856 from a total of 767177 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3157 -82.77324 11.56789 0.71630 INTE EXTERN> -31.35076 -51.42248 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7732" Parameter: A <- "-82.7732" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3508" Parameter: B <- "-31.3508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4225" Parameter: C <- "-51.4225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3157 TOTAL ENERGY = -82.7732 RDTITL> * VAN DER WAALS = -31.3508 ELECTROSTATIC = -51.4225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3157" Parameter: CONF_N -> "8002" Comparing "3157" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3158" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767177 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762449 ATOM PAIRS WERE FOUND FOR ATOM LIST 42027 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30532 from a total of 762449 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3158 -69.02411 -13.74913 0.68517 INTE EXTERN> -27.64592 -41.37819 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0241" Parameter: A <- "-69.0241" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6459" Parameter: B <- "-27.6459" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3782" Parameter: C <- "-41.3782" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3158 TOTAL ENERGY = -69.0241 RDTITL> * VAN DER WAALS = -27.6459 ELECTROSTATIC = -41.3782 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3158" Parameter: CONF_N -> "8002" Comparing "3158" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3159" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762449 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763240 ATOM PAIRS WERE FOUND FOR ATOM LIST 42051 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30533 from a total of 763240 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3159 -73.66484 4.64073 0.78094 INTE EXTERN> -25.36895 -48.29589 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6648" Parameter: A <- "-73.6648" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.369" Parameter: B <- "-25.369" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2959" Parameter: C <- "-48.2959" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3159 TOTAL ENERGY = -73.6648 RDTITL> * VAN DER WAALS = -25.369 ELECTROSTATIC = -48.2959 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3159" Parameter: CONF_N -> "8002" Comparing "3159" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3160" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763240 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763721 ATOM PAIRS WERE FOUND FOR ATOM LIST 42075 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30340 from a total of 763721 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3160 -81.10149 7.43665 0.76460 INTE EXTERN> -28.74570 -52.35579 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1015" Parameter: A <- "-81.1015" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7457" Parameter: B <- "-28.7457" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3558" Parameter: C <- "-52.3558" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3160 TOTAL ENERGY = -81.1015 RDTITL> * VAN DER WAALS = -28.7457 ELECTROSTATIC = -52.3558 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3160" Parameter: CONF_N -> "8002" Comparing "3160" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3161" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763721 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762064 ATOM PAIRS WERE FOUND FOR ATOM LIST 41972 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30608 from a total of 762064 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3161 -81.14623 0.04475 0.69618 INTE EXTERN> -31.10142 -50.04481 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1462" Parameter: A <- "-81.1462" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1014" Parameter: B <- "-31.1014" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0448" Parameter: C <- "-50.0448" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3161 TOTAL ENERGY = -81.1462 RDTITL> * VAN DER WAALS = -31.1014 ELECTROSTATIC = -50.0448 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3161" Parameter: CONF_N -> "8002" Comparing "3161" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3162" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762064 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763919 ATOM PAIRS WERE FOUND FOR ATOM LIST 42022 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30317 from a total of 763919 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3162 -81.43660 0.29037 0.64323 INTE EXTERN> -32.99628 -48.44032 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4366" Parameter: A <- "-81.4366" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9963" Parameter: B <- "-32.9963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4403" Parameter: C <- "-48.4403" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3162 TOTAL ENERGY = -81.4366 RDTITL> * VAN DER WAALS = -32.9963 ELECTROSTATIC = -48.4403 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3162" Parameter: CONF_N -> "8002" Comparing "3162" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3163" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763919 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765910 ATOM PAIRS WERE FOUND FOR ATOM LIST 42000 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30542 from a total of 765910 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3163 -79.54950 -1.88710 0.69866 INTE EXTERN> -29.97643 -49.57307 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5495" Parameter: A <- "-79.5495" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9764" Parameter: B <- "-29.9764" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5731" Parameter: C <- "-49.5731" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3163 TOTAL ENERGY = -79.5495 RDTITL> * VAN DER WAALS = -29.9764 ELECTROSTATIC = -49.5731 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3163" Parameter: CONF_N -> "8002" Comparing "3163" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3164" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765910 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760950 ATOM PAIRS WERE FOUND FOR ATOM LIST 41954 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30866 from a total of 760950 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3164 -79.52576 -0.02374 0.63878 INTE EXTERN> -35.54237 -43.98339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5258" Parameter: A <- "-79.5258" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.5424" Parameter: B <- "-35.5424" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9834" Parameter: C <- "-43.9834" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3164 TOTAL ENERGY = -79.5258 RDTITL> * VAN DER WAALS = -35.5424 ELECTROSTATIC = -43.9834 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3164" Parameter: CONF_N -> "8002" Comparing "3164" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3165" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760950 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764346 ATOM PAIRS WERE FOUND FOR ATOM LIST 42252 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30475 from a total of 764346 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3165 -85.06757 5.54180 0.70055 INTE EXTERN> -31.83872 -53.22884 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.0676" Parameter: A <- "-85.0676" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8387" Parameter: B <- "-31.8387" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.2288" Parameter: C <- "-53.2288" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3165 TOTAL ENERGY = -85.0676 RDTITL> * VAN DER WAALS = -31.8387 ELECTROSTATIC = -53.2288 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3165" Parameter: CONF_N -> "8002" Comparing "3165" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3166" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764346 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760100 ATOM PAIRS WERE FOUND FOR ATOM LIST 42103 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30174 from a total of 760100 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3166 -72.95066 -12.11690 0.56801 INTE EXTERN> -33.68373 -39.26694 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9507" Parameter: A <- "-72.9507" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6837" Parameter: B <- "-33.6837" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2669" Parameter: C <- "-39.2669" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3166 TOTAL ENERGY = -72.9507 RDTITL> * VAN DER WAALS = -33.6837 ELECTROSTATIC = -39.2669 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3166" Parameter: CONF_N -> "8002" Comparing "3166" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3167" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760100 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760939 ATOM PAIRS WERE FOUND FOR ATOM LIST 42011 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29925 from a total of 760939 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3167 -75.62494 2.67428 0.70256 INTE EXTERN> -27.34285 -48.28209 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6249" Parameter: A <- "-75.6249" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3429" Parameter: B <- "-27.3429" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2821" Parameter: C <- "-48.2821" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3167 TOTAL ENERGY = -75.6249 RDTITL> * VAN DER WAALS = -27.3429 ELECTROSTATIC = -48.2821 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3167" Parameter: CONF_N -> "8002" Comparing "3167" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3168" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760939 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760646 ATOM PAIRS WERE FOUND FOR ATOM LIST 41838 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30078 from a total of 760646 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3168 -75.03779 -0.58715 0.64625 INTE EXTERN> -31.76361 -43.27419 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0378" Parameter: A <- "-75.0378" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7636" Parameter: B <- "-31.7636" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2742" Parameter: C <- "-43.2742" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3168 TOTAL ENERGY = -75.0378 RDTITL> * VAN DER WAALS = -31.7636 ELECTROSTATIC = -43.2742 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3168" Parameter: CONF_N -> "8002" Comparing "3168" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3169" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760646 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764626 ATOM PAIRS WERE FOUND FOR ATOM LIST 42046 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30024 from a total of 764626 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3169 -69.69870 -5.33909 0.62293 INTE EXTERN> -32.04314 -37.65557 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6987" Parameter: A <- "-69.6987" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0431" Parameter: B <- "-32.0431" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6556" Parameter: C <- "-37.6556" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3169 TOTAL ENERGY = -69.6987 RDTITL> * VAN DER WAALS = -32.0431 ELECTROSTATIC = -37.6556 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3169" Parameter: CONF_N -> "8002" Comparing "3169" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3170" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764626 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757178 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29872 from a total of 757178 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3170 -77.14540 7.44670 0.65904 INTE EXTERN> -32.89091 -44.25449 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1454" Parameter: A <- "-77.1454" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8909" Parameter: B <- "-32.8909" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2545" Parameter: C <- "-44.2545" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3170 TOTAL ENERGY = -77.1454 RDTITL> * VAN DER WAALS = -32.8909 ELECTROSTATIC = -44.2545 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3170" Parameter: CONF_N -> "8002" Comparing "3170" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3171" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757178 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761746 ATOM PAIRS WERE FOUND FOR ATOM LIST 41770 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29805 from a total of 761746 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3171 -76.19930 -0.94610 0.68366 INTE EXTERN> -32.08479 -44.11451 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1993" Parameter: A <- "-76.1993" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0848" Parameter: B <- "-32.0848" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1145" Parameter: C <- "-44.1145" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3171 TOTAL ENERGY = -76.1993 RDTITL> * VAN DER WAALS = -32.0848 ELECTROSTATIC = -44.1145 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3171" Parameter: CONF_N -> "8002" Comparing "3171" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3172" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761746 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761828 ATOM PAIRS WERE FOUND FOR ATOM LIST 41858 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29771 from a total of 761828 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3172 -74.82093 -1.37837 0.68750 INTE EXTERN> -27.86745 -46.95348 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8209" Parameter: A <- "-74.8209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8675" Parameter: B <- "-27.8675" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9535" Parameter: C <- "-46.9535" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3172 TOTAL ENERGY = -74.8209 RDTITL> * VAN DER WAALS = -27.8675 ELECTROSTATIC = -46.9535 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3172" Parameter: CONF_N -> "8002" Comparing "3172" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3173" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761828 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766278 ATOM PAIRS WERE FOUND FOR ATOM LIST 42179 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30336 from a total of 766278 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3173 -79.79865 4.97772 0.67209 INTE EXTERN> -31.42891 -48.36975 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7987" Parameter: A <- "-79.7987" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4289" Parameter: B <- "-31.4289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3697" Parameter: C <- "-48.3697" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3173 TOTAL ENERGY = -79.7987 RDTITL> * VAN DER WAALS = -31.4289 ELECTROSTATIC = -48.3697 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3173" Parameter: CONF_N -> "8002" Comparing "3173" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3174" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766278 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767693 ATOM PAIRS WERE FOUND FOR ATOM LIST 42258 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30315 from a total of 767693 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3174 -77.69966 -2.09899 0.77044 INTE EXTERN> -26.73987 -50.95979 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6997" Parameter: A <- "-77.6997" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7399" Parameter: B <- "-26.7399" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9598" Parameter: C <- "-50.9598" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3174 TOTAL ENERGY = -77.6997 RDTITL> * VAN DER WAALS = -26.7399 ELECTROSTATIC = -50.9598 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3174" Parameter: CONF_N -> "8002" Comparing "3174" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3175" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767693 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765402 ATOM PAIRS WERE FOUND FOR ATOM LIST 42098 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30023 from a total of 765402 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3175 -76.41520 -1.28446 0.58035 INTE EXTERN> -35.57612 -40.83908 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4152" Parameter: A <- "-76.4152" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.5761" Parameter: B <- "-35.5761" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8391" Parameter: C <- "-40.8391" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3175 TOTAL ENERGY = -76.4152 RDTITL> * VAN DER WAALS = -35.5761 ELECTROSTATIC = -40.8391 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3175" Parameter: CONF_N -> "8002" Comparing "3175" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3176" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765402 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765098 ATOM PAIRS WERE FOUND FOR ATOM LIST 42002 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29731 from a total of 765098 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3176 -74.45557 -1.95963 0.77967 INTE EXTERN> -26.59478 -47.86079 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4556" Parameter: A <- "-74.4556" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5948" Parameter: B <- "-26.5948" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8608" Parameter: C <- "-47.8608" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3176 TOTAL ENERGY = -74.4556 RDTITL> * VAN DER WAALS = -26.5948 ELECTROSTATIC = -47.8608 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3176" Parameter: CONF_N -> "8002" Comparing "3176" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3177" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765098 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758943 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29504 from a total of 758943 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3177 -77.40730 2.95173 0.61382 INTE EXTERN> -31.96315 -45.44415 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4073" Parameter: A <- "-77.4073" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9632" Parameter: B <- "-31.9632" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4441" Parameter: C <- "-45.4441" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3177 TOTAL ENERGY = -77.4073 RDTITL> * VAN DER WAALS = -31.9632 ELECTROSTATIC = -45.4441 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3177" Parameter: CONF_N -> "8002" Comparing "3177" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3178" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758943 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765924 ATOM PAIRS WERE FOUND FOR ATOM LIST 42013 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29705 from a total of 765924 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3178 -79.32561 1.91830 0.72649 INTE EXTERN> -28.24548 -51.08012 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.3256" Parameter: A <- "-79.3256" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2455" Parameter: B <- "-28.2455" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0801" Parameter: C <- "-51.0801" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3178 TOTAL ENERGY = -79.3256 RDTITL> * VAN DER WAALS = -28.2455 ELECTROSTATIC = -51.0801 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3178" Parameter: CONF_N -> "8002" Comparing "3178" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3179" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765924 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764544 ATOM PAIRS WERE FOUND FOR ATOM LIST 42118 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30493 from a total of 764544 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3179 -84.06828 4.74268 0.81504 INTE EXTERN> -28.03374 -56.03455 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.0683" Parameter: A <- "-84.0683" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0337" Parameter: B <- "-28.0337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.0345" Parameter: C <- "-56.0345" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3179 TOTAL ENERGY = -84.0683 RDTITL> * VAN DER WAALS = -28.0337 ELECTROSTATIC = -56.0345 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3179" Parameter: CONF_N -> "8002" Comparing "3179" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3180" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764544 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770282 ATOM PAIRS WERE FOUND FOR ATOM LIST 42214 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30632 from a total of 770282 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3180 -77.27641 -6.79187 0.69762 INTE EXTERN> -32.05722 -45.21919 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2764" Parameter: A <- "-77.2764" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0572" Parameter: B <- "-32.0572" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2192" Parameter: C <- "-45.2192" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3180 TOTAL ENERGY = -77.2764 RDTITL> * VAN DER WAALS = -32.0572 ELECTROSTATIC = -45.2192 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3180" Parameter: CONF_N -> "8002" Comparing "3180" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3181" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770282 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755538 ATOM PAIRS WERE FOUND FOR ATOM LIST 41516 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29894 from a total of 755538 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3181 -76.00703 -1.26938 0.63869 INTE EXTERN> -32.28471 -43.72232 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.007" Parameter: A <- "-76.007" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2847" Parameter: B <- "-32.2847" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7223" Parameter: C <- "-43.7223" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3181 TOTAL ENERGY = -76.007 RDTITL> * VAN DER WAALS = -32.2847 ELECTROSTATIC = -43.7223 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3181" Parameter: CONF_N -> "8002" Comparing "3181" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3182" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755538 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762161 ATOM PAIRS WERE FOUND FOR ATOM LIST 41804 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29639 from a total of 762161 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3182 -76.70581 0.69878 0.74326 INTE EXTERN> -29.52423 -47.18158 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7058" Parameter: A <- "-76.7058" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5242" Parameter: B <- "-29.5242" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1816" Parameter: C <- "-47.1816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3182 TOTAL ENERGY = -76.7058 RDTITL> * VAN DER WAALS = -29.5242 ELECTROSTATIC = -47.1816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3182" Parameter: CONF_N -> "8002" Comparing "3182" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3183" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762161 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763637 ATOM PAIRS WERE FOUND FOR ATOM LIST 41847 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29791 from a total of 763637 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3183 -78.93971 2.23390 0.66616 INTE EXTERN> -31.78444 -47.15527 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9397" Parameter: A <- "-78.9397" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7844" Parameter: B <- "-31.7844" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1553" Parameter: C <- "-47.1553" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3183 TOTAL ENERGY = -78.9397 RDTITL> * VAN DER WAALS = -31.7844 ELECTROSTATIC = -47.1553 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3183" Parameter: CONF_N -> "8002" Comparing "3183" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3184" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763637 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769175 ATOM PAIRS WERE FOUND FOR ATOM LIST 42206 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29790 from a total of 769175 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3184 -77.23418 -1.70553 0.75538 INTE EXTERN> -28.77659 -48.45759 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2342" Parameter: A <- "-77.2342" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7766" Parameter: B <- "-28.7766" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4576" Parameter: C <- "-48.4576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3184 TOTAL ENERGY = -77.2342 RDTITL> * VAN DER WAALS = -28.7766 ELECTROSTATIC = -48.4576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3184" Parameter: CONF_N -> "8002" Comparing "3184" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3185" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769175 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760489 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29115 from a total of 760489 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3185 -78.99166 1.75748 0.71266 INTE EXTERN> -31.31412 -47.67754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9917" Parameter: A <- "-78.9917" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3141" Parameter: B <- "-31.3141" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6775" Parameter: C <- "-47.6775" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3185 TOTAL ENERGY = -78.9917 RDTITL> * VAN DER WAALS = -31.3141 ELECTROSTATIC = -47.6775 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3185" Parameter: CONF_N -> "8002" Comparing "3185" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3186" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760489 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764723 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29478 from a total of 764723 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3186 -69.47609 -9.51557 0.79250 INTE EXTERN> -26.11552 -43.36058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4761" Parameter: A <- "-69.4761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1155" Parameter: B <- "-26.1155" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3606" Parameter: C <- "-43.3606" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3186 TOTAL ENERGY = -69.4761 RDTITL> * VAN DER WAALS = -26.1155 ELECTROSTATIC = -43.3606 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3186" Parameter: CONF_N -> "8002" Comparing "3186" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3187" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764723 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761929 ATOM PAIRS WERE FOUND FOR ATOM LIST 41721 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29805 from a total of 761929 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3187 -71.74876 2.27267 0.73390 INTE EXTERN> -25.94805 -45.80071 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7488" Parameter: A <- "-71.7488" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9481" Parameter: B <- "-25.9481" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8007" Parameter: C <- "-45.8007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3187 TOTAL ENERGY = -71.7488 RDTITL> * VAN DER WAALS = -25.9481 ELECTROSTATIC = -45.8007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3187" Parameter: CONF_N -> "8002" Comparing "3187" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3188" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761929 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757789 ATOM PAIRS WERE FOUND FOR ATOM LIST 41704 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29621 from a total of 757789 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3188 -72.23181 0.48305 0.56789 INTE EXTERN> -33.57803 -38.65379 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2318" Parameter: A <- "-72.2318" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.578" Parameter: B <- "-33.578" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6538" Parameter: C <- "-38.6538" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3188 TOTAL ENERGY = -72.2318 RDTITL> * VAN DER WAALS = -33.578 ELECTROSTATIC = -38.6538 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3188" Parameter: CONF_N -> "8002" Comparing "3188" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3189" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757789 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763480 ATOM PAIRS WERE FOUND FOR ATOM LIST 42102 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30078 from a total of 763480 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3189 -67.62883 -4.60299 0.55899 INTE EXTERN> -31.95736 -35.67147 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6288" Parameter: A <- "-67.6288" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9574" Parameter: B <- "-31.9574" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6715" Parameter: C <- "-35.6715" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3189 TOTAL ENERGY = -67.6288 RDTITL> * VAN DER WAALS = -31.9574 ELECTROSTATIC = -35.6715 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3189" Parameter: CONF_N -> "8002" Comparing "3189" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3190" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763480 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762765 ATOM PAIRS WERE FOUND FOR ATOM LIST 41830 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29583 from a total of 762765 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3190 -76.30960 8.68077 0.61782 INTE EXTERN> -31.30846 -45.00114 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3096" Parameter: A <- "-76.3096" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3085" Parameter: B <- "-31.3085" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0011" Parameter: C <- "-45.0011" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3190 TOTAL ENERGY = -76.3096 RDTITL> * VAN DER WAALS = -31.3085 ELECTROSTATIC = -45.0011 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3190" Parameter: CONF_N -> "8002" Comparing "3190" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3191" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762765 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757534 ATOM PAIRS WERE FOUND FOR ATOM LIST 41835 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29562 from a total of 757534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3191 -64.08557 -12.22403 0.62701 INTE EXTERN> -29.01846 -35.06710 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0856" Parameter: A <- "-64.0856" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0185" Parameter: B <- "-29.0185" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0671" Parameter: C <- "-35.0671" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3191 TOTAL ENERGY = -64.0856 RDTITL> * VAN DER WAALS = -29.0185 ELECTROSTATIC = -35.0671 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3191" Parameter: CONF_N -> "8002" Comparing "3191" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3192" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29232 from a total of 765422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3192 -68.85599 4.77042 0.65977 INTE EXTERN> -26.48456 -42.37144 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.856" Parameter: A <- "-68.856" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4846" Parameter: B <- "-26.4846" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3714" Parameter: C <- "-42.3714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3192 TOTAL ENERGY = -68.856 RDTITL> * VAN DER WAALS = -26.4846 ELECTROSTATIC = -42.3714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3192" Parameter: CONF_N -> "8002" Comparing "3192" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3193" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766849 ATOM PAIRS WERE FOUND FOR ATOM LIST 42067 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29888 from a total of 766849 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3193 -66.09049 -2.76550 0.64508 INTE EXTERN> -27.01888 -39.07161 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0905" Parameter: A <- "-66.0905" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0189" Parameter: B <- "-27.0189" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0716" Parameter: C <- "-39.0716" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3193 TOTAL ENERGY = -66.0905 RDTITL> * VAN DER WAALS = -27.0189 ELECTROSTATIC = -39.0716 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3193" Parameter: CONF_N -> "8002" Comparing "3193" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3194" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766849 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762520 ATOM PAIRS WERE FOUND FOR ATOM LIST 41859 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29268 from a total of 762520 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3194 -68.46662 2.37613 0.69274 INTE EXTERN> -23.85370 -44.61292 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4666" Parameter: A <- "-68.4666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8537" Parameter: B <- "-23.8537" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6129" Parameter: C <- "-44.6129" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3194 TOTAL ENERGY = -68.4666 RDTITL> * VAN DER WAALS = -23.8537 ELECTROSTATIC = -44.6129 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3194" Parameter: CONF_N -> "8002" Comparing "3194" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3195" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762520 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761233 ATOM PAIRS WERE FOUND FOR ATOM LIST 42013 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29568 from a total of 761233 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3195 -66.72686 -1.73976 0.64371 INTE EXTERN> -27.05345 -39.67341 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7269" Parameter: A <- "-66.7269" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0534" Parameter: B <- "-27.0534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6734" Parameter: C <- "-39.6734" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3195 TOTAL ENERGY = -66.7269 RDTITL> * VAN DER WAALS = -27.0534 ELECTROSTATIC = -39.6734 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3195" Parameter: CONF_N -> "8002" Comparing "3195" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3196" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761233 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760937 ATOM PAIRS WERE FOUND FOR ATOM LIST 41548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29925 from a total of 760937 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3196 -74.51359 7.78672 0.64511 INTE EXTERN> -27.00691 -47.50668 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5136" Parameter: A <- "-74.5136" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0069" Parameter: B <- "-27.0069" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5067" Parameter: C <- "-47.5067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3196 TOTAL ENERGY = -74.5136 RDTITL> * VAN DER WAALS = -27.0069 ELECTROSTATIC = -47.5067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3196" Parameter: CONF_N -> "8002" Comparing "3196" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3197" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760937 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763545 ATOM PAIRS WERE FOUND FOR ATOM LIST 42037 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29899 from a total of 763545 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3197 -64.79659 -9.71700 0.57786 INTE EXTERN> -30.85433 -33.94226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7966" Parameter: A <- "-64.7966" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8543" Parameter: B <- "-30.8543" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9423" Parameter: C <- "-33.9423" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3197 TOTAL ENERGY = -64.7966 RDTITL> * VAN DER WAALS = -30.8543 ELECTROSTATIC = -33.9423 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3197" Parameter: CONF_N -> "8002" Comparing "3197" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3198" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763545 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770101 ATOM PAIRS WERE FOUND FOR ATOM LIST 42261 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30074 from a total of 770101 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3198 -66.96636 2.16977 0.59920 INTE EXTERN> -30.08359 -36.88277 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9664" Parameter: A <- "-66.9664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0836" Parameter: B <- "-30.0836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8828" Parameter: C <- "-36.8828" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3198 TOTAL ENERGY = -66.9664 RDTITL> * VAN DER WAALS = -30.0836 ELECTROSTATIC = -36.8828 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3198" Parameter: CONF_N -> "8002" Comparing "3198" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3199" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770101 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760271 ATOM PAIRS WERE FOUND FOR ATOM LIST 41880 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28990 from a total of 760271 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3199 -71.22159 4.25523 0.77298 INTE EXTERN> -25.34092 -45.88067 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2216" Parameter: A <- "-71.2216" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3409" Parameter: B <- "-25.3409" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8807" Parameter: C <- "-45.8807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3199 TOTAL ENERGY = -71.2216 RDTITL> * VAN DER WAALS = -25.3409 ELECTROSTATIC = -45.8807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3199" Parameter: CONF_N -> "8002" Comparing "3199" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3200" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760271 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762858 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29661 from a total of 762858 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3200 -66.76651 -4.45508 0.66906 INTE EXTERN> -30.57372 -36.19280 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7665" Parameter: A <- "-66.7665" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5737" Parameter: B <- "-30.5737" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1928" Parameter: C <- "-36.1928" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3200 TOTAL ENERGY = -66.7665 RDTITL> * VAN DER WAALS = -30.5737 ELECTROSTATIC = -36.1928 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3200" Parameter: CONF_N -> "8002" Comparing "3200" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3201" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762858 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756357 ATOM PAIRS WERE FOUND FOR ATOM LIST 41545 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29335 from a total of 756357 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3201 -70.77289 4.00638 0.60759 INTE EXTERN> -31.17802 -39.59487 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7729" Parameter: A <- "-70.7729" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.178" Parameter: B <- "-31.178" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5949" Parameter: C <- "-39.5949" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3201 TOTAL ENERGY = -70.7729 RDTITL> * VAN DER WAALS = -31.178 ELECTROSTATIC = -39.5949 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3201" Parameter: CONF_N -> "8002" Comparing "3201" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3202" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756357 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764490 ATOM PAIRS WERE FOUND FOR ATOM LIST 42041 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29805 from a total of 764490 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3202 -69.80286 -0.97004 0.58101 INTE EXTERN> -31.19468 -38.60817 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8029" Parameter: A <- "-69.8029" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1947" Parameter: B <- "-31.1947" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6082" Parameter: C <- "-38.6082" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3202 TOTAL ENERGY = -69.8029 RDTITL> * VAN DER WAALS = -31.1947 ELECTROSTATIC = -38.6082 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3202" Parameter: CONF_N -> "8002" Comparing "3202" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3203" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764490 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759371 ATOM PAIRS WERE FOUND FOR ATOM LIST 41506 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29605 from a total of 759371 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3203 -70.86108 1.05822 0.74080 INTE EXTERN> -27.55193 -43.30914 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8611" Parameter: A <- "-70.8611" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5519" Parameter: B <- "-27.5519" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3091" Parameter: C <- "-43.3091" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3203 TOTAL ENERGY = -70.8611 RDTITL> * VAN DER WAALS = -27.5519 ELECTROSTATIC = -43.3091 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3203" Parameter: CONF_N -> "8002" Comparing "3203" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3204" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759371 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758908 ATOM PAIRS WERE FOUND FOR ATOM LIST 41704 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29783 from a total of 758908 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3204 -70.87950 0.01842 0.72305 INTE EXTERN> -25.59538 -45.28412 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8795" Parameter: A <- "-70.8795" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5954" Parameter: B <- "-25.5954" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2841" Parameter: C <- "-45.2841" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3204 TOTAL ENERGY = -70.8795 RDTITL> * VAN DER WAALS = -25.5954 ELECTROSTATIC = -45.2841 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3204" Parameter: CONF_N -> "8002" Comparing "3204" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3205" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758908 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755542 ATOM PAIRS WERE FOUND FOR ATOM LIST 41466 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29439 from a total of 755542 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3205 -70.75840 -0.12110 0.60646 INTE EXTERN> -30.87135 -39.88705 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7584" Parameter: A <- "-70.7584" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8714" Parameter: B <- "-30.8714" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.887" Parameter: C <- "-39.887" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3205 TOTAL ENERGY = -70.7584 RDTITL> * VAN DER WAALS = -30.8714 ELECTROSTATIC = -39.887 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3205" Parameter: CONF_N -> "8002" Comparing "3205" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3206" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755542 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760063 ATOM PAIRS WERE FOUND FOR ATOM LIST 41768 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29351 from a total of 760063 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3206 -66.01832 -4.74008 0.57846 INTE EXTERN> -28.55186 -37.46646 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0183" Parameter: A <- "-66.0183" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5519" Parameter: B <- "-28.5519" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4665" Parameter: C <- "-37.4665" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3206 TOTAL ENERGY = -66.0183 RDTITL> * VAN DER WAALS = -28.5519 ELECTROSTATIC = -37.4665 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3206" Parameter: CONF_N -> "8002" Comparing "3206" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3207" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760063 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762274 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29397 from a total of 762274 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3207 -68.58192 2.56360 0.53620 INTE EXTERN> -31.43098 -37.15094 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5819" Parameter: A <- "-68.5819" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.431" Parameter: B <- "-31.431" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1509" Parameter: C <- "-37.1509" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3207 TOTAL ENERGY = -68.5819 RDTITL> * VAN DER WAALS = -31.431 ELECTROSTATIC = -37.1509 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3207" Parameter: CONF_N -> "8002" Comparing "3207" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3208" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762274 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760364 ATOM PAIRS WERE FOUND FOR ATOM LIST 41965 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29516 from a total of 760364 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3208 -66.93976 -1.64216 0.66203 INTE EXTERN> -28.19183 -38.74793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9398" Parameter: A <- "-66.9398" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1918" Parameter: B <- "-28.1918" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7479" Parameter: C <- "-38.7479" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3208 TOTAL ENERGY = -66.9398 RDTITL> * VAN DER WAALS = -28.1918 ELECTROSTATIC = -38.7479 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3208" Parameter: CONF_N -> "8002" Comparing "3208" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3209" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760364 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757373 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29174 from a total of 757373 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3209 -64.64816 -2.29160 0.66381 INTE EXTERN> -26.16389 -38.48427 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6482" Parameter: A <- "-64.6482" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1639" Parameter: B <- "-26.1639" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4843" Parameter: C <- "-38.4843" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3209 TOTAL ENERGY = -64.6482 RDTITL> * VAN DER WAALS = -26.1639 ELECTROSTATIC = -38.4843 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3209" Parameter: CONF_N -> "8002" Comparing "3209" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3210" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757373 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762592 ATOM PAIRS WERE FOUND FOR ATOM LIST 42046 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29477 from a total of 762592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3210 -71.04136 6.39320 0.60075 INTE EXTERN> -31.53103 -39.51033 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0414" Parameter: A <- "-71.0414" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.531" Parameter: B <- "-31.531" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5103" Parameter: C <- "-39.5103" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3210 TOTAL ENERGY = -71.0414 RDTITL> * VAN DER WAALS = -31.531 ELECTROSTATIC = -39.5103 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3210" Parameter: CONF_N -> "8002" Comparing "3210" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3211" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759387 ATOM PAIRS WERE FOUND FOR ATOM LIST 41856 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29370 from a total of 759387 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3211 -63.44107 -7.60029 0.56293 INTE EXTERN> -29.06108 -34.37999 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4411" Parameter: A <- "-63.4411" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0611" Parameter: B <- "-29.0611" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.38" Parameter: C <- "-34.38" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3211 TOTAL ENERGY = -63.4411 RDTITL> * VAN DER WAALS = -29.0611 ELECTROSTATIC = -34.38 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3211" Parameter: CONF_N -> "8002" Comparing "3211" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3212" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759387 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761875 ATOM PAIRS WERE FOUND FOR ATOM LIST 41737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29586 from a total of 761875 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3212 -71.79604 8.35497 0.61651 INTE EXTERN> -26.51085 -45.28519 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.796" Parameter: A <- "-71.796" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5108" Parameter: B <- "-26.5108" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2852" Parameter: C <- "-45.2852" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3212 TOTAL ENERGY = -71.796 RDTITL> * VAN DER WAALS = -26.5108 ELECTROSTATIC = -45.2852 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3212" Parameter: CONF_N -> "8002" Comparing "3212" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3213" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761875 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760631 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29169 from a total of 760631 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3213 -72.44130 0.64526 0.65888 INTE EXTERN> -28.22908 -44.21221 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4413" Parameter: A <- "-72.4413" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2291" Parameter: B <- "-28.2291" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2122" Parameter: C <- "-44.2122" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3213 TOTAL ENERGY = -72.4413 RDTITL> * VAN DER WAALS = -28.2291 ELECTROSTATIC = -44.2122 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3213" Parameter: CONF_N -> "8002" Comparing "3213" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3214" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760631 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758989 ATOM PAIRS WERE FOUND FOR ATOM LIST 41623 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29313 from a total of 758989 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3214 -69.70020 -2.74110 0.63438 INTE EXTERN> -28.71328 -40.98692 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7002" Parameter: A <- "-69.7002" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7133" Parameter: B <- "-28.7133" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9869" Parameter: C <- "-40.9869" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3214 TOTAL ENERGY = -69.7002 RDTITL> * VAN DER WAALS = -28.7133 ELECTROSTATIC = -40.9869 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3214" Parameter: CONF_N -> "8002" Comparing "3214" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3215" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758989 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765597 ATOM PAIRS WERE FOUND FOR ATOM LIST 41964 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28982 from a total of 765597 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3215 -63.82700 -5.87320 0.59164 INTE EXTERN> -28.22026 -35.60675 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.827" Parameter: A <- "-63.827" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2203" Parameter: B <- "-28.2203" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6067" Parameter: C <- "-35.6067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3215 TOTAL ENERGY = -63.827 RDTITL> * VAN DER WAALS = -28.2203 ELECTROSTATIC = -35.6067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3215" Parameter: CONF_N -> "8002" Comparing "3215" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3216" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765597 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763384 ATOM PAIRS WERE FOUND FOR ATOM LIST 41890 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29815 from a total of 763384 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3216 -71.96632 8.13932 0.63678 INTE EXTERN> -28.71101 -43.25531 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9663" Parameter: A <- "-71.9663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.711" Parameter: B <- "-28.711" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2553" Parameter: C <- "-43.2553" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3216 TOTAL ENERGY = -71.9663 RDTITL> * VAN DER WAALS = -28.711 ELECTROSTATIC = -43.2553 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3216" Parameter: CONF_N -> "8002" Comparing "3216" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3217" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763384 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759187 ATOM PAIRS WERE FOUND FOR ATOM LIST 41738 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29229 from a total of 759187 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3217 -67.47355 -4.49277 0.60112 INTE EXTERN> -28.83149 -38.64207 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4736" Parameter: A <- "-67.4736" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8315" Parameter: B <- "-28.8315" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6421" Parameter: C <- "-38.6421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3217 TOTAL ENERGY = -67.4736 RDTITL> * VAN DER WAALS = -28.8315 ELECTROSTATIC = -38.6421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3217" Parameter: CONF_N -> "8002" Comparing "3217" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3218" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759187 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761397 ATOM PAIRS WERE FOUND FOR ATOM LIST 41848 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29021 from a total of 761397 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3218 -66.19788 -1.27568 0.59521 INTE EXTERN> -30.10903 -36.08885 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1979" Parameter: A <- "-66.1979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.109" Parameter: B <- "-30.109" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0889" Parameter: C <- "-36.0889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3218 TOTAL ENERGY = -66.1979 RDTITL> * VAN DER WAALS = -30.109 ELECTROSTATIC = -36.0889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3218" Parameter: CONF_N -> "8002" Comparing "3218" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3219" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761397 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760752 ATOM PAIRS WERE FOUND FOR ATOM LIST 41803 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29107 from a total of 760752 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3219 -68.62638 2.42850 0.64141 INTE EXTERN> -30.16661 -38.45977 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6264" Parameter: A <- "-68.6264" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1666" Parameter: B <- "-30.1666" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4598" Parameter: C <- "-38.4598" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3219 TOTAL ENERGY = -68.6264 RDTITL> * VAN DER WAALS = -30.1666 ELECTROSTATIC = -38.4598 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3219" Parameter: CONF_N -> "8002" Comparing "3219" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3220" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760752 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763548 ATOM PAIRS WERE FOUND FOR ATOM LIST 41979 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29626 from a total of 763548 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3220 -70.78311 2.15673 0.53628 INTE EXTERN> -32.94708 -37.83603 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7831" Parameter: A <- "-70.7831" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9471" Parameter: B <- "-32.9471" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.836" Parameter: C <- "-37.836" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3220 TOTAL ENERGY = -70.7831 RDTITL> * VAN DER WAALS = -32.9471 ELECTROSTATIC = -37.836 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3220" Parameter: CONF_N -> "8002" Comparing "3220" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3221" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763548 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766515 ATOM PAIRS WERE FOUND FOR ATOM LIST 41997 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29925 from a total of 766515 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3221 -65.18540 -5.59771 0.76226 INTE EXTERN> -23.16542 -42.01999 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1854" Parameter: A <- "-65.1854" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.1654" Parameter: B <- "-23.1654" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.02" Parameter: C <- "-42.02" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3221 TOTAL ENERGY = -65.1854 RDTITL> * VAN DER WAALS = -23.1654 ELECTROSTATIC = -42.02 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3221" Parameter: CONF_N -> "8002" Comparing "3221" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3222" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766515 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768983 ATOM PAIRS WERE FOUND FOR ATOM LIST 41953 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29247 from a total of 768983 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3222 -67.81993 2.63453 0.58420 INTE EXTERN> -30.50855 -37.31138 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8199" Parameter: A <- "-67.8199" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5086" Parameter: B <- "-30.5086" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3114" Parameter: C <- "-37.3114" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3222 TOTAL ENERGY = -67.8199 RDTITL> * VAN DER WAALS = -30.5086 ELECTROSTATIC = -37.3114 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3222" Parameter: CONF_N -> "8002" Comparing "3222" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3223" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768983 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768092 ATOM PAIRS WERE FOUND FOR ATOM LIST 42038 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29806 from a total of 768092 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3223 -65.87449 -1.94544 0.75657 INTE EXTERN> -23.25465 -42.61984 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8745" Parameter: A <- "-65.8745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.2546" Parameter: B <- "-23.2546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6198" Parameter: C <- "-42.6198" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3223 TOTAL ENERGY = -65.8745 RDTITL> * VAN DER WAALS = -23.2546 ELECTROSTATIC = -42.6198 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3223" Parameter: CONF_N -> "8002" Comparing "3223" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3224" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768092 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762117 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29697 from a total of 762117 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3224 -66.51505 0.64056 0.61840 INTE EXTERN> -28.70965 -37.80540 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.515" Parameter: A <- "-66.515" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7096" Parameter: B <- "-28.7096" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8054" Parameter: C <- "-37.8054" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3224 TOTAL ENERGY = -66.515 RDTITL> * VAN DER WAALS = -28.7096 ELECTROSTATIC = -37.8054 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3224" Parameter: CONF_N -> "8002" Comparing "3224" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3225" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762117 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769628 ATOM PAIRS WERE FOUND FOR ATOM LIST 42090 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30362 from a total of 769628 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3225 -65.78092 -0.73412 0.66466 INTE EXTERN> -29.04388 -36.73704 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7809" Parameter: A <- "-65.7809" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0439" Parameter: B <- "-29.0439" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.737" Parameter: C <- "-36.737" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3225 TOTAL ENERGY = -65.7809 RDTITL> * VAN DER WAALS = -29.0439 ELECTROSTATIC = -36.737 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3225" Parameter: CONF_N -> "8002" Comparing "3225" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3226" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769628 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765867 ATOM PAIRS WERE FOUND FOR ATOM LIST 41913 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29914 from a total of 765867 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3226 -65.96049 0.17956 0.59619 INTE EXTERN> -32.01312 -33.94737 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9605" Parameter: A <- "-65.9605" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0131" Parameter: B <- "-32.0131" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9474" Parameter: C <- "-33.9474" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3226 TOTAL ENERGY = -65.9605 RDTITL> * VAN DER WAALS = -32.0131 ELECTROSTATIC = -33.9474 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3226" Parameter: CONF_N -> "8002" Comparing "3226" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3227" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765867 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764245 ATOM PAIRS WERE FOUND FOR ATOM LIST 41941 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29899 from a total of 764245 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3227 -73.03468 7.07419 0.63223 INTE EXTERN> -31.17720 -41.85748 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0347" Parameter: A <- "-73.0347" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1772" Parameter: B <- "-31.1772" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8575" Parameter: C <- "-41.8575" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3227 TOTAL ENERGY = -73.0347 RDTITL> * VAN DER WAALS = -31.1772 ELECTROSTATIC = -41.8575 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3227" Parameter: CONF_N -> "8002" Comparing "3227" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3228" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764245 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767401 ATOM PAIRS WERE FOUND FOR ATOM LIST 42090 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30056 from a total of 767401 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3228 -73.65619 0.62151 0.70714 INTE EXTERN> -29.56020 -44.09599 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6562" Parameter: A <- "-73.6562" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5602" Parameter: B <- "-29.5602" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.096" Parameter: C <- "-44.096" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3228 TOTAL ENERGY = -73.6562 RDTITL> * VAN DER WAALS = -29.5602 ELECTROSTATIC = -44.096 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3228" Parameter: CONF_N -> "8002" Comparing "3228" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3229" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767401 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762260 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29629 from a total of 762260 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3229 -70.86517 -2.79102 0.61859 INTE EXTERN> -32.69440 -38.17077 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8652" Parameter: A <- "-70.8652" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6944" Parameter: B <- "-32.6944" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1708" Parameter: C <- "-38.1708" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3229 TOTAL ENERGY = -70.8652 RDTITL> * VAN DER WAALS = -32.6944 ELECTROSTATIC = -38.1708 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3229" Parameter: CONF_N -> "8002" Comparing "3229" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3230" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762260 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759157 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30159 from a total of 759157 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3230 -70.53107 -0.33410 0.57847 INTE EXTERN> -32.79815 -37.73291 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5311" Parameter: A <- "-70.5311" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7982" Parameter: B <- "-32.7982" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7329" Parameter: C <- "-37.7329" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3230 TOTAL ENERGY = -70.5311 RDTITL> * VAN DER WAALS = -32.7982 ELECTROSTATIC = -37.7329 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3230" Parameter: CONF_N -> "8002" Comparing "3230" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3231" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759157 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764838 ATOM PAIRS WERE FOUND FOR ATOM LIST 42234 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30044 from a total of 764838 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3231 -69.55960 -0.97146 0.53808 INTE EXTERN> -32.85372 -36.70588 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5596" Parameter: A <- "-69.5596" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8537" Parameter: B <- "-32.8537" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7059" Parameter: C <- "-36.7059" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3231 TOTAL ENERGY = -69.5596 RDTITL> * VAN DER WAALS = -32.8537 ELECTROSTATIC = -36.7059 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3231" Parameter: CONF_N -> "8002" Comparing "3231" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3232" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764838 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758577 ATOM PAIRS WERE FOUND FOR ATOM LIST 41642 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29040 from a total of 758577 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3232 -66.11975 -3.43986 0.75502 INTE EXTERN> -26.40868 -39.71107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1197" Parameter: A <- "-66.1197" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4087" Parameter: B <- "-26.4087" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7111" Parameter: C <- "-39.7111" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3232 TOTAL ENERGY = -66.1197 RDTITL> * VAN DER WAALS = -26.4087 ELECTROSTATIC = -39.7111 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3232" Parameter: CONF_N -> "8002" Comparing "3232" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3233" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758577 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761987 ATOM PAIRS WERE FOUND FOR ATOM LIST 41851 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29271 from a total of 761987 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3233 -76.00349 9.88374 0.70693 INTE EXTERN> -26.91608 -49.08741 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0035" Parameter: A <- "-76.0035" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9161" Parameter: B <- "-26.9161" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0874" Parameter: C <- "-49.0874" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3233 TOTAL ENERGY = -76.0035 RDTITL> * VAN DER WAALS = -26.9161 ELECTROSTATIC = -49.0874 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3233" Parameter: CONF_N -> "8002" Comparing "3233" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3234" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761987 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770241 ATOM PAIRS WERE FOUND FOR ATOM LIST 42287 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30149 from a total of 770241 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3234 -72.66829 -3.33520 0.69834 INTE EXTERN> -28.48919 -44.17910 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6683" Parameter: A <- "-72.6683" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4892" Parameter: B <- "-28.4892" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1791" Parameter: C <- "-44.1791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3234 TOTAL ENERGY = -72.6683 RDTITL> * VAN DER WAALS = -28.4892 ELECTROSTATIC = -44.1791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3234" Parameter: CONF_N -> "8002" Comparing "3234" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3235" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770241 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766078 ATOM PAIRS WERE FOUND FOR ATOM LIST 42179 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30235 from a total of 766078 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3235 -66.39406 -6.27423 0.60006 INTE EXTERN> -29.93644 -36.45762 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3941" Parameter: A <- "-66.3941" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9364" Parameter: B <- "-29.9364" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4576" Parameter: C <- "-36.4576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3235 TOTAL ENERGY = -66.3941 RDTITL> * VAN DER WAALS = -29.9364 ELECTROSTATIC = -36.4576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3235" Parameter: CONF_N -> "8002" Comparing "3235" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3236" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766078 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759300 ATOM PAIRS WERE FOUND FOR ATOM LIST 41734 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29874 from a total of 759300 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3236 -71.99361 5.59954 0.60059 INTE EXTERN> -31.11900 -40.87460 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9936" Parameter: A <- "-71.9936" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.119" Parameter: B <- "-31.119" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8746" Parameter: C <- "-40.8746" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3236 TOTAL ENERGY = -71.9936 RDTITL> * VAN DER WAALS = -31.119 ELECTROSTATIC = -40.8746 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3236" Parameter: CONF_N -> "8002" Comparing "3236" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3237" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759300 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756763 ATOM PAIRS WERE FOUND FOR ATOM LIST 41578 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29969 from a total of 756763 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3237 -69.54426 -2.44935 0.60733 INTE EXTERN> -31.28271 -38.26155 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5443" Parameter: A <- "-69.5443" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2827" Parameter: B <- "-31.2827" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2616" Parameter: C <- "-38.2616" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3237 TOTAL ENERGY = -69.5443 RDTITL> * VAN DER WAALS = -31.2827 ELECTROSTATIC = -38.2616 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3237" Parameter: CONF_N -> "8002" Comparing "3237" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3238" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756763 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757780 ATOM PAIRS WERE FOUND FOR ATOM LIST 41519 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29348 from a total of 757780 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3238 -74.56846 5.02420 0.56198 INTE EXTERN> -33.16425 -41.40420 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5685" Parameter: A <- "-74.5685" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1643" Parameter: B <- "-33.1643" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4042" Parameter: C <- "-41.4042" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3238 TOTAL ENERGY = -74.5685 RDTITL> * VAN DER WAALS = -33.1643 ELECTROSTATIC = -41.4042 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3238" Parameter: CONF_N -> "8002" Comparing "3238" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3239" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757780 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770674 ATOM PAIRS WERE FOUND FOR ATOM LIST 42349 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30394 from a total of 770674 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3239 -72.67753 -1.89093 0.58408 INTE EXTERN> -33.65964 -39.01789 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6775" Parameter: A <- "-72.6775" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6596" Parameter: B <- "-33.6596" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0179" Parameter: C <- "-39.0179" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3239 TOTAL ENERGY = -72.6775 RDTITL> * VAN DER WAALS = -33.6596 ELECTROSTATIC = -39.0179 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3239" Parameter: CONF_N -> "8002" Comparing "3239" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3240" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770674 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763826 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29697 from a total of 763826 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3240 -73.39138 0.71385 0.60945 INTE EXTERN> -31.25341 -42.13797 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3914" Parameter: A <- "-73.3914" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2534" Parameter: B <- "-31.2534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.138" Parameter: C <- "-42.138" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3240 TOTAL ENERGY = -73.3914 RDTITL> * VAN DER WAALS = -31.2534 ELECTROSTATIC = -42.138 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3240" Parameter: CONF_N -> "8002" Comparing "3240" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3241" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763826 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762899 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30254 from a total of 762899 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3241 -74.78189 1.39051 0.79882 INTE EXTERN> -23.59173 -51.19017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7819" Parameter: A <- "-74.7819" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.5917" Parameter: B <- "-23.5917" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1902" Parameter: C <- "-51.1902" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3241 TOTAL ENERGY = -74.7819 RDTITL> * VAN DER WAALS = -23.5917 ELECTROSTATIC = -51.1902 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3241" Parameter: CONF_N -> "8002" Comparing "3241" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3242" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762899 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764918 ATOM PAIRS WERE FOUND FOR ATOM LIST 41927 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30337 from a total of 764918 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3242 -78.97578 4.19388 0.70609 INTE EXTERN> -30.71936 -48.25641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9758" Parameter: A <- "-78.9758" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7194" Parameter: B <- "-30.7194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2564" Parameter: C <- "-48.2564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3242 TOTAL ENERGY = -78.9758 RDTITL> * VAN DER WAALS = -30.7194 ELECTROSTATIC = -48.2564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3242" Parameter: CONF_N -> "8002" Comparing "3242" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3243" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764918 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760591 ATOM PAIRS WERE FOUND FOR ATOM LIST 41871 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30144 from a total of 760591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3243 -76.71510 -2.26068 0.64147 INTE EXTERN> -32.89364 -43.82146 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7151" Parameter: A <- "-76.7151" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8936" Parameter: B <- "-32.8936" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8215" Parameter: C <- "-43.8215" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3243 TOTAL ENERGY = -76.7151 RDTITL> * VAN DER WAALS = -32.8936 ELECTROSTATIC = -43.8215 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3243" Parameter: CONF_N -> "8002" Comparing "3243" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3244" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760840 ATOM PAIRS WERE FOUND FOR ATOM LIST 41750 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30169 from a total of 760840 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3244 -69.45014 -7.26496 0.68767 INTE EXTERN> -29.34400 -40.10614 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4501" Parameter: A <- "-69.4501" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.344" Parameter: B <- "-29.344" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1061" Parameter: C <- "-40.1061" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3244 TOTAL ENERGY = -69.4501 RDTITL> * VAN DER WAALS = -29.344 ELECTROSTATIC = -40.1061 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3244" Parameter: CONF_N -> "8002" Comparing "3244" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3245" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760840 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759603 ATOM PAIRS WERE FOUND FOR ATOM LIST 42087 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29668 from a total of 759603 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3245 -69.79857 0.34843 0.62999 INTE EXTERN> -30.88418 -38.91438 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7986" Parameter: A <- "-69.7986" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8842" Parameter: B <- "-30.8842" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9144" Parameter: C <- "-38.9144" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3245 TOTAL ENERGY = -69.7986 RDTITL> * VAN DER WAALS = -30.8842 ELECTROSTATIC = -38.9144 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3245" Parameter: CONF_N -> "8002" Comparing "3245" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3246" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759603 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761174 ATOM PAIRS WERE FOUND FOR ATOM LIST 41970 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29684 from a total of 761174 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3246 -77.36912 7.57055 0.68319 INTE EXTERN> -30.98584 -46.38328 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3691" Parameter: A <- "-77.3691" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9858" Parameter: B <- "-30.9858" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3833" Parameter: C <- "-46.3833" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3246 TOTAL ENERGY = -77.3691 RDTITL> * VAN DER WAALS = -30.9858 ELECTROSTATIC = -46.3833 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3246" Parameter: CONF_N -> "8002" Comparing "3246" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3247" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761174 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759596 ATOM PAIRS WERE FOUND FOR ATOM LIST 41787 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30243 from a total of 759596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3247 -81.15997 3.79086 0.77914 INTE EXTERN> -25.87401 -55.28596 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.16" Parameter: A <- "-81.16" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.874" Parameter: B <- "-25.874" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.286" Parameter: C <- "-55.286" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3247 TOTAL ENERGY = -81.16 RDTITL> * VAN DER WAALS = -25.874 ELECTROSTATIC = -55.286 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3247" Parameter: CONF_N -> "8002" Comparing "3247" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3248" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764004 ATOM PAIRS WERE FOUND FOR ATOM LIST 41931 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29580 from a total of 764004 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3248 -74.04746 -7.11251 0.66892 INTE EXTERN> -27.80061 -46.24685 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0475" Parameter: A <- "-74.0475" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8006" Parameter: B <- "-27.8006" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2469" Parameter: C <- "-46.2469" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3248 TOTAL ENERGY = -74.0475 RDTITL> * VAN DER WAALS = -27.8006 ELECTROSTATIC = -46.2469 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3248" Parameter: CONF_N -> "8002" Comparing "3248" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3249" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764004 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765822 ATOM PAIRS WERE FOUND FOR ATOM LIST 42109 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30543 from a total of 765822 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3249 -85.26958 11.22211 0.68274 INTE EXTERN> -31.12616 -54.14342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.2696" Parameter: A <- "-85.2696" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1262" Parameter: B <- "-31.1262" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.1434" Parameter: C <- "-54.1434" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3249 TOTAL ENERGY = -85.2696 RDTITL> * VAN DER WAALS = -31.1262 ELECTROSTATIC = -54.1434 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3249" Parameter: CONF_N -> "8002" Comparing "3249" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3250" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765822 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759563 ATOM PAIRS WERE FOUND FOR ATOM LIST 41825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29926 from a total of 759563 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3250 -82.86296 -2.40661 0.77475 INTE EXTERN> -27.12404 -55.73892 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.863" Parameter: A <- "-82.863" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.124" Parameter: B <- "-27.124" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.7389" Parameter: C <- "-55.7389" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3250 TOTAL ENERGY = -82.863 RDTITL> * VAN DER WAALS = -27.124 ELECTROSTATIC = -55.7389 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3250" Parameter: CONF_N -> "8002" Comparing "3250" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3251" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759563 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765194 ATOM PAIRS WERE FOUND FOR ATOM LIST 41950 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30135 from a total of 765194 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3251 -82.72894 -0.13403 0.66371 INTE EXTERN> -30.38878 -52.34016 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7289" Parameter: A <- "-82.7289" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3888" Parameter: B <- "-30.3888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3402" Parameter: C <- "-52.3402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3251 TOTAL ENERGY = -82.7289 RDTITL> * VAN DER WAALS = -30.3888 ELECTROSTATIC = -52.3402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3251" Parameter: CONF_N -> "8002" Comparing "3251" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3252" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765194 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762146 ATOM PAIRS WERE FOUND FOR ATOM LIST 41868 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29602 from a total of 762146 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3252 -79.42376 -3.30518 0.74944 INTE EXTERN> -26.80310 -52.62066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4238" Parameter: A <- "-79.4238" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8031" Parameter: B <- "-26.8031" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6207" Parameter: C <- "-52.6207" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3252 TOTAL ENERGY = -79.4238 RDTITL> * VAN DER WAALS = -26.8031 ELECTROSTATIC = -52.6207 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3252" Parameter: CONF_N -> "8002" Comparing "3252" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3253" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762146 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761385 ATOM PAIRS WERE FOUND FOR ATOM LIST 41850 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29210 from a total of 761385 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3253 -83.04646 3.62270 0.62860 INTE EXTERN> -32.87650 -50.16996 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.0465" Parameter: A <- "-83.0465" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8765" Parameter: B <- "-32.8765" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.17" Parameter: C <- "-50.17" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3253 TOTAL ENERGY = -83.0465 RDTITL> * VAN DER WAALS = -32.8765 ELECTROSTATIC = -50.17 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3253" Parameter: CONF_N -> "8002" Comparing "3253" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3254" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761385 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756573 ATOM PAIRS WERE FOUND FOR ATOM LIST 41460 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29148 from a total of 756573 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3254 -78.18483 -4.86163 0.68584 INTE EXTERN> -29.01487 -49.16997 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1848" Parameter: A <- "-78.1848" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0149" Parameter: B <- "-29.0149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.17" Parameter: C <- "-49.17" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3254 TOTAL ENERGY = -78.1848 RDTITL> * VAN DER WAALS = -29.0149 ELECTROSTATIC = -49.17 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3254" Parameter: CONF_N -> "8002" Comparing "3254" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3255" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756573 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758375 ATOM PAIRS WERE FOUND FOR ATOM LIST 41617 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29428 from a total of 758375 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3255 -80.67114 2.48630 0.65282 INTE EXTERN> -29.90314 -50.76800 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6711" Parameter: A <- "-80.6711" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9031" Parameter: B <- "-29.9031" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.768" Parameter: C <- "-50.768" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3255 TOTAL ENERGY = -80.6711 RDTITL> * VAN DER WAALS = -29.9031 ELECTROSTATIC = -50.768 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3255" Parameter: CONF_N -> "8002" Comparing "3255" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3256" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758375 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761590 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29236 from a total of 761590 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3256 -86.90049 6.22936 0.72080 INTE EXTERN> -27.62368 -59.27681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.9005" Parameter: A <- "-86.9005" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6237" Parameter: B <- "-27.6237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.2768" Parameter: C <- "-59.2768" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3256 TOTAL ENERGY = -86.9005 RDTITL> * VAN DER WAALS = -27.6237 ELECTROSTATIC = -59.2768 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3256" Parameter: CONF_N -> "8002" Comparing "3256" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3257" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761590 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762165 ATOM PAIRS WERE FOUND FOR ATOM LIST 41913 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29438 from a total of 762165 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3257 -85.01075 -1.88974 0.68248 INTE EXTERN> -32.07091 -52.93985 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.0108" Parameter: A <- "-85.0108" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0709" Parameter: B <- "-32.0709" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9398" Parameter: C <- "-52.9398" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3257 TOTAL ENERGY = -85.0108 RDTITL> * VAN DER WAALS = -32.0709 ELECTROSTATIC = -52.9398 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3257" Parameter: CONF_N -> "8002" Comparing "3257" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3258" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762165 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763073 ATOM PAIRS WERE FOUND FOR ATOM LIST 41815 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30142 from a total of 763073 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3258 -82.62004 -2.39072 0.65340 INTE EXTERN> -32.06504 -50.55500 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.62" Parameter: A <- "-82.62" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.065" Parameter: B <- "-32.065" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.555" Parameter: C <- "-50.555" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3258 TOTAL ENERGY = -82.62 RDTITL> * VAN DER WAALS = -32.065 ELECTROSTATIC = -50.555 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3258" Parameter: CONF_N -> "8002" Comparing "3258" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3259" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763073 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758098 ATOM PAIRS WERE FOUND FOR ATOM LIST 41886 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29959 from a total of 758098 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3259 -85.33703 2.71699 0.67038 INTE EXTERN> -30.52523 -54.81180 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.337" Parameter: A <- "-85.337" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5252" Parameter: B <- "-30.5252" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8118" Parameter: C <- "-54.8118" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3259 TOTAL ENERGY = -85.337 RDTITL> * VAN DER WAALS = -30.5252 ELECTROSTATIC = -54.8118 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3259" Parameter: CONF_N -> "8002" Comparing "3259" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3260" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758098 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762519 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29667 from a total of 762519 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3260 -74.41760 -10.91943 0.58742 INTE EXTERN> -30.91414 -43.50345 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4176" Parameter: A <- "-74.4176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9141" Parameter: B <- "-30.9141" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5035" Parameter: C <- "-43.5035" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3260 TOTAL ENERGY = -74.4176 RDTITL> * VAN DER WAALS = -30.9141 ELECTROSTATIC = -43.5035 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3260" Parameter: CONF_N -> "8002" Comparing "3260" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3261" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762519 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762742 ATOM PAIRS WERE FOUND FOR ATOM LIST 41908 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29517 from a total of 762742 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3261 -73.74503 -0.67257 0.60275 INTE EXTERN> -34.23635 -39.50868 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.745" Parameter: A <- "-73.745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.2364" Parameter: B <- "-34.2364" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5087" Parameter: C <- "-39.5087" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3261 TOTAL ENERGY = -73.745 RDTITL> * VAN DER WAALS = -34.2364 ELECTROSTATIC = -39.5087 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3261" Parameter: CONF_N -> "8002" Comparing "3261" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3262" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762742 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756953 ATOM PAIRS WERE FOUND FOR ATOM LIST 41669 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29650 from a total of 756953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3262 -75.69537 1.95034 0.63207 INTE EXTERN> -31.27115 -44.42422 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6954" Parameter: A <- "-75.6954" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2712" Parameter: B <- "-31.2712" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4242" Parameter: C <- "-44.4242" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3262 TOTAL ENERGY = -75.6954 RDTITL> * VAN DER WAALS = -31.2712 ELECTROSTATIC = -44.4242 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3262" Parameter: CONF_N -> "8002" Comparing "3262" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3263" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760306 ATOM PAIRS WERE FOUND FOR ATOM LIST 41840 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29371 from a total of 760306 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3263 -71.81180 -3.88357 0.59531 INTE EXTERN> -30.35293 -41.45887 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8118" Parameter: A <- "-71.8118" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3529" Parameter: B <- "-30.3529" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4589" Parameter: C <- "-41.4589" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3263 TOTAL ENERGY = -71.8118 RDTITL> * VAN DER WAALS = -30.3529 ELECTROSTATIC = -41.4589 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3263" Parameter: CONF_N -> "8002" Comparing "3263" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3264" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760306 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757270 ATOM PAIRS WERE FOUND FOR ATOM LIST 41626 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29026 from a total of 757270 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3264 -71.58294 -0.22886 0.56199 INTE EXTERN> -31.67136 -39.91158 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5829" Parameter: A <- "-71.5829" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6714" Parameter: B <- "-31.6714" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9116" Parameter: C <- "-39.9116" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3264 TOTAL ENERGY = -71.5829 RDTITL> * VAN DER WAALS = -31.6714 ELECTROSTATIC = -39.9116 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3264" Parameter: CONF_N -> "8002" Comparing "3264" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3265" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757270 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755265 ATOM PAIRS WERE FOUND FOR ATOM LIST 41367 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28804 from a total of 755265 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3265 -70.76029 -0.82265 0.61122 INTE EXTERN> -31.30504 -39.45524 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7603" Parameter: A <- "-70.7603" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.305" Parameter: B <- "-31.305" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4552" Parameter: C <- "-39.4552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3265 TOTAL ENERGY = -70.7603 RDTITL> * VAN DER WAALS = -31.305 ELECTROSTATIC = -39.4552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3265" Parameter: CONF_N -> "8002" Comparing "3265" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3266" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755265 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753516 ATOM PAIRS WERE FOUND FOR ATOM LIST 41503 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29071 from a total of 753516 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3266 -76.35343 5.59315 0.74107 INTE EXTERN> -27.71594 -48.63750 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3534" Parameter: A <- "-76.3534" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7159" Parameter: B <- "-27.7159" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6375" Parameter: C <- "-48.6375" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3266 TOTAL ENERGY = -76.3534 RDTITL> * VAN DER WAALS = -27.7159 ELECTROSTATIC = -48.6375 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3266" Parameter: CONF_N -> "8002" Comparing "3266" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3267" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753516 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759111 ATOM PAIRS WERE FOUND FOR ATOM LIST 41579 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29091 from a total of 759111 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3267 -73.82130 -2.53214 0.65646 INTE EXTERN> -29.83697 -43.98433 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8213" Parameter: A <- "-73.8213" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.837" Parameter: B <- "-29.837" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9843" Parameter: C <- "-43.9843" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3267 TOTAL ENERGY = -73.8213 RDTITL> * VAN DER WAALS = -29.837 ELECTROSTATIC = -43.9843 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3267" Parameter: CONF_N -> "8002" Comparing "3267" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3268" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759111 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760428 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29123 from a total of 760428 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3268 -66.84822 -6.97308 0.62303 INTE EXTERN> -28.16525 -38.68297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8482" Parameter: A <- "-66.8482" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1652" Parameter: B <- "-28.1652" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.683" Parameter: C <- "-38.683" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3268 TOTAL ENERGY = -66.8482 RDTITL> * VAN DER WAALS = -28.1652 ELECTROSTATIC = -38.683 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3268" Parameter: CONF_N -> "8002" Comparing "3268" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3269" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760428 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767562 ATOM PAIRS WERE FOUND FOR ATOM LIST 41940 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30607 from a total of 767562 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3269 -75.49342 8.64520 0.75550 INTE EXTERN> -24.91186 -50.58156 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4934" Parameter: A <- "-75.4934" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9119" Parameter: B <- "-24.9119" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5816" Parameter: C <- "-50.5816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3269 TOTAL ENERGY = -75.4934 RDTITL> * VAN DER WAALS = -24.9119 ELECTROSTATIC = -50.5816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3269" Parameter: CONF_N -> "8002" Comparing "3269" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3270" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767562 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757187 ATOM PAIRS WERE FOUND FOR ATOM LIST 41694 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29180 from a total of 757187 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3270 -66.70985 -8.78357 0.54680 INTE EXTERN> -30.92367 -35.78617 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7098" Parameter: A <- "-66.7098" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9237" Parameter: B <- "-30.9237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7862" Parameter: C <- "-35.7862" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3270 TOTAL ENERGY = -66.7098 RDTITL> * VAN DER WAALS = -30.9237 ELECTROSTATIC = -35.7862 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3270" Parameter: CONF_N -> "8002" Comparing "3270" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3271" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757187 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761400 ATOM PAIRS WERE FOUND FOR ATOM LIST 41876 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29921 from a total of 761400 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3271 -81.18307 14.47322 0.71365 INTE EXTERN> -27.83083 -53.35224 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1831" Parameter: A <- "-81.1831" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8308" Parameter: B <- "-27.8308" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3522" Parameter: C <- "-53.3522" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3271 TOTAL ENERGY = -81.1831 RDTITL> * VAN DER WAALS = -27.8308 ELECTROSTATIC = -53.3522 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3271" Parameter: CONF_N -> "8002" Comparing "3271" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3272" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761400 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764943 ATOM PAIRS WERE FOUND FOR ATOM LIST 41928 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30609 from a total of 764943 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3272 -73.69180 -7.49127 0.67160 INTE EXTERN> -27.69338 -45.99842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6918" Parameter: A <- "-73.6918" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6934" Parameter: B <- "-27.6934" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9984" Parameter: C <- "-45.9984" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3272 TOTAL ENERGY = -73.6918 RDTITL> * VAN DER WAALS = -27.6934 ELECTROSTATIC = -45.9984 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3272" Parameter: CONF_N -> "8002" Comparing "3272" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3273" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764943 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41511 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29921 from a total of 757601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3273 -75.92716 2.23537 0.68872 INTE EXTERN> -29.00972 -46.91745 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9272" Parameter: A <- "-75.9272" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0097" Parameter: B <- "-29.0097" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9174" Parameter: C <- "-46.9174" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3273 TOTAL ENERGY = -75.9272 RDTITL> * VAN DER WAALS = -29.0097 ELECTROSTATIC = -46.9174 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3273" Parameter: CONF_N -> "8002" Comparing "3273" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3274" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763129 ATOM PAIRS WERE FOUND FOR ATOM LIST 42056 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30325 from a total of 763129 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3274 -73.87550 -2.05166 0.79597 INTE EXTERN> -25.44112 -48.43439 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8755" Parameter: A <- "-73.8755" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4411" Parameter: B <- "-25.4411" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4344" Parameter: C <- "-48.4344" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3274 TOTAL ENERGY = -73.8755 RDTITL> * VAN DER WAALS = -25.4411 ELECTROSTATIC = -48.4344 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3274" Parameter: CONF_N -> "8002" Comparing "3274" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3275" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763129 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760301 ATOM PAIRS WERE FOUND FOR ATOM LIST 41684 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30221 from a total of 760301 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3275 -66.92296 -6.95255 0.55827 INTE EXTERN> -28.80272 -38.12024 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.923" Parameter: A <- "-66.923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8027" Parameter: B <- "-28.8027" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1202" Parameter: C <- "-38.1202" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3275 TOTAL ENERGY = -66.923 RDTITL> * VAN DER WAALS = -28.8027 ELECTROSTATIC = -38.1202 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3275" Parameter: CONF_N -> "8002" Comparing "3275" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3276" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760301 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754633 ATOM PAIRS WERE FOUND FOR ATOM LIST 41342 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29198 from a total of 754633 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3276 -74.01581 7.09285 0.56086 INTE EXTERN> -30.99523 -43.02058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0158" Parameter: A <- "-74.0158" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9952" Parameter: B <- "-30.9952" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0206" Parameter: C <- "-43.0206" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3276 TOTAL ENERGY = -74.0158 RDTITL> * VAN DER WAALS = -30.9952 ELECTROSTATIC = -43.0206 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3276" Parameter: CONF_N -> "8002" Comparing "3276" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3277" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754633 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761440 ATOM PAIRS WERE FOUND FOR ATOM LIST 41966 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29030 from a total of 761440 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3277 -69.39557 -4.62024 0.58859 INTE EXTERN> -30.23947 -39.15610 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3956" Parameter: A <- "-69.3956" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2395" Parameter: B <- "-30.2395" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1561" Parameter: C <- "-39.1561" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3277 TOTAL ENERGY = -69.3956 RDTITL> * VAN DER WAALS = -30.2395 ELECTROSTATIC = -39.1561 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3277" Parameter: CONF_N -> "8002" Comparing "3277" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3278" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761440 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759593 ATOM PAIRS WERE FOUND FOR ATOM LIST 41803 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29149 from a total of 759593 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3278 -68.10764 -1.28792 0.56842 INTE EXTERN> -30.85707 -37.25058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1076" Parameter: A <- "-68.1076" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8571" Parameter: B <- "-30.8571" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2506" Parameter: C <- "-37.2506" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3278 TOTAL ENERGY = -68.1076 RDTITL> * VAN DER WAALS = -30.8571 ELECTROSTATIC = -37.2506 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3278" Parameter: CONF_N -> "8002" Comparing "3278" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3279" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759593 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757968 ATOM PAIRS WERE FOUND FOR ATOM LIST 41706 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29422 from a total of 757968 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3279 -67.70644 -0.40120 0.63806 INTE EXTERN> -29.92826 -37.77818 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7064" Parameter: A <- "-67.7064" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9283" Parameter: B <- "-29.9283" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7782" Parameter: C <- "-37.7782" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3279 TOTAL ENERGY = -67.7064 RDTITL> * VAN DER WAALS = -29.9283 ELECTROSTATIC = -37.7782 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3279" Parameter: CONF_N -> "8002" Comparing "3279" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3280" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757968 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759953 ATOM PAIRS WERE FOUND FOR ATOM LIST 41737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29271 from a total of 759953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3280 -67.28614 -0.42030 0.53639 INTE EXTERN> -30.81560 -36.47054 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2861" Parameter: A <- "-67.2861" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8156" Parameter: B <- "-30.8156" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4705" Parameter: C <- "-36.4705" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3280 TOTAL ENERGY = -67.2861 RDTITL> * VAN DER WAALS = -30.8156 ELECTROSTATIC = -36.4705 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3280" Parameter: CONF_N -> "8002" Comparing "3280" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3281" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757092 ATOM PAIRS WERE FOUND FOR ATOM LIST 41440 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29191 from a total of 757092 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3281 -72.02995 4.74381 0.64431 INTE EXTERN> -27.66527 -44.36468 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.03" Parameter: A <- "-72.03" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6653" Parameter: B <- "-27.6653" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3647" Parameter: C <- "-44.3647" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3281 TOTAL ENERGY = -72.03 RDTITL> * VAN DER WAALS = -27.6653 ELECTROSTATIC = -44.3647 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3281" Parameter: CONF_N -> "8002" Comparing "3281" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3282" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757092 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756947 ATOM PAIRS WERE FOUND FOR ATOM LIST 41906 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29168 from a total of 756947 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3282 -71.26675 -0.76320 0.59107 INTE EXTERN> -32.34617 -38.92058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2668" Parameter: A <- "-71.2668" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3462" Parameter: B <- "-32.3462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9206" Parameter: C <- "-38.9206" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3282 TOTAL ENERGY = -71.2668 RDTITL> * VAN DER WAALS = -32.3462 ELECTROSTATIC = -38.9206 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3282" Parameter: CONF_N -> "8002" Comparing "3282" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3283" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756947 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756519 ATOM PAIRS WERE FOUND FOR ATOM LIST 41559 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29228 from a total of 756519 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3283 -70.28880 -0.97796 0.49151 INTE EXTERN> -32.69993 -37.58886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2888" Parameter: A <- "-70.2888" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6999" Parameter: B <- "-32.6999" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5889" Parameter: C <- "-37.5889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3283 TOTAL ENERGY = -70.2888 RDTITL> * VAN DER WAALS = -32.6999 ELECTROSTATIC = -37.5889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3283" Parameter: CONF_N -> "8002" Comparing "3283" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3284" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756519 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759132 ATOM PAIRS WERE FOUND FOR ATOM LIST 41777 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29454 from a total of 759132 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3284 -71.03407 0.74527 0.71308 INTE EXTERN> -26.76423 -44.26984 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0341" Parameter: A <- "-71.0341" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7642" Parameter: B <- "-26.7642" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2698" Parameter: C <- "-44.2698" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3284 TOTAL ENERGY = -71.0341 RDTITL> * VAN DER WAALS = -26.7642 ELECTROSTATIC = -44.2698 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3284" Parameter: CONF_N -> "8002" Comparing "3284" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3285" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759132 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755666 ATOM PAIRS WERE FOUND FOR ATOM LIST 41516 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29346 from a total of 755666 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3285 -72.09859 1.06452 0.60100 INTE EXTERN> -29.90192 -42.19667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0986" Parameter: A <- "-72.0986" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9019" Parameter: B <- "-29.9019" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1967" Parameter: C <- "-42.1967" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3285 TOTAL ENERGY = -72.0986 RDTITL> * VAN DER WAALS = -29.9019 ELECTROSTATIC = -42.1967 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3285" Parameter: CONF_N -> "8002" Comparing "3285" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3286" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755666 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756732 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29170 from a total of 756732 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3286 -70.58907 -1.50952 0.62633 INTE EXTERN> -31.60656 -38.98251 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5891" Parameter: A <- "-70.5891" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6066" Parameter: B <- "-31.6066" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9825" Parameter: C <- "-38.9825" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3286 TOTAL ENERGY = -70.5891 RDTITL> * VAN DER WAALS = -31.6066 ELECTROSTATIC = -38.9825 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3286" Parameter: CONF_N -> "8002" Comparing "3286" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3287" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756732 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758578 ATOM PAIRS WERE FOUND FOR ATOM LIST 41829 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29119 from a total of 758578 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3287 -64.75549 -5.83358 0.63072 INTE EXTERN> -27.17477 -37.58072 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7555" Parameter: A <- "-64.7555" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1748" Parameter: B <- "-27.1748" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5807" Parameter: C <- "-37.5807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3287 TOTAL ENERGY = -64.7555 RDTITL> * VAN DER WAALS = -27.1748 ELECTROSTATIC = -37.5807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3287" Parameter: CONF_N -> "8002" Comparing "3287" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3288" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758578 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755857 ATOM PAIRS WERE FOUND FOR ATOM LIST 41566 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29694 from a total of 755857 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3288 -64.05638 -0.69911 0.70916 INTE EXTERN> -21.94097 -42.11541 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0564" Parameter: A <- "-64.0564" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.941" Parameter: B <- "-21.941" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1154" Parameter: C <- "-42.1154" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3288 TOTAL ENERGY = -64.0564 RDTITL> * VAN DER WAALS = -21.941 ELECTROSTATIC = -42.1154 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3288" Parameter: CONF_N -> "8002" Comparing "3288" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3289" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755857 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757986 ATOM PAIRS WERE FOUND FOR ATOM LIST 41554 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29506 from a total of 757986 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3289 -70.19590 6.13952 0.62182 INTE EXTERN> -30.23398 -39.96192 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1959" Parameter: A <- "-70.1959" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.234" Parameter: B <- "-30.234" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9619" Parameter: C <- "-39.9619" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3289 TOTAL ENERGY = -70.1959 RDTITL> * VAN DER WAALS = -30.234 ELECTROSTATIC = -39.9619 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3289" Parameter: CONF_N -> "8002" Comparing "3289" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3290" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757986 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757996 ATOM PAIRS WERE FOUND FOR ATOM LIST 41564 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29719 from a total of 757996 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3290 -56.92124 -13.27466 0.88089 INTE EXTERN> -22.40979 -34.51145 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-56.9212" Parameter: A <- "-56.9212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.4098" Parameter: B <- "-22.4098" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5115" Parameter: C <- "-34.5115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3290 TOTAL ENERGY = -56.9212 RDTITL> * VAN DER WAALS = -22.4098 ELECTROSTATIC = -34.5115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3290" Parameter: CONF_N -> "8002" Comparing "3290" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3291" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757996 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761707 ATOM PAIRS WERE FOUND FOR ATOM LIST 41982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29566 from a total of 761707 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3291 -69.32874 12.40750 0.66006 INTE EXTERN> -32.09144 -37.23730 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3287" Parameter: A <- "-69.3287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0914" Parameter: B <- "-32.0914" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2373" Parameter: C <- "-37.2373" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3291 TOTAL ENERGY = -69.3287 RDTITL> * VAN DER WAALS = -32.0914 ELECTROSTATIC = -37.2373 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3291" Parameter: CONF_N -> "8002" Comparing "3291" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3292" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761707 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760659 ATOM PAIRS WERE FOUND FOR ATOM LIST 41954 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30241 from a total of 760659 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3292 -68.13797 -1.19078 0.67940 INTE EXTERN> -28.99831 -39.13965 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.138" Parameter: A <- "-68.138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9983" Parameter: B <- "-28.9983" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1397" Parameter: C <- "-39.1397" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3292 TOTAL ENERGY = -68.138 RDTITL> * VAN DER WAALS = -28.9983 ELECTROSTATIC = -39.1397 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3292" Parameter: CONF_N -> "8002" Comparing "3292" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3293" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760659 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764018 ATOM PAIRS WERE FOUND FOR ATOM LIST 42176 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29537 from a total of 764018 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3293 -66.23731 -1.90065 0.51229 INTE EXTERN> -34.26291 -31.97441 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2373" Parameter: A <- "-66.2373" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.2629" Parameter: B <- "-34.2629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.9744" Parameter: C <- "-31.9744" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3293 TOTAL ENERGY = -66.2373 RDTITL> * VAN DER WAALS = -34.2629 ELECTROSTATIC = -31.9744 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3293" Parameter: CONF_N -> "8002" Comparing "3293" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3294" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764018 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764224 ATOM PAIRS WERE FOUND FOR ATOM LIST 42028 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30011 from a total of 764224 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3294 -63.83987 -2.39745 0.57582 INTE EXTERN> -29.42530 -34.41456 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.8399" Parameter: A <- "-63.8399" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4253" Parameter: B <- "-29.4253" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4146" Parameter: C <- "-34.4146" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3294 TOTAL ENERGY = -63.8399 RDTITL> * VAN DER WAALS = -29.4253 ELECTROSTATIC = -34.4146 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3294" Parameter: CONF_N -> "8002" Comparing "3294" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3295" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764224 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753536 ATOM PAIRS WERE FOUND FOR ATOM LIST 41302 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29314 from a total of 753536 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3295 -67.48440 3.64454 0.69068 INTE EXTERN> -29.14342 -38.34099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4844" Parameter: A <- "-67.4844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1434" Parameter: B <- "-29.1434" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.341" Parameter: C <- "-38.341" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3295 TOTAL ENERGY = -67.4844 RDTITL> * VAN DER WAALS = -29.1434 ELECTROSTATIC = -38.341 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3295" Parameter: CONF_N -> "8002" Comparing "3295" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3296" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753536 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753556 ATOM PAIRS WERE FOUND FOR ATOM LIST 41369 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29293 from a total of 753556 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3296 -61.58777 -5.89663 0.64968 INTE EXTERN> -27.94606 -33.64171 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.5878" Parameter: A <- "-61.5878" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9461" Parameter: B <- "-27.9461" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6417" Parameter: C <- "-33.6417" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3296 TOTAL ENERGY = -61.5878 RDTITL> * VAN DER WAALS = -27.9461 ELECTROSTATIC = -33.6417 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3296" Parameter: CONF_N -> "8002" Comparing "3296" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3297" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753556 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746653 ATOM PAIRS WERE FOUND FOR ATOM LIST 41256 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29061 from a total of 746653 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3297 -64.99536 3.40760 0.59417 INTE EXTERN> -29.14060 -35.85477 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9954" Parameter: A <- "-64.9954" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1406" Parameter: B <- "-29.1406" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8548" Parameter: C <- "-35.8548" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3297 TOTAL ENERGY = -64.9954 RDTITL> * VAN DER WAALS = -29.1406 ELECTROSTATIC = -35.8548 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3297" Parameter: CONF_N -> "8002" Comparing "3297" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3298" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746653 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750800 ATOM PAIRS WERE FOUND FOR ATOM LIST 41387 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29231 from a total of 750800 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3298 -76.27157 11.27620 0.65038 INTE EXTERN> -30.29975 -45.97182 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2716" Parameter: A <- "-76.2716" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2997" Parameter: B <- "-30.2997" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9718" Parameter: C <- "-45.9718" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3298 TOTAL ENERGY = -76.2716 RDTITL> * VAN DER WAALS = -30.2997 ELECTROSTATIC = -45.9718 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3298" Parameter: CONF_N -> "8002" Comparing "3298" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3299" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750800 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756108 ATOM PAIRS WERE FOUND FOR ATOM LIST 41430 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29654 from a total of 756108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3299 -69.12391 -7.14766 0.61953 INTE EXTERN> -30.02572 -39.09819 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1239" Parameter: A <- "-69.1239" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0257" Parameter: B <- "-30.0257" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0982" Parameter: C <- "-39.0982" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3299 TOTAL ENERGY = -69.1239 RDTITL> * VAN DER WAALS = -30.0257 ELECTROSTATIC = -39.0982 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3299" Parameter: CONF_N -> "8002" Comparing "3299" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3300" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754199 ATOM PAIRS WERE FOUND FOR ATOM LIST 41516 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29401 from a total of 754199 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3300 -73.92309 4.79918 0.65528 INTE EXTERN> -28.04081 -45.88228 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9231" Parameter: A <- "-73.9231" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0408" Parameter: B <- "-28.0408" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8823" Parameter: C <- "-45.8823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3300 TOTAL ENERGY = -73.9231 RDTITL> * VAN DER WAALS = -28.0408 ELECTROSTATIC = -45.8823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3300" Parameter: CONF_N -> "8002" Comparing "3300" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3301" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754199 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754643 ATOM PAIRS WERE FOUND FOR ATOM LIST 41664 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29342 from a total of 754643 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3301 -69.36746 -4.55563 0.56535 INTE EXTERN> -31.13925 -38.22821 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3675" Parameter: A <- "-69.3675" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1392" Parameter: B <- "-31.1392" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2282" Parameter: C <- "-38.2282" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3301 TOTAL ENERGY = -69.3675 RDTITL> * VAN DER WAALS = -31.1392 ELECTROSTATIC = -38.2282 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3301" Parameter: CONF_N -> "8002" Comparing "3301" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3302" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754643 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755093 ATOM PAIRS WERE FOUND FOR ATOM LIST 41687 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29363 from a total of 755093 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3302 -71.79633 2.42886 0.65787 INTE EXTERN> -30.41439 -41.38194 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7963" Parameter: A <- "-71.7963" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4144" Parameter: B <- "-30.4144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3819" Parameter: C <- "-41.3819" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3302 TOTAL ENERGY = -71.7963 RDTITL> * VAN DER WAALS = -30.4144 ELECTROSTATIC = -41.3819 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3302" Parameter: CONF_N -> "8002" Comparing "3302" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3303" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755093 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750437 ATOM PAIRS WERE FOUND FOR ATOM LIST 41414 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28706 from a total of 750437 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3303 -72.02718 0.23086 0.58385 INTE EXTERN> -31.92493 -40.10225 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0272" Parameter: A <- "-72.0272" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9249" Parameter: B <- "-31.9249" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1023" Parameter: C <- "-40.1023" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3303 TOTAL ENERGY = -72.0272 RDTITL> * VAN DER WAALS = -31.9249 ELECTROSTATIC = -40.1023 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3303" Parameter: CONF_N -> "8002" Comparing "3303" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3304" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750437 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753331 ATOM PAIRS WERE FOUND FOR ATOM LIST 41469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29807 from a total of 753331 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3304 -69.91620 -2.11099 0.63410 INTE EXTERN> -29.53726 -40.37894 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9162" Parameter: A <- "-69.9162" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5373" Parameter: B <- "-29.5373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3789" Parameter: C <- "-40.3789" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3304 TOTAL ENERGY = -69.9162 RDTITL> * VAN DER WAALS = -29.5373 ELECTROSTATIC = -40.3789 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3304" Parameter: CONF_N -> "8002" Comparing "3304" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3305" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753331 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753715 ATOM PAIRS WERE FOUND FOR ATOM LIST 41530 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29751 from a total of 753715 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3305 -63.34325 -6.57295 0.55100 INTE EXTERN> -31.85498 -31.48827 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3432" Parameter: A <- "-63.3432" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.855" Parameter: B <- "-31.855" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4883" Parameter: C <- "-31.4883" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3305 TOTAL ENERGY = -63.3432 RDTITL> * VAN DER WAALS = -31.855 ELECTROSTATIC = -31.4883 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3305" Parameter: CONF_N -> "8002" Comparing "3305" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3306" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753715 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765774 ATOM PAIRS WERE FOUND FOR ATOM LIST 42321 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29568 from a total of 765774 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3306 -67.43994 4.09670 0.72011 INTE EXTERN> -27.34442 -40.09552 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4399" Parameter: A <- "-67.4399" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3444" Parameter: B <- "-27.3444" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0955" Parameter: C <- "-40.0955" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3306 TOTAL ENERGY = -67.4399 RDTITL> * VAN DER WAALS = -27.3444 ELECTROSTATIC = -40.0955 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3306" Parameter: CONF_N -> "8002" Comparing "3306" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3307" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765774 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756918 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30003 from a total of 756918 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3307 -67.73113 0.29118 0.79129 INTE EXTERN> -24.39226 -43.33886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7311" Parameter: A <- "-67.7311" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3923" Parameter: B <- "-24.3923" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3389" Parameter: C <- "-43.3389" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3307 TOTAL ENERGY = -67.7311 RDTITL> * VAN DER WAALS = -24.3923 ELECTROSTATIC = -43.3389 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3307" Parameter: CONF_N -> "8002" Comparing "3307" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3308" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756918 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754117 ATOM PAIRS WERE FOUND FOR ATOM LIST 41520 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29983 from a total of 754117 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3308 -62.01617 -5.71495 0.65116 INTE EXTERN> -26.97401 -35.04216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.0162" Parameter: A <- "-62.0162" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.974" Parameter: B <- "-26.974" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0422" Parameter: C <- "-35.0422" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3308 TOTAL ENERGY = -62.0162 RDTITL> * VAN DER WAALS = -26.974 ELECTROSTATIC = -35.0422 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3308" Parameter: CONF_N -> "8002" Comparing "3308" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3309" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754117 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757971 ATOM PAIRS WERE FOUND FOR ATOM LIST 41631 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29942 from a total of 757971 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3309 -65.50888 3.49271 0.75453 INTE EXTERN> -26.14130 -39.36758 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5089" Parameter: A <- "-65.5089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1413" Parameter: B <- "-26.1413" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3676" Parameter: C <- "-39.3676" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3309 TOTAL ENERGY = -65.5089 RDTITL> * VAN DER WAALS = -26.1413 ELECTROSTATIC = -39.3676 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3309" Parameter: CONF_N -> "8002" Comparing "3309" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3310" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757971 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41757 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30150 from a total of 757422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3310 -76.36363 10.85474 0.66228 INTE EXTERN> -29.70795 -46.65568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3636" Parameter: A <- "-76.3636" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7079" Parameter: B <- "-29.7079" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6557" Parameter: C <- "-46.6557" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3310 TOTAL ENERGY = -76.3636 RDTITL> * VAN DER WAALS = -29.7079 ELECTROSTATIC = -46.6557 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3310" Parameter: CONF_N -> "8002" Comparing "3310" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3311" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41815 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29655 from a total of 759526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3311 -70.48558 -5.87805 0.64666 INTE EXTERN> -25.55113 -44.93445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4856" Parameter: A <- "-70.4856" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5511" Parameter: B <- "-25.5511" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9344" Parameter: C <- "-44.9344" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3311 TOTAL ENERGY = -70.4856 RDTITL> * VAN DER WAALS = -25.5511 ELECTROSTATIC = -44.9344 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3311" Parameter: CONF_N -> "8002" Comparing "3311" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3312" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758663 ATOM PAIRS WERE FOUND FOR ATOM LIST 41789 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29759 from a total of 758663 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3312 -69.58214 -0.90344 0.60600 INTE EXTERN> -28.88502 -40.69712 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5821" Parameter: A <- "-69.5821" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.885" Parameter: B <- "-28.885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6971" Parameter: C <- "-40.6971" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3312 TOTAL ENERGY = -69.5821 RDTITL> * VAN DER WAALS = -28.885 ELECTROSTATIC = -40.6971 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3312" Parameter: CONF_N -> "8002" Comparing "3312" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3313" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758663 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756003 ATOM PAIRS WERE FOUND FOR ATOM LIST 41685 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30309 from a total of 756003 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3313 -65.84607 -3.73607 0.57256 INTE EXTERN> -26.91661 -38.92946 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8461" Parameter: A <- "-65.8461" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9166" Parameter: B <- "-26.9166" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9295" Parameter: C <- "-38.9295" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3313 TOTAL ENERGY = -65.8461 RDTITL> * VAN DER WAALS = -26.9166 ELECTROSTATIC = -38.9295 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3313" Parameter: CONF_N -> "8002" Comparing "3313" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3314" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756003 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760663 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29089 from a total of 760663 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3314 -69.38990 3.54383 0.54929 INTE EXTERN> -28.88095 -40.50895 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3899" Parameter: A <- "-69.3899" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.881" Parameter: B <- "-28.881" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.509" Parameter: C <- "-40.509" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3314 TOTAL ENERGY = -69.3899 RDTITL> * VAN DER WAALS = -28.881 ELECTROSTATIC = -40.509 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3314" Parameter: CONF_N -> "8002" Comparing "3314" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3315" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760663 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763234 ATOM PAIRS WERE FOUND FOR ATOM LIST 41834 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29740 from a total of 763234 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3315 -69.90506 0.51516 0.90612 INTE EXTERN> -20.97446 -48.93061 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9051" Parameter: A <- "-69.9051" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.9745" Parameter: B <- "-20.9745" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9306" Parameter: C <- "-48.9306" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3315 TOTAL ENERGY = -69.9051 RDTITL> * VAN DER WAALS = -20.9745 ELECTROSTATIC = -48.9306 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3315" Parameter: CONF_N -> "8002" Comparing "3315" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3316" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763234 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761057 ATOM PAIRS WERE FOUND FOR ATOM LIST 41887 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29345 from a total of 761057 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3316 -81.81589 11.91083 0.73662 INTE EXTERN> -27.55757 -54.25832 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8159" Parameter: A <- "-81.8159" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5576" Parameter: B <- "-27.5576" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2583" Parameter: C <- "-54.2583" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3316 TOTAL ENERGY = -81.8159 RDTITL> * VAN DER WAALS = -27.5576 ELECTROSTATIC = -54.2583 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3316" Parameter: CONF_N -> "8002" Comparing "3316" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3317" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761057 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769393 ATOM PAIRS WERE FOUND FOR ATOM LIST 42279 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30208 from a total of 769393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3317 -77.89853 -3.91736 0.63795 INTE EXTERN> -31.95136 -45.94717 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8985" Parameter: A <- "-77.8985" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9514" Parameter: B <- "-31.9514" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9472" Parameter: C <- "-45.9472" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3317 TOTAL ENERGY = -77.8985 RDTITL> * VAN DER WAALS = -31.9514 ELECTROSTATIC = -45.9472 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3317" Parameter: CONF_N -> "8002" Comparing "3317" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3318" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41689 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29667 from a total of 759009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3318 -66.84975 -11.04878 0.71752 INTE EXTERN> -26.95636 -39.89339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8497" Parameter: A <- "-66.8497" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9564" Parameter: B <- "-26.9564" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8934" Parameter: C <- "-39.8934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3318 TOTAL ENERGY = -66.8497 RDTITL> * VAN DER WAALS = -26.9564 ELECTROSTATIC = -39.8934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3318" Parameter: CONF_N -> "8002" Comparing "3318" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3319" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758918 ATOM PAIRS WERE FOUND FOR ATOM LIST 41626 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29993 from a total of 758918 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3319 -74.90413 8.05438 0.58145 INTE EXTERN> -30.92165 -43.98248 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9041" Parameter: A <- "-74.9041" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9217" Parameter: B <- "-30.9217" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9825" Parameter: C <- "-43.9825" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3319 TOTAL ENERGY = -74.9041 RDTITL> * VAN DER WAALS = -30.9217 ELECTROSTATIC = -43.9825 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3319" Parameter: CONF_N -> "8002" Comparing "3319" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3320" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758918 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761732 ATOM PAIRS WERE FOUND FOR ATOM LIST 41908 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29976 from a total of 761732 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3320 -71.76640 -3.13773 0.70463 INTE EXTERN> -24.88203 -46.88437 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7664" Parameter: A <- "-71.7664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.882" Parameter: B <- "-24.882" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8844" Parameter: C <- "-46.8844" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3320 TOTAL ENERGY = -71.7664 RDTITL> * VAN DER WAALS = -24.882 ELECTROSTATIC = -46.8844 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3320" Parameter: CONF_N -> "8002" Comparing "3320" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3321" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761732 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766809 ATOM PAIRS WERE FOUND FOR ATOM LIST 42096 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30470 from a total of 766809 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3321 -81.06393 9.29753 0.73595 INTE EXTERN> -27.85446 -53.20946 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.0639" Parameter: A <- "-81.0639" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8545" Parameter: B <- "-27.8545" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.2095" Parameter: C <- "-53.2095" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3321 TOTAL ENERGY = -81.0639 RDTITL> * VAN DER WAALS = -27.8545 ELECTROSTATIC = -53.2095 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3321" Parameter: CONF_N -> "8002" Comparing "3321" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3322" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766809 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761406 ATOM PAIRS WERE FOUND FOR ATOM LIST 42042 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29472 from a total of 761406 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3322 -75.02127 -6.04266 0.65847 INTE EXTERN> -28.25809 -46.76317 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0213" Parameter: A <- "-75.0213" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2581" Parameter: B <- "-28.2581" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7632" Parameter: C <- "-46.7632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3322 TOTAL ENERGY = -75.0213 RDTITL> * VAN DER WAALS = -28.2581 ELECTROSTATIC = -46.7632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3322" Parameter: CONF_N -> "8002" Comparing "3322" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3323" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761406 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762688 ATOM PAIRS WERE FOUND FOR ATOM LIST 42040 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29828 from a total of 762688 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3323 -78.42304 3.40178 0.64561 INTE EXTERN> -29.59342 -48.82962 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.423" Parameter: A <- "-78.423" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5934" Parameter: B <- "-29.5934" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8296" Parameter: C <- "-48.8296" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3323 TOTAL ENERGY = -78.423 RDTITL> * VAN DER WAALS = -29.5934 ELECTROSTATIC = -48.8296 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3323" Parameter: CONF_N -> "8002" Comparing "3323" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3324" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762688 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759255 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29313 from a total of 759255 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3324 -75.68524 -2.73780 0.59793 INTE EXTERN> -27.95449 -47.73075 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6852" Parameter: A <- "-75.6852" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9545" Parameter: B <- "-27.9545" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7307" Parameter: C <- "-47.7307" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3324 TOTAL ENERGY = -75.6852 RDTITL> * VAN DER WAALS = -27.9545 ELECTROSTATIC = -47.7307 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3324" Parameter: CONF_N -> "8002" Comparing "3324" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3325" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759255 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755494 ATOM PAIRS WERE FOUND FOR ATOM LIST 41725 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30032 from a total of 755494 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3325 -72.88854 -2.79670 0.65341 INTE EXTERN> -27.99418 -44.89436 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8885" Parameter: A <- "-72.8885" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9942" Parameter: B <- "-27.9942" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8944" Parameter: C <- "-44.8944" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3325 TOTAL ENERGY = -72.8885 RDTITL> * VAN DER WAALS = -27.9942 ELECTROSTATIC = -44.8944 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3325" Parameter: CONF_N -> "8002" Comparing "3325" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3326" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755494 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757463 ATOM PAIRS WERE FOUND FOR ATOM LIST 41746 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29076 from a total of 757463 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3326 -81.45385 8.56531 0.62431 INTE EXTERN> -28.93144 -52.52240 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4538" Parameter: A <- "-81.4538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9314" Parameter: B <- "-28.9314" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5224" Parameter: C <- "-52.5224" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3326 TOTAL ENERGY = -81.4538 RDTITL> * VAN DER WAALS = -28.9314 ELECTROSTATIC = -52.5224 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3326" Parameter: CONF_N -> "8002" Comparing "3326" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3327" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757463 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762345 ATOM PAIRS WERE FOUND FOR ATOM LIST 42022 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29413 from a total of 762345 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3327 -72.77712 -8.67673 0.67700 INTE EXTERN> -26.52731 -46.24981 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7771" Parameter: A <- "-72.7771" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5273" Parameter: B <- "-26.5273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2498" Parameter: C <- "-46.2498" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3327 TOTAL ENERGY = -72.7771 RDTITL> * VAN DER WAALS = -26.5273 ELECTROSTATIC = -46.2498 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3327" Parameter: CONF_N -> "8002" Comparing "3327" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3328" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762345 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762308 ATOM PAIRS WERE FOUND FOR ATOM LIST 41899 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28662 from a total of 762308 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3328 -78.39774 5.62062 0.59697 INTE EXTERN> -31.38703 -47.01071 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3977" Parameter: A <- "-78.3977" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.387" Parameter: B <- "-31.387" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0107" Parameter: C <- "-47.0107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3328 TOTAL ENERGY = -78.3977 RDTITL> * VAN DER WAALS = -31.387 ELECTROSTATIC = -47.0107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3328" Parameter: CONF_N -> "8002" Comparing "3328" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3329" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762308 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752606 ATOM PAIRS WERE FOUND FOR ATOM LIST 41603 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28921 from a total of 752606 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3329 -74.76967 -3.62808 0.59361 INTE EXTERN> -27.74936 -47.02030 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7697" Parameter: A <- "-74.7697" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7494" Parameter: B <- "-27.7494" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0203" Parameter: C <- "-47.0203" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3329 TOTAL ENERGY = -74.7697 RDTITL> * VAN DER WAALS = -27.7494 ELECTROSTATIC = -47.0203 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3329" Parameter: CONF_N -> "8002" Comparing "3329" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3330" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752606 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755323 ATOM PAIRS WERE FOUND FOR ATOM LIST 41838 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29210 from a total of 755323 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3330 -70.99050 -3.77917 0.69877 INTE EXTERN> -22.66936 -48.32113 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9905" Parameter: A <- "-70.9905" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.6694" Parameter: B <- "-22.6694" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3211" Parameter: C <- "-48.3211" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3330 TOTAL ENERGY = -70.9905 RDTITL> * VAN DER WAALS = -22.6694 ELECTROSTATIC = -48.3211 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3330" Parameter: CONF_N -> "8002" Comparing "3330" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3331" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755323 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758477 ATOM PAIRS WERE FOUND FOR ATOM LIST 42007 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29006 from a total of 758477 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3331 -77.98387 6.99337 0.78509 INTE EXTERN> -20.16611 -57.81775 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9839" Parameter: A <- "-77.9839" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.1661" Parameter: B <- "-20.1661" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.8178" Parameter: C <- "-57.8178" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3331 TOTAL ENERGY = -77.9839 RDTITL> * VAN DER WAALS = -20.1661 ELECTROSTATIC = -57.8178 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3331" Parameter: CONF_N -> "8002" Comparing "3331" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3332" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758477 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756973 ATOM PAIRS WERE FOUND FOR ATOM LIST 41845 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29027 from a total of 756973 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3332 -72.75287 -5.23100 0.82622 INTE EXTERN> -24.10075 -48.65212 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7529" Parameter: A <- "-72.7529" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1007" Parameter: B <- "-24.1007" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6521" Parameter: C <- "-48.6521" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3332 TOTAL ENERGY = -72.7529 RDTITL> * VAN DER WAALS = -24.1007 ELECTROSTATIC = -48.6521 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3332" Parameter: CONF_N -> "8002" Comparing "3332" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3333" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756973 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761354 ATOM PAIRS WERE FOUND FOR ATOM LIST 42134 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29426 from a total of 761354 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3333 -74.55055 1.79768 0.71126 INTE EXTERN> -29.51896 -45.03159 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5505" Parameter: A <- "-74.5505" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.519" Parameter: B <- "-29.519" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0316" Parameter: C <- "-45.0316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3333 TOTAL ENERGY = -74.5505 RDTITL> * VAN DER WAALS = -29.519 ELECTROSTATIC = -45.0316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3333" Parameter: CONF_N -> "8002" Comparing "3333" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3334" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761354 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753645 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29194 from a total of 753645 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3334 -80.40598 5.85543 0.69353 INTE EXTERN> -27.53285 -52.87312 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.406" Parameter: A <- "-80.406" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5329" Parameter: B <- "-27.5329" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8731" Parameter: C <- "-52.8731" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3334 TOTAL ENERGY = -80.406 RDTITL> * VAN DER WAALS = -27.5329 ELECTROSTATIC = -52.8731 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3334" Parameter: CONF_N -> "8002" Comparing "3334" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3335" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753645 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753623 ATOM PAIRS WERE FOUND FOR ATOM LIST 41579 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29242 from a total of 753623 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3335 -72.87262 -7.53336 0.70437 INTE EXTERN> -26.57750 -46.29511 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8726" Parameter: A <- "-72.8726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5775" Parameter: B <- "-26.5775" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2951" Parameter: C <- "-46.2951" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3335 TOTAL ENERGY = -72.8726 RDTITL> * VAN DER WAALS = -26.5775 ELECTROSTATIC = -46.2951 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3335" Parameter: CONF_N -> "8002" Comparing "3335" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3336" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753623 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757308 ATOM PAIRS WERE FOUND FOR ATOM LIST 41899 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29382 from a total of 757308 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3336 -78.86440 5.99178 0.62312 INTE EXTERN> -30.46895 -48.39545 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8644" Parameter: A <- "-78.8644" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4689" Parameter: B <- "-30.4689" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3954" Parameter: C <- "-48.3954" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3336 TOTAL ENERGY = -78.8644 RDTITL> * VAN DER WAALS = -30.4689 ELECTROSTATIC = -48.3954 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3336" Parameter: CONF_N -> "8002" Comparing "3336" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3337" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757308 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757100 ATOM PAIRS WERE FOUND FOR ATOM LIST 41854 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28968 from a total of 757100 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3337 -73.85542 -5.00898 0.66841 INTE EXTERN> -26.86789 -46.98753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8554" Parameter: A <- "-73.8554" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8679" Parameter: B <- "-26.8679" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9875" Parameter: C <- "-46.9875" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3337 TOTAL ENERGY = -73.8554 RDTITL> * VAN DER WAALS = -26.8679 ELECTROSTATIC = -46.9875 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3337" Parameter: CONF_N -> "8002" Comparing "3337" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3338" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757100 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757683 ATOM PAIRS WERE FOUND FOR ATOM LIST 41796 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29608 from a total of 757683 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3338 -68.42493 -5.43049 0.60539 INTE EXTERN> -32.39285 -36.03208 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4249" Parameter: A <- "-68.4249" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3928" Parameter: B <- "-32.3928" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0321" Parameter: C <- "-36.0321" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3338 TOTAL ENERGY = -68.4249 RDTITL> * VAN DER WAALS = -32.3928 ELECTROSTATIC = -36.0321 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3338" Parameter: CONF_N -> "8002" Comparing "3338" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3339" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757683 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757312 ATOM PAIRS WERE FOUND FOR ATOM LIST 41651 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29315 from a total of 757312 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3339 -63.67048 -4.75444 0.45292 INTE EXTERN> -33.50120 -30.16928 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6705" Parameter: A <- "-63.6705" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5012" Parameter: B <- "-33.5012" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.1693" Parameter: C <- "-30.1693" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3339 TOTAL ENERGY = -63.6705 RDTITL> * VAN DER WAALS = -33.5012 ELECTROSTATIC = -30.1693 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3339" Parameter: CONF_N -> "8002" Comparing "3339" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3340" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757312 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755357 ATOM PAIRS WERE FOUND FOR ATOM LIST 41711 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29646 from a total of 755357 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3340 -70.83932 7.16884 0.59383 INTE EXTERN> -30.01418 -40.82514 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8393" Parameter: A <- "-70.8393" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0142" Parameter: B <- "-30.0142" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8251" Parameter: C <- "-40.8251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3340 TOTAL ENERGY = -70.8393 RDTITL> * VAN DER WAALS = -30.0142 ELECTROSTATIC = -40.8251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3340" Parameter: CONF_N -> "8002" Comparing "3340" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3341" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755357 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761820 ATOM PAIRS WERE FOUND FOR ATOM LIST 42058 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30360 from a total of 761820 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3341 -69.96878 -0.87054 0.59072 INTE EXTERN> -30.66963 -39.29915 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9688" Parameter: A <- "-69.9688" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6696" Parameter: B <- "-30.6696" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2991" Parameter: C <- "-39.2991" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3341 TOTAL ENERGY = -69.9688 RDTITL> * VAN DER WAALS = -30.6696 ELECTROSTATIC = -39.2991 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3341" Parameter: CONF_N -> "8002" Comparing "3341" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3342" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761820 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756925 ATOM PAIRS WERE FOUND FOR ATOM LIST 41731 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30179 from a total of 756925 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3342 -68.12588 -1.84289 0.61139 INTE EXTERN> -29.39184 -38.73404 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1259" Parameter: A <- "-68.1259" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3918" Parameter: B <- "-29.3918" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.734" Parameter: C <- "-38.734" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3342 TOTAL ENERGY = -68.1259 RDTITL> * VAN DER WAALS = -29.3918 ELECTROSTATIC = -38.734 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3342" Parameter: CONF_N -> "8002" Comparing "3342" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3343" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756925 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748431 ATOM PAIRS WERE FOUND FOR ATOM LIST 41163 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29768 from a total of 748431 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3343 -68.85738 0.73150 0.57774 INTE EXTERN> -31.91717 -36.94021 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8574" Parameter: A <- "-68.8574" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9172" Parameter: B <- "-31.9172" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9402" Parameter: C <- "-36.9402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3343 TOTAL ENERGY = -68.8574 RDTITL> * VAN DER WAALS = -31.9172 ELECTROSTATIC = -36.9402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3343" Parameter: CONF_N -> "8002" Comparing "3343" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3344" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748431 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755354 ATOM PAIRS WERE FOUND FOR ATOM LIST 41608 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30030 from a total of 755354 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3344 -69.76401 0.90663 0.69565 INTE EXTERN> -29.19594 -40.56807 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.764" Parameter: A <- "-69.764" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1959" Parameter: B <- "-29.1959" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5681" Parameter: C <- "-40.5681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3344 TOTAL ENERGY = -69.764 RDTITL> * VAN DER WAALS = -29.1959 ELECTROSTATIC = -40.5681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3344" Parameter: CONF_N -> "8002" Comparing "3344" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3345" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755354 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41505 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28974 from a total of 751110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3345 -69.79524 0.03123 0.68217 INTE EXTERN> -29.38782 -40.40742 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7952" Parameter: A <- "-69.7952" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3878" Parameter: B <- "-29.3878" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4074" Parameter: C <- "-40.4074" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3345 TOTAL ENERGY = -69.7952 RDTITL> * VAN DER WAALS = -29.3878 ELECTROSTATIC = -40.4074 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3345" Parameter: CONF_N -> "8002" Comparing "3345" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3346" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761416 ATOM PAIRS WERE FOUND FOR ATOM LIST 41991 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29695 from a total of 761416 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3346 -71.45215 1.65691 0.66096 INTE EXTERN> -30.07303 -41.37913 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4522" Parameter: A <- "-71.4522" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.073" Parameter: B <- "-30.073" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3791" Parameter: C <- "-41.3791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3346 TOTAL ENERGY = -71.4522 RDTITL> * VAN DER WAALS = -30.073 ELECTROSTATIC = -41.3791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3346" Parameter: CONF_N -> "8002" Comparing "3346" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3347" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761416 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759352 ATOM PAIRS WERE FOUND FOR ATOM LIST 41739 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29441 from a total of 759352 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3347 -69.32472 -2.12743 0.65980 INTE EXTERN> -27.03857 -42.28615 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3247" Parameter: A <- "-69.3247" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0386" Parameter: B <- "-27.0386" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2862" Parameter: C <- "-42.2862" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3347 TOTAL ENERGY = -69.3247 RDTITL> * VAN DER WAALS = -27.0386 ELECTROSTATIC = -42.2862 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3347" Parameter: CONF_N -> "8002" Comparing "3347" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3348" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759352 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752666 ATOM PAIRS WERE FOUND FOR ATOM LIST 41440 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29437 from a total of 752666 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3348 -62.64049 -6.68423 0.61639 INTE EXTERN> -27.74849 -34.89200 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.6405" Parameter: A <- "-62.6405" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7485" Parameter: B <- "-27.7485" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.892" Parameter: C <- "-34.892" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3348 TOTAL ENERGY = -62.6405 RDTITL> * VAN DER WAALS = -27.7485 ELECTROSTATIC = -34.892 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3348" Parameter: CONF_N -> "8002" Comparing "3348" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3349" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752666 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755905 ATOM PAIRS WERE FOUND FOR ATOM LIST 41520 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29890 from a total of 755905 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3349 -73.67830 11.03780 0.65861 INTE EXTERN> -28.65677 -45.02152 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6783" Parameter: A <- "-73.6783" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6568" Parameter: B <- "-28.6568" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0215" Parameter: C <- "-45.0215" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3349 TOTAL ENERGY = -73.6783 RDTITL> * VAN DER WAALS = -28.6568 ELECTROSTATIC = -45.0215 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3349" Parameter: CONF_N -> "8002" Comparing "3349" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3350" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755905 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755261 ATOM PAIRS WERE FOUND FOR ATOM LIST 41511 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29771 from a total of 755261 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3350 -71.29809 -2.38021 0.63161 INTE EXTERN> -30.15384 -41.14425 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2981" Parameter: A <- "-71.2981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1538" Parameter: B <- "-30.1538" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1442" Parameter: C <- "-41.1442" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3350 TOTAL ENERGY = -71.2981 RDTITL> * VAN DER WAALS = -30.1538 ELECTROSTATIC = -41.1442 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3350" Parameter: CONF_N -> "8002" Comparing "3350" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3351" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755261 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754844 ATOM PAIRS WERE FOUND FOR ATOM LIST 41424 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29459 from a total of 754844 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3351 -68.89715 -2.40094 0.64974 INTE EXTERN> -30.14636 -38.75079 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8972" Parameter: A <- "-68.8972" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1464" Parameter: B <- "-30.1464" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7508" Parameter: C <- "-38.7508" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3351 TOTAL ENERGY = -68.8972 RDTITL> * VAN DER WAALS = -30.1464 ELECTROSTATIC = -38.7508 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3351" Parameter: CONF_N -> "8002" Comparing "3351" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3352" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754844 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760037 ATOM PAIRS WERE FOUND FOR ATOM LIST 41832 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30111 from a total of 760037 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3352 -69.78716 0.89001 0.56294 INTE EXTERN> -32.69247 -37.09470 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7872" Parameter: A <- "-69.7872" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6925" Parameter: B <- "-32.6925" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0947" Parameter: C <- "-37.0947" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3352 TOTAL ENERGY = -69.7872 RDTITL> * VAN DER WAALS = -32.6925 ELECTROSTATIC = -37.0947 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3352" Parameter: CONF_N -> "8002" Comparing "3352" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3353" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760037 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763614 ATOM PAIRS WERE FOUND FOR ATOM LIST 41977 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29546 from a total of 763614 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3353 -68.10107 -1.68610 0.64122 INTE EXTERN> -30.83847 -37.26259 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1011" Parameter: A <- "-68.1011" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8385" Parameter: B <- "-30.8385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2626" Parameter: C <- "-37.2626" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3353 TOTAL ENERGY = -68.1011 RDTITL> * VAN DER WAALS = -30.8385 ELECTROSTATIC = -37.2626 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3353" Parameter: CONF_N -> "8002" Comparing "3353" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3354" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763614 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763140 ATOM PAIRS WERE FOUND FOR ATOM LIST 42012 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29612 from a total of 763140 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3354 -75.47991 7.37885 0.65657 INTE EXTERN> -30.29721 -45.18270 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4799" Parameter: A <- "-75.4799" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2972" Parameter: B <- "-30.2972" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1827" Parameter: C <- "-45.1827" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3354 TOTAL ENERGY = -75.4799 RDTITL> * VAN DER WAALS = -30.2972 ELECTROSTATIC = -45.1827 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3354" Parameter: CONF_N -> "8002" Comparing "3354" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3355" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763140 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754565 ATOM PAIRS WERE FOUND FOR ATOM LIST 41861 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29317 from a total of 754565 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3355 -72.98219 -2.49772 0.61746 INTE EXTERN> -33.80472 -39.17747 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9822" Parameter: A <- "-72.9822" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8047" Parameter: B <- "-33.8047" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1775" Parameter: C <- "-39.1775" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3355 TOTAL ENERGY = -72.9822 RDTITL> * VAN DER WAALS = -33.8047 ELECTROSTATIC = -39.1775 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3355" Parameter: CONF_N -> "8002" Comparing "3355" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3356" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754565 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757327 ATOM PAIRS WERE FOUND FOR ATOM LIST 41673 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29551 from a total of 757327 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3356 -70.61011 -2.37208 0.62199 INTE EXTERN> -29.86704 -40.74307 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6101" Parameter: A <- "-70.6101" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.867" Parameter: B <- "-29.867" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7431" Parameter: C <- "-40.7431" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3356 TOTAL ENERGY = -70.6101 RDTITL> * VAN DER WAALS = -29.867 ELECTROSTATIC = -40.7431 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3356" Parameter: CONF_N -> "8002" Comparing "3356" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3357" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757327 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755981 ATOM PAIRS WERE FOUND FOR ATOM LIST 41641 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29160 from a total of 755981 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3357 -75.48573 4.87562 0.57383 INTE EXTERN> -33.28357 -42.20216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4857" Parameter: A <- "-75.4857" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2836" Parameter: B <- "-33.2836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2022" Parameter: C <- "-42.2022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3357 TOTAL ENERGY = -75.4857 RDTITL> * VAN DER WAALS = -33.2836 ELECTROSTATIC = -42.2022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3357" Parameter: CONF_N -> "8002" Comparing "3357" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3358" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755981 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763109 ATOM PAIRS WERE FOUND FOR ATOM LIST 41800 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30271 from a total of 763109 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3358 -67.92536 -7.56037 0.69906 INTE EXTERN> -28.48722 -39.43814 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9254" Parameter: A <- "-67.9254" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4872" Parameter: B <- "-28.4872" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4381" Parameter: C <- "-39.4381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3358 TOTAL ENERGY = -67.9254 RDTITL> * VAN DER WAALS = -28.4872 ELECTROSTATIC = -39.4381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3358" Parameter: CONF_N -> "8002" Comparing "3358" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3359" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763109 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764600 ATOM PAIRS WERE FOUND FOR ATOM LIST 42107 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30162 from a total of 764600 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3359 -69.62398 1.69862 0.75852 INTE EXTERN> -24.12166 -45.50232 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.624" Parameter: A <- "-69.624" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1217" Parameter: B <- "-24.1217" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5023" Parameter: C <- "-45.5023" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3359 TOTAL ENERGY = -69.624 RDTITL> * VAN DER WAALS = -24.1217 ELECTROSTATIC = -45.5023 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3359" Parameter: CONF_N -> "8002" Comparing "3359" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3360" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764600 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760995 ATOM PAIRS WERE FOUND FOR ATOM LIST 41922 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29624 from a total of 760995 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3360 -74.09458 4.47060 0.66534 INTE EXTERN> -28.67860 -45.41598 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0946" Parameter: A <- "-74.0946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6786" Parameter: B <- "-28.6786" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.416" Parameter: C <- "-45.416" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3360 TOTAL ENERGY = -74.0946 RDTITL> * VAN DER WAALS = -28.6786 ELECTROSTATIC = -45.416 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3360" Parameter: CONF_N -> "8002" Comparing "3360" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3361" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760995 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761364 ATOM PAIRS WERE FOUND FOR ATOM LIST 41860 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29494 from a total of 761364 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3361 -72.59558 -1.49900 0.68493 INTE EXTERN> -27.91775 -44.67782 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5956" Parameter: A <- "-72.5956" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9178" Parameter: B <- "-27.9178" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6778" Parameter: C <- "-44.6778" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3361 TOTAL ENERGY = -72.5956 RDTITL> * VAN DER WAALS = -27.9178 ELECTROSTATIC = -44.6778 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3361" Parameter: CONF_N -> "8002" Comparing "3361" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3362" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761364 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763611 ATOM PAIRS WERE FOUND FOR ATOM LIST 41993 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29739 from a total of 763611 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3362 -78.06642 5.47084 0.60652 INTE EXTERN> -33.21863 -44.84779 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0664" Parameter: A <- "-78.0664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2186" Parameter: B <- "-33.2186" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8478" Parameter: C <- "-44.8478" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3362 TOTAL ENERGY = -78.0664 RDTITL> * VAN DER WAALS = -33.2186 ELECTROSTATIC = -44.8478 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3362" Parameter: CONF_N -> "8002" Comparing "3362" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3363" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763611 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757531 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29005 from a total of 757531 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3363 -75.24277 -2.82365 0.70162 INTE EXTERN> -28.34385 -46.89892 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2428" Parameter: A <- "-75.2428" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3438" Parameter: B <- "-28.3438" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8989" Parameter: C <- "-46.8989" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3363 TOTAL ENERGY = -75.2428 RDTITL> * VAN DER WAALS = -28.3438 ELECTROSTATIC = -46.8989 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3363" Parameter: CONF_N -> "8002" Comparing "3363" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3364" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757531 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41857 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29882 from a total of 760601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3364 -68.42611 -6.81666 0.68528 INTE EXTERN> -26.01971 -42.40639 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4261" Parameter: A <- "-68.4261" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0197" Parameter: B <- "-26.0197" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4064" Parameter: C <- "-42.4064" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3364 TOTAL ENERGY = -68.4261 RDTITL> * VAN DER WAALS = -26.0197 ELECTROSTATIC = -42.4064 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3364" Parameter: CONF_N -> "8002" Comparing "3364" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3365" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764246 ATOM PAIRS WERE FOUND FOR ATOM LIST 42129 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29413 from a total of 764246 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3365 -70.78624 2.36014 0.77027 INTE EXTERN> -24.17794 -46.60831 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7862" Parameter: A <- "-70.7862" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1779" Parameter: B <- "-24.1779" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6083" Parameter: C <- "-46.6083" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3365 TOTAL ENERGY = -70.7862 RDTITL> * VAN DER WAALS = -24.1779 ELECTROSTATIC = -46.6083 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3365" Parameter: CONF_N -> "8002" Comparing "3365" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3366" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764246 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763978 ATOM PAIRS WERE FOUND FOR ATOM LIST 42009 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30070 from a total of 763978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3366 -77.51848 6.73224 0.62596 INTE EXTERN> -30.91001 -46.60848 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5185" Parameter: A <- "-77.5185" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.91" Parameter: B <- "-30.91" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6085" Parameter: C <- "-46.6085" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3366 TOTAL ENERGY = -77.5185 RDTITL> * VAN DER WAALS = -30.91 ELECTROSTATIC = -46.6085 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3366" Parameter: CONF_N -> "8002" Comparing "3366" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3367" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754852 ATOM PAIRS WERE FOUND FOR ATOM LIST 41589 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29415 from a total of 754852 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3367 -66.93366 -10.58482 0.60248 INTE EXTERN> -29.25056 -37.68310 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9337" Parameter: A <- "-66.9337" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2506" Parameter: B <- "-29.2506" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6831" Parameter: C <- "-37.6831" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3367 TOTAL ENERGY = -66.9337 RDTITL> * VAN DER WAALS = -29.2506 ELECTROSTATIC = -37.6831 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3367" Parameter: CONF_N -> "8002" Comparing "3367" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3368" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754852 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762444 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29892 from a total of 762444 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3368 -65.64047 -1.29320 0.54082 INTE EXTERN> -32.48209 -33.15838 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6405" Parameter: A <- "-65.6405" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4821" Parameter: B <- "-32.4821" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1584" Parameter: C <- "-33.1584" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3368 TOTAL ENERGY = -65.6405 RDTITL> * VAN DER WAALS = -32.4821 ELECTROSTATIC = -33.1584 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3368" Parameter: CONF_N -> "8002" Comparing "3368" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3369" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762444 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753896 ATOM PAIRS WERE FOUND FOR ATOM LIST 41529 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29824 from a total of 753896 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3369 -67.30847 1.66800 0.62180 INTE EXTERN> -30.55325 -36.75521 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3085" Parameter: A <- "-67.3085" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5533" Parameter: B <- "-30.5533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7552" Parameter: C <- "-36.7552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3369 TOTAL ENERGY = -67.3085 RDTITL> * VAN DER WAALS = -30.5533 ELECTROSTATIC = -36.7552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3369" Parameter: CONF_N -> "8002" Comparing "3369" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3370" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753896 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757392 ATOM PAIRS WERE FOUND FOR ATOM LIST 41533 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29636 from a total of 757392 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3370 -75.39896 8.09049 0.67153 INTE EXTERN> -29.03280 -46.36615 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.399" Parameter: A <- "-75.399" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0328" Parameter: B <- "-29.0328" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3662" Parameter: C <- "-46.3662" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3370 TOTAL ENERGY = -75.399 RDTITL> * VAN DER WAALS = -29.0328 ELECTROSTATIC = -46.3662 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3370" Parameter: CONF_N -> "8002" Comparing "3370" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3371" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757392 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765225 ATOM PAIRS WERE FOUND FOR ATOM LIST 42084 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29494 from a total of 765225 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3371 -71.34486 -4.05410 0.64124 INTE EXTERN> -30.28810 -41.05676 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3449" Parameter: A <- "-71.3449" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2881" Parameter: B <- "-30.2881" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0568" Parameter: C <- "-41.0568" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3371 TOTAL ENERGY = -71.3449 RDTITL> * VAN DER WAALS = -30.2881 ELECTROSTATIC = -41.0568 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3371" Parameter: CONF_N -> "8002" Comparing "3371" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3372" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765225 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761036 ATOM PAIRS WERE FOUND FOR ATOM LIST 41760 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29536 from a total of 761036 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3372 -70.24537 -1.09949 0.61078 INTE EXTERN> -28.97184 -41.27354 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2454" Parameter: A <- "-70.2454" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9718" Parameter: B <- "-28.9718" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2735" Parameter: C <- "-41.2735" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3372 TOTAL ENERGY = -70.2454 RDTITL> * VAN DER WAALS = -28.9718 ELECTROSTATIC = -41.2735 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3372" Parameter: CONF_N -> "8002" Comparing "3372" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3373" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761036 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761327 ATOM PAIRS WERE FOUND FOR ATOM LIST 41759 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29058 from a total of 761327 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3373 -72.85056 2.60519 0.65369 INTE EXTERN> -28.18130 -44.66926 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8506" Parameter: A <- "-72.8506" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1813" Parameter: B <- "-28.1813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6693" Parameter: C <- "-44.6693" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3373 TOTAL ENERGY = -72.8506 RDTITL> * VAN DER WAALS = -28.1813 ELECTROSTATIC = -44.6693 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3373" Parameter: CONF_N -> "8002" Comparing "3373" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3374" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761327 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760721 ATOM PAIRS WERE FOUND FOR ATOM LIST 41793 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29476 from a total of 760721 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3374 -70.91427 -1.93629 0.58417 INTE EXTERN> -31.26835 -39.64591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9143" Parameter: A <- "-70.9143" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2684" Parameter: B <- "-31.2684" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6459" Parameter: C <- "-39.6459" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3374 TOTAL ENERGY = -70.9143 RDTITL> * VAN DER WAALS = -31.2684 ELECTROSTATIC = -39.6459 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3374" Parameter: CONF_N -> "8002" Comparing "3374" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3375" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760721 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761816 ATOM PAIRS WERE FOUND FOR ATOM LIST 41915 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28617 from a total of 761816 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3375 -58.79477 -12.11949 0.53874 INTE EXTERN> -29.75028 -29.04450 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.7948" Parameter: A <- "-58.7948" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7503" Parameter: B <- "-29.7503" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.0445" Parameter: C <- "-29.0445" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3375 TOTAL ENERGY = -58.7948 RDTITL> * VAN DER WAALS = -29.7503 ELECTROSTATIC = -29.0445 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3375" Parameter: CONF_N -> "8002" Comparing "3375" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3376" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761816 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767070 ATOM PAIRS WERE FOUND FOR ATOM LIST 42140 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29689 from a total of 767070 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3376 -63.09795 4.30317 0.70053 INTE EXTERN> -25.93684 -37.16111 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.0979" Parameter: A <- "-63.0979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9368" Parameter: B <- "-25.9368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1611" Parameter: C <- "-37.1611" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3376 TOTAL ENERGY = -63.0979 RDTITL> * VAN DER WAALS = -25.9368 ELECTROSTATIC = -37.1611 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3376" Parameter: CONF_N -> "8002" Comparing "3376" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3377" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767070 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760365 ATOM PAIRS WERE FOUND FOR ATOM LIST 41931 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29781 from a total of 760365 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3377 -70.94054 7.84260 0.76302 INTE EXTERN> -23.65598 -47.28456 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9405" Parameter: A <- "-70.9405" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.656" Parameter: B <- "-23.656" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2846" Parameter: C <- "-47.2846" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3377 TOTAL ENERGY = -70.9405 RDTITL> * VAN DER WAALS = -23.656 ELECTROSTATIC = -47.2846 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3377" Parameter: CONF_N -> "8002" Comparing "3377" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3378" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760365 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29788 from a total of 758526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3378 -75.13414 4.19360 0.67629 INTE EXTERN> -28.52140 -46.61274 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1341" Parameter: A <- "-75.1341" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5214" Parameter: B <- "-28.5214" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6127" Parameter: C <- "-46.6127" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3378 TOTAL ENERGY = -75.1341 RDTITL> * VAN DER WAALS = -28.5214 ELECTROSTATIC = -46.6127 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3378" Parameter: CONF_N -> "8002" Comparing "3378" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3379" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763281 ATOM PAIRS WERE FOUND FOR ATOM LIST 41913 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29025 from a total of 763281 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3379 -76.86659 1.73245 0.71947 INTE EXTERN> -26.20695 -50.65964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8666" Parameter: A <- "-76.8666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2069" Parameter: B <- "-26.2069" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6596" Parameter: C <- "-50.6596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3379 TOTAL ENERGY = -76.8666 RDTITL> * VAN DER WAALS = -26.2069 ELECTROSTATIC = -50.6596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3379" Parameter: CONF_N -> "8002" Comparing "3379" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3380" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763281 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763687 ATOM PAIRS WERE FOUND FOR ATOM LIST 42195 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29774 from a total of 763687 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3380 -76.78706 -0.07953 0.56320 INTE EXTERN> -32.95321 -43.83385 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7871" Parameter: A <- "-76.7871" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9532" Parameter: B <- "-32.9532" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8338" Parameter: C <- "-43.8338" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3380 TOTAL ENERGY = -76.7871 RDTITL> * VAN DER WAALS = -32.9532 ELECTROSTATIC = -43.8338 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3380" Parameter: CONF_N -> "8002" Comparing "3380" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3381" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763687 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764029 ATOM PAIRS WERE FOUND FOR ATOM LIST 42174 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28837 from a total of 764029 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3381 -80.88051 4.09345 0.70947 INTE EXTERN> -27.00678 -53.87373 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.8805" Parameter: A <- "-80.8805" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0068" Parameter: B <- "-27.0068" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8737" Parameter: C <- "-53.8737" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3381 TOTAL ENERGY = -80.8805 RDTITL> * VAN DER WAALS = -27.0068 ELECTROSTATIC = -53.8737 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3381" Parameter: CONF_N -> "8002" Comparing "3381" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3382" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764029 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765819 ATOM PAIRS WERE FOUND FOR ATOM LIST 42202 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29134 from a total of 765819 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3382 -82.26502 1.38451 0.76197 INTE EXTERN> -25.60367 -56.66135 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.265" Parameter: A <- "-82.265" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6037" Parameter: B <- "-25.6037" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.6614" Parameter: C <- "-56.6614" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3382 TOTAL ENERGY = -82.265 RDTITL> * VAN DER WAALS = -25.6037 ELECTROSTATIC = -56.6614 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3382" Parameter: CONF_N -> "8002" Comparing "3382" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3383" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765819 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763912 ATOM PAIRS WERE FOUND FOR ATOM LIST 42140 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28951 from a total of 763912 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3383 -74.32495 -7.94007 0.61998 INTE EXTERN> -28.58890 -45.73605 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.325" Parameter: A <- "-74.325" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5889" Parameter: B <- "-28.5889" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.736" Parameter: C <- "-45.736" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3383 TOTAL ENERGY = -74.325 RDTITL> * VAN DER WAALS = -28.5889 ELECTROSTATIC = -45.736 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3383" Parameter: CONF_N -> "8002" Comparing "3383" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3384" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763912 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766058 ATOM PAIRS WERE FOUND FOR ATOM LIST 42059 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29319 from a total of 766058 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3384 -78.57767 4.25272 0.62581 INTE EXTERN> -29.10772 -49.46994 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5777" Parameter: A <- "-78.5777" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1077" Parameter: B <- "-29.1077" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4699" Parameter: C <- "-49.4699" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3384 TOTAL ENERGY = -78.5777 RDTITL> * VAN DER WAALS = -29.1077 ELECTROSTATIC = -49.4699 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3384" Parameter: CONF_N -> "8002" Comparing "3384" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3385" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766058 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766377 ATOM PAIRS WERE FOUND FOR ATOM LIST 42266 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29732 from a total of 766377 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3385 -80.44381 1.86614 0.74486 INTE EXTERN> -24.60577 -55.83804 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4438" Parameter: A <- "-80.4438" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6058" Parameter: B <- "-24.6058" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.838" Parameter: C <- "-55.838" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3385 TOTAL ENERGY = -80.4438 RDTITL> * VAN DER WAALS = -24.6058 ELECTROSTATIC = -55.838 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3385" Parameter: CONF_N -> "8002" Comparing "3385" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3386" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766377 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763131 ATOM PAIRS WERE FOUND FOR ATOM LIST 41979 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29242 from a total of 763131 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3386 -78.61900 -1.82481 0.58974 INTE EXTERN> -31.16950 -47.44950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.619" Parameter: A <- "-78.619" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1695" Parameter: B <- "-31.1695" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4495" Parameter: C <- "-47.4495" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3386 TOTAL ENERGY = -78.619 RDTITL> * VAN DER WAALS = -31.1695 ELECTROSTATIC = -47.4495 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3386" Parameter: CONF_N -> "8002" Comparing "3386" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3387" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763131 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764510 ATOM PAIRS WERE FOUND FOR ATOM LIST 42091 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29034 from a total of 764510 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3387 -79.09009 0.47108 0.59279 INTE EXTERN> -32.04837 -47.04172 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0901" Parameter: A <- "-79.0901" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0484" Parameter: B <- "-32.0484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0417" Parameter: C <- "-47.0417" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3387 TOTAL ENERGY = -79.0901 RDTITL> * VAN DER WAALS = -32.0484 ELECTROSTATIC = -47.0417 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3387" Parameter: CONF_N -> "8002" Comparing "3387" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3388" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764510 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766216 ATOM PAIRS WERE FOUND FOR ATOM LIST 42127 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30196 from a total of 766216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3388 -85.15722 6.06713 0.72712 INTE EXTERN> -28.21475 -56.94247 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.1572" Parameter: A <- "-85.1572" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2148" Parameter: B <- "-28.2148" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.9425" Parameter: C <- "-56.9425" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3388 TOTAL ENERGY = -85.1572 RDTITL> * VAN DER WAALS = -28.2148 ELECTROSTATIC = -56.9425 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3388" Parameter: CONF_N -> "8002" Comparing "3388" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3389" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763984 ATOM PAIRS WERE FOUND FOR ATOM LIST 42083 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29952 from a total of 763984 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3389 -81.13821 -4.01901 0.80373 INTE EXTERN> -24.29901 -56.83919 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1382" Parameter: A <- "-81.1382" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.299" Parameter: B <- "-24.299" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.8392" Parameter: C <- "-56.8392" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3389 TOTAL ENERGY = -81.1382 RDTITL> * VAN DER WAALS = -24.299 ELECTROSTATIC = -56.8392 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3389" Parameter: CONF_N -> "8002" Comparing "3389" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3390" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763984 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762983 ATOM PAIRS WERE FOUND FOR ATOM LIST 42086 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29195 from a total of 762983 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3390 -82.36857 1.23036 0.75464 INTE EXTERN> -28.57226 -53.79631 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3686" Parameter: A <- "-82.3686" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5723" Parameter: B <- "-28.5723" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.7963" Parameter: C <- "-53.7963" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3390 TOTAL ENERGY = -82.3686 RDTITL> * VAN DER WAALS = -28.5723 ELECTROSTATIC = -53.7963 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3390" Parameter: CONF_N -> "8002" Comparing "3390" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3391" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762983 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758099 ATOM PAIRS WERE FOUND FOR ATOM LIST 41543 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29270 from a total of 758099 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3391 -82.28461 -0.08396 0.69387 INTE EXTERN> -24.90235 -57.38226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.2846" Parameter: A <- "-82.2846" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9023" Parameter: B <- "-24.9023" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.3823" Parameter: C <- "-57.3823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3391 TOTAL ENERGY = -82.2846 RDTITL> * VAN DER WAALS = -24.9023 ELECTROSTATIC = -57.3823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3391" Parameter: CONF_N -> "8002" Comparing "3391" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3392" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758099 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760878 ATOM PAIRS WERE FOUND FOR ATOM LIST 41831 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29277 from a total of 760878 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3392 -85.05053 2.76593 0.65997 INTE EXTERN> -27.53363 -57.51690 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.0505" Parameter: A <- "-85.0505" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5336" Parameter: B <- "-27.5336" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.5169" Parameter: C <- "-57.5169" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3392 TOTAL ENERGY = -85.0505 RDTITL> * VAN DER WAALS = -27.5336 ELECTROSTATIC = -57.5169 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3392" Parameter: CONF_N -> "8002" Comparing "3392" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3393" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760878 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763828 ATOM PAIRS WERE FOUND FOR ATOM LIST 42161 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28832 from a total of 763828 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3393 -80.95663 -4.09391 0.72675 INTE EXTERN> -26.67512 -54.28151 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9566" Parameter: A <- "-80.9566" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6751" Parameter: B <- "-26.6751" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2815" Parameter: C <- "-54.2815" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3393 TOTAL ENERGY = -80.9566 RDTITL> * VAN DER WAALS = -26.6751 ELECTROSTATIC = -54.2815 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3393" Parameter: CONF_N -> "8002" Comparing "3393" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3394" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763828 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761431 ATOM PAIRS WERE FOUND FOR ATOM LIST 41816 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29329 from a total of 761431 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3394 -82.36521 1.40858 0.82883 INTE EXTERN> -26.16803 -56.19718 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3652" Parameter: A <- "-82.3652" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.168" Parameter: B <- "-26.168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.1972" Parameter: C <- "-56.1972" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3394 TOTAL ENERGY = -82.3652 RDTITL> * VAN DER WAALS = -26.168 ELECTROSTATIC = -56.1972 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3394" Parameter: CONF_N -> "8002" Comparing "3394" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3395" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761431 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763674 ATOM PAIRS WERE FOUND FOR ATOM LIST 41889 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28375 from a total of 763674 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3395 -70.80266 -11.56254 0.62810 INTE EXTERN> -28.37299 -42.42968 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8027" Parameter: A <- "-70.8027" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.373" Parameter: B <- "-28.373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4297" Parameter: C <- "-42.4297" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3395 TOTAL ENERGY = -70.8027 RDTITL> * VAN DER WAALS = -28.373 ELECTROSTATIC = -42.4297 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3395" Parameter: CONF_N -> "8002" Comparing "3395" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3396" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763674 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763509 ATOM PAIRS WERE FOUND FOR ATOM LIST 42079 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29086 from a total of 763509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3396 -82.98257 12.17991 0.73101 INTE EXTERN> -27.69604 -55.28653 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9826" Parameter: A <- "-82.9826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.696" Parameter: B <- "-27.696" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.2865" Parameter: C <- "-55.2865" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3396 TOTAL ENERGY = -82.9826 RDTITL> * VAN DER WAALS = -27.696 ELECTROSTATIC = -55.2865 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3396" Parameter: CONF_N -> "8002" Comparing "3396" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3397" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760733 ATOM PAIRS WERE FOUND FOR ATOM LIST 41979 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28635 from a total of 760733 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3397 -82.88544 -0.09713 0.69123 INTE EXTERN> -29.71588 -53.16957 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.8854" Parameter: A <- "-82.8854" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7159" Parameter: B <- "-29.7159" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.1696" Parameter: C <- "-53.1696" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3397 TOTAL ENERGY = -82.8854 RDTITL> * VAN DER WAALS = -29.7159 ELECTROSTATIC = -53.1696 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3397" Parameter: CONF_N -> "8002" Comparing "3397" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3398" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760733 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764069 ATOM PAIRS WERE FOUND FOR ATOM LIST 41905 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29590 from a total of 764069 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3398 -72.66654 -10.21890 0.71088 INTE EXTERN> -25.92370 -46.74284 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6665" Parameter: A <- "-72.6665" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9237" Parameter: B <- "-25.9237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7428" Parameter: C <- "-46.7428" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3398 TOTAL ENERGY = -72.6665 RDTITL> * VAN DER WAALS = -25.9237 ELECTROSTATIC = -46.7428 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3398" Parameter: CONF_N -> "8002" Comparing "3398" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3399" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764069 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762219 ATOM PAIRS WERE FOUND FOR ATOM LIST 42077 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29305 from a total of 762219 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3399 -76.75465 4.08811 0.75827 INTE EXTERN> -26.66616 -50.08848 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7546" Parameter: A <- "-76.7546" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6662" Parameter: B <- "-26.6662" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0885" Parameter: C <- "-50.0885" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3399 TOTAL ENERGY = -76.7546 RDTITL> * VAN DER WAALS = -26.6662 ELECTROSTATIC = -50.0885 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3399" Parameter: CONF_N -> "8002" Comparing "3399" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3400" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762219 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757805 ATOM PAIRS WERE FOUND FOR ATOM LIST 41924 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28575 from a total of 757805 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3400 -88.41476 11.66011 0.65436 INTE EXTERN> -32.09877 -56.31599 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.4148" Parameter: A <- "-88.4148" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0988" Parameter: B <- "-32.0988" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.316" Parameter: C <- "-56.316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3400 TOTAL ENERGY = -88.4148 RDTITL> * VAN DER WAALS = -32.0988 ELECTROSTATIC = -56.316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3400" Parameter: CONF_N -> "8002" Comparing "3400" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3401" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757805 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755988 ATOM PAIRS WERE FOUND FOR ATOM LIST 41614 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28915 from a total of 755988 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3401 -78.51374 -9.90102 0.78722 INTE EXTERN> -24.33637 -54.17737 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5137" Parameter: A <- "-78.5137" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3364" Parameter: B <- "-24.3364" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.1774" Parameter: C <- "-54.1774" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3401 TOTAL ENERGY = -78.5137 RDTITL> * VAN DER WAALS = -24.3364 ELECTROSTATIC = -54.1774 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3401" Parameter: CONF_N -> "8002" Comparing "3401" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3402" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755988 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764638 ATOM PAIRS WERE FOUND FOR ATOM LIST 42056 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28774 from a total of 764638 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3402 -71.31742 -7.19632 0.64787 INTE EXTERN> -29.89942 -41.41800 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3174" Parameter: A <- "-71.3174" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8994" Parameter: B <- "-29.8994" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.418" Parameter: C <- "-41.418" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3402 TOTAL ENERGY = -71.3174 RDTITL> * VAN DER WAALS = -29.8994 ELECTROSTATIC = -41.418 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3402" Parameter: CONF_N -> "8002" Comparing "3402" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3403" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764638 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760546 ATOM PAIRS WERE FOUND FOR ATOM LIST 41783 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29613 from a total of 760546 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3403 -76.12446 4.80704 0.58599 INTE EXTERN> -34.20667 -41.91779 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1245" Parameter: A <- "-76.1245" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.2067" Parameter: B <- "-34.2067" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9178" Parameter: C <- "-41.9178" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3403 TOTAL ENERGY = -76.1245 RDTITL> * VAN DER WAALS = -34.2067 ELECTROSTATIC = -41.9178 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3403" Parameter: CONF_N -> "8002" Comparing "3403" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3404" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760546 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761517 ATOM PAIRS WERE FOUND FOR ATOM LIST 41771 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29807 from a total of 761517 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3404 -74.66774 -1.45672 0.60104 INTE EXTERN> -31.39400 -43.27373 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6677" Parameter: A <- "-74.6677" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.394" Parameter: B <- "-31.394" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2737" Parameter: C <- "-43.2737" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3404 TOTAL ENERGY = -74.6677 RDTITL> * VAN DER WAALS = -31.394 ELECTROSTATIC = -43.2737 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3404" Parameter: CONF_N -> "8002" Comparing "3404" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3405" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761517 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761330 ATOM PAIRS WERE FOUND FOR ATOM LIST 41830 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29807 from a total of 761330 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3405 -79.50745 4.83971 0.64745 INTE EXTERN> -31.73127 -47.77618 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5074" Parameter: A <- "-79.5074" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7313" Parameter: B <- "-31.7313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7762" Parameter: C <- "-47.7762" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3405 TOTAL ENERGY = -79.5074 RDTITL> * VAN DER WAALS = -31.7313 ELECTROSTATIC = -47.7762 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3405" Parameter: CONF_N -> "8002" Comparing "3405" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3406" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761330 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763733 ATOM PAIRS WERE FOUND FOR ATOM LIST 42009 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28916 from a total of 763733 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3406 -76.34712 -3.16033 0.56698 INTE EXTERN> -32.89108 -43.45604 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3471" Parameter: A <- "-76.3471" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8911" Parameter: B <- "-32.8911" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.456" Parameter: C <- "-43.456" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3406 TOTAL ENERGY = -76.3471 RDTITL> * VAN DER WAALS = -32.8911 ELECTROSTATIC = -43.456 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3406" Parameter: CONF_N -> "8002" Comparing "3406" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3407" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763733 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763875 ATOM PAIRS WERE FOUND FOR ATOM LIST 42148 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29481 from a total of 763875 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3407 -75.44290 -0.90421 0.82990 INTE EXTERN> -22.46541 -52.97749 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4429" Parameter: A <- "-75.4429" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.4654" Parameter: B <- "-22.4654" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9775" Parameter: C <- "-52.9775" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3407 TOTAL ENERGY = -75.4429 RDTITL> * VAN DER WAALS = -22.4654 ELECTROSTATIC = -52.9775 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3407" Parameter: CONF_N -> "8002" Comparing "3407" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3408" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763875 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763234 ATOM PAIRS WERE FOUND FOR ATOM LIST 41957 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29561 from a total of 763234 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3408 -77.30788 1.86498 0.62609 INTE EXTERN> -30.87595 -46.43193 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3079" Parameter: A <- "-77.3079" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.876" Parameter: B <- "-30.876" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4319" Parameter: C <- "-46.4319" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3408 TOTAL ENERGY = -77.3079 RDTITL> * VAN DER WAALS = -30.876 ELECTROSTATIC = -46.4319 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3408" Parameter: CONF_N -> "8002" Comparing "3408" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3409" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763234 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757412 ATOM PAIRS WERE FOUND FOR ATOM LIST 41792 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29300 from a total of 757412 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3409 -69.83540 -7.47248 0.57902 INTE EXTERN> -31.47660 -38.35880 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8354" Parameter: A <- "-69.8354" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4766" Parameter: B <- "-31.4766" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3588" Parameter: C <- "-38.3588" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3409 TOTAL ENERGY = -69.8354 RDTITL> * VAN DER WAALS = -31.4766 ELECTROSTATIC = -38.3588 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3409" Parameter: CONF_N -> "8002" Comparing "3409" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3410" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757412 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763938 ATOM PAIRS WERE FOUND FOR ATOM LIST 42083 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29666 from a total of 763938 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3410 -79.92738 10.09198 0.74284 INTE EXTERN> -28.41491 -51.51247 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9274" Parameter: A <- "-79.9274" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4149" Parameter: B <- "-28.4149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5125" Parameter: C <- "-51.5125" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3410 TOTAL ENERGY = -79.9274 RDTITL> * VAN DER WAALS = -28.4149 ELECTROSTATIC = -51.5125 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3410" Parameter: CONF_N -> "8002" Comparing "3410" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3411" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763938 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755457 ATOM PAIRS WERE FOUND FOR ATOM LIST 41511 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29204 from a total of 755457 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3411 -80.08423 0.15685 0.64555 INTE EXTERN> -32.12470 -47.95954 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0842" Parameter: A <- "-80.0842" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1247" Parameter: B <- "-32.1247" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9595" Parameter: C <- "-47.9595" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3411 TOTAL ENERGY = -80.0842 RDTITL> * VAN DER WAALS = -32.1247 ELECTROSTATIC = -47.9595 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3411" Parameter: CONF_N -> "8002" Comparing "3411" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3412" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755457 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759952 ATOM PAIRS WERE FOUND FOR ATOM LIST 42010 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29683 from a total of 759952 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3412 -79.14266 -0.94157 0.63313 INTE EXTERN> -33.38115 -45.76151 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1427" Parameter: A <- "-79.1427" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3811" Parameter: B <- "-33.3811" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7615" Parameter: C <- "-45.7615" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3412 TOTAL ENERGY = -79.1427 RDTITL> * VAN DER WAALS = -33.3811 ELECTROSTATIC = -45.7615 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3412" Parameter: CONF_N -> "8002" Comparing "3412" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3413" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759952 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760414 ATOM PAIRS WERE FOUND FOR ATOM LIST 41945 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29840 from a total of 760414 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3413 -71.81064 -7.33202 0.60826 INTE EXTERN> -31.31055 -40.50009 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8106" Parameter: A <- "-71.8106" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3106" Parameter: B <- "-31.3106" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5001" Parameter: C <- "-40.5001" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3413 TOTAL ENERGY = -71.8106 RDTITL> * VAN DER WAALS = -31.3106 ELECTROSTATIC = -40.5001 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3413" Parameter: CONF_N -> "8002" Comparing "3413" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3414" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760414 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758805 ATOM PAIRS WERE FOUND FOR ATOM LIST 41767 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29057 from a total of 758805 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3414 -69.62843 -2.18221 0.65480 INTE EXTERN> -30.20485 -39.42359 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6284" Parameter: A <- "-69.6284" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2048" Parameter: B <- "-30.2048" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4236" Parameter: C <- "-39.4236" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3414 TOTAL ENERGY = -69.6284 RDTITL> * VAN DER WAALS = -30.2048 ELECTROSTATIC = -39.4236 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3414" Parameter: CONF_N -> "8002" Comparing "3414" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3415" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758805 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762463 ATOM PAIRS WERE FOUND FOR ATOM LIST 41944 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29285 from a total of 762463 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3415 -75.76504 6.13661 0.61445 INTE EXTERN> -32.02567 -43.73938 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.765" Parameter: A <- "-75.765" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0257" Parameter: B <- "-32.0257" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7394" Parameter: C <- "-43.7394" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3415 TOTAL ENERGY = -75.765 RDTITL> * VAN DER WAALS = -32.0257 ELECTROSTATIC = -43.7394 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3415" Parameter: CONF_N -> "8002" Comparing "3415" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3416" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762463 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757117 ATOM PAIRS WERE FOUND FOR ATOM LIST 41781 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29401 from a total of 757117 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3416 -75.78060 0.01556 0.58504 INTE EXTERN> -32.44012 -43.34048 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7806" Parameter: A <- "-75.7806" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4401" Parameter: B <- "-32.4401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3405" Parameter: C <- "-43.3405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3416 TOTAL ENERGY = -75.7806 RDTITL> * VAN DER WAALS = -32.4401 ELECTROSTATIC = -43.3405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3416" Parameter: CONF_N -> "8002" Comparing "3416" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3417" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757117 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761666 ATOM PAIRS WERE FOUND FOR ATOM LIST 41973 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30096 from a total of 761666 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3417 -75.29313 -0.48747 0.78116 INTE EXTERN> -23.42174 -51.87140 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2931" Parameter: A <- "-75.2931" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4217" Parameter: B <- "-23.4217" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8714" Parameter: C <- "-51.8714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3417 TOTAL ENERGY = -75.2931 RDTITL> * VAN DER WAALS = -23.4217 ELECTROSTATIC = -51.8714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3417" Parameter: CONF_N -> "8002" Comparing "3417" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3418" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761666 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762026 ATOM PAIRS WERE FOUND FOR ATOM LIST 41955 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29858 from a total of 762026 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3418 -72.77525 -2.51788 0.63729 INTE EXTERN> -28.22642 -44.54883 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7753" Parameter: A <- "-72.7753" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2264" Parameter: B <- "-28.2264" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5488" Parameter: C <- "-44.5488" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3418 TOTAL ENERGY = -72.7753 RDTITL> * VAN DER WAALS = -28.2264 ELECTROSTATIC = -44.5488 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3418" Parameter: CONF_N -> "8002" Comparing "3418" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3419" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762026 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760175 ATOM PAIRS WERE FOUND FOR ATOM LIST 41739 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29062 from a total of 760175 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3419 -78.36490 5.58964 0.58196 INTE EXTERN> -33.46662 -44.89828 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3649" Parameter: A <- "-78.3649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4666" Parameter: B <- "-33.4666" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8983" Parameter: C <- "-44.8983" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3419 TOTAL ENERGY = -78.3649 RDTITL> * VAN DER WAALS = -33.4666 ELECTROSTATIC = -44.8983 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3419" Parameter: CONF_N -> "8002" Comparing "3419" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3420" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760175 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764963 ATOM PAIRS WERE FOUND FOR ATOM LIST 42007 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29432 from a total of 764963 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3420 -66.41437 -11.95053 0.59347 INTE EXTERN> -31.14704 -35.26733 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4144" Parameter: A <- "-66.4144" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.147" Parameter: B <- "-31.147" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2673" Parameter: C <- "-35.2673" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3420 TOTAL ENERGY = -66.4144 RDTITL> * VAN DER WAALS = -31.147 ELECTROSTATIC = -35.2673 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3420" Parameter: CONF_N -> "8002" Comparing "3420" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3421" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764963 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760529 ATOM PAIRS WERE FOUND FOR ATOM LIST 41833 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29531 from a total of 760529 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3421 -73.60404 7.18967 0.56901 INTE EXTERN> -31.13878 -42.46526 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.604" Parameter: A <- "-73.604" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1388" Parameter: B <- "-31.1388" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4653" Parameter: C <- "-42.4653" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3421 TOTAL ENERGY = -73.604 RDTITL> * VAN DER WAALS = -31.1388 ELECTROSTATIC = -42.4653 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3421" Parameter: CONF_N -> "8002" Comparing "3421" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3422" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760529 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755349 ATOM PAIRS WERE FOUND FOR ATOM LIST 41645 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28871 from a total of 755349 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3422 -73.80721 0.20316 0.54939 INTE EXTERN> -32.48723 -41.31998 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8072" Parameter: A <- "-73.8072" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4872" Parameter: B <- "-32.4872" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.32" Parameter: C <- "-41.32" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3422 TOTAL ENERGY = -73.8072 RDTITL> * VAN DER WAALS = -32.4872 ELECTROSTATIC = -41.32 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3422" Parameter: CONF_N -> "8002" Comparing "3422" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3423" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755349 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754734 ATOM PAIRS WERE FOUND FOR ATOM LIST 41716 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28944 from a total of 754734 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3423 -70.99827 -2.80893 0.65283 INTE EXTERN> -28.88562 -42.11265 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9983" Parameter: A <- "-70.9983" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8856" Parameter: B <- "-28.8856" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1126" Parameter: C <- "-42.1126" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3423 TOTAL ENERGY = -70.9983 RDTITL> * VAN DER WAALS = -28.8856 ELECTROSTATIC = -42.1126 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3423" Parameter: CONF_N -> "8002" Comparing "3423" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3424" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754734 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756393 ATOM PAIRS WERE FOUND FOR ATOM LIST 41570 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28614 from a total of 756393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3424 -67.69761 -3.30066 0.54543 INTE EXTERN> -33.81285 -33.88476 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6976" Parameter: A <- "-67.6976" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8128" Parameter: B <- "-33.8128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8848" Parameter: C <- "-33.8848" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3424 TOTAL ENERGY = -67.6976 RDTITL> * VAN DER WAALS = -33.8128 ELECTROSTATIC = -33.8848 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3424" Parameter: CONF_N -> "8002" Comparing "3424" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3425" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749838 ATOM PAIRS WERE FOUND FOR ATOM LIST 41583 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28704 from a total of 749838 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3425 -74.82366 7.12605 0.56180 INTE EXTERN> -32.62127 -42.20239 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8237" Parameter: A <- "-74.8237" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6213" Parameter: B <- "-32.6213" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2024" Parameter: C <- "-42.2024" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3425 TOTAL ENERGY = -74.8237 RDTITL> * VAN DER WAALS = -32.6213 ELECTROSTATIC = -42.2024 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3425" Parameter: CONF_N -> "8002" Comparing "3425" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3426" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749838 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753268 ATOM PAIRS WERE FOUND FOR ATOM LIST 41417 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29176 from a total of 753268 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3426 -72.37856 -2.44510 0.54966 INTE EXTERN> -33.48782 -38.89073 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3786" Parameter: A <- "-72.3786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4878" Parameter: B <- "-33.4878" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8907" Parameter: C <- "-38.8907" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3426 TOTAL ENERGY = -72.3786 RDTITL> * VAN DER WAALS = -33.4878 ELECTROSTATIC = -38.8907 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3426" Parameter: CONF_N -> "8002" Comparing "3426" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3427" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753268 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755629 ATOM PAIRS WERE FOUND FOR ATOM LIST 41707 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28929 from a total of 755629 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3427 -70.38552 -1.99304 0.58546 INTE EXTERN> -31.82218 -38.56334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3855" Parameter: A <- "-70.3855" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8222" Parameter: B <- "-31.8222" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5633" Parameter: C <- "-38.5633" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3427 TOTAL ENERGY = -70.3855 RDTITL> * VAN DER WAALS = -31.8222 ELECTROSTATIC = -38.5633 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3427" Parameter: CONF_N -> "8002" Comparing "3427" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3428" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755629 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763391 ATOM PAIRS WERE FOUND FOR ATOM LIST 42018 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29344 from a total of 763391 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3428 -75.12603 4.74051 0.65862 INTE EXTERN> -30.97317 -44.15286 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.126" Parameter: A <- "-75.126" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9732" Parameter: B <- "-30.9732" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1529" Parameter: C <- "-44.1529" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3428 TOTAL ENERGY = -75.126 RDTITL> * VAN DER WAALS = -30.9732 ELECTROSTATIC = -44.1529 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3428" Parameter: CONF_N -> "8002" Comparing "3428" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3429" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763391 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765234 ATOM PAIRS WERE FOUND FOR ATOM LIST 42079 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29160 from a total of 765234 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3429 -71.79375 -3.33227 0.54498 INTE EXTERN> -32.81011 -38.98364 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7938" Parameter: A <- "-71.7938" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8101" Parameter: B <- "-32.8101" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9836" Parameter: C <- "-38.9836" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3429 TOTAL ENERGY = -71.7938 RDTITL> * VAN DER WAALS = -32.8101 ELECTROSTATIC = -38.9836 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3429" Parameter: CONF_N -> "8002" Comparing "3429" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3430" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765234 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757366 ATOM PAIRS WERE FOUND FOR ATOM LIST 41823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28709 from a total of 757366 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3430 -65.10874 -6.68501 0.60017 INTE EXTERN> -28.42952 -36.67922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1087" Parameter: A <- "-65.1087" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4295" Parameter: B <- "-28.4295" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6792" Parameter: C <- "-36.6792" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3430 TOTAL ENERGY = -65.1087 RDTITL> * VAN DER WAALS = -28.4295 ELECTROSTATIC = -36.6792 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3430" Parameter: CONF_N -> "8002" Comparing "3430" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3431" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757366 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755113 ATOM PAIRS WERE FOUND FOR ATOM LIST 41497 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28750 from a total of 755113 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3431 -70.19500 5.08626 0.61208 INTE EXTERN> -30.56933 -39.62567 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.195" Parameter: A <- "-70.195" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5693" Parameter: B <- "-30.5693" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6257" Parameter: C <- "-39.6257" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3431 TOTAL ENERGY = -70.195 RDTITL> * VAN DER WAALS = -30.5693 ELECTROSTATIC = -39.6257 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3431" Parameter: CONF_N -> "8002" Comparing "3431" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3432" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755113 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761239 ATOM PAIRS WERE FOUND FOR ATOM LIST 41731 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28870 from a total of 761239 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3432 -67.55525 -2.63975 0.75301 INTE EXTERN> -25.73391 -41.82134 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5553" Parameter: A <- "-67.5553" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7339" Parameter: B <- "-25.7339" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8213" Parameter: C <- "-41.8213" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3432 TOTAL ENERGY = -67.5553 RDTITL> * VAN DER WAALS = -25.7339 ELECTROSTATIC = -41.8213 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3432" Parameter: CONF_N -> "8002" Comparing "3432" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3433" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761239 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760306 ATOM PAIRS WERE FOUND FOR ATOM LIST 41831 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29356 from a total of 760306 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3433 -73.96998 6.41472 0.59039 INTE EXTERN> -30.65231 -43.31767 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.97" Parameter: A <- "-73.97" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6523" Parameter: B <- "-30.6523" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3177" Parameter: C <- "-43.3177" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3433 TOTAL ENERGY = -73.97 RDTITL> * VAN DER WAALS = -30.6523 ELECTROSTATIC = -43.3177 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3433" Parameter: CONF_N -> "8002" Comparing "3433" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3434" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760306 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765039 ATOM PAIRS WERE FOUND FOR ATOM LIST 42143 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29395 from a total of 765039 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3434 -74.22916 0.25919 0.70246 INTE EXTERN> -27.96246 -46.26670 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2292" Parameter: A <- "-74.2292" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9625" Parameter: B <- "-27.9625" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2667" Parameter: C <- "-46.2667" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3434 TOTAL ENERGY = -74.2292 RDTITL> * VAN DER WAALS = -27.9625 ELECTROSTATIC = -46.2667 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3434" Parameter: CONF_N -> "8002" Comparing "3434" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3435" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765039 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770165 ATOM PAIRS WERE FOUND FOR ATOM LIST 42277 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29778 from a total of 770165 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3435 -66.22207 -8.00709 0.53224 INTE EXTERN> -31.79897 -34.42310 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2221" Parameter: A <- "-66.2221" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.799" Parameter: B <- "-31.799" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4231" Parameter: C <- "-34.4231" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3435 TOTAL ENERGY = -66.2221 RDTITL> * VAN DER WAALS = -31.799 ELECTROSTATIC = -34.4231 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3435" Parameter: CONF_N -> "8002" Comparing "3435" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3436" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770165 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766652 ATOM PAIRS WERE FOUND FOR ATOM LIST 42316 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28776 from a total of 766652 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3436 -73.11643 6.89436 0.57056 INTE EXTERN> -31.45463 -41.66180 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1164" Parameter: A <- "-73.1164" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4546" Parameter: B <- "-31.4546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6618" Parameter: C <- "-41.6618" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3436 TOTAL ENERGY = -73.1164 RDTITL> * VAN DER WAALS = -31.4546 ELECTROSTATIC = -41.6618 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3436" Parameter: CONF_N -> "8002" Comparing "3436" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3437" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766652 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764771 ATOM PAIRS WERE FOUND FOR ATOM LIST 42223 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29571 from a total of 764771 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3437 -70.09762 -3.01881 0.65676 INTE EXTERN> -29.78162 -40.31600 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0976" Parameter: A <- "-70.0976" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7816" Parameter: B <- "-29.7816" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.316" Parameter: C <- "-40.316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3437 TOTAL ENERGY = -70.0976 RDTITL> * VAN DER WAALS = -29.7816 ELECTROSTATIC = -40.316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3437" Parameter: CONF_N -> "8002" Comparing "3437" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3438" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764771 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765527 ATOM PAIRS WERE FOUND FOR ATOM LIST 42205 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29597 from a total of 765527 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3438 -70.12797 0.03034 0.58129 INTE EXTERN> -31.08388 -39.04409 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.128" Parameter: A <- "-70.128" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0839" Parameter: B <- "-31.0839" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0441" Parameter: C <- "-39.0441" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3438 TOTAL ENERGY = -70.128 RDTITL> * VAN DER WAALS = -31.0839 ELECTROSTATIC = -39.0441 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3438" Parameter: CONF_N -> "8002" Comparing "3438" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3439" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765527 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766850 ATOM PAIRS WERE FOUND FOR ATOM LIST 42222 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29055 from a total of 766850 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3439 -71.73716 1.60919 0.62188 INTE EXTERN> -31.47957 -40.25759 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7372" Parameter: A <- "-71.7372" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4796" Parameter: B <- "-31.4796" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2576" Parameter: C <- "-40.2576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3439 TOTAL ENERGY = -71.7372 RDTITL> * VAN DER WAALS = -31.4796 ELECTROSTATIC = -40.2576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3439" Parameter: CONF_N -> "8002" Comparing "3439" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3440" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766850 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760837 ATOM PAIRS WERE FOUND FOR ATOM LIST 42040 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28741 from a total of 760837 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3440 -65.25149 -6.48568 0.62670 INTE EXTERN> -28.04672 -37.20477 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2515" Parameter: A <- "-65.2515" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0467" Parameter: B <- "-28.0467" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2048" Parameter: C <- "-37.2048" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3440 TOTAL ENERGY = -65.2515 RDTITL> * VAN DER WAALS = -28.0467 ELECTROSTATIC = -37.2048 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3440" Parameter: CONF_N -> "8002" Comparing "3440" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3441" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760837 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766877 ATOM PAIRS WERE FOUND FOR ATOM LIST 42262 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29649 from a total of 766877 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3441 -70.48044 5.22895 0.63829 INTE EXTERN> -29.26101 -41.21943 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4804" Parameter: A <- "-70.4804" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.261" Parameter: B <- "-29.261" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2194" Parameter: C <- "-41.2194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3441 TOTAL ENERGY = -70.4804 RDTITL> * VAN DER WAALS = -29.261 ELECTROSTATIC = -41.2194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3441" Parameter: CONF_N -> "8002" Comparing "3441" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3442" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766877 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764430 ATOM PAIRS WERE FOUND FOR ATOM LIST 42052 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29486 from a total of 764430 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3442 -70.43129 -0.04915 0.62300 INTE EXTERN> -30.33322 -40.09807 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4313" Parameter: A <- "-70.4313" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3332" Parameter: B <- "-30.3332" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0981" Parameter: C <- "-40.0981" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3442 TOTAL ENERGY = -70.4313 RDTITL> * VAN DER WAALS = -30.3332 ELECTROSTATIC = -40.0981 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3442" Parameter: CONF_N -> "8002" Comparing "3442" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3443" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764430 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758856 ATOM PAIRS WERE FOUND FOR ATOM LIST 41962 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29066 from a total of 758856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3443 -66.52125 -3.91005 0.52973 INTE EXTERN> -33.01079 -33.51046 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5212" Parameter: A <- "-66.5212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0108" Parameter: B <- "-33.0108" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.5105" Parameter: C <- "-33.5105" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3443 TOTAL ENERGY = -66.5212 RDTITL> * VAN DER WAALS = -33.0108 ELECTROSTATIC = -33.5105 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3443" Parameter: CONF_N -> "8002" Comparing "3443" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3444" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762744 ATOM PAIRS WERE FOUND FOR ATOM LIST 41962 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29682 from a total of 762744 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3444 -73.51587 6.99462 0.63307 INTE EXTERN> -29.64773 -43.86814 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5159" Parameter: A <- "-73.5159" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6477" Parameter: B <- "-29.6477" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8681" Parameter: C <- "-43.8681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3444 TOTAL ENERGY = -73.5159 RDTITL> * VAN DER WAALS = -29.6477 ELECTROSTATIC = -43.8681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3444" Parameter: CONF_N -> "8002" Comparing "3444" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3445" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762744 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757126 ATOM PAIRS WERE FOUND FOR ATOM LIST 41781 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28913 from a total of 757126 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3445 -64.84400 -8.67187 0.56507 INTE EXTERN> -31.92612 -32.91787 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.844" Parameter: A <- "-64.844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9261" Parameter: B <- "-31.9261" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.9179" Parameter: C <- "-32.9179" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3445 TOTAL ENERGY = -64.844 RDTITL> * VAN DER WAALS = -31.9261 ELECTROSTATIC = -32.9179 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3445" Parameter: CONF_N -> "8002" Comparing "3445" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3446" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757126 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760669 ATOM PAIRS WERE FOUND FOR ATOM LIST 41965 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29548 from a total of 760669 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3446 -61.99834 -2.84565 0.69137 INTE EXTERN> -26.46200 -35.53634 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.9983" Parameter: A <- "-61.9983" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.462" Parameter: B <- "-26.462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5363" Parameter: C <- "-35.5363" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3446 TOTAL ENERGY = -61.9983 RDTITL> * VAN DER WAALS = -26.462 ELECTROSTATIC = -35.5363 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3446" Parameter: CONF_N -> "8002" Comparing "3446" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3447" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760669 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765471 ATOM PAIRS WERE FOUND FOR ATOM LIST 42324 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29561 from a total of 765471 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3447 -63.03550 1.03716 0.64498 INTE EXTERN> -29.36233 -33.67317 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.0355" Parameter: A <- "-63.0355" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3623" Parameter: B <- "-29.3623" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6732" Parameter: C <- "-33.6732" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3447 TOTAL ENERGY = -63.0355 RDTITL> * VAN DER WAALS = -29.3623 ELECTROSTATIC = -33.6732 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3447" Parameter: CONF_N -> "8002" Comparing "3447" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3448" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765471 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767474 ATOM PAIRS WERE FOUND FOR ATOM LIST 42348 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29858 from a total of 767474 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3448 -72.94775 9.91225 0.71370 INTE EXTERN> -28.44593 -44.50182 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9478" Parameter: A <- "-72.9478" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4459" Parameter: B <- "-28.4459" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5018" Parameter: C <- "-44.5018" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3448 TOTAL ENERGY = -72.9478 RDTITL> * VAN DER WAALS = -28.4459 ELECTROSTATIC = -44.5018 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3448" Parameter: CONF_N -> "8002" Comparing "3448" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3449" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767474 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767347 ATOM PAIRS WERE FOUND FOR ATOM LIST 42381 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29393 from a total of 767347 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3449 -71.19145 -1.75630 0.61694 INTE EXTERN> -29.03998 -42.15147 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1914" Parameter: A <- "-71.1914" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.04" Parameter: B <- "-29.04" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1515" Parameter: C <- "-42.1515" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3449 TOTAL ENERGY = -71.1914 RDTITL> * VAN DER WAALS = -29.04 ELECTROSTATIC = -42.1515 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3449" Parameter: CONF_N -> "8002" Comparing "3449" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3450" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767347 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767231 ATOM PAIRS WERE FOUND FOR ATOM LIST 42398 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29510 from a total of 767231 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3450 -73.21680 2.02535 0.66376 INTE EXTERN> -30.00704 -43.20976 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2168" Parameter: A <- "-73.2168" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.007" Parameter: B <- "-30.007" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2098" Parameter: C <- "-43.2098" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3450 TOTAL ENERGY = -73.2168 RDTITL> * VAN DER WAALS = -30.007 ELECTROSTATIC = -43.2098 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3450" Parameter: CONF_N -> "8002" Comparing "3450" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3451" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767231 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765784 ATOM PAIRS WERE FOUND FOR ATOM LIST 42368 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29550 from a total of 765784 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3451 -73.17280 -0.04400 0.69188 INTE EXTERN> -27.89595 -45.27685 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1728" Parameter: A <- "-73.1728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8959" Parameter: B <- "-27.8959" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2768" Parameter: C <- "-45.2768" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3451 TOTAL ENERGY = -73.1728 RDTITL> * VAN DER WAALS = -27.8959 ELECTROSTATIC = -45.2768 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3451" Parameter: CONF_N -> "8002" Comparing "3451" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3452" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765784 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772053 ATOM PAIRS WERE FOUND FOR ATOM LIST 42439 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29554 from a total of 772053 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3452 -79.56637 6.39358 0.67132 INTE EXTERN> -30.45556 -49.11082 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5664" Parameter: A <- "-79.5664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4556" Parameter: B <- "-30.4556" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1108" Parameter: C <- "-49.1108" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3452 TOTAL ENERGY = -79.5664 RDTITL> * VAN DER WAALS = -30.4556 ELECTROSTATIC = -49.1108 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3452" Parameter: CONF_N -> "8002" Comparing "3452" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3453" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772053 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 772064 ATOM PAIRS WERE FOUND FOR ATOM LIST 42427 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30100 from a total of 772064 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3453 -70.46219 -9.10418 0.63936 INTE EXTERN> -30.51816 -39.94403 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4622" Parameter: A <- "-70.4622" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5182" Parameter: B <- "-30.5182" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.944" Parameter: C <- "-39.944" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3453 TOTAL ENERGY = -70.4622 RDTITL> * VAN DER WAALS = -30.5182 ELECTROSTATIC = -39.944 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3453" Parameter: CONF_N -> "8002" Comparing "3453" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3454" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 772064 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764904 ATOM PAIRS WERE FOUND FOR ATOM LIST 42208 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29126 from a total of 764904 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3454 -68.30945 -2.15274 0.62519 INTE EXTERN> -28.67818 -39.63127 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3095" Parameter: A <- "-68.3095" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6782" Parameter: B <- "-28.6782" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6313" Parameter: C <- "-39.6313" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3454 TOTAL ENERGY = -68.3095 RDTITL> * VAN DER WAALS = -28.6782 ELECTROSTATIC = -39.6313 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3454" Parameter: CONF_N -> "8002" Comparing "3454" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3455" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764904 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768095 ATOM PAIRS WERE FOUND FOR ATOM LIST 42451 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29542 from a total of 768095 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3455 -75.96836 7.65891 0.68915 INTE EXTERN> -26.47328 -49.49509 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9684" Parameter: A <- "-75.9684" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4733" Parameter: B <- "-26.4733" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4951" Parameter: C <- "-49.4951" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3455 TOTAL ENERGY = -75.9684 RDTITL> * VAN DER WAALS = -26.4733 ELECTROSTATIC = -49.4951 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3455" Parameter: CONF_N -> "8002" Comparing "3455" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3456" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768095 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767874 ATOM PAIRS WERE FOUND FOR ATOM LIST 42381 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29670 from a total of 767874 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3456 -73.30812 -2.66025 0.77006 INTE EXTERN> -25.14675 -48.16137 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3081" Parameter: A <- "-73.3081" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1467" Parameter: B <- "-25.1467" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1614" Parameter: C <- "-48.1614" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3456 TOTAL ENERGY = -73.3081 RDTITL> * VAN DER WAALS = -25.1467 ELECTROSTATIC = -48.1614 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3456" Parameter: CONF_N -> "8002" Comparing "3456" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3457" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767874 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767048 ATOM PAIRS WERE FOUND FOR ATOM LIST 42388 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30427 from a total of 767048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3457 -67.94066 -5.36746 0.59882 INTE EXTERN> -30.96752 -36.97314 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9407" Parameter: A <- "-67.9407" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9675" Parameter: B <- "-30.9675" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9731" Parameter: C <- "-36.9731" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3457 TOTAL ENERGY = -67.9407 RDTITL> * VAN DER WAALS = -30.9675 ELECTROSTATIC = -36.9731 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3457" Parameter: CONF_N -> "8002" Comparing "3457" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3458" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769468 ATOM PAIRS WERE FOUND FOR ATOM LIST 42422 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29521 from a total of 769468 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3458 -72.16118 4.22052 0.63790 INTE EXTERN> -27.99028 -44.17090 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1612" Parameter: A <- "-72.1612" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9903" Parameter: B <- "-27.9903" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1709" Parameter: C <- "-44.1709" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3458 TOTAL ENERGY = -72.1612 RDTITL> * VAN DER WAALS = -27.9903 ELECTROSTATIC = -44.1709 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3458" Parameter: CONF_N -> "8002" Comparing "3458" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3459" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769468 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763499 ATOM PAIRS WERE FOUND FOR ATOM LIST 42316 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29438 from a total of 763499 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3459 -75.72990 3.56872 0.61377 INTE EXTERN> -32.33061 -43.39929 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7299" Parameter: A <- "-75.7299" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3306" Parameter: B <- "-32.3306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3993" Parameter: C <- "-43.3993" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3459 TOTAL ENERGY = -75.7299 RDTITL> * VAN DER WAALS = -32.3306 ELECTROSTATIC = -43.3993 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3459" Parameter: CONF_N -> "8002" Comparing "3459" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3460" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763499 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761469 ATOM PAIRS WERE FOUND FOR ATOM LIST 41934 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29522 from a total of 761469 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3460 -71.72822 -4.00169 0.62134 INTE EXTERN> -29.77984 -41.94838 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7282" Parameter: A <- "-71.7282" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7798" Parameter: B <- "-29.7798" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9484" Parameter: C <- "-41.9484" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3460 TOTAL ENERGY = -71.7282 RDTITL> * VAN DER WAALS = -29.7798 ELECTROSTATIC = -41.9484 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3460" Parameter: CONF_N -> "8002" Comparing "3460" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3461" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761469 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759309 ATOM PAIRS WERE FOUND FOR ATOM LIST 42040 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28793 from a total of 759309 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3461 -61.26832 -10.45990 0.46307 INTE EXTERN> -34.18652 -27.08180 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.2683" Parameter: A <- "-61.2683" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1865" Parameter: B <- "-34.1865" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.0818" Parameter: C <- "-27.0818" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3461 TOTAL ENERGY = -61.2683 RDTITL> * VAN DER WAALS = -34.1865 ELECTROSTATIC = -27.0818 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3461" Parameter: CONF_N -> "8002" Comparing "3461" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3462" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759309 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764998 ATOM PAIRS WERE FOUND FOR ATOM LIST 42322 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29499 from a total of 764998 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3462 -71.48583 10.21751 0.57755 INTE EXTERN> -30.59625 -40.88959 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4858" Parameter: A <- "-71.4858" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5962" Parameter: B <- "-30.5962" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8896" Parameter: C <- "-40.8896" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3462 TOTAL ENERGY = -71.4858 RDTITL> * VAN DER WAALS = -30.5962 ELECTROSTATIC = -40.8896 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3462" Parameter: CONF_N -> "8002" Comparing "3462" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3463" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764998 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763886 ATOM PAIRS WERE FOUND FOR ATOM LIST 42215 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29024 from a total of 763886 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3463 -71.12710 -0.35873 0.60455 INTE EXTERN> -29.09057 -42.03653 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1271" Parameter: A <- "-71.1271" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0906" Parameter: B <- "-29.0906" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0365" Parameter: C <- "-42.0365" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3463 TOTAL ENERGY = -71.1271 RDTITL> * VAN DER WAALS = -29.0906 ELECTROSTATIC = -42.0365 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3463" Parameter: CONF_N -> "8002" Comparing "3463" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3464" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763886 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763264 ATOM PAIRS WERE FOUND FOR ATOM LIST 42163 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29680 from a total of 763264 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3464 -73.07841 1.95131 0.62535 INTE EXTERN> -29.72521 -43.35320 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0784" Parameter: A <- "-73.0784" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7252" Parameter: B <- "-29.7252" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3532" Parameter: C <- "-43.3532" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3464 TOTAL ENERGY = -73.0784 RDTITL> * VAN DER WAALS = -29.7252 ELECTROSTATIC = -43.3532 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3464" Parameter: CONF_N -> "8002" Comparing "3464" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3465" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763264 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770776 ATOM PAIRS WERE FOUND FOR ATOM LIST 42568 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29191 from a total of 770776 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3465 -70.54272 -2.53569 0.52107 INTE EXTERN> -33.73424 -36.80848 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5427" Parameter: A <- "-70.5427" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7342" Parameter: B <- "-33.7342" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8085" Parameter: C <- "-36.8085" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3465 TOTAL ENERGY = -70.5427 RDTITL> * VAN DER WAALS = -33.7342 ELECTROSTATIC = -36.8085 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3465" Parameter: CONF_N -> "8002" Comparing "3465" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3466" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770776 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768515 ATOM PAIRS WERE FOUND FOR ATOM LIST 42380 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29457 from a total of 768515 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3466 -70.71893 0.17621 0.68599 INTE EXTERN> -28.99915 -41.71978 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7189" Parameter: A <- "-70.7189" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9992" Parameter: B <- "-28.9992" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7198" Parameter: C <- "-41.7198" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3466 TOTAL ENERGY = -70.7189 RDTITL> * VAN DER WAALS = -28.9992 ELECTROSTATIC = -41.7198 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3466" Parameter: CONF_N -> "8002" Comparing "3466" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3467" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768515 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767584 ATOM PAIRS WERE FOUND FOR ATOM LIST 42215 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29557 from a total of 767584 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3467 -69.28394 -1.43499 0.53146 INTE EXTERN> -33.35969 -35.92425 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2839" Parameter: A <- "-69.2839" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3597" Parameter: B <- "-33.3597" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9242" Parameter: C <- "-35.9242" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3467 TOTAL ENERGY = -69.2839 RDTITL> * VAN DER WAALS = -33.3597 ELECTROSTATIC = -35.9242 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3467" Parameter: CONF_N -> "8002" Comparing "3467" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3468" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767584 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768105 ATOM PAIRS WERE FOUND FOR ATOM LIST 42355 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29562 from a total of 768105 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3468 -67.48038 -1.80356 0.53163 INTE EXTERN> -32.06281 -35.41757 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4804" Parameter: A <- "-67.4804" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0628" Parameter: B <- "-32.0628" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4176" Parameter: C <- "-35.4176" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3468 TOTAL ENERGY = -67.4804 RDTITL> * VAN DER WAALS = -32.0628 ELECTROSTATIC = -35.4176 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3468" Parameter: CONF_N -> "8002" Comparing "3468" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3469" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768105 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769339 ATOM PAIRS WERE FOUND FOR ATOM LIST 42459 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29659 from a total of 769339 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3469 -70.27311 2.79274 0.59058 INTE EXTERN> -32.20328 -38.06983 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2731" Parameter: A <- "-70.2731" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2033" Parameter: B <- "-32.2033" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0698" Parameter: C <- "-38.0698" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3469 TOTAL ENERGY = -70.2731 RDTITL> * VAN DER WAALS = -32.2033 ELECTROSTATIC = -38.0698 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3469" Parameter: CONF_N -> "8002" Comparing "3469" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3470" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769339 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765006 ATOM PAIRS WERE FOUND FOR ATOM LIST 42324 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29584 from a total of 765006 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3470 -72.22845 1.95534 0.59803 INTE EXTERN> -31.31584 -40.91261 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2285" Parameter: A <- "-72.2285" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3158" Parameter: B <- "-31.3158" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9126" Parameter: C <- "-40.9126" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3470 TOTAL ENERGY = -72.2285 RDTITL> * VAN DER WAALS = -31.3158 ELECTROSTATIC = -40.9126 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3470" Parameter: CONF_N -> "8002" Comparing "3470" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3471" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765006 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768824 ATOM PAIRS WERE FOUND FOR ATOM LIST 42377 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28871 from a total of 768824 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3471 -76.99798 4.76953 0.69248 INTE EXTERN> -28.94728 -48.05070 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.998" Parameter: A <- "-76.998" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9473" Parameter: B <- "-28.9473" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0507" Parameter: C <- "-48.0507" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3471 TOTAL ENERGY = -76.998 RDTITL> * VAN DER WAALS = -28.9473 ELECTROSTATIC = -48.0507 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3471" Parameter: CONF_N -> "8002" Comparing "3471" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3472" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768824 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766704 ATOM PAIRS WERE FOUND FOR ATOM LIST 42274 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28811 from a total of 766704 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3472 -69.45208 -7.54590 0.77810 INTE EXTERN> -23.68164 -45.77043 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4521" Parameter: A <- "-69.4521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6816" Parameter: B <- "-23.6816" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7704" Parameter: C <- "-45.7704" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3472 TOTAL ENERGY = -69.4521 RDTITL> * VAN DER WAALS = -23.6816 ELECTROSTATIC = -45.7704 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3472" Parameter: CONF_N -> "8002" Comparing "3472" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3473" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766704 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768411 ATOM PAIRS WERE FOUND FOR ATOM LIST 42265 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29217 from a total of 768411 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3473 -74.77294 5.32086 0.65321 INTE EXTERN> -29.91266 -44.86029 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7729" Parameter: A <- "-74.7729" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9127" Parameter: B <- "-29.9127" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8603" Parameter: C <- "-44.8603" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3473 TOTAL ENERGY = -74.7729 RDTITL> * VAN DER WAALS = -29.9127 ELECTROSTATIC = -44.8603 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3473" Parameter: CONF_N -> "8002" Comparing "3473" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3474" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768411 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768227 ATOM PAIRS WERE FOUND FOR ATOM LIST 42398 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29459 from a total of 768227 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3474 -72.22944 -2.54350 0.64245 INTE EXTERN> -30.43739 -41.79205 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2294" Parameter: A <- "-72.2294" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4374" Parameter: B <- "-30.4374" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7921" Parameter: C <- "-41.7921" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3474 TOTAL ENERGY = -72.2294 RDTITL> * VAN DER WAALS = -30.4374 ELECTROSTATIC = -41.7921 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3474" Parameter: CONF_N -> "8002" Comparing "3474" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3475" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768227 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767473 ATOM PAIRS WERE FOUND FOR ATOM LIST 42383 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29097 from a total of 767473 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3475 -70.23993 -1.98952 0.65494 INTE EXTERN> -29.28694 -40.95299 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2399" Parameter: A <- "-70.2399" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2869" Parameter: B <- "-29.2869" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.953" Parameter: C <- "-40.953" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3475 TOTAL ENERGY = -70.2399 RDTITL> * VAN DER WAALS = -29.2869 ELECTROSTATIC = -40.953 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3475" Parameter: CONF_N -> "8002" Comparing "3475" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3476" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767473 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767717 ATOM PAIRS WERE FOUND FOR ATOM LIST 42256 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29363 from a total of 767717 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3476 -70.72986 0.48993 0.65414 INTE EXTERN> -28.10324 -42.62662 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7299" Parameter: A <- "-70.7299" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1032" Parameter: B <- "-28.1032" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6266" Parameter: C <- "-42.6266" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3476 TOTAL ENERGY = -70.7299 RDTITL> * VAN DER WAALS = -28.1032 ELECTROSTATIC = -42.6266 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3476" Parameter: CONF_N -> "8002" Comparing "3476" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3477" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767717 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758722 ATOM PAIRS WERE FOUND FOR ATOM LIST 41951 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29556 from a total of 758722 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3477 -76.65962 5.92976 0.64796 INTE EXTERN> -30.70265 -45.95697 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6596" Parameter: A <- "-76.6596" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7026" Parameter: B <- "-30.7026" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.957" Parameter: C <- "-45.957" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3477 TOTAL ENERGY = -76.6596 RDTITL> * VAN DER WAALS = -30.7026 ELECTROSTATIC = -45.957 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3477" Parameter: CONF_N -> "8002" Comparing "3477" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3478" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758722 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768624 ATOM PAIRS WERE FOUND FOR ATOM LIST 42464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29252 from a total of 768624 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3478 -73.00395 -3.65567 0.69874 INTE EXTERN> -28.42675 -44.57720 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0039" Parameter: A <- "-73.0039" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4267" Parameter: B <- "-28.4267" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5772" Parameter: C <- "-44.5772" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3478 TOTAL ENERGY = -73.0039 RDTITL> * VAN DER WAALS = -28.4267 ELECTROSTATIC = -44.5772 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3478" Parameter: CONF_N -> "8002" Comparing "3478" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3479" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768624 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761269 ATOM PAIRS WERE FOUND FOR ATOM LIST 41944 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29432 from a total of 761269 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3479 -71.54265 -1.46130 0.59296 INTE EXTERN> -30.97075 -40.57189 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5426" Parameter: A <- "-71.5426" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9708" Parameter: B <- "-30.9708" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5719" Parameter: C <- "-40.5719" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3479 TOTAL ENERGY = -71.5426 RDTITL> * VAN DER WAALS = -30.9708 ELECTROSTATIC = -40.5719 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3479" Parameter: CONF_N -> "8002" Comparing "3479" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3480" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761269 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765140 ATOM PAIRS WERE FOUND FOR ATOM LIST 42354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29069 from a total of 765140 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3480 -81.65836 10.11571 0.65511 INTE EXTERN> -28.01395 -53.64441 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6584" Parameter: A <- "-81.6584" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.014" Parameter: B <- "-28.014" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6444" Parameter: C <- "-53.6444" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3480 TOTAL ENERGY = -81.6584 RDTITL> * VAN DER WAALS = -28.014 ELECTROSTATIC = -53.6444 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3480" Parameter: CONF_N -> "8002" Comparing "3480" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3481" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765140 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759509 ATOM PAIRS WERE FOUND FOR ATOM LIST 42138 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28800 from a total of 759509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3481 -79.15669 -2.50167 0.54638 INTE EXTERN> -33.80587 -45.35082 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1567" Parameter: A <- "-79.1567" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8059" Parameter: B <- "-33.8059" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3508" Parameter: C <- "-45.3508" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3481 TOTAL ENERGY = -79.1567 RDTITL> * VAN DER WAALS = -33.8059 ELECTROSTATIC = -45.3508 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3481" Parameter: CONF_N -> "8002" Comparing "3481" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3482" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762841 ATOM PAIRS WERE FOUND FOR ATOM LIST 42082 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29329 from a total of 762841 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3482 -74.01171 -5.14498 0.66397 INTE EXTERN> -29.70286 -44.30885 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0117" Parameter: A <- "-74.0117" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7029" Parameter: B <- "-29.7029" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3089" Parameter: C <- "-44.3089" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3482 TOTAL ENERGY = -74.0117 RDTITL> * VAN DER WAALS = -29.7029 ELECTROSTATIC = -44.3089 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3482" Parameter: CONF_N -> "8002" Comparing "3482" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3483" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762841 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766277 ATOM PAIRS WERE FOUND FOR ATOM LIST 42074 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28898 from a total of 766277 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3483 -74.96615 0.95444 0.59569 INTE EXTERN> -32.39348 -42.57267 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9662" Parameter: A <- "-74.9662" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3935" Parameter: B <- "-32.3935" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5727" Parameter: C <- "-42.5727" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3483 TOTAL ENERGY = -74.9662 RDTITL> * VAN DER WAALS = -32.3935 ELECTROSTATIC = -42.5727 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3483" Parameter: CONF_N -> "8002" Comparing "3483" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3484" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766277 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761916 ATOM PAIRS WERE FOUND FOR ATOM LIST 42034 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29250 from a total of 761916 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3484 -75.62225 0.65610 0.55811 INTE EXTERN> -33.39772 -42.22453 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6223" Parameter: A <- "-75.6223" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3977" Parameter: B <- "-33.3977" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2245" Parameter: C <- "-42.2245" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3484 TOTAL ENERGY = -75.6223 RDTITL> * VAN DER WAALS = -33.3977 ELECTROSTATIC = -42.2245 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3484" Parameter: CONF_N -> "8002" Comparing "3484" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3485" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761916 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756795 ATOM PAIRS WERE FOUND FOR ATOM LIST 41836 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29040 from a total of 756795 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3485 -72.59685 -3.02540 0.53481 INTE EXTERN> -33.28929 -39.30756 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5969" Parameter: A <- "-72.5969" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2893" Parameter: B <- "-33.2893" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3076" Parameter: C <- "-39.3076" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3485 TOTAL ENERGY = -72.5969 RDTITL> * VAN DER WAALS = -33.2893 ELECTROSTATIC = -39.3076 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3485" Parameter: CONF_N -> "8002" Comparing "3485" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3486" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756795 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755296 ATOM PAIRS WERE FOUND FOR ATOM LIST 41858 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28780 from a total of 755296 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3486 -67.36039 -5.23646 0.53098 INTE EXTERN> -30.01595 -37.34445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3604" Parameter: A <- "-67.3604" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0159" Parameter: B <- "-30.0159" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3444" Parameter: C <- "-37.3444" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3486 TOTAL ENERGY = -67.3604 RDTITL> * VAN DER WAALS = -30.0159 ELECTROSTATIC = -37.3444 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3486" Parameter: CONF_N -> "8002" Comparing "3486" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3487" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755296 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763454 ATOM PAIRS WERE FOUND FOR ATOM LIST 42090 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29379 from a total of 763454 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3487 -76.87259 9.51220 0.53692 INTE EXTERN> -31.89087 -44.98173 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8726" Parameter: A <- "-76.8726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8909" Parameter: B <- "-31.8909" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9817" Parameter: C <- "-44.9817" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3487 TOTAL ENERGY = -76.8726 RDTITL> * VAN DER WAALS = -31.8909 ELECTROSTATIC = -44.9817 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3487" Parameter: CONF_N -> "8002" Comparing "3487" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3488" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763454 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762452 ATOM PAIRS WERE FOUND FOR ATOM LIST 42194 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29132 from a total of 762452 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3488 -75.50881 -1.36378 0.78353 INTE EXTERN> -25.13952 -50.36929 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5088" Parameter: A <- "-75.5088" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1395" Parameter: B <- "-25.1395" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3693" Parameter: C <- "-50.3693" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3488 TOTAL ENERGY = -75.5088 RDTITL> * VAN DER WAALS = -25.1395 ELECTROSTATIC = -50.3693 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3488" Parameter: CONF_N -> "8002" Comparing "3488" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3489" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762452 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765238 ATOM PAIRS WERE FOUND FOR ATOM LIST 42317 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29540 from a total of 765238 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3489 -72.17688 -3.33193 0.57205 INTE EXTERN> -32.46364 -39.71324 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1769" Parameter: A <- "-72.1769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4636" Parameter: B <- "-32.4636" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7132" Parameter: C <- "-39.7132" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3489 TOTAL ENERGY = -72.1769 RDTITL> * VAN DER WAALS = -32.4636 ELECTROSTATIC = -39.7132 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3489" Parameter: CONF_N -> "8002" Comparing "3489" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3490" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765238 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767375 ATOM PAIRS WERE FOUND FOR ATOM LIST 42291 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29872 from a total of 767375 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3490 -70.17590 -2.00099 0.83029 INTE EXTERN> -26.28657 -43.88933 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1759" Parameter: A <- "-70.1759" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2866" Parameter: B <- "-26.2866" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8893" Parameter: C <- "-43.8893" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3490 TOTAL ENERGY = -70.1759 RDTITL> * VAN DER WAALS = -26.2866 ELECTROSTATIC = -43.8893 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3490" Parameter: CONF_N -> "8002" Comparing "3490" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3491" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767375 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762318 ATOM PAIRS WERE FOUND FOR ATOM LIST 42130 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29141 from a total of 762318 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3491 -69.59075 -0.58515 0.56419 INTE EXTERN> -31.31067 -38.28007 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5907" Parameter: A <- "-69.5907" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3107" Parameter: B <- "-31.3107" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2801" Parameter: C <- "-38.2801" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3491 TOTAL ENERGY = -69.5907 RDTITL> * VAN DER WAALS = -31.3107 ELECTROSTATIC = -38.2801 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3491" Parameter: CONF_N -> "8002" Comparing "3491" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3492" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762318 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760493 ATOM PAIRS WERE FOUND FOR ATOM LIST 41977 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29366 from a total of 760493 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3492 -74.53896 4.94821 0.59123 INTE EXTERN> -31.78832 -42.75063 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.539" Parameter: A <- "-74.539" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7883" Parameter: B <- "-31.7883" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7506" Parameter: C <- "-42.7506" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3492 TOTAL ENERGY = -74.539 RDTITL> * VAN DER WAALS = -31.7883 ELECTROSTATIC = -42.7506 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3492" Parameter: CONF_N -> "8002" Comparing "3492" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3493" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760493 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764410 ATOM PAIRS WERE FOUND FOR ATOM LIST 42328 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29290 from a total of 764410 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3493 -70.57461 -3.96434 0.55893 INTE EXTERN> -32.06128 -38.51333 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5746" Parameter: A <- "-70.5746" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0613" Parameter: B <- "-32.0613" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5133" Parameter: C <- "-38.5133" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3493 TOTAL ENERGY = -70.5746 RDTITL> * VAN DER WAALS = -32.0613 ELECTROSTATIC = -38.5133 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3493" Parameter: CONF_N -> "8002" Comparing "3493" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3494" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764410 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763616 ATOM PAIRS WERE FOUND FOR ATOM LIST 42192 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30071 from a total of 763616 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3494 -73.13451 2.55989 0.70561 INTE EXTERN> -27.68643 -45.44808 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1345" Parameter: A <- "-73.1345" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6864" Parameter: B <- "-27.6864" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4481" Parameter: C <- "-45.4481" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3494 TOTAL ENERGY = -73.1345 RDTITL> * VAN DER WAALS = -27.6864 ELECTROSTATIC = -45.4481 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3494" Parameter: CONF_N -> "8002" Comparing "3494" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3495" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763616 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769378 ATOM PAIRS WERE FOUND FOR ATOM LIST 42354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30358 from a total of 769378 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3495 -75.85036 2.71585 0.60023 INTE EXTERN> -31.27163 -44.57873 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8504" Parameter: A <- "-75.8504" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2716" Parameter: B <- "-31.2716" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5787" Parameter: C <- "-44.5787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3495 TOTAL ENERGY = -75.8504 RDTITL> * VAN DER WAALS = -31.2716 ELECTROSTATIC = -44.5787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3495" Parameter: CONF_N -> "8002" Comparing "3495" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3496" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769378 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759338 ATOM PAIRS WERE FOUND FOR ATOM LIST 41990 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30018 from a total of 759338 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3496 -75.32710 -0.52326 0.62095 INTE EXTERN> -31.03424 -44.29287 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3271" Parameter: A <- "-75.3271" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0342" Parameter: B <- "-31.0342" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2929" Parameter: C <- "-44.2929" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3496 TOTAL ENERGY = -75.3271 RDTITL> * VAN DER WAALS = -31.0342 ELECTROSTATIC = -44.2929 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3496" Parameter: CONF_N -> "8002" Comparing "3496" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3497" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759338 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761327 ATOM PAIRS WERE FOUND FOR ATOM LIST 42184 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29842 from a total of 761327 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3497 -81.57687 6.24977 0.72269 INTE EXTERN> -26.07124 -55.50563 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5769" Parameter: A <- "-81.5769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0712" Parameter: B <- "-26.0712" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.5056" Parameter: C <- "-55.5056" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3497 TOTAL ENERGY = -81.5769 RDTITL> * VAN DER WAALS = -26.0712 ELECTROSTATIC = -55.5056 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3497" Parameter: CONF_N -> "8002" Comparing "3497" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3498" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761327 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767307 ATOM PAIRS WERE FOUND FOR ATOM LIST 42468 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30043 from a total of 767307 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3498 -76.34910 -5.22777 0.56640 INTE EXTERN> -33.05466 -43.29445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3491" Parameter: A <- "-76.3491" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0547" Parameter: B <- "-33.0547" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2944" Parameter: C <- "-43.2944" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3498 TOTAL ENERGY = -76.3491 RDTITL> * VAN DER WAALS = -33.0547 ELECTROSTATIC = -43.2944 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3498" Parameter: CONF_N -> "8002" Comparing "3498" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3499" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767307 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763353 ATOM PAIRS WERE FOUND FOR ATOM LIST 42044 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30092 from a total of 763353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3499 -69.60683 -6.74228 0.52661 INTE EXTERN> -35.16464 -34.44219 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6068" Parameter: A <- "-69.6068" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.1646" Parameter: B <- "-35.1646" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4422" Parameter: C <- "-34.4422" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3499 TOTAL ENERGY = -69.6068 RDTITL> * VAN DER WAALS = -35.1646 ELECTROSTATIC = -34.4422 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3499" Parameter: CONF_N -> "8002" Comparing "3499" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3500" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760832 ATOM PAIRS WERE FOUND FOR ATOM LIST 41933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29421 from a total of 760832 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3500 -72.31164 2.70482 0.52524 INTE EXTERN> -33.35145 -38.96019 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3116" Parameter: A <- "-72.3116" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3515" Parameter: B <- "-33.3515" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9602" Parameter: C <- "-38.9602" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3500 TOTAL ENERGY = -72.3116 RDTITL> * VAN DER WAALS = -33.3515 ELECTROSTATIC = -38.9602 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3500" Parameter: CONF_N -> "8002" Comparing "3500" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3501" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760832 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768745 ATOM PAIRS WERE FOUND FOR ATOM LIST 42415 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29658 from a total of 768745 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3501 -73.38278 1.07114 0.56911 INTE EXTERN> -31.78364 -41.59914 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3828" Parameter: A <- "-73.3828" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7836" Parameter: B <- "-31.7836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5991" Parameter: C <- "-41.5991" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3501 TOTAL ENERGY = -73.3828 RDTITL> * VAN DER WAALS = -31.7836 ELECTROSTATIC = -41.5991 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3501" Parameter: CONF_N -> "8002" Comparing "3501" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3502" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768745 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765326 ATOM PAIRS WERE FOUND FOR ATOM LIST 42040 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29740 from a total of 765326 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3502 -74.61379 1.23101 0.75405 INTE EXTERN> -26.04637 -48.56742 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6138" Parameter: A <- "-74.6138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0464" Parameter: B <- "-26.0464" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5674" Parameter: C <- "-48.5674" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3502 TOTAL ENERGY = -74.6138 RDTITL> * VAN DER WAALS = -26.0464 ELECTROSTATIC = -48.5674 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3502" Parameter: CONF_N -> "8002" Comparing "3502" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3503" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765326 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768173 ATOM PAIRS WERE FOUND FOR ATOM LIST 42558 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30351 from a total of 768173 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3503 -71.71098 -2.90281 0.65141 INTE EXTERN> -27.88654 -43.82444 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.711" Parameter: A <- "-71.711" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8865" Parameter: B <- "-27.8865" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8244" Parameter: C <- "-43.8244" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3503 TOTAL ENERGY = -71.711 RDTITL> * VAN DER WAALS = -27.8865 ELECTROSTATIC = -43.8244 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3503" Parameter: CONF_N -> "8002" Comparing "3503" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3504" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768173 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765829 ATOM PAIRS WERE FOUND FOR ATOM LIST 42016 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29759 from a total of 765829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3504 -74.35728 2.64630 0.67505 INTE EXTERN> -29.65715 -44.70013 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3573" Parameter: A <- "-74.3573" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6572" Parameter: B <- "-29.6572" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7001" Parameter: C <- "-44.7001" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3504 TOTAL ENERGY = -74.3573 RDTITL> * VAN DER WAALS = -29.6572 ELECTROSTATIC = -44.7001 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3504" Parameter: CONF_N -> "8002" Comparing "3504" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3505" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769101 ATOM PAIRS WERE FOUND FOR ATOM LIST 42315 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29915 from a total of 769101 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3505 -75.06524 0.70795 0.62145 INTE EXTERN> -32.89773 -42.16750 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0652" Parameter: A <- "-75.0652" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8977" Parameter: B <- "-32.8977" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1675" Parameter: C <- "-42.1675" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3505 TOTAL ENERGY = -75.0652 RDTITL> * VAN DER WAALS = -32.8977 ELECTROSTATIC = -42.1675 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3505" Parameter: CONF_N -> "8002" Comparing "3505" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3506" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769101 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765761 ATOM PAIRS WERE FOUND FOR ATOM LIST 42531 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30342 from a total of 765761 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3506 -78.57691 3.51167 0.70718 INTE EXTERN> -26.90771 -51.66920 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5769" Parameter: A <- "-78.5769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9077" Parameter: B <- "-26.9077" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6692" Parameter: C <- "-51.6692" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3506 TOTAL ENERGY = -78.5769 RDTITL> * VAN DER WAALS = -26.9077 ELECTROSTATIC = -51.6692 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3506" Parameter: CONF_N -> "8002" Comparing "3506" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3507" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765761 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769046 ATOM PAIRS WERE FOUND FOR ATOM LIST 42636 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29622 from a total of 769046 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3507 -75.10504 -3.47187 0.72709 INTE EXTERN> -25.36594 -49.73909 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.105" Parameter: A <- "-75.105" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3659" Parameter: B <- "-25.3659" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7391" Parameter: C <- "-49.7391" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3507 TOTAL ENERGY = -75.105 RDTITL> * VAN DER WAALS = -25.3659 ELECTROSTATIC = -49.7391 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3507" Parameter: CONF_N -> "8002" Comparing "3507" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3508" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769046 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 773131 ATOM PAIRS WERE FOUND FOR ATOM LIST 42694 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30151 from a total of 773131 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3508 -69.71279 -5.39225 0.70518 INTE EXTERN> -27.30656 -42.40623 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7128" Parameter: A <- "-69.7128" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3066" Parameter: B <- "-27.3066" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4062" Parameter: C <- "-42.4062" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3508 TOTAL ENERGY = -69.7128 RDTITL> * VAN DER WAALS = -27.3066 ELECTROSTATIC = -42.4062 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3508" Parameter: CONF_N -> "8002" Comparing "3508" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3509" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 773131 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770960 ATOM PAIRS WERE FOUND FOR ATOM LIST 42348 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30137 from a total of 770960 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3509 -68.39614 -1.31665 0.56423 INTE EXTERN> -31.04671 -37.34943 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3961" Parameter: A <- "-68.3961" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0467" Parameter: B <- "-31.0467" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3494" Parameter: C <- "-37.3494" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3509 TOTAL ENERGY = -68.3961 RDTITL> * VAN DER WAALS = -31.0467 ELECTROSTATIC = -37.3494 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3509" Parameter: CONF_N -> "8002" Comparing "3509" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3510" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770960 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764528 ATOM PAIRS WERE FOUND FOR ATOM LIST 42108 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29402 from a total of 764528 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3510 -74.83655 6.44040 0.63117 INTE EXTERN> -28.49609 -46.34046 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8365" Parameter: A <- "-74.8365" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4961" Parameter: B <- "-28.4961" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3405" Parameter: C <- "-46.3405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3510 TOTAL ENERGY = -74.8365 RDTITL> * VAN DER WAALS = -28.4961 ELECTROSTATIC = -46.3405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3510" Parameter: CONF_N -> "8002" Comparing "3510" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3511" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764528 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762709 ATOM PAIRS WERE FOUND FOR ATOM LIST 42093 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29854 from a total of 762709 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3511 -77.57192 2.73537 0.65031 INTE EXTERN> -28.30073 -49.27119 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5719" Parameter: A <- "-77.5719" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3007" Parameter: B <- "-28.3007" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2712" Parameter: C <- "-49.2712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3511 TOTAL ENERGY = -77.5719 RDTITL> * VAN DER WAALS = -28.3007 ELECTROSTATIC = -49.2712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3511" Parameter: CONF_N -> "8002" Comparing "3511" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3512" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762709 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768318 ATOM PAIRS WERE FOUND FOR ATOM LIST 42214 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29688 from a total of 768318 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3512 -78.23295 0.66103 0.68226 INTE EXTERN> -27.63703 -50.59592 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2329" Parameter: A <- "-78.2329" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.637" Parameter: B <- "-27.637" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5959" Parameter: C <- "-50.5959" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3512 TOTAL ENERGY = -78.2329 RDTITL> * VAN DER WAALS = -27.637 ELECTROSTATIC = -50.5959 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3512" Parameter: CONF_N -> "8002" Comparing "3512" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3513" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768318 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761995 ATOM PAIRS WERE FOUND FOR ATOM LIST 42070 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28973 from a total of 761995 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3513 -79.53879 1.30584 0.63369 INTE EXTERN> -29.06750 -50.47128 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5388" Parameter: A <- "-79.5388" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0675" Parameter: B <- "-29.0675" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4713" Parameter: C <- "-50.4713" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3513 TOTAL ENERGY = -79.5388 RDTITL> * VAN DER WAALS = -29.0675 ELECTROSTATIC = -50.4713 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3513" Parameter: CONF_N -> "8002" Comparing "3513" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3514" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761995 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765874 ATOM PAIRS WERE FOUND FOR ATOM LIST 42248 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29120 from a total of 765874 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3514 -68.48513 -11.05365 0.61455 INTE EXTERN> -29.89691 -38.58823 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4851" Parameter: A <- "-68.4851" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8969" Parameter: B <- "-29.8969" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5882" Parameter: C <- "-38.5882" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3514 TOTAL ENERGY = -68.4851 RDTITL> * VAN DER WAALS = -29.8969 ELECTROSTATIC = -38.5882 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3514" Parameter: CONF_N -> "8002" Comparing "3514" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3515" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765874 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764234 ATOM PAIRS WERE FOUND FOR ATOM LIST 42108 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29557 from a total of 764234 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3515 -80.90536 12.42023 0.65905 INTE EXTERN> -30.22545 -50.67991 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9054" Parameter: A <- "-80.9054" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2255" Parameter: B <- "-30.2255" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6799" Parameter: C <- "-50.6799" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3515 TOTAL ENERGY = -80.9054 RDTITL> * VAN DER WAALS = -30.2255 ELECTROSTATIC = -50.6799 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3515" Parameter: CONF_N -> "8002" Comparing "3515" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3516" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764234 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765057 ATOM PAIRS WERE FOUND FOR ATOM LIST 42408 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29135 from a total of 765057 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3516 -73.26441 -7.64095 0.67270 INTE EXTERN> -28.50547 -44.75895 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2644" Parameter: A <- "-73.2644" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5055" Parameter: B <- "-28.5055" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7589" Parameter: C <- "-44.7589" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3516 TOTAL ENERGY = -73.2644 RDTITL> * VAN DER WAALS = -28.5055 ELECTROSTATIC = -44.7589 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3516" Parameter: CONF_N -> "8002" Comparing "3516" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3517" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765057 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753418 ATOM PAIRS WERE FOUND FOR ATOM LIST 41763 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28653 from a total of 753418 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3517 -71.15265 -2.11177 0.61332 INTE EXTERN> -28.51750 -42.63515 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1526" Parameter: A <- "-71.1526" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5175" Parameter: B <- "-28.5175" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6352" Parameter: C <- "-42.6352" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3517 TOTAL ENERGY = -71.1526 RDTITL> * VAN DER WAALS = -28.5175 ELECTROSTATIC = -42.6352 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3517" Parameter: CONF_N -> "8002" Comparing "3517" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3518" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753418 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761609 ATOM PAIRS WERE FOUND FOR ATOM LIST 42055 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29077 from a total of 761609 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3518 -71.14203 -0.01062 0.50530 INTE EXTERN> -32.59405 -38.54798 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.142" Parameter: A <- "-71.142" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.594" Parameter: B <- "-32.594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.548" Parameter: C <- "-38.548" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3518 TOTAL ENERGY = -71.142 RDTITL> * VAN DER WAALS = -32.594 ELECTROSTATIC = -38.548 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3518" Parameter: CONF_N -> "8002" Comparing "3518" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3519" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761609 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758834 ATOM PAIRS WERE FOUND FOR ATOM LIST 42035 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28504 from a total of 758834 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3519 -75.19622 4.05420 0.66914 INTE EXTERN> -26.62637 -48.56986 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1962" Parameter: A <- "-75.1962" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6264" Parameter: B <- "-26.6264" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5699" Parameter: C <- "-48.5699" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3519 TOTAL ENERGY = -75.1962 RDTITL> * VAN DER WAALS = -26.6264 ELECTROSTATIC = -48.5699 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3519" Parameter: CONF_N -> "8002" Comparing "3519" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3520" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758834 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763897 ATOM PAIRS WERE FOUND FOR ATOM LIST 42326 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28804 from a total of 763897 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3520 -74.49511 -0.70111 0.59675 INTE EXTERN> -29.47497 -45.02014 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4951" Parameter: A <- "-74.4951" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.475" Parameter: B <- "-29.475" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0201" Parameter: C <- "-45.0201" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3520 TOTAL ENERGY = -74.4951 RDTITL> * VAN DER WAALS = -29.475 ELECTROSTATIC = -45.0201 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3520" Parameter: CONF_N -> "8002" Comparing "3520" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3521" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763897 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758849 ATOM PAIRS WERE FOUND FOR ATOM LIST 42051 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29291 from a total of 758849 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3521 -72.65292 -1.84219 0.66310 INTE EXTERN> -29.17868 -43.47425 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6529" Parameter: A <- "-72.6529" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1787" Parameter: B <- "-29.1787" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4742" Parameter: C <- "-43.4742" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3521 TOTAL ENERGY = -72.6529 RDTITL> * VAN DER WAALS = -29.1787 ELECTROSTATIC = -43.4742 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3521" Parameter: CONF_N -> "8002" Comparing "3521" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3522" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758849 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759062 ATOM PAIRS WERE FOUND FOR ATOM LIST 42004 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28569 from a total of 759062 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3522 -74.04924 1.39632 0.52842 INTE EXTERN> -33.76636 -40.28288 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0492" Parameter: A <- "-74.0492" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7664" Parameter: B <- "-33.7664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2829" Parameter: C <- "-40.2829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3522 TOTAL ENERGY = -74.0492 RDTITL> * VAN DER WAALS = -33.7664 ELECTROSTATIC = -40.2829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3522" Parameter: CONF_N -> "8002" Comparing "3522" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3523" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759062 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759770 ATOM PAIRS WERE FOUND FOR ATOM LIST 42077 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29024 from a total of 759770 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3523 -61.21240 -12.83684 0.54756 INTE EXTERN> -27.79570 -33.41670 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.2124" Parameter: A <- "-61.2124" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7957" Parameter: B <- "-27.7957" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.4167" Parameter: C <- "-33.4167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3523 TOTAL ENERGY = -61.2124 RDTITL> * VAN DER WAALS = -27.7957 ELECTROSTATIC = -33.4167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3523" Parameter: CONF_N -> "8002" Comparing "3523" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3524" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759770 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757642 ATOM PAIRS WERE FOUND FOR ATOM LIST 41784 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28951 from a total of 757642 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3524 -74.12358 12.91118 0.64681 INTE EXTERN> -28.66404 -45.45954 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1236" Parameter: A <- "-74.1236" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.664" Parameter: B <- "-28.664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4595" Parameter: C <- "-45.4595" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3524 TOTAL ENERGY = -74.1236 RDTITL> * VAN DER WAALS = -28.664 ELECTROSTATIC = -45.4595 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3524" Parameter: CONF_N -> "8002" Comparing "3524" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3525" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757642 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768833 ATOM PAIRS WERE FOUND FOR ATOM LIST 42554 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28511 from a total of 768833 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3525 -70.39089 -3.73269 0.54788 INTE EXTERN> -30.85108 -39.53982 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3909" Parameter: A <- "-70.3909" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8511" Parameter: B <- "-30.8511" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5398" Parameter: C <- "-39.5398" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3525 TOTAL ENERGY = -70.3909 RDTITL> * VAN DER WAALS = -30.8511 ELECTROSTATIC = -39.5398 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3525" Parameter: CONF_N -> "8002" Comparing "3525" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3526" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768833 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767234 ATOM PAIRS WERE FOUND FOR ATOM LIST 42467 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29308 from a total of 767234 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3526 -77.05024 6.65935 0.60943 INTE EXTERN> -30.97491 -46.07533 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0502" Parameter: A <- "-77.0502" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9749" Parameter: B <- "-30.9749" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0753" Parameter: C <- "-46.0753" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3526 TOTAL ENERGY = -77.0502 RDTITL> * VAN DER WAALS = -30.9749 ELECTROSTATIC = -46.0753 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3526" Parameter: CONF_N -> "8002" Comparing "3526" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3527" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767234 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762917 ATOM PAIRS WERE FOUND FOR ATOM LIST 42161 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29372 from a total of 762917 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3527 -70.45762 -6.59262 0.77949 INTE EXTERN> -25.43376 -45.02386 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4576" Parameter: A <- "-70.4576" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4338" Parameter: B <- "-25.4338" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0239" Parameter: C <- "-45.0239" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3527 TOTAL ENERGY = -70.4576 RDTITL> * VAN DER WAALS = -25.4338 ELECTROSTATIC = -45.0239 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3527" Parameter: CONF_N -> "8002" Comparing "3527" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3528" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762917 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760618 ATOM PAIRS WERE FOUND FOR ATOM LIST 42025 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28727 from a total of 760618 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3528 -68.15353 -2.30409 0.62583 INTE EXTERN> -28.88991 -39.26362 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1535" Parameter: A <- "-68.1535" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8899" Parameter: B <- "-28.8899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2636" Parameter: C <- "-39.2636" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3528 TOTAL ENERGY = -68.1535 RDTITL> * VAN DER WAALS = -28.8899 ELECTROSTATIC = -39.2636 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3528" Parameter: CONF_N -> "8002" Comparing "3528" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3529" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760618 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767983 ATOM PAIRS WERE FOUND FOR ATOM LIST 42536 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29293 from a total of 767983 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3529 -66.66368 -1.48985 0.71422 INTE EXTERN> -24.23437 -42.42931 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6637" Parameter: A <- "-66.6637" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2344" Parameter: B <- "-24.2344" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4293" Parameter: C <- "-42.4293" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3529 TOTAL ENERGY = -66.6637 RDTITL> * VAN DER WAALS = -24.2344 ELECTROSTATIC = -42.4293 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3529" Parameter: CONF_N -> "8002" Comparing "3529" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3530" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767983 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762190 ATOM PAIRS WERE FOUND FOR ATOM LIST 42323 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29112 from a total of 762190 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3530 -75.27454 8.61086 0.72923 INTE EXTERN> -26.03122 -49.24332 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2745" Parameter: A <- "-75.2745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0312" Parameter: B <- "-26.0312" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2433" Parameter: C <- "-49.2433" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3530 TOTAL ENERGY = -75.2745 RDTITL> * VAN DER WAALS = -26.0312 ELECTROSTATIC = -49.2433 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3530" Parameter: CONF_N -> "8002" Comparing "3530" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3531" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762190 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762638 ATOM PAIRS WERE FOUND FOR ATOM LIST 42264 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28589 from a total of 762638 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3531 -67.30600 -7.96854 0.70579 INTE EXTERN> -25.66764 -41.63835 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.306" Parameter: A <- "-67.306" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6676" Parameter: B <- "-25.6676" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6384" Parameter: C <- "-41.6384" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3531 TOTAL ENERGY = -67.306 RDTITL> * VAN DER WAALS = -25.6676 ELECTROSTATIC = -41.6384 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3531" Parameter: CONF_N -> "8002" Comparing "3531" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3532" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762638 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762221 ATOM PAIRS WERE FOUND FOR ATOM LIST 41939 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28959 from a total of 762221 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3532 -72.48817 5.18217 0.63053 INTE EXTERN> -28.68006 -43.80811 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4882" Parameter: A <- "-72.4882" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6801" Parameter: B <- "-28.6801" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8081" Parameter: C <- "-43.8081" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3532 TOTAL ENERGY = -72.4882 RDTITL> * VAN DER WAALS = -28.6801 ELECTROSTATIC = -43.8081 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3532" Parameter: CONF_N -> "8002" Comparing "3532" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3533" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762221 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767925 ATOM PAIRS WERE FOUND FOR ATOM LIST 42346 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29165 from a total of 767925 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3533 -79.83307 7.34490 0.63366 INTE EXTERN> -31.22702 -48.60605 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8331" Parameter: A <- "-79.8331" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.227" Parameter: B <- "-31.227" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.606" Parameter: C <- "-48.606" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3533 TOTAL ENERGY = -79.8331 RDTITL> * VAN DER WAALS = -31.227 ELECTROSTATIC = -48.606 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3533" Parameter: CONF_N -> "8002" Comparing "3533" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3534" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767925 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764654 ATOM PAIRS WERE FOUND FOR ATOM LIST 42469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29529 from a total of 764654 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3534 -74.81432 -5.01876 0.82294 INTE EXTERN> -22.02267 -52.79165 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8143" Parameter: A <- "-74.8143" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.0227" Parameter: B <- "-22.0227" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.7916" Parameter: C <- "-52.7916" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3534 TOTAL ENERGY = -74.8143 RDTITL> * VAN DER WAALS = -22.0227 ELECTROSTATIC = -52.7916 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3534" Parameter: CONF_N -> "8002" Comparing "3534" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3535" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764654 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760802 ATOM PAIRS WERE FOUND FOR ATOM LIST 42065 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28491 from a total of 760802 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3535 -76.78894 1.97463 0.63445 INTE EXTERN> -29.40229 -47.38665 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7889" Parameter: A <- "-76.7889" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4023" Parameter: B <- "-29.4023" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3867" Parameter: C <- "-47.3867" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3535 TOTAL ENERGY = -76.7889 RDTITL> * VAN DER WAALS = -29.4023 ELECTROSTATIC = -47.3867 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3535" Parameter: CONF_N -> "8002" Comparing "3535" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3536" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760802 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760447 ATOM PAIRS WERE FOUND FOR ATOM LIST 41937 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29265 from a total of 760447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3536 -79.04322 2.25428 0.72591 INTE EXTERN> -29.45292 -49.59029 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0432" Parameter: A <- "-79.0432" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4529" Parameter: B <- "-29.4529" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5903" Parameter: C <- "-49.5903" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3536 TOTAL ENERGY = -79.0432 RDTITL> * VAN DER WAALS = -29.4529 ELECTROSTATIC = -49.5903 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3536" Parameter: CONF_N -> "8002" Comparing "3536" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3537" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759906 ATOM PAIRS WERE FOUND FOR ATOM LIST 42035 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28720 from a total of 759906 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3537 -69.98926 -9.05396 0.64426 INTE EXTERN> -29.20826 -40.78100 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9893" Parameter: A <- "-69.9893" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2083" Parameter: B <- "-29.2083" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.781" Parameter: C <- "-40.781" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3537 TOTAL ENERGY = -69.9893 RDTITL> * VAN DER WAALS = -29.2083 ELECTROSTATIC = -40.781 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3537" Parameter: CONF_N -> "8002" Comparing "3537" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3538" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759906 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762772 ATOM PAIRS WERE FOUND FOR ATOM LIST 42240 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28919 from a total of 762772 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3538 -71.43747 1.44821 0.61234 INTE EXTERN> -29.24342 -42.19405 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4375" Parameter: A <- "-71.4375" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2434" Parameter: B <- "-29.2434" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.194" Parameter: C <- "-42.194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3538 TOTAL ENERGY = -71.4375 RDTITL> * VAN DER WAALS = -29.2434 ELECTROSTATIC = -42.194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3538" Parameter: CONF_N -> "8002" Comparing "3538" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3539" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762772 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765378 ATOM PAIRS WERE FOUND FOR ATOM LIST 42199 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28907 from a total of 765378 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3539 -74.07694 2.63948 0.54862 INTE EXTERN> -32.31993 -41.75701 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0769" Parameter: A <- "-74.0769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3199" Parameter: B <- "-32.3199" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.757" Parameter: C <- "-41.757" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3539 TOTAL ENERGY = -74.0769 RDTITL> * VAN DER WAALS = -32.3199 ELECTROSTATIC = -41.757 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3539" Parameter: CONF_N -> "8002" Comparing "3539" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3540" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765378 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760960 ATOM PAIRS WERE FOUND FOR ATOM LIST 42008 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28819 from a total of 760960 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3540 -71.55874 -2.51820 0.62880 INTE EXTERN> -26.96374 -44.59500 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5587" Parameter: A <- "-71.5587" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9637" Parameter: B <- "-26.9637" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.595" Parameter: C <- "-44.595" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3540 TOTAL ENERGY = -71.5587 RDTITL> * VAN DER WAALS = -26.9637 ELECTROSTATIC = -44.595 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3540" Parameter: CONF_N -> "8002" Comparing "3540" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3541" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760960 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759282 ATOM PAIRS WERE FOUND FOR ATOM LIST 41955 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28555 from a total of 759282 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3541 -71.83148 0.27274 0.57034 INTE EXTERN> -30.28622 -41.54526 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8315" Parameter: A <- "-71.8315" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2862" Parameter: B <- "-30.2862" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5453" Parameter: C <- "-41.5453" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3541 TOTAL ENERGY = -71.8315 RDTITL> * VAN DER WAALS = -30.2862 ELECTROSTATIC = -41.5453 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3541" Parameter: CONF_N -> "8002" Comparing "3541" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3542" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759282 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760723 ATOM PAIRS WERE FOUND FOR ATOM LIST 42150 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28885 from a total of 760723 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3542 -71.29219 -0.53929 0.73207 INTE EXTERN> -25.60430 -45.68789 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2922" Parameter: A <- "-71.2922" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6043" Parameter: B <- "-25.6043" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6879" Parameter: C <- "-45.6879" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3542 TOTAL ENERGY = -71.2922 RDTITL> * VAN DER WAALS = -25.6043 ELECTROSTATIC = -45.6879 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3542" Parameter: CONF_N -> "8002" Comparing "3542" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3543" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760723 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758101 ATOM PAIRS WERE FOUND FOR ATOM LIST 41868 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28903 from a total of 758101 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3543 -79.26097 7.96879 0.60899 INTE EXTERN> -32.51100 -46.74997 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.261" Parameter: A <- "-79.261" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.511" Parameter: B <- "-32.511" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.75" Parameter: C <- "-46.75" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3543 TOTAL ENERGY = -79.261 RDTITL> * VAN DER WAALS = -32.511 ELECTROSTATIC = -46.75 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3543" Parameter: CONF_N -> "8002" Comparing "3543" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3544" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758101 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762146 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28099 from a total of 762146 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3544 -75.17116 -4.08982 0.65908 INTE EXTERN> -29.84687 -45.32429 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1712" Parameter: A <- "-75.1712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8469" Parameter: B <- "-29.8469" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3243" Parameter: C <- "-45.3243" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3544 TOTAL ENERGY = -75.1712 RDTITL> * VAN DER WAALS = -29.8469 ELECTROSTATIC = -45.3243 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3544" Parameter: CONF_N -> "8002" Comparing "3544" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3545" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762146 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762973 ATOM PAIRS WERE FOUND FOR ATOM LIST 42175 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29003 from a total of 762973 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3545 -64.41286 -10.75830 0.65494 INTE EXTERN> -27.31752 -37.09534 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.4129" Parameter: A <- "-64.4129" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3175" Parameter: B <- "-27.3175" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0953" Parameter: C <- "-37.0953" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3545 TOTAL ENERGY = -64.4129 RDTITL> * VAN DER WAALS = -27.3175 ELECTROSTATIC = -37.0953 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3545" Parameter: CONF_N -> "8002" Comparing "3545" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3546" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762973 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756996 ATOM PAIRS WERE FOUND FOR ATOM LIST 41885 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28019 from a total of 756996 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3546 -72.35569 7.94283 0.73718 INTE EXTERN> -27.04077 -45.31493 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3557" Parameter: A <- "-72.3557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0408" Parameter: B <- "-27.0408" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3149" Parameter: C <- "-45.3149" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3546 TOTAL ENERGY = -72.3557 RDTITL> * VAN DER WAALS = -27.0408 ELECTROSTATIC = -45.3149 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3546" Parameter: CONF_N -> "8002" Comparing "3546" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3547" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756996 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758357 ATOM PAIRS WERE FOUND FOR ATOM LIST 41945 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28746 from a total of 758357 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3547 -73.24557 0.88988 0.73295 INTE EXTERN> -26.05620 -47.18937 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2456" Parameter: A <- "-73.2456" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0562" Parameter: B <- "-26.0562" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1894" Parameter: C <- "-47.1894" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3547 TOTAL ENERGY = -73.2456 RDTITL> * VAN DER WAALS = -26.0562 ELECTROSTATIC = -47.1894 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3547" Parameter: CONF_N -> "8002" Comparing "3547" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3548" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758357 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763278 ATOM PAIRS WERE FOUND FOR ATOM LIST 42179 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29551 from a total of 763278 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3548 -73.15495 -0.09062 0.78823 INTE EXTERN> -24.58507 -48.56988 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1549" Parameter: A <- "-73.1549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5851" Parameter: B <- "-24.5851" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5699" Parameter: C <- "-48.5699" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3548 TOTAL ENERGY = -73.1549 RDTITL> * VAN DER WAALS = -24.5851 ELECTROSTATIC = -48.5699 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3548" Parameter: CONF_N -> "8002" Comparing "3548" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3549" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763278 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762678 ATOM PAIRS WERE FOUND FOR ATOM LIST 42220 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29448 from a total of 762678 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3549 -76.72584 3.57089 0.72768 INTE EXTERN> -28.93386 -47.79198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7258" Parameter: A <- "-76.7258" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9339" Parameter: B <- "-28.9339" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.792" Parameter: C <- "-47.792" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3549 TOTAL ENERGY = -76.7258 RDTITL> * VAN DER WAALS = -28.9339 ELECTROSTATIC = -47.792 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3549" Parameter: CONF_N -> "8002" Comparing "3549" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3550" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762678 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761089 ATOM PAIRS WERE FOUND FOR ATOM LIST 41995 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29469 from a total of 761089 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3550 -74.49348 -2.23236 0.72333 INTE EXTERN> -28.21653 -46.27695 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4935" Parameter: A <- "-74.4935" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2165" Parameter: B <- "-28.2165" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2769" Parameter: C <- "-46.2769" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3550 TOTAL ENERGY = -74.4935 RDTITL> * VAN DER WAALS = -28.2165 ELECTROSTATIC = -46.2769 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3550" Parameter: CONF_N -> "8002" Comparing "3550" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3551" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761089 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760306 ATOM PAIRS WERE FOUND FOR ATOM LIST 42015 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29535 from a total of 760306 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3551 -73.19271 -1.30077 0.57637 INTE EXTERN> -31.21747 -41.97524 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1927" Parameter: A <- "-73.1927" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2175" Parameter: B <- "-31.2175" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9752" Parameter: C <- "-41.9752" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3551 TOTAL ENERGY = -73.1927 RDTITL> * VAN DER WAALS = -31.2175 ELECTROSTATIC = -41.9752 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3551" Parameter: CONF_N -> "8002" Comparing "3551" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3552" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760306 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762792 ATOM PAIRS WERE FOUND FOR ATOM LIST 42123 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29106 from a total of 762792 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3552 -69.98814 -3.20457 0.68092 INTE EXTERN> -26.69062 -43.29751 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9881" Parameter: A <- "-69.9881" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6906" Parameter: B <- "-26.6906" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2975" Parameter: C <- "-43.2975" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3552 TOTAL ENERGY = -69.9881 RDTITL> * VAN DER WAALS = -26.6906 ELECTROSTATIC = -43.2975 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3552" Parameter: CONF_N -> "8002" Comparing "3552" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3553" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762792 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758589 ATOM PAIRS WERE FOUND FOR ATOM LIST 41733 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29174 from a total of 758589 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3553 -74.46185 4.47371 0.71360 INTE EXTERN> -29.03881 -45.42303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4618" Parameter: A <- "-74.4618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0388" Parameter: B <- "-29.0388" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.423" Parameter: C <- "-45.423" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3553 TOTAL ENERGY = -74.4618 RDTITL> * VAN DER WAALS = -29.0388 ELECTROSTATIC = -45.423 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3553" Parameter: CONF_N -> "8002" Comparing "3553" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3554" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758589 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762265 ATOM PAIRS WERE FOUND FOR ATOM LIST 41939 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29294 from a total of 762265 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3554 -72.83848 -1.62337 0.61872 INTE EXTERN> -30.40411 -42.43437 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8385" Parameter: A <- "-72.8385" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4041" Parameter: B <- "-30.4041" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4344" Parameter: C <- "-42.4344" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3554 TOTAL ENERGY = -72.8385 RDTITL> * VAN DER WAALS = -30.4041 ELECTROSTATIC = -42.4344 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3554" Parameter: CONF_N -> "8002" Comparing "3554" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3555" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762265 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758812 ATOM PAIRS WERE FOUND FOR ATOM LIST 41844 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29031 from a total of 758812 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3555 -75.98910 3.15062 0.62302 INTE EXTERN> -30.21326 -45.77584 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9891" Parameter: A <- "-75.9891" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2133" Parameter: B <- "-30.2133" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7758" Parameter: C <- "-45.7758" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3555 TOTAL ENERGY = -75.9891 RDTITL> * VAN DER WAALS = -30.2133 ELECTROSTATIC = -45.7758 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3555" Parameter: CONF_N -> "8002" Comparing "3555" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3556" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758812 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754348 ATOM PAIRS WERE FOUND FOR ATOM LIST 41806 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28340 from a total of 754348 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3556 -67.99534 -7.99376 0.67436 INTE EXTERN> -28.25882 -39.73651 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9953" Parameter: A <- "-67.9953" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2588" Parameter: B <- "-28.2588" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7365" Parameter: C <- "-39.7365" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3556 TOTAL ENERGY = -67.9953 RDTITL> * VAN DER WAALS = -28.2588 ELECTROSTATIC = -39.7365 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3556" Parameter: CONF_N -> "8002" Comparing "3556" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3557" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754348 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753280 ATOM PAIRS WERE FOUND FOR ATOM LIST 41590 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28870 from a total of 753280 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3557 -75.75978 7.76444 0.62981 INTE EXTERN> -29.93499 -45.82479 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7598" Parameter: A <- "-75.7598" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.935" Parameter: B <- "-29.935" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8248" Parameter: C <- "-45.8248" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3557 TOTAL ENERGY = -75.7598 RDTITL> * VAN DER WAALS = -29.935 ELECTROSTATIC = -45.8248 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3557" Parameter: CONF_N -> "8002" Comparing "3557" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3558" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753280 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755796 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28637 from a total of 755796 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3558 -67.69119 -8.06859 0.56624 INTE EXTERN> -30.73020 -36.96099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6912" Parameter: A <- "-67.6912" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7302" Parameter: B <- "-30.7302" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.961" Parameter: C <- "-36.961" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3558 TOTAL ENERGY = -67.6912 RDTITL> * VAN DER WAALS = -30.7302 ELECTROSTATIC = -36.961 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3558" Parameter: CONF_N -> "8002" Comparing "3558" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3559" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755796 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755573 ATOM PAIRS WERE FOUND FOR ATOM LIST 41838 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29386 from a total of 755573 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3559 -74.03603 6.34484 0.74094 INTE EXTERN> -25.98020 -48.05583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.036" Parameter: A <- "-74.036" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9802" Parameter: B <- "-25.9802" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0558" Parameter: C <- "-48.0558" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3559 TOTAL ENERGY = -74.036 RDTITL> * VAN DER WAALS = -25.9802 ELECTROSTATIC = -48.0558 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3559" Parameter: CONF_N -> "8002" Comparing "3559" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3560" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755573 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753597 ATOM PAIRS WERE FOUND FOR ATOM LIST 41947 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28856 from a total of 753597 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3560 -69.06853 -4.96750 0.66420 INTE EXTERN> -26.72215 -42.34638 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0685" Parameter: A <- "-69.0685" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7221" Parameter: B <- "-26.7221" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3464" Parameter: C <- "-42.3464" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3560 TOTAL ENERGY = -69.0685 RDTITL> * VAN DER WAALS = -26.7221 ELECTROSTATIC = -42.3464 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3560" Parameter: CONF_N -> "8002" Comparing "3560" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3561" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753597 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760874 ATOM PAIRS WERE FOUND FOR ATOM LIST 42217 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29293 from a total of 760874 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3561 -76.75255 7.68403 0.61549 INTE EXTERN> -32.47192 -44.28064 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7526" Parameter: A <- "-76.7526" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4719" Parameter: B <- "-32.4719" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2806" Parameter: C <- "-44.2806" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3561 TOTAL ENERGY = -76.7526 RDTITL> * VAN DER WAALS = -32.4719 ELECTROSTATIC = -44.2806 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3561" Parameter: CONF_N -> "8002" Comparing "3561" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3562" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760874 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759614 ATOM PAIRS WERE FOUND FOR ATOM LIST 42104 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28454 from a total of 759614 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3562 -78.76502 2.01246 0.60750 INTE EXTERN> -31.35154 -47.41348 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.765" Parameter: A <- "-78.765" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3515" Parameter: B <- "-31.3515" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4135" Parameter: C <- "-47.4135" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3562 TOTAL ENERGY = -78.765 RDTITL> * VAN DER WAALS = -31.3515 ELECTROSTATIC = -47.4135 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3562" Parameter: CONF_N -> "8002" Comparing "3562" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3563" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759614 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754829 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29357 from a total of 754829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3563 -74.36812 -4.39690 0.56973 INTE EXTERN> -30.74757 -43.62055 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3681" Parameter: A <- "-74.3681" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7476" Parameter: B <- "-30.7476" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6205" Parameter: C <- "-43.6205" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3563 TOTAL ENERGY = -74.3681 RDTITL> * VAN DER WAALS = -30.7476 ELECTROSTATIC = -43.6205 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3563" Parameter: CONF_N -> "8002" Comparing "3563" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3564" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755894 ATOM PAIRS WERE FOUND FOR ATOM LIST 41780 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29484 from a total of 755894 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3564 -70.18159 -4.18653 0.51557 INTE EXTERN> -33.91263 -36.26896 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1816" Parameter: A <- "-70.1816" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9126" Parameter: B <- "-33.9126" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.269" Parameter: C <- "-36.269" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3564 TOTAL ENERGY = -70.1816 RDTITL> * VAN DER WAALS = -33.9126 ELECTROSTATIC = -36.269 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3564" Parameter: CONF_N -> "8002" Comparing "3564" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3565" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755894 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41808 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28750 from a total of 757110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3565 -75.11637 4.93478 0.56455 INTE EXTERN> -30.94925 -44.16712 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1164" Parameter: A <- "-75.1164" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9492" Parameter: B <- "-30.9492" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1671" Parameter: C <- "-44.1671" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3565 TOTAL ENERGY = -75.1164 RDTITL> * VAN DER WAALS = -30.9492 ELECTROSTATIC = -44.1671 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3565" Parameter: CONF_N -> "8002" Comparing "3565" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3566" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764177 ATOM PAIRS WERE FOUND FOR ATOM LIST 42331 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29459 from a total of 764177 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3566 -72.03082 -3.08556 0.67836 INTE EXTERN> -28.67226 -43.35856 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0308" Parameter: A <- "-72.0308" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6723" Parameter: B <- "-28.6723" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3586" Parameter: C <- "-43.3586" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3566 TOTAL ENERGY = -72.0308 RDTITL> * VAN DER WAALS = -28.6723 ELECTROSTATIC = -43.3586 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3566" Parameter: CONF_N -> "8002" Comparing "3566" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3567" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764177 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763886 ATOM PAIRS WERE FOUND FOR ATOM LIST 42265 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29450 from a total of 763886 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3567 -68.93173 -3.09909 0.49759 INTE EXTERN> -34.65632 -34.27541 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9317" Parameter: A <- "-68.9317" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6563" Parameter: B <- "-34.6563" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2754" Parameter: C <- "-34.2754" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3567 TOTAL ENERGY = -68.9317 RDTITL> * VAN DER WAALS = -34.6563 ELECTROSTATIC = -34.2754 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3567" Parameter: CONF_N -> "8002" Comparing "3567" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3568" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763886 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758302 ATOM PAIRS WERE FOUND FOR ATOM LIST 41941 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29311 from a total of 758302 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3568 -69.95746 1.02573 0.65621 INTE EXTERN> -26.08416 -43.87330 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9575" Parameter: A <- "-69.9575" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0842" Parameter: B <- "-26.0842" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8733" Parameter: C <- "-43.8733" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3568 TOTAL ENERGY = -69.9575 RDTITL> * VAN DER WAALS = -26.0842 ELECTROSTATIC = -43.8733 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3568" Parameter: CONF_N -> "8002" Comparing "3568" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3569" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758302 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763665 ATOM PAIRS WERE FOUND FOR ATOM LIST 42178 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28708 from a total of 763665 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3569 -76.71358 6.75612 0.65101 INTE EXTERN> -28.91360 -47.79998 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7136" Parameter: A <- "-76.7136" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9136" Parameter: B <- "-28.9136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8" Parameter: C <- "-47.8" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3569 TOTAL ENERGY = -76.7136 RDTITL> * VAN DER WAALS = -28.9136 ELECTROSTATIC = -47.8 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3569" Parameter: CONF_N -> "8002" Comparing "3569" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3570" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763665 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760191 ATOM PAIRS WERE FOUND FOR ATOM LIST 41931 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28763 from a total of 760191 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3570 -73.84122 -2.87236 0.59896 INTE EXTERN> -29.41458 -44.42665 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8412" Parameter: A <- "-73.8412" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4146" Parameter: B <- "-29.4146" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4266" Parameter: C <- "-44.4266" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3570 TOTAL ENERGY = -73.8412 RDTITL> * VAN DER WAALS = -29.4146 ELECTROSTATIC = -44.4266 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3570" Parameter: CONF_N -> "8002" Comparing "3570" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3571" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760191 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759011 ATOM PAIRS WERE FOUND FOR ATOM LIST 41824 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29558 from a total of 759011 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3571 -69.84863 -3.99259 0.64826 INTE EXTERN> -28.07054 -41.77810 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8486" Parameter: A <- "-69.8486" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0705" Parameter: B <- "-28.0705" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7781" Parameter: C <- "-41.7781" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3571 TOTAL ENERGY = -69.8486 RDTITL> * VAN DER WAALS = -28.0705 ELECTROSTATIC = -41.7781 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3571" Parameter: CONF_N -> "8002" Comparing "3571" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3572" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759011 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756863 ATOM PAIRS WERE FOUND FOR ATOM LIST 41831 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29271 from a total of 756863 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3572 -75.45993 5.61130 0.55519 INTE EXTERN> -31.21529 -44.24464 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4599" Parameter: A <- "-75.4599" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2153" Parameter: B <- "-31.2153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2446" Parameter: C <- "-44.2446" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3572 TOTAL ENERGY = -75.4599 RDTITL> * VAN DER WAALS = -31.2153 ELECTROSTATIC = -44.2446 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3572" Parameter: CONF_N -> "8002" Comparing "3572" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3573" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756863 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762074 ATOM PAIRS WERE FOUND FOR ATOM LIST 42081 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28987 from a total of 762074 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3573 -72.35242 -3.10751 0.56881 INTE EXTERN> -30.84336 -41.50906 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3524" Parameter: A <- "-72.3524" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8434" Parameter: B <- "-30.8434" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5091" Parameter: C <- "-41.5091" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3573 TOTAL ENERGY = -72.3524 RDTITL> * VAN DER WAALS = -30.8434 ELECTROSTATIC = -41.5091 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3573" Parameter: CONF_N -> "8002" Comparing "3573" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3574" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762074 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761891 ATOM PAIRS WERE FOUND FOR ATOM LIST 42035 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28965 from a total of 761891 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3574 -72.43177 0.07935 0.54235 INTE EXTERN> -31.43777 -40.99400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4318" Parameter: A <- "-72.4318" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4378" Parameter: B <- "-31.4378" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.994" Parameter: C <- "-40.994" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3574 TOTAL ENERGY = -72.4318 RDTITL> * VAN DER WAALS = -31.4378 ELECTROSTATIC = -40.994 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3574" Parameter: CONF_N -> "8002" Comparing "3574" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3575" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761891 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760307 ATOM PAIRS WERE FOUND FOR ATOM LIST 42188 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28821 from a total of 760307 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3575 -69.85203 -2.57974 0.55415 INTE EXTERN> -32.29632 -37.55571 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.852" Parameter: A <- "-69.852" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2963" Parameter: B <- "-32.2963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5557" Parameter: C <- "-37.5557" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3575 TOTAL ENERGY = -69.852 RDTITL> * VAN DER WAALS = -32.2963 ELECTROSTATIC = -37.5557 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3575" Parameter: CONF_N -> "8002" Comparing "3575" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3576" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760307 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759521 ATOM PAIRS WERE FOUND FOR ATOM LIST 41942 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28903 from a total of 759521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3576 -69.47098 -0.38105 0.65386 INTE EXTERN> -29.09754 -40.37344 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.471" Parameter: A <- "-69.471" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0975" Parameter: B <- "-29.0975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3734" Parameter: C <- "-40.3734" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3576 TOTAL ENERGY = -69.471 RDTITL> * VAN DER WAALS = -29.0975 ELECTROSTATIC = -40.3734 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3576" Parameter: CONF_N -> "8002" Comparing "3576" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3577" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761005 ATOM PAIRS WERE FOUND FOR ATOM LIST 42050 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29184 from a total of 761005 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3577 -74.10920 4.63822 0.68476 INTE EXTERN> -24.64142 -49.46778 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1092" Parameter: A <- "-74.1092" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6414" Parameter: B <- "-24.6414" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4678" Parameter: C <- "-49.4678" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3577 TOTAL ENERGY = -74.1092 RDTITL> * VAN DER WAALS = -24.6414 ELECTROSTATIC = -49.4678 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3577" Parameter: CONF_N -> "8002" Comparing "3577" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3578" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761005 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758922 ATOM PAIRS WERE FOUND FOR ATOM LIST 41813 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29271 from a total of 758922 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3578 -74.69742 0.58822 0.65119 INTE EXTERN> -28.78169 -45.91572 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6974" Parameter: A <- "-74.6974" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7817" Parameter: B <- "-28.7817" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9157" Parameter: C <- "-45.9157" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3578 TOTAL ENERGY = -74.6974 RDTITL> * VAN DER WAALS = -28.7817 ELECTROSTATIC = -45.9157 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3578" Parameter: CONF_N -> "8002" Comparing "3578" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3579" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758922 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759885 ATOM PAIRS WERE FOUND FOR ATOM LIST 41929 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29073 from a total of 759885 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3579 -77.45746 2.76005 0.60851 INTE EXTERN> -32.79978 -44.65768 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4575" Parameter: A <- "-77.4575" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7998" Parameter: B <- "-32.7998" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6577" Parameter: C <- "-44.6577" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3579 TOTAL ENERGY = -77.4575 RDTITL> * VAN DER WAALS = -32.7998 ELECTROSTATIC = -44.6577 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3579" Parameter: CONF_N -> "8002" Comparing "3579" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3580" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759885 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760177 ATOM PAIRS WERE FOUND FOR ATOM LIST 41944 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29858 from a total of 760177 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3580 -71.50936 -5.94810 0.59727 INTE EXTERN> -33.16370 -38.34567 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5094" Parameter: A <- "-71.5094" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1637" Parameter: B <- "-33.1637" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3457" Parameter: C <- "-38.3457" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3580 TOTAL ENERGY = -71.5094 RDTITL> * VAN DER WAALS = -33.1637 ELECTROSTATIC = -38.3457 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3580" Parameter: CONF_N -> "8002" Comparing "3580" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3581" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760177 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760210 ATOM PAIRS WERE FOUND FOR ATOM LIST 41972 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29606 from a total of 760210 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3581 -75.22829 3.71892 0.57931 INTE EXTERN> -33.15635 -42.07193 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2283" Parameter: A <- "-75.2283" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1564" Parameter: B <- "-33.1564" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0719" Parameter: C <- "-42.0719" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3581 TOTAL ENERGY = -75.2283 RDTITL> * VAN DER WAALS = -33.1564 ELECTROSTATIC = -42.0719 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3581" Parameter: CONF_N -> "8002" Comparing "3581" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3582" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760210 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754486 ATOM PAIRS WERE FOUND FOR ATOM LIST 41794 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28942 from a total of 754486 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3582 -71.85939 -3.36890 0.58857 INTE EXTERN> -31.75787 -40.10152 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8594" Parameter: A <- "-71.8594" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7579" Parameter: B <- "-31.7579" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1015" Parameter: C <- "-40.1015" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3582 TOTAL ENERGY = -71.8594 RDTITL> * VAN DER WAALS = -31.7579 ELECTROSTATIC = -40.1015 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3582" Parameter: CONF_N -> "8002" Comparing "3582" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3583" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754486 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757173 ATOM PAIRS WERE FOUND FOR ATOM LIST 41919 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29234 from a total of 757173 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3583 -76.64261 4.78322 0.56506 INTE EXTERN> -32.32003 -44.32257 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6426" Parameter: A <- "-76.6426" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.32" Parameter: B <- "-32.32" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3226" Parameter: C <- "-44.3226" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3583 TOTAL ENERGY = -76.6426 RDTITL> * VAN DER WAALS = -32.32 ELECTROSTATIC = -44.3226 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3583" Parameter: CONF_N -> "8002" Comparing "3583" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3584" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757173 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755740 ATOM PAIRS WERE FOUND FOR ATOM LIST 41795 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29329 from a total of 755740 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3584 -75.46578 -1.17682 0.71095 INTE EXTERN> -27.50179 -47.96399 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4658" Parameter: A <- "-75.4658" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5018" Parameter: B <- "-27.5018" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.964" Parameter: C <- "-47.964" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3584 TOTAL ENERGY = -75.4658 RDTITL> * VAN DER WAALS = -27.5018 ELECTROSTATIC = -47.964 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3584" Parameter: CONF_N -> "8002" Comparing "3584" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3585" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755740 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759787 ATOM PAIRS WERE FOUND FOR ATOM LIST 41815 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29409 from a total of 759787 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3585 -83.82807 8.36229 0.68986 INTE EXTERN> -30.31451 -53.51356 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.8281" Parameter: A <- "-83.8281" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3145" Parameter: B <- "-30.3145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.5136" Parameter: C <- "-53.5136" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3585 TOTAL ENERGY = -83.8281 RDTITL> * VAN DER WAALS = -30.3145 ELECTROSTATIC = -53.5136 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3585" Parameter: CONF_N -> "8002" Comparing "3585" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3586" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759787 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746838 ATOM PAIRS WERE FOUND FOR ATOM LIST 41440 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29429 from a total of 746838 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3586 -74.69683 -9.13124 0.73008 INTE EXTERN> -25.73676 -48.96007 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6968" Parameter: A <- "-74.6968" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7368" Parameter: B <- "-25.7368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9601" Parameter: C <- "-48.9601" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3586 TOTAL ENERGY = -74.6968 RDTITL> * VAN DER WAALS = -25.7368 ELECTROSTATIC = -48.9601 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3586" Parameter: CONF_N -> "8002" Comparing "3586" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3587" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746838 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755388 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29354 from a total of 755388 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3587 -72.86857 -1.82826 0.61273 INTE EXTERN> -28.80010 -44.06847 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8686" Parameter: A <- "-72.8686" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8001" Parameter: B <- "-28.8001" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0685" Parameter: C <- "-44.0685" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3587 TOTAL ENERGY = -72.8686 RDTITL> * VAN DER WAALS = -28.8001 ELECTROSTATIC = -44.0685 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3587" Parameter: CONF_N -> "8002" Comparing "3587" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3588" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755388 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755884 ATOM PAIRS WERE FOUND FOR ATOM LIST 41810 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29344 from a total of 755884 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3588 -74.02509 1.15651 0.57274 INTE EXTERN> -31.31116 -42.71393 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0251" Parameter: A <- "-74.0251" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3112" Parameter: B <- "-31.3112" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7139" Parameter: C <- "-42.7139" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3588 TOTAL ENERGY = -74.0251 RDTITL> * VAN DER WAALS = -31.3112 ELECTROSTATIC = -42.7139 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3588" Parameter: CONF_N -> "8002" Comparing "3588" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3589" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755884 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759264 ATOM PAIRS WERE FOUND FOR ATOM LIST 41990 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29944 from a total of 759264 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3589 -77.01217 2.98708 0.59038 INTE EXTERN> -33.63839 -43.37378 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0122" Parameter: A <- "-77.0122" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6384" Parameter: B <- "-33.6384" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3738" Parameter: C <- "-43.3738" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3589 TOTAL ENERGY = -77.0122 RDTITL> * VAN DER WAALS = -33.6384 ELECTROSTATIC = -43.3738 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3589" Parameter: CONF_N -> "8002" Comparing "3589" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3590" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759264 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762296 ATOM PAIRS WERE FOUND FOR ATOM LIST 42136 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29559 from a total of 762296 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3590 -76.59755 -0.41461 0.64560 INTE EXTERN> -29.71667 -46.88089 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5976" Parameter: A <- "-76.5976" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7167" Parameter: B <- "-29.7167" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8809" Parameter: C <- "-46.8809" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3590 TOTAL ENERGY = -76.5976 RDTITL> * VAN DER WAALS = -29.7167 ELECTROSTATIC = -46.8809 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3590" Parameter: CONF_N -> "8002" Comparing "3590" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3591" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762296 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769315 ATOM PAIRS WERE FOUND FOR ATOM LIST 42481 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29207 from a total of 769315 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3591 -80.72883 4.13128 0.59191 INTE EXTERN> -33.26415 -47.46468 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7288" Parameter: A <- "-80.7288" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2642" Parameter: B <- "-33.2642" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4647" Parameter: C <- "-47.4647" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3591 TOTAL ENERGY = -80.7288 RDTITL> * VAN DER WAALS = -33.2642 ELECTROSTATIC = -47.4647 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3591" Parameter: CONF_N -> "8002" Comparing "3591" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3592" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769315 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764017 ATOM PAIRS WERE FOUND FOR ATOM LIST 42073 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28970 from a total of 764017 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3592 -73.27939 -7.44944 0.58939 INTE EXTERN> -30.47750 -42.80189 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2794" Parameter: A <- "-73.2794" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4775" Parameter: B <- "-30.4775" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8019" Parameter: C <- "-42.8019" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3592 TOTAL ENERGY = -73.2794 RDTITL> * VAN DER WAALS = -30.4775 ELECTROSTATIC = -42.8019 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3592" Parameter: CONF_N -> "8002" Comparing "3592" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3593" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764017 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764110 ATOM PAIRS WERE FOUND FOR ATOM LIST 42192 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29433 from a total of 764110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3593 -76.88928 3.60989 0.59708 INTE EXTERN> -30.96084 -45.92845 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8893" Parameter: A <- "-76.8893" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9608" Parameter: B <- "-30.9608" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9284" Parameter: C <- "-45.9284" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3593 TOTAL ENERGY = -76.8893 RDTITL> * VAN DER WAALS = -30.9608 ELECTROSTATIC = -45.9284 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3593" Parameter: CONF_N -> "8002" Comparing "3593" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3594" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761873 ATOM PAIRS WERE FOUND FOR ATOM LIST 42069 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28398 from a total of 761873 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3594 -75.02859 -1.86069 0.66517 INTE EXTERN> -27.07755 -47.95103 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0286" Parameter: A <- "-75.0286" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0776" Parameter: B <- "-27.0776" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.951" Parameter: C <- "-47.951" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3594 TOTAL ENERGY = -75.0286 RDTITL> * VAN DER WAALS = -27.0776 ELECTROSTATIC = -47.951 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3594" Parameter: CONF_N -> "8002" Comparing "3594" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3595" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761873 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759150 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28225 from a total of 759150 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3595 -68.95747 -6.07112 0.61201 INTE EXTERN> -27.50238 -41.45509 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9575" Parameter: A <- "-68.9575" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5024" Parameter: B <- "-27.5024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4551" Parameter: C <- "-41.4551" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3595 TOTAL ENERGY = -68.9575 RDTITL> * VAN DER WAALS = -27.5024 ELECTROSTATIC = -41.4551 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3595" Parameter: CONF_N -> "8002" Comparing "3595" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3596" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759150 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752725 ATOM PAIRS WERE FOUND FOR ATOM LIST 41658 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27684 from a total of 752725 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3596 -63.10310 -5.85437 0.61492 INTE EXTERN> -26.76752 -36.33558 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1031" Parameter: A <- "-63.1031" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7675" Parameter: B <- "-26.7675" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3356" Parameter: C <- "-36.3356" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3596 TOTAL ENERGY = -63.1031 RDTITL> * VAN DER WAALS = -26.7675 ELECTROSTATIC = -36.3356 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3596" Parameter: CONF_N -> "8002" Comparing "3596" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3597" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752725 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752485 ATOM PAIRS WERE FOUND FOR ATOM LIST 41676 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29272 from a total of 752485 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3597 -71.50131 8.39821 0.75720 INTE EXTERN> -23.00162 -48.49969 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5013" Parameter: A <- "-71.5013" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.0016" Parameter: B <- "-23.0016" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4997" Parameter: C <- "-48.4997" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3597 TOTAL ENERGY = -71.5013 RDTITL> * VAN DER WAALS = -23.0016 ELECTROSTATIC = -48.4997 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3597" Parameter: CONF_N -> "8002" Comparing "3597" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3598" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752485 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754116 ATOM PAIRS WERE FOUND FOR ATOM LIST 41708 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28505 from a total of 754116 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3598 -71.75082 0.24951 0.67855 INTE EXTERN> -26.89474 -44.85608 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7508" Parameter: A <- "-71.7508" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8947" Parameter: B <- "-26.8947" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8561" Parameter: C <- "-44.8561" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3598 TOTAL ENERGY = -71.7508 RDTITL> * VAN DER WAALS = -26.8947 ELECTROSTATIC = -44.8561 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3598" Parameter: CONF_N -> "8002" Comparing "3598" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3599" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754116 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753622 ATOM PAIRS WERE FOUND FOR ATOM LIST 41643 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28560 from a total of 753622 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3599 -73.64810 1.89727 0.60654 INTE EXTERN> -29.85680 -43.79129 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6481" Parameter: A <- "-73.6481" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8568" Parameter: B <- "-29.8568" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7913" Parameter: C <- "-43.7913" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3599 TOTAL ENERGY = -73.6481 RDTITL> * VAN DER WAALS = -29.8568 ELECTROSTATIC = -43.7913 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3599" Parameter: CONF_N -> "8002" Comparing "3599" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3600" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753622 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756304 ATOM PAIRS WERE FOUND FOR ATOM LIST 41854 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28984 from a total of 756304 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3600 -75.65555 2.00745 0.63459 INTE EXTERN> -28.62885 -47.02670 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6555" Parameter: A <- "-75.6555" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6289" Parameter: B <- "-28.6289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0267" Parameter: C <- "-47.0267" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3600 TOTAL ENERGY = -75.6555 RDTITL> * VAN DER WAALS = -28.6289 ELECTROSTATIC = -47.0267 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3600" Parameter: CONF_N -> "8002" Comparing "3600" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3601" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756304 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757576 ATOM PAIRS WERE FOUND FOR ATOM LIST 41784 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28775 from a total of 757576 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3601 -73.79407 -1.86148 0.69164 INTE EXTERN> -26.98848 -46.80558 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7941" Parameter: A <- "-73.7941" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9885" Parameter: B <- "-26.9885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8056" Parameter: C <- "-46.8056" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3601 TOTAL ENERGY = -73.7941 RDTITL> * VAN DER WAALS = -26.9885 ELECTROSTATIC = -46.8056 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3601" Parameter: CONF_N -> "8002" Comparing "3601" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3602" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757576 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757306 ATOM PAIRS WERE FOUND FOR ATOM LIST 41993 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28796 from a total of 757306 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3602 -76.94622 3.15216 0.55452 INTE EXTERN> -31.31972 -45.62650 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9462" Parameter: A <- "-76.9462" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3197" Parameter: B <- "-31.3197" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6265" Parameter: C <- "-45.6265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3602 TOTAL ENERGY = -76.9462 RDTITL> * VAN DER WAALS = -31.3197 ELECTROSTATIC = -45.6265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3602" Parameter: CONF_N -> "8002" Comparing "3602" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3603" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757306 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755980 ATOM PAIRS WERE FOUND FOR ATOM LIST 42030 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29169 from a total of 755980 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3603 -75.22491 -1.72131 0.62625 INTE EXTERN> -30.33985 -44.88507 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2249" Parameter: A <- "-75.2249" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3398" Parameter: B <- "-30.3398" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8851" Parameter: C <- "-44.8851" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3603 TOTAL ENERGY = -75.2249 RDTITL> * VAN DER WAALS = -30.3398 ELECTROSTATIC = -44.8851 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3603" Parameter: CONF_N -> "8002" Comparing "3603" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3604" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755980 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750070 ATOM PAIRS WERE FOUND FOR ATOM LIST 41490 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28578 from a total of 750070 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3604 -68.80939 -6.41553 0.51762 INTE EXTERN> -32.90528 -35.90411 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8094" Parameter: A <- "-68.8094" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9053" Parameter: B <- "-32.9053" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9041" Parameter: C <- "-35.9041" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3604 TOTAL ENERGY = -68.8094 RDTITL> * VAN DER WAALS = -32.9053 ELECTROSTATIC = -35.9041 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3604" Parameter: CONF_N -> "8002" Comparing "3604" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3605" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750070 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755377 ATOM PAIRS WERE FOUND FOR ATOM LIST 41874 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28607 from a total of 755377 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3605 -75.39288 6.58349 0.63992 INTE EXTERN> -28.98592 -46.40696 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3929" Parameter: A <- "-75.3929" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9859" Parameter: B <- "-28.9859" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.407" Parameter: C <- "-46.407" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3605 TOTAL ENERGY = -75.3929 RDTITL> * VAN DER WAALS = -28.9859 ELECTROSTATIC = -46.407 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3605" Parameter: CONF_N -> "8002" Comparing "3605" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3606" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755377 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763847 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28621 from a total of 763847 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3606 -68.18657 -7.20630 0.48679 INTE EXTERN> -32.91112 -35.27545 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1866" Parameter: A <- "-68.1866" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9111" Parameter: B <- "-32.9111" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2755" Parameter: C <- "-35.2755" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3606 TOTAL ENERGY = -68.1866 RDTITL> * VAN DER WAALS = -32.9111 ELECTROSTATIC = -35.2755 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3606" Parameter: CONF_N -> "8002" Comparing "3606" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3607" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763847 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762051 ATOM PAIRS WERE FOUND FOR ATOM LIST 42009 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29281 from a total of 762051 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3607 -75.13202 6.94545 0.55248 INTE EXTERN> -32.55846 -42.57356 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.132" Parameter: A <- "-75.132" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5585" Parameter: B <- "-32.5585" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5736" Parameter: C <- "-42.5736" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3607 TOTAL ENERGY = -75.132 RDTITL> * VAN DER WAALS = -32.5585 ELECTROSTATIC = -42.5736 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3607" Parameter: CONF_N -> "8002" Comparing "3607" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3608" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762051 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759924 ATOM PAIRS WERE FOUND FOR ATOM LIST 41923 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29253 from a total of 759924 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3608 -65.15440 -9.97762 0.60709 INTE EXTERN> -27.71937 -37.43504 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1544" Parameter: A <- "-65.1544" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7194" Parameter: B <- "-27.7194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.435" Parameter: C <- "-37.435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3608 TOTAL ENERGY = -65.1544 RDTITL> * VAN DER WAALS = -27.7194 ELECTROSTATIC = -37.435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3608" Parameter: CONF_N -> "8002" Comparing "3608" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3609" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759924 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759967 ATOM PAIRS WERE FOUND FOR ATOM LIST 41965 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28496 from a total of 759967 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3609 -64.33860 -0.81580 0.52664 INTE EXTERN> -30.51684 -33.82177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3386" Parameter: A <- "-64.3386" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5168" Parameter: B <- "-30.5168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8218" Parameter: C <- "-33.8218" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3609 TOTAL ENERGY = -64.3386 RDTITL> * VAN DER WAALS = -30.5168 ELECTROSTATIC = -33.8218 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3609" Parameter: CONF_N -> "8002" Comparing "3609" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3610" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759967 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759395 ATOM PAIRS WERE FOUND FOR ATOM LIST 42107 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28736 from a total of 759395 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3610 -63.50205 -0.83655 0.54105 INTE EXTERN> -31.05563 -32.44642 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.5021" Parameter: A <- "-63.5021" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0556" Parameter: B <- "-31.0556" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.4464" Parameter: C <- "-32.4464" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3610 TOTAL ENERGY = -63.5021 RDTITL> * VAN DER WAALS = -31.0556 ELECTROSTATIC = -32.4464 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3610" Parameter: CONF_N -> "8002" Comparing "3610" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3611" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759395 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758035 ATOM PAIRS WERE FOUND FOR ATOM LIST 41828 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29684 from a total of 758035 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3611 -73.71929 10.21724 0.56889 INTE EXTERN> -31.36240 -42.35689 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7193" Parameter: A <- "-73.7193" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3624" Parameter: B <- "-31.3624" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3569" Parameter: C <- "-42.3569" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3611 TOTAL ENERGY = -73.7193 RDTITL> * VAN DER WAALS = -31.3624 ELECTROSTATIC = -42.3569 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3611" Parameter: CONF_N -> "8002" Comparing "3611" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3612" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758035 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757232 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29064 from a total of 757232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3612 -74.60322 0.88392 0.60594 INTE EXTERN> -31.58777 -43.01544 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6032" Parameter: A <- "-74.6032" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5878" Parameter: B <- "-31.5878" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0154" Parameter: C <- "-43.0154" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3612 TOTAL ENERGY = -74.6032 RDTITL> * VAN DER WAALS = -31.5878 ELECTROSTATIC = -43.0154 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3612" Parameter: CONF_N -> "8002" Comparing "3612" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3613" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754189 ATOM PAIRS WERE FOUND FOR ATOM LIST 41742 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28206 from a total of 754189 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3613 -62.98694 -11.61627 0.55008 INTE EXTERN> -30.67205 -32.31489 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9869" Parameter: A <- "-62.9869" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.672" Parameter: B <- "-30.672" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.3149" Parameter: C <- "-32.3149" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3613 TOTAL ENERGY = -62.9869 RDTITL> * VAN DER WAALS = -30.672 ELECTROSTATIC = -32.3149 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3613" Parameter: CONF_N -> "8002" Comparing "3613" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3614" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754189 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754210 ATOM PAIRS WERE FOUND FOR ATOM LIST 41654 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29366 from a total of 754210 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3614 -70.34816 7.36121 0.56798 INTE EXTERN> -31.57372 -38.77444 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3482" Parameter: A <- "-70.3482" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5737" Parameter: B <- "-31.5737" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7744" Parameter: C <- "-38.7744" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3614 TOTAL ENERGY = -70.3482 RDTITL> * VAN DER WAALS = -31.5737 ELECTROSTATIC = -38.7744 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3614" Parameter: CONF_N -> "8002" Comparing "3614" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3615" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754210 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761102 ATOM PAIRS WERE FOUND FOR ATOM LIST 42066 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29514 from a total of 761102 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3615 -70.34307 -0.00509 0.56708 INTE EXTERN> -33.37176 -36.97131 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3431" Parameter: A <- "-70.3431" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3718" Parameter: B <- "-33.3718" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9713" Parameter: C <- "-36.9713" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3615 TOTAL ENERGY = -70.3431 RDTITL> * VAN DER WAALS = -33.3718 ELECTROSTATIC = -36.9713 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3615" Parameter: CONF_N -> "8002" Comparing "3615" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3616" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761102 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764017 ATOM PAIRS WERE FOUND FOR ATOM LIST 42126 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29304 from a total of 764017 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3616 -70.78659 0.44352 0.51984 INTE EXTERN> -32.01925 -38.76734 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7866" Parameter: A <- "-70.7866" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0192" Parameter: B <- "-32.0192" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7673" Parameter: C <- "-38.7673" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3616 TOTAL ENERGY = -70.7866 RDTITL> * VAN DER WAALS = -32.0192 ELECTROSTATIC = -38.7673 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3616" Parameter: CONF_N -> "8002" Comparing "3616" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3617" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764017 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757670 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28835 from a total of 757670 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3617 -73.53582 2.74923 0.64208 INTE EXTERN> -28.84762 -44.68821 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5358" Parameter: A <- "-73.5358" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8476" Parameter: B <- "-28.8476" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6882" Parameter: C <- "-44.6882" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3617 TOTAL ENERGY = -73.5358 RDTITL> * VAN DER WAALS = -28.8476 ELECTROSTATIC = -44.6882 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3617" Parameter: CONF_N -> "8002" Comparing "3617" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3618" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757670 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749906 ATOM PAIRS WERE FOUND FOR ATOM LIST 41395 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28396 from a total of 749906 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3618 -66.71482 -6.82101 0.58420 INTE EXTERN> -29.31360 -37.40122 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7148" Parameter: A <- "-66.7148" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3136" Parameter: B <- "-29.3136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4012" Parameter: C <- "-37.4012" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3618 TOTAL ENERGY = -66.7148 RDTITL> * VAN DER WAALS = -29.3136 ELECTROSTATIC = -37.4012 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3618" Parameter: CONF_N -> "8002" Comparing "3618" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3619" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749906 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749032 ATOM PAIRS WERE FOUND FOR ATOM LIST 41484 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28748 from a total of 749032 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3619 -72.38805 5.67324 0.59140 INTE EXTERN> -30.14766 -42.24040 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3881" Parameter: A <- "-72.3881" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1477" Parameter: B <- "-30.1477" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2404" Parameter: C <- "-42.2404" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3619 TOTAL ENERGY = -72.3881 RDTITL> * VAN DER WAALS = -30.1477 ELECTROSTATIC = -42.2404 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3619" Parameter: CONF_N -> "8002" Comparing "3619" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3620" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749032 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759392 ATOM PAIRS WERE FOUND FOR ATOM LIST 41864 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29186 from a total of 759392 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3620 -71.20251 -1.18554 0.71148 INTE EXTERN> -27.07599 -44.12652 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2025" Parameter: A <- "-71.2025" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.076" Parameter: B <- "-27.076" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1265" Parameter: C <- "-44.1265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3620 TOTAL ENERGY = -71.2025 RDTITL> * VAN DER WAALS = -27.076 ELECTROSTATIC = -44.1265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3620" Parameter: CONF_N -> "8002" Comparing "3620" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3621" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759392 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754760 ATOM PAIRS WERE FOUND FOR ATOM LIST 41795 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28668 from a total of 754760 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3621 -69.64929 -1.55323 0.52837 INTE EXTERN> -31.86636 -37.78293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6493" Parameter: A <- "-69.6493" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8664" Parameter: B <- "-31.8664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7829" Parameter: C <- "-37.7829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3621 TOTAL ENERGY = -69.6493 RDTITL> * VAN DER WAALS = -31.8664 ELECTROSTATIC = -37.7829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3621" Parameter: CONF_N -> "8002" Comparing "3621" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3622" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754760 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753521 ATOM PAIRS WERE FOUND FOR ATOM LIST 41801 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28486 from a total of 753521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3622 -76.62548 6.97619 0.61810 INTE EXTERN> -30.71868 -45.90680 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6255" Parameter: A <- "-76.6255" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7187" Parameter: B <- "-30.7187" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9068" Parameter: C <- "-45.9068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3622 TOTAL ENERGY = -76.6255 RDTITL> * VAN DER WAALS = -30.7187 ELECTROSTATIC = -45.9068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3622" Parameter: CONF_N -> "8002" Comparing "3622" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3623" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749230 ATOM PAIRS WERE FOUND FOR ATOM LIST 41723 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28519 from a total of 749230 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3623 -63.29186 -13.33362 0.55509 INTE EXTERN> -29.96724 -33.32462 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.2919" Parameter: A <- "-63.2919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9672" Parameter: B <- "-29.9672" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.3246" Parameter: C <- "-33.3246" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3623 TOTAL ENERGY = -63.2919 RDTITL> * VAN DER WAALS = -29.9672 ELECTROSTATIC = -33.3246 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3623" Parameter: CONF_N -> "8002" Comparing "3623" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3624" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749230 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755899 ATOM PAIRS WERE FOUND FOR ATOM LIST 41767 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28719 from a total of 755899 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3624 -69.50403 6.21217 0.55872 INTE EXTERN> -30.00205 -39.50198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.504" Parameter: A <- "-69.504" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0021" Parameter: B <- "-30.0021" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.502" Parameter: C <- "-39.502" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3624 TOTAL ENERGY = -69.504 RDTITL> * VAN DER WAALS = -30.0021 ELECTROSTATIC = -39.502 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3624" Parameter: CONF_N -> "8002" Comparing "3624" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3625" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755899 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753906 ATOM PAIRS WERE FOUND FOR ATOM LIST 41576 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28977 from a total of 753906 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3625 -73.28492 3.78089 0.61438 INTE EXTERN> -29.65801 -43.62691 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2849" Parameter: A <- "-73.2849" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.658" Parameter: B <- "-29.658" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6269" Parameter: C <- "-43.6269" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3625 TOTAL ENERGY = -73.2849 RDTITL> * VAN DER WAALS = -29.658 ELECTROSTATIC = -43.6269 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3625" Parameter: CONF_N -> "8002" Comparing "3625" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3626" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753906 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757937 ATOM PAIRS WERE FOUND FOR ATOM LIST 42098 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28866 from a total of 757937 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3626 -76.45682 3.17190 0.62289 INTE EXTERN> -29.44619 -47.01063 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4568" Parameter: A <- "-76.4568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4462" Parameter: B <- "-29.4462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0106" Parameter: C <- "-47.0106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3626 TOTAL ENERGY = -76.4568 RDTITL> * VAN DER WAALS = -29.4462 ELECTROSTATIC = -47.0106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3626" Parameter: CONF_N -> "8002" Comparing "3626" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3627" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757937 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760663 ATOM PAIRS WERE FOUND FOR ATOM LIST 42170 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29110 from a total of 760663 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3627 -66.89767 -9.55915 0.69255 INTE EXTERN> -25.13141 -41.76626 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8977" Parameter: A <- "-66.8977" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1314" Parameter: B <- "-25.1314" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7663" Parameter: C <- "-41.7663" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3627 TOTAL ENERGY = -66.8977 RDTITL> * VAN DER WAALS = -25.1314 ELECTROSTATIC = -41.7663 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3627" Parameter: CONF_N -> "8002" Comparing "3627" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3628" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760663 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757634 ATOM PAIRS WERE FOUND FOR ATOM LIST 41952 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29458 from a total of 757634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3628 -66.90068 0.00300 0.57828 INTE EXTERN> -29.59508 -37.30560 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9007" Parameter: A <- "-66.9007" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5951" Parameter: B <- "-29.5951" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3056" Parameter: C <- "-37.3056" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3628 TOTAL ENERGY = -66.9007 RDTITL> * VAN DER WAALS = -29.5951 ELECTROSTATIC = -37.3056 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3628" Parameter: CONF_N -> "8002" Comparing "3628" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3629" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757523 ATOM PAIRS WERE FOUND FOR ATOM LIST 41992 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29026 from a total of 757523 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3629 -77.59505 10.69437 0.60596 INTE EXTERN> -31.91812 -45.67693 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.595" Parameter: A <- "-77.595" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9181" Parameter: B <- "-31.9181" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6769" Parameter: C <- "-45.6769" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3629 TOTAL ENERGY = -77.595 RDTITL> * VAN DER WAALS = -31.9181 ELECTROSTATIC = -45.6769 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3629" Parameter: CONF_N -> "8002" Comparing "3629" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3630" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757523 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760329 ATOM PAIRS WERE FOUND FOR ATOM LIST 42079 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29303 from a total of 760329 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3630 -65.40330 -12.19174 0.68464 INTE EXTERN> -24.80899 -40.59432 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4033" Parameter: A <- "-65.4033" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.809" Parameter: B <- "-24.809" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5943" Parameter: C <- "-40.5943" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3630 TOTAL ENERGY = -65.4033 RDTITL> * VAN DER WAALS = -24.809 ELECTROSTATIC = -40.5943 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3630" Parameter: CONF_N -> "8002" Comparing "3630" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3631" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760329 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759947 ATOM PAIRS WERE FOUND FOR ATOM LIST 42062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28700 from a total of 759947 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3631 -67.87400 2.47069 0.53730 INTE EXTERN> -31.85735 -36.01664 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.874" Parameter: A <- "-67.874" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8574" Parameter: B <- "-31.8574" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0166" Parameter: C <- "-36.0166" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3631 TOTAL ENERGY = -67.874 RDTITL> * VAN DER WAALS = -31.8574 ELECTROSTATIC = -36.0166 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3631" Parameter: CONF_N -> "8002" Comparing "3631" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3632" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759947 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768953 ATOM PAIRS WERE FOUND FOR ATOM LIST 42492 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29636 from a total of 768953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3632 -68.04429 0.17029 0.75605 INTE EXTERN> -24.03670 -44.00759 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0443" Parameter: A <- "-68.0443" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0367" Parameter: B <- "-24.0367" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0076" Parameter: C <- "-44.0076" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3632 TOTAL ENERGY = -68.0443 RDTITL> * VAN DER WAALS = -24.0367 ELECTROSTATIC = -44.0076 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3632" Parameter: CONF_N -> "8002" Comparing "3632" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3633" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764822 ATOM PAIRS WERE FOUND FOR ATOM LIST 42262 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29396 from a total of 764822 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3633 -68.38450 0.34021 0.60688 INTE EXTERN> -29.00848 -39.37602 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3845" Parameter: A <- "-68.3845" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0085" Parameter: B <- "-29.0085" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.376" Parameter: C <- "-39.376" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3633 TOTAL ENERGY = -68.3845 RDTITL> * VAN DER WAALS = -29.0085 ELECTROSTATIC = -39.376 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3633" Parameter: CONF_N -> "8002" Comparing "3633" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3634" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764822 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764832 ATOM PAIRS WERE FOUND FOR ATOM LIST 42216 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29017 from a total of 764832 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3634 -71.32002 2.93552 0.64627 INTE EXTERN> -30.04893 -41.27109 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.32" Parameter: A <- "-71.32" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0489" Parameter: B <- "-30.0489" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2711" Parameter: C <- "-41.2711" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3634 TOTAL ENERGY = -71.32 RDTITL> * VAN DER WAALS = -30.0489 ELECTROSTATIC = -41.2711 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3634" Parameter: CONF_N -> "8002" Comparing "3634" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3635" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764832 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766426 ATOM PAIRS WERE FOUND FOR ATOM LIST 42325 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29426 from a total of 766426 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3635 -65.52381 -5.79621 0.57071 INTE EXTERN> -29.40253 -36.12128 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5238" Parameter: A <- "-65.5238" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4025" Parameter: B <- "-29.4025" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1213" Parameter: C <- "-36.1213" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3635 TOTAL ENERGY = -65.5238 RDTITL> * VAN DER WAALS = -29.4025 ELECTROSTATIC = -36.1213 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3635" Parameter: CONF_N -> "8002" Comparing "3635" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3636" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766426 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759325 ATOM PAIRS WERE FOUND FOR ATOM LIST 41978 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29412 from a total of 759325 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3636 -67.34430 1.82049 0.54130 INTE EXTERN> -32.11381 -35.23050 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3443" Parameter: A <- "-67.3443" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1138" Parameter: B <- "-32.1138" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2305" Parameter: C <- "-35.2305" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3636 TOTAL ENERGY = -67.3443 RDTITL> * VAN DER WAALS = -32.1138 ELECTROSTATIC = -35.2305 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3636" Parameter: CONF_N -> "8002" Comparing "3636" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3637" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759325 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764715 ATOM PAIRS WERE FOUND FOR ATOM LIST 42285 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29609 from a total of 764715 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3637 -75.92088 8.57658 0.61431 INTE EXTERN> -28.44418 -47.47669 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9209" Parameter: A <- "-75.9209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4442" Parameter: B <- "-28.4442" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4767" Parameter: C <- "-47.4767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3637 TOTAL ENERGY = -75.9209 RDTITL> * VAN DER WAALS = -28.4442 ELECTROSTATIC = -47.4767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3637" Parameter: CONF_N -> "8002" Comparing "3637" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3638" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764715 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761688 ATOM PAIRS WERE FOUND FOR ATOM LIST 41961 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28746 from a total of 761688 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3638 -70.53119 -5.38969 0.72293 INTE EXTERN> -27.91277 -42.61842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5312" Parameter: A <- "-70.5312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9128" Parameter: B <- "-27.9128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6184" Parameter: C <- "-42.6184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3638 TOTAL ENERGY = -70.5312 RDTITL> * VAN DER WAALS = -27.9128 ELECTROSTATIC = -42.6184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3638" Parameter: CONF_N -> "8002" Comparing "3638" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3639" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761688 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758497 ATOM PAIRS WERE FOUND FOR ATOM LIST 41871 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29153 from a total of 758497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3639 -76.91244 6.38125 0.63718 INTE EXTERN> -30.24485 -46.66760 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9124" Parameter: A <- "-76.9124" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2448" Parameter: B <- "-30.2448" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6676" Parameter: C <- "-46.6676" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3639 TOTAL ENERGY = -76.9124 RDTITL> * VAN DER WAALS = -30.2448 ELECTROSTATIC = -46.6676 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3639" Parameter: CONF_N -> "8002" Comparing "3639" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3640" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759568 ATOM PAIRS WERE FOUND FOR ATOM LIST 41876 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29070 from a total of 759568 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3640 -65.12431 -11.78814 0.62924 INTE EXTERN> -27.61847 -37.50584 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1243" Parameter: A <- "-65.1243" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6185" Parameter: B <- "-27.6185" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5058" Parameter: C <- "-37.5058" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3640 TOTAL ENERGY = -65.1243 RDTITL> * VAN DER WAALS = -27.6185 ELECTROSTATIC = -37.5058 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3640" Parameter: CONF_N -> "8002" Comparing "3640" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3641" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759568 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763675 ATOM PAIRS WERE FOUND FOR ATOM LIST 42178 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29851 from a total of 763675 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3641 -66.52398 1.39967 0.78058 INTE EXTERN> -22.44616 -44.07782 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.524" Parameter: A <- "-66.524" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.4462" Parameter: B <- "-22.4462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0778" Parameter: C <- "-44.0778" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3641 TOTAL ENERGY = -66.524 RDTITL> * VAN DER WAALS = -22.4462 ELECTROSTATIC = -44.0778 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3641" Parameter: CONF_N -> "8002" Comparing "3641" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3642" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763675 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767823 ATOM PAIRS WERE FOUND FOR ATOM LIST 42437 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29028 from a total of 767823 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3642 -63.09369 -3.43029 0.65750 INTE EXTERN> -29.45204 -33.64166 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.0937" Parameter: A <- "-63.0937" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.452" Parameter: B <- "-29.452" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6417" Parameter: C <- "-33.6417" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3642 TOTAL ENERGY = -63.0937 RDTITL> * VAN DER WAALS = -29.452 ELECTROSTATIC = -33.6417 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3642" Parameter: CONF_N -> "8002" Comparing "3642" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3643" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767823 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764000 ATOM PAIRS WERE FOUND FOR ATOM LIST 42292 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29438 from a total of 764000 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3643 -60.20854 -2.88516 0.52713 INTE EXTERN> -29.13427 -31.07426 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.2085" Parameter: A <- "-60.2085" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1343" Parameter: B <- "-29.1343" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.0743" Parameter: C <- "-31.0743" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3643 TOTAL ENERGY = -60.2085 RDTITL> * VAN DER WAALS = -29.1343 ELECTROSTATIC = -31.0743 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3643" Parameter: CONF_N -> "8002" Comparing "3643" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3644" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764000 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763152 ATOM PAIRS WERE FOUND FOR ATOM LIST 42194 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28750 from a total of 763152 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3644 -70.05964 9.85110 0.54667 INTE EXTERN> -31.76147 -38.29816 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0596" Parameter: A <- "-70.0596" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7615" Parameter: B <- "-31.7615" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2982" Parameter: C <- "-38.2982" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3644 TOTAL ENERGY = -70.0596 RDTITL> * VAN DER WAALS = -31.7615 ELECTROSTATIC = -38.2982 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3644" Parameter: CONF_N -> "8002" Comparing "3644" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3645" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763152 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758451 ATOM PAIRS WERE FOUND FOR ATOM LIST 41848 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29069 from a total of 758451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3645 -67.54049 -2.51915 0.58754 INTE EXTERN> -30.01021 -37.53027 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5405" Parameter: A <- "-67.5405" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0102" Parameter: B <- "-30.0102" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5303" Parameter: C <- "-37.5303" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3645 TOTAL ENERGY = -67.5405 RDTITL> * VAN DER WAALS = -30.0102 ELECTROSTATIC = -37.5303 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3645" Parameter: CONF_N -> "8002" Comparing "3645" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3646" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763517 ATOM PAIRS WERE FOUND FOR ATOM LIST 42221 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29224 from a total of 763517 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3646 -73.63992 6.09944 0.56151 INTE EXTERN> -33.95472 -39.68520 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6399" Parameter: A <- "-73.6399" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9547" Parameter: B <- "-33.9547" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6852" Parameter: C <- "-39.6852" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3646 TOTAL ENERGY = -73.6399 RDTITL> * VAN DER WAALS = -33.9547 ELECTROSTATIC = -39.6852 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3646" Parameter: CONF_N -> "8002" Comparing "3646" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3647" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763517 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759777 ATOM PAIRS WERE FOUND FOR ATOM LIST 42029 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29277 from a total of 759777 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3647 -64.18625 -9.45368 0.64087 INTE EXTERN> -26.87127 -37.31498 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1862" Parameter: A <- "-64.1862" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8713" Parameter: B <- "-26.8713" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.315" Parameter: C <- "-37.315" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3647 TOTAL ENERGY = -64.1862 RDTITL> * VAN DER WAALS = -26.8713 ELECTROSTATIC = -37.315 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3647" Parameter: CONF_N -> "8002" Comparing "3647" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3648" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759777 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766591 ATOM PAIRS WERE FOUND FOR ATOM LIST 42307 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29848 from a total of 766591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3648 -78.87140 14.68516 0.74068 INTE EXTERN> -27.84314 -51.02826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8714" Parameter: A <- "-78.8714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8431" Parameter: B <- "-27.8431" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0283" Parameter: C <- "-51.0283" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3648 TOTAL ENERGY = -78.8714 RDTITL> * VAN DER WAALS = -27.8431 ELECTROSTATIC = -51.0283 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3648" Parameter: CONF_N -> "8002" Comparing "3648" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3649" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759899 ATOM PAIRS WERE FOUND FOR ATOM LIST 42102 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28912 from a total of 759899 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3649 -74.23497 -4.63643 0.60611 INTE EXTERN> -31.79584 -42.43913 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.235" Parameter: A <- "-74.235" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7958" Parameter: B <- "-31.7958" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4391" Parameter: C <- "-42.4391" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3649 TOTAL ENERGY = -74.235 RDTITL> * VAN DER WAALS = -31.7958 ELECTROSTATIC = -42.4391 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3649" Parameter: CONF_N -> "8002" Comparing "3649" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3650" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759899 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757789 ATOM PAIRS WERE FOUND FOR ATOM LIST 41682 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29044 from a total of 757789 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3650 -76.28287 2.04790 0.64619 INTE EXTERN> -27.10943 -49.17344 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2829" Parameter: A <- "-76.2829" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1094" Parameter: B <- "-27.1094" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1734" Parameter: C <- "-49.1734" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3650 TOTAL ENERGY = -76.2829 RDTITL> * VAN DER WAALS = -27.1094 ELECTROSTATIC = -49.1734 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3650" Parameter: CONF_N -> "8002" Comparing "3650" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3651" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757789 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756445 ATOM PAIRS WERE FOUND FOR ATOM LIST 41802 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28772 from a total of 756445 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3651 -65.87670 -10.40617 0.63938 INTE EXTERN> -28.06600 -37.81071 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8767" Parameter: A <- "-65.8767" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.066" Parameter: B <- "-28.066" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8107" Parameter: C <- "-37.8107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3651 TOTAL ENERGY = -65.8767 RDTITL> * VAN DER WAALS = -28.066 ELECTROSTATIC = -37.8107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3651" Parameter: CONF_N -> "8002" Comparing "3651" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3652" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756445 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759890 ATOM PAIRS WERE FOUND FOR ATOM LIST 42042 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29046 from a total of 759890 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3652 -75.25941 9.38270 0.60784 INTE EXTERN> -30.21135 -45.04806 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2594" Parameter: A <- "-75.2594" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2114" Parameter: B <- "-30.2114" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0481" Parameter: C <- "-45.0481" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3652 TOTAL ENERGY = -75.2594 RDTITL> * VAN DER WAALS = -30.2114 ELECTROSTATIC = -45.0481 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3652" Parameter: CONF_N -> "8002" Comparing "3652" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3653" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759890 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767136 ATOM PAIRS WERE FOUND FOR ATOM LIST 42348 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29465 from a total of 767136 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3653 -79.16323 3.90383 0.78087 INTE EXTERN> -23.32492 -55.83831 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1632" Parameter: A <- "-79.1632" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.3249" Parameter: B <- "-23.3249" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.8383" Parameter: C <- "-55.8383" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3653 TOTAL ENERGY = -79.1632 RDTITL> * VAN DER WAALS = -23.3249 ELECTROSTATIC = -55.8383 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3653" Parameter: CONF_N -> "8002" Comparing "3653" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3654" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767136 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753866 ATOM PAIRS WERE FOUND FOR ATOM LIST 41690 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28688 from a total of 753866 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3654 -78.95376 -0.20947 0.66627 INTE EXTERN> -27.69746 -51.25630 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9538" Parameter: A <- "-78.9538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6975" Parameter: B <- "-27.6975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2563" Parameter: C <- "-51.2563" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3654 TOTAL ENERGY = -78.9538 RDTITL> * VAN DER WAALS = -27.6975 ELECTROSTATIC = -51.2563 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3654" Parameter: CONF_N -> "8002" Comparing "3654" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3655" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753866 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763034 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29248 from a total of 763034 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3655 -68.35018 -10.60359 0.68836 INTE EXTERN> -27.45789 -40.89228 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3502" Parameter: A <- "-68.3502" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4579" Parameter: B <- "-27.4579" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8923" Parameter: C <- "-40.8923" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3655 TOTAL ENERGY = -68.3502 RDTITL> * VAN DER WAALS = -27.4579 ELECTROSTATIC = -40.8923 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3655" Parameter: CONF_N -> "8002" Comparing "3655" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3656" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763034 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765750 ATOM PAIRS WERE FOUND FOR ATOM LIST 42208 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29328 from a total of 765750 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3656 -71.88348 3.53330 0.59099 INTE EXTERN> -30.88771 -40.99576 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8835" Parameter: A <- "-71.8835" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8877" Parameter: B <- "-30.8877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9958" Parameter: C <- "-40.9958" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3656 TOTAL ENERGY = -71.8835 RDTITL> * VAN DER WAALS = -30.8877 ELECTROSTATIC = -40.9958 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3656" Parameter: CONF_N -> "8002" Comparing "3656" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3657" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765750 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762901 ATOM PAIRS WERE FOUND FOR ATOM LIST 42171 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29125 from a total of 762901 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3657 -74.16555 2.28207 0.62624 INTE EXTERN> -26.33131 -47.83424 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1656" Parameter: A <- "-74.1656" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3313" Parameter: B <- "-26.3313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8342" Parameter: C <- "-47.8342" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3657 TOTAL ENERGY = -74.1656 RDTITL> * VAN DER WAALS = -26.3313 ELECTROSTATIC = -47.8342 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3657" Parameter: CONF_N -> "8002" Comparing "3657" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3658" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762901 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768888 ATOM PAIRS WERE FOUND FOR ATOM LIST 42441 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29482 from a total of 768888 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3658 -77.18293 3.01738 0.60134 INTE EXTERN> -31.64873 -45.53419 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1829" Parameter: A <- "-77.1829" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6487" Parameter: B <- "-31.6487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5342" Parameter: C <- "-45.5342" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3658 TOTAL ENERGY = -77.1829 RDTITL> * VAN DER WAALS = -31.6487 ELECTROSTATIC = -45.5342 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3658" Parameter: CONF_N -> "8002" Comparing "3658" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3659" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768888 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763141 ATOM PAIRS WERE FOUND FOR ATOM LIST 42317 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29455 from a total of 763141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3659 -77.20308 0.02016 0.70712 INTE EXTERN> -27.32416 -49.87892 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2031" Parameter: A <- "-77.2031" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3242" Parameter: B <- "-27.3242" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8789" Parameter: C <- "-49.8789" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3659 TOTAL ENERGY = -77.2031 RDTITL> * VAN DER WAALS = -27.3242 ELECTROSTATIC = -49.8789 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3659" Parameter: CONF_N -> "8002" Comparing "3659" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3660" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761742 ATOM PAIRS WERE FOUND FOR ATOM LIST 42235 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28812 from a total of 761742 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3660 -76.60496 -0.59812 0.58737 INTE EXTERN> -31.48319 -45.12177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.605" Parameter: A <- "-76.605" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4832" Parameter: B <- "-31.4832" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1218" Parameter: C <- "-45.1218" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3660 TOTAL ENERGY = -76.605 RDTITL> * VAN DER WAALS = -31.4832 ELECTROSTATIC = -45.1218 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3660" Parameter: CONF_N -> "8002" Comparing "3660" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3661" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761742 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767216 ATOM PAIRS WERE FOUND FOR ATOM LIST 42314 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28773 from a total of 767216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3661 -73.49545 -3.10951 0.58305 INTE EXTERN> -29.62203 -43.87342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4955" Parameter: A <- "-73.4955" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.622" Parameter: B <- "-29.622" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8734" Parameter: C <- "-43.8734" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3661 TOTAL ENERGY = -73.4955 RDTITL> * VAN DER WAALS = -29.622 ELECTROSTATIC = -43.8734 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3661" Parameter: CONF_N -> "8002" Comparing "3661" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3662" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766938 ATOM PAIRS WERE FOUND FOR ATOM LIST 42435 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28958 from a total of 766938 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3662 -75.31843 1.82298 0.63623 INTE EXTERN> -28.45255 -46.86587 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3184" Parameter: A <- "-75.3184" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4526" Parameter: B <- "-28.4526" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8659" Parameter: C <- "-46.8659" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3662 TOTAL ENERGY = -75.3184 RDTITL> * VAN DER WAALS = -28.4526 ELECTROSTATIC = -46.8659 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3662" Parameter: CONF_N -> "8002" Comparing "3662" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3663" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766938 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761508 ATOM PAIRS WERE FOUND FOR ATOM LIST 42085 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28769 from a total of 761508 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3663 -80.75405 5.43562 0.60704 INTE EXTERN> -31.28863 -49.46542 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.754" Parameter: A <- "-80.754" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2886" Parameter: B <- "-31.2886" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4654" Parameter: C <- "-49.4654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3663 TOTAL ENERGY = -80.754 RDTITL> * VAN DER WAALS = -31.2886 ELECTROSTATIC = -49.4654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3663" Parameter: CONF_N -> "8002" Comparing "3663" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3664" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761508 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764517 ATOM PAIRS WERE FOUND FOR ATOM LIST 42388 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28393 from a total of 764517 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3664 -71.78565 -8.96839 0.61703 INTE EXTERN> -26.72241 -45.06325 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7857" Parameter: A <- "-71.7857" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7224" Parameter: B <- "-26.7224" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0632" Parameter: C <- "-45.0632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3664 TOTAL ENERGY = -71.7857 RDTITL> * VAN DER WAALS = -26.7224 ELECTROSTATIC = -45.0632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3664" Parameter: CONF_N -> "8002" Comparing "3664" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3665" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764517 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762233 ATOM PAIRS WERE FOUND FOR ATOM LIST 42101 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28295 from a total of 762233 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3665 -73.42706 1.64140 0.60503 INTE EXTERN> -29.90322 -43.52383 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4271" Parameter: A <- "-73.4271" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9032" Parameter: B <- "-29.9032" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5238" Parameter: C <- "-43.5238" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3665 TOTAL ENERGY = -73.4271 RDTITL> * VAN DER WAALS = -29.9032 ELECTROSTATIC = -43.5238 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3665" Parameter: CONF_N -> "8002" Comparing "3665" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3666" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762233 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765504 ATOM PAIRS WERE FOUND FOR ATOM LIST 42347 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28660 from a total of 765504 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3666 -76.37075 2.94369 0.65602 INTE EXTERN> -28.69238 -47.67837 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3708" Parameter: A <- "-76.3708" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6924" Parameter: B <- "-28.6924" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6784" Parameter: C <- "-47.6784" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3666 TOTAL ENERGY = -76.3708 RDTITL> * VAN DER WAALS = -28.6924 ELECTROSTATIC = -47.6784 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3666" Parameter: CONF_N -> "8002" Comparing "3666" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3667" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765504 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760439 ATOM PAIRS WERE FOUND FOR ATOM LIST 42145 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28997 from a total of 760439 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3667 -68.35622 -8.01453 0.73729 INTE EXTERN> -22.06272 -46.29350 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3562" Parameter: A <- "-68.3562" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.0627" Parameter: B <- "-22.0627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2935" Parameter: C <- "-46.2935" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3667 TOTAL ENERGY = -68.3562 RDTITL> * VAN DER WAALS = -22.0627 ELECTROSTATIC = -46.2935 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3667" Parameter: CONF_N -> "8002" Comparing "3667" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3668" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760439 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758016 ATOM PAIRS WERE FOUND FOR ATOM LIST 42146 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29092 from a total of 758016 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3668 -74.22086 5.86464 0.65149 INTE EXTERN> -26.72223 -47.49863 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2209" Parameter: A <- "-74.2209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7222" Parameter: B <- "-26.7222" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4986" Parameter: C <- "-47.4986" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3668 TOTAL ENERGY = -74.2209 RDTITL> * VAN DER WAALS = -26.7222 ELECTROSTATIC = -47.4986 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3668" Parameter: CONF_N -> "8002" Comparing "3668" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3669" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758016 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757234 ATOM PAIRS WERE FOUND FOR ATOM LIST 42036 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29120 from a total of 757234 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3669 -70.28829 -3.93257 0.55284 INTE EXTERN> -30.66353 -39.62476 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2883" Parameter: A <- "-70.2883" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6635" Parameter: B <- "-30.6635" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6248" Parameter: C <- "-39.6248" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3669 TOTAL ENERGY = -70.2883 RDTITL> * VAN DER WAALS = -30.6635 ELECTROSTATIC = -39.6248 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3669" Parameter: CONF_N -> "8002" Comparing "3669" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3670" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757234 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762385 ATOM PAIRS WERE FOUND FOR ATOM LIST 42340 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28914 from a total of 762385 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3670 -76.22083 5.93254 0.63962 INTE EXTERN> -28.63132 -47.58950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2208" Parameter: A <- "-76.2208" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6313" Parameter: B <- "-28.6313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5895" Parameter: C <- "-47.5895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3670 TOTAL ENERGY = -76.2208 RDTITL> * VAN DER WAALS = -28.6313 ELECTROSTATIC = -47.5895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3670" Parameter: CONF_N -> "8002" Comparing "3670" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3671" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762385 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759098 ATOM PAIRS WERE FOUND FOR ATOM LIST 42133 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27988 from a total of 759098 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3671 -67.00691 -9.21391 0.52014 INTE EXTERN> -31.41356 -35.59335 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0069" Parameter: A <- "-67.0069" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4136" Parameter: B <- "-31.4136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5934" Parameter: C <- "-35.5934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3671 TOTAL ENERGY = -67.0069 RDTITL> * VAN DER WAALS = -31.4136 ELECTROSTATIC = -35.5934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3671" Parameter: CONF_N -> "8002" Comparing "3671" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3672" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759098 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761161 ATOM PAIRS WERE FOUND FOR ATOM LIST 42077 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28502 from a total of 761161 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3672 -72.65904 5.65212 0.59531 INTE EXTERN> -31.20145 -41.45759 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.659" Parameter: A <- "-72.659" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2015" Parameter: B <- "-31.2015" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4576" Parameter: C <- "-41.4576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3672 TOTAL ENERGY = -72.659 RDTITL> * VAN DER WAALS = -31.2015 ELECTROSTATIC = -41.4576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3672" Parameter: CONF_N -> "8002" Comparing "3672" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3673" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761161 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758133 ATOM PAIRS WERE FOUND FOR ATOM LIST 41934 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28276 from a total of 758133 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3673 -78.88408 6.22505 0.58399 INTE EXTERN> -31.21288 -47.67120 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8841" Parameter: A <- "-78.8841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2129" Parameter: B <- "-31.2129" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6712" Parameter: C <- "-47.6712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3673 TOTAL ENERGY = -78.8841 RDTITL> * VAN DER WAALS = -31.2129 ELECTROSTATIC = -47.6712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3673" Parameter: CONF_N -> "8002" Comparing "3673" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3674" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758133 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763590 ATOM PAIRS WERE FOUND FOR ATOM LIST 42076 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28738 from a total of 763590 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3674 -74.90814 -3.97595 0.69614 INTE EXTERN> -28.71803 -46.19011 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9081" Parameter: A <- "-74.9081" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.718" Parameter: B <- "-28.718" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1901" Parameter: C <- "-46.1901" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3674 TOTAL ENERGY = -74.9081 RDTITL> * VAN DER WAALS = -28.718 ELECTROSTATIC = -46.1901 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3674" Parameter: CONF_N -> "8002" Comparing "3674" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3675" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763590 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763909 ATOM PAIRS WERE FOUND FOR ATOM LIST 42135 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29895 from a total of 763909 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3675 -77.65981 2.75167 0.58862 INTE EXTERN> -30.24511 -47.41470 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6598" Parameter: A <- "-77.6598" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2451" Parameter: B <- "-30.2451" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4147" Parameter: C <- "-47.4147" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3675 TOTAL ENERGY = -77.6598 RDTITL> * VAN DER WAALS = -30.2451 ELECTROSTATIC = -47.4147 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3675" Parameter: CONF_N -> "8002" Comparing "3675" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3676" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763909 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764801 ATOM PAIRS WERE FOUND FOR ATOM LIST 42129 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29076 from a total of 764801 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3676 -80.58956 2.92975 0.66488 INTE EXTERN> -28.85617 -51.73339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5896" Parameter: A <- "-80.5896" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8562" Parameter: B <- "-28.8562" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7334" Parameter: C <- "-51.7334" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3676 TOTAL ENERGY = -80.5896 RDTITL> * VAN DER WAALS = -28.8562 ELECTROSTATIC = -51.7334 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3676" Parameter: CONF_N -> "8002" Comparing "3676" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3677" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764801 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760528 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29056 from a total of 760528 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3677 -74.66439 -5.92517 0.63075 INTE EXTERN> -30.32886 -44.33554 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6644" Parameter: A <- "-74.6644" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3289" Parameter: B <- "-30.3289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3355" Parameter: C <- "-44.3355" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3677 TOTAL ENERGY = -74.6644 RDTITL> * VAN DER WAALS = -30.3289 ELECTROSTATIC = -44.3355 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3677" Parameter: CONF_N -> "8002" Comparing "3677" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3678" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760528 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762109 ATOM PAIRS WERE FOUND FOR ATOM LIST 42013 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28863 from a total of 762109 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3678 -71.27642 -3.38797 0.60808 INTE EXTERN> -28.57571 -42.70071 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2764" Parameter: A <- "-71.2764" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5757" Parameter: B <- "-28.5757" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7007" Parameter: C <- "-42.7007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3678 TOTAL ENERGY = -71.2764 RDTITL> * VAN DER WAALS = -28.5757 ELECTROSTATIC = -42.7007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3678" Parameter: CONF_N -> "8002" Comparing "3678" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3679" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762109 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755533 ATOM PAIRS WERE FOUND FOR ATOM LIST 41646 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28547 from a total of 755533 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3679 -79.24414 7.96772 0.64413 INTE EXTERN> -27.40403 -51.84011 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2441" Parameter: A <- "-79.2441" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.404" Parameter: B <- "-27.404" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8401" Parameter: C <- "-51.8401" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3679 TOTAL ENERGY = -79.2441 RDTITL> * VAN DER WAALS = -27.404 ELECTROSTATIC = -51.8401 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3679" Parameter: CONF_N -> "8002" Comparing "3679" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3680" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755533 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759087 ATOM PAIRS WERE FOUND FOR ATOM LIST 41910 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29004 from a total of 759087 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3680 -72.41154 -6.83261 0.59640 INTE EXTERN> -30.36977 -42.04177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4115" Parameter: A <- "-72.4115" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3698" Parameter: B <- "-30.3698" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0418" Parameter: C <- "-42.0418" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3680 TOTAL ENERGY = -72.4115 RDTITL> * VAN DER WAALS = -30.3698 ELECTROSTATIC = -42.0418 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3680" Parameter: CONF_N -> "8002" Comparing "3680" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3681" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759087 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767756 ATOM PAIRS WERE FOUND FOR ATOM LIST 42210 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29573 from a total of 767756 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3681 -80.41351 8.00198 0.69007 INTE EXTERN> -28.05027 -52.36325 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4135" Parameter: A <- "-80.4135" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0503" Parameter: B <- "-28.0503" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3632" Parameter: C <- "-52.3632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3681 TOTAL ENERGY = -80.4135 RDTITL> * VAN DER WAALS = -28.0503 ELECTROSTATIC = -52.3632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3681" Parameter: CONF_N -> "8002" Comparing "3681" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3682" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767756 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765980 ATOM PAIRS WERE FOUND FOR ATOM LIST 42212 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28824 from a total of 765980 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3682 -76.85777 -3.55575 0.61403 INTE EXTERN> -29.57778 -47.27999 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8578" Parameter: A <- "-76.8578" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5778" Parameter: B <- "-29.5778" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.28" Parameter: C <- "-47.28" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3682 TOTAL ENERGY = -76.8578 RDTITL> * VAN DER WAALS = -29.5778 ELECTROSTATIC = -47.28 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3682" Parameter: CONF_N -> "8002" Comparing "3682" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3683" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765980 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759882 ATOM PAIRS WERE FOUND FOR ATOM LIST 41963 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28849 from a total of 759882 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3683 -78.73537 1.87760 0.65818 INTE EXTERN> -27.43953 -51.29583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7354" Parameter: A <- "-78.7354" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4395" Parameter: B <- "-27.4395" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2958" Parameter: C <- "-51.2958" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3683 TOTAL ENERGY = -78.7354 RDTITL> * VAN DER WAALS = -27.4395 ELECTROSTATIC = -51.2958 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3683" Parameter: CONF_N -> "8002" Comparing "3683" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3684" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759882 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762458 ATOM PAIRS WERE FOUND FOR ATOM LIST 42273 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29135 from a total of 762458 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3684 -76.63204 -2.10332 0.57496 INTE EXTERN> -31.45974 -45.17230 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.632" Parameter: A <- "-76.632" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4597" Parameter: B <- "-31.4597" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1723" Parameter: C <- "-45.1723" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3684 TOTAL ENERGY = -76.632 RDTITL> * VAN DER WAALS = -31.4597 ELECTROSTATIC = -45.1723 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3684" Parameter: CONF_N -> "8002" Comparing "3684" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3685" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762458 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759621 ATOM PAIRS WERE FOUND FOR ATOM LIST 42076 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28851 from a total of 759621 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3685 -68.20806 -8.42398 0.71785 INTE EXTERN> -25.51967 -42.68839 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2081" Parameter: A <- "-68.2081" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5197" Parameter: B <- "-25.5197" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6884" Parameter: C <- "-42.6884" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3685 TOTAL ENERGY = -68.2081 RDTITL> * VAN DER WAALS = -25.5197 ELECTROSTATIC = -42.6884 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3685" Parameter: CONF_N -> "8002" Comparing "3685" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3686" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759621 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759109 ATOM PAIRS WERE FOUND FOR ATOM LIST 41882 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29111 from a total of 759109 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3686 -60.27262 -7.93545 0.53269 INTE EXTERN> -28.61359 -31.65903 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.2726" Parameter: A <- "-60.2726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6136" Parameter: B <- "-28.6136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.659" Parameter: C <- "-31.659" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3686 TOTAL ENERGY = -60.2726 RDTITL> * VAN DER WAALS = -28.6136 ELECTROSTATIC = -31.659 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3686" Parameter: CONF_N -> "8002" Comparing "3686" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3687" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759109 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759797 ATOM PAIRS WERE FOUND FOR ATOM LIST 42025 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29287 from a total of 759797 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3687 -68.38440 8.11178 0.56112 INTE EXTERN> -31.09772 -37.28668 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3844" Parameter: A <- "-68.3844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0977" Parameter: B <- "-31.0977" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2867" Parameter: C <- "-37.2867" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3687 TOTAL ENERGY = -68.3844 RDTITL> * VAN DER WAALS = -31.0977 ELECTROSTATIC = -37.2867 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3687" Parameter: CONF_N -> "8002" Comparing "3687" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3688" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759797 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757951 ATOM PAIRS WERE FOUND FOR ATOM LIST 41800 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28664 from a total of 757951 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3688 -70.89449 2.51009 0.63844 INTE EXTERN> -28.07722 -42.81726 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8945" Parameter: A <- "-70.8945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0772" Parameter: B <- "-28.0772" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8173" Parameter: C <- "-42.8173" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3688 TOTAL ENERGY = -70.8945 RDTITL> * VAN DER WAALS = -28.0772 ELECTROSTATIC = -42.8173 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3688" Parameter: CONF_N -> "8002" Comparing "3688" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3689" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757951 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759852 ATOM PAIRS WERE FOUND FOR ATOM LIST 42008 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29150 from a total of 759852 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3689 -74.96710 4.07262 0.61734 INTE EXTERN> -30.02124 -44.94586 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9671" Parameter: A <- "-74.9671" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0212" Parameter: B <- "-30.0212" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9459" Parameter: C <- "-44.9459" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3689 TOTAL ENERGY = -74.9671 RDTITL> * VAN DER WAALS = -30.0212 ELECTROSTATIC = -44.9459 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3689" Parameter: CONF_N -> "8002" Comparing "3689" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3690" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759852 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41876 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28817 from a total of 760586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3690 -69.95903 -5.00807 0.59630 INTE EXTERN> -31.35267 -38.60637 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.959" Parameter: A <- "-69.959" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3527" Parameter: B <- "-31.3527" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6064" Parameter: C <- "-38.6064" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3690 TOTAL ENERGY = -69.959 RDTITL> * VAN DER WAALS = -31.3527 ELECTROSTATIC = -38.6064 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3690" Parameter: CONF_N -> "8002" Comparing "3690" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3691" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763774 ATOM PAIRS WERE FOUND FOR ATOM LIST 42035 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28838 from a total of 763774 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3691 -67.28502 -2.67401 0.54554 INTE EXTERN> -32.44655 -34.83847 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.285" Parameter: A <- "-67.285" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4465" Parameter: B <- "-32.4465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8385" Parameter: C <- "-34.8385" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3691 TOTAL ENERGY = -67.285 RDTITL> * VAN DER WAALS = -32.4465 ELECTROSTATIC = -34.8385 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3691" Parameter: CONF_N -> "8002" Comparing "3691" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3692" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763774 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754362 ATOM PAIRS WERE FOUND FOR ATOM LIST 41736 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28773 from a total of 754362 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3692 -70.33424 3.04922 0.61864 INTE EXTERN> -30.30647 -40.02777 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3342" Parameter: A <- "-70.3342" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3065" Parameter: B <- "-30.3065" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0278" Parameter: C <- "-40.0278" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3692 TOTAL ENERGY = -70.3342 RDTITL> * VAN DER WAALS = -30.3065 ELECTROSTATIC = -40.0278 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3692" Parameter: CONF_N -> "8002" Comparing "3692" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3693" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754362 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758115 ATOM PAIRS WERE FOUND FOR ATOM LIST 41763 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28380 from a total of 758115 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3693 -69.07360 -1.26064 0.62721 INTE EXTERN> -28.79456 -40.27904 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0736" Parameter: A <- "-69.0736" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7946" Parameter: B <- "-28.7946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.279" Parameter: C <- "-40.279" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3693 TOTAL ENERGY = -69.0736 RDTITL> * VAN DER WAALS = -28.7946 ELECTROSTATIC = -40.279 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3693" Parameter: CONF_N -> "8002" Comparing "3693" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3694" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758115 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759154 ATOM PAIRS WERE FOUND FOR ATOM LIST 41687 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28483 from a total of 759154 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3694 -72.54106 3.46746 0.57862 INTE EXTERN> -30.65886 -41.88221 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5411" Parameter: A <- "-72.5411" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6589" Parameter: B <- "-30.6589" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8822" Parameter: C <- "-41.8822" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3694 TOTAL ENERGY = -72.5411 RDTITL> * VAN DER WAALS = -30.6589 ELECTROSTATIC = -41.8822 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3694" Parameter: CONF_N -> "8002" Comparing "3694" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3695" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759154 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758131 ATOM PAIRS WERE FOUND FOR ATOM LIST 41935 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28333 from a total of 758131 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3695 -72.32521 -0.21585 0.71868 INTE EXTERN> -24.73538 -47.58983 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3252" Parameter: A <- "-72.3252" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7354" Parameter: B <- "-24.7354" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5898" Parameter: C <- "-47.5898" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3695 TOTAL ENERGY = -72.3252 RDTITL> * VAN DER WAALS = -24.7354 ELECTROSTATIC = -47.5898 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3695" Parameter: CONF_N -> "8002" Comparing "3695" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3696" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758131 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761738 ATOM PAIRS WERE FOUND FOR ATOM LIST 41924 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29110 from a total of 761738 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3696 -71.34241 -0.98280 0.72549 INTE EXTERN> -22.99155 -48.35086 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3424" Parameter: A <- "-71.3424" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.9915" Parameter: B <- "-22.9915" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3509" Parameter: C <- "-48.3509" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3696 TOTAL ENERGY = -71.3424 RDTITL> * VAN DER WAALS = -22.9915 ELECTROSTATIC = -48.3509 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3696" Parameter: CONF_N -> "8002" Comparing "3696" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3697" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761738 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762965 ATOM PAIRS WERE FOUND FOR ATOM LIST 41998 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29495 from a total of 762965 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3697 -71.05327 -0.28914 0.67655 INTE EXTERN> -27.55870 -43.49457 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0533" Parameter: A <- "-71.0533" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5587" Parameter: B <- "-27.5587" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4946" Parameter: C <- "-43.4946" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3697 TOTAL ENERGY = -71.0533 RDTITL> * VAN DER WAALS = -27.5587 ELECTROSTATIC = -43.4946 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3697" Parameter: CONF_N -> "8002" Comparing "3697" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3698" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762965 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756519 ATOM PAIRS WERE FOUND FOR ATOM LIST 41740 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28983 from a total of 756519 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3698 -76.07071 5.01744 0.62641 INTE EXTERN> -29.79794 -46.27277 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0707" Parameter: A <- "-76.0707" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7979" Parameter: B <- "-29.7979" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2728" Parameter: C <- "-46.2728" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3698 TOTAL ENERGY = -76.0707 RDTITL> * VAN DER WAALS = -29.7979 ELECTROSTATIC = -46.2728 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3698" Parameter: CONF_N -> "8002" Comparing "3698" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3699" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756519 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762930 ATOM PAIRS WERE FOUND FOR ATOM LIST 42032 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28666 from a total of 762930 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3699 -81.52126 5.45056 0.67421 INTE EXTERN> -28.16246 -53.35881 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5213" Parameter: A <- "-81.5213" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1625" Parameter: B <- "-28.1625" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3588" Parameter: C <- "-53.3588" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3699 TOTAL ENERGY = -81.5213 RDTITL> * VAN DER WAALS = -28.1625 ELECTROSTATIC = -53.3588 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3699" Parameter: CONF_N -> "8002" Comparing "3699" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3700" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762930 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758932 ATOM PAIRS WERE FOUND FOR ATOM LIST 41960 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28685 from a total of 758932 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3700 -70.94658 -10.57468 0.54339 INTE EXTERN> -30.39854 -40.54804 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9466" Parameter: A <- "-70.9466" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3985" Parameter: B <- "-30.3985" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.548" Parameter: C <- "-40.548" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3700 TOTAL ENERGY = -70.9466 RDTITL> * VAN DER WAALS = -30.3985 ELECTROSTATIC = -40.548 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3700" Parameter: CONF_N -> "8002" Comparing "3700" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3701" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758932 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753246 ATOM PAIRS WERE FOUND FOR ATOM LIST 41701 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28625 from a total of 753246 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3701 -69.85432 -1.09226 0.81080 INTE EXTERN> -21.07352 -48.78080 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8543" Parameter: A <- "-69.8543" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.0735" Parameter: B <- "-21.0735" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7808" Parameter: C <- "-48.7808" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3701 TOTAL ENERGY = -69.8543 RDTITL> * VAN DER WAALS = -21.0735 ELECTROSTATIC = -48.7808 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3701" Parameter: CONF_N -> "8002" Comparing "3701" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3702" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753246 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764004 ATOM PAIRS WERE FOUND FOR ATOM LIST 42295 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28357 from a total of 764004 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3702 -70.45814 0.60382 0.63335 INTE EXTERN> -25.98497 -44.47318 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4581" Parameter: A <- "-70.4581" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.985" Parameter: B <- "-25.985" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4732" Parameter: C <- "-44.4732" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3702 TOTAL ENERGY = -70.4581 RDTITL> * VAN DER WAALS = -25.985 ELECTROSTATIC = -44.4732 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3702" Parameter: CONF_N -> "8002" Comparing "3702" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3703" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764004 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758351 ATOM PAIRS WERE FOUND FOR ATOM LIST 41797 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28437 from a total of 758351 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3703 -77.29407 6.83593 0.72874 INTE EXTERN> -27.20162 -50.09246 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2941" Parameter: A <- "-77.2941" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2016" Parameter: B <- "-27.2016" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0925" Parameter: C <- "-50.0925" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3703 TOTAL ENERGY = -77.2941 RDTITL> * VAN DER WAALS = -27.2016 ELECTROSTATIC = -50.0925 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3703" Parameter: CONF_N -> "8002" Comparing "3703" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3704" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758351 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762600 ATOM PAIRS WERE FOUND FOR ATOM LIST 42130 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28504 from a total of 762600 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3704 -69.50318 -7.79089 0.58663 INTE EXTERN> -28.51973 -40.98345 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5032" Parameter: A <- "-69.5032" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5197" Parameter: B <- "-28.5197" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9834" Parameter: C <- "-40.9834" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3704 TOTAL ENERGY = -69.5032 RDTITL> * VAN DER WAALS = -28.5197 ELECTROSTATIC = -40.9834 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3704" Parameter: CONF_N -> "8002" Comparing "3704" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3705" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762600 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762740 ATOM PAIRS WERE FOUND FOR ATOM LIST 41992 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28332 from a total of 762740 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3705 -74.84083 5.33765 0.55598 INTE EXTERN> -30.71677 -44.12406 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8408" Parameter: A <- "-74.8408" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7168" Parameter: B <- "-30.7168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1241" Parameter: C <- "-44.1241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3705 TOTAL ENERGY = -74.8408 RDTITL> * VAN DER WAALS = -30.7168 ELECTROSTATIC = -44.1241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3705" Parameter: CONF_N -> "8002" Comparing "3705" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3706" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762740 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765987 ATOM PAIRS WERE FOUND FOR ATOM LIST 42175 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28952 from a total of 765987 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3706 -76.95319 2.11236 0.71454 INTE EXTERN> -24.46434 -52.48885 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9532" Parameter: A <- "-76.9532" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4643" Parameter: B <- "-24.4643" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.4888" Parameter: C <- "-52.4888" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3706 TOTAL ENERGY = -76.9532 RDTITL> * VAN DER WAALS = -24.4643 ELECTROSTATIC = -52.4888 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3706" Parameter: CONF_N -> "8002" Comparing "3706" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3707" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765987 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763904 ATOM PAIRS WERE FOUND FOR ATOM LIST 42016 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28174 from a total of 763904 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3707 -69.46061 -7.49258 0.57564 INTE EXTERN> -28.04552 -41.41509 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4606" Parameter: A <- "-69.4606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0455" Parameter: B <- "-28.0455" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4151" Parameter: C <- "-41.4151" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3707 TOTAL ENERGY = -69.4606 RDTITL> * VAN DER WAALS = -28.0455 ELECTROSTATIC = -41.4151 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3707" Parameter: CONF_N -> "8002" Comparing "3707" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3708" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763904 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755842 ATOM PAIRS WERE FOUND FOR ATOM LIST 41704 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28186 from a total of 755842 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3708 -80.33985 10.87924 0.60124 INTE EXTERN> -29.05719 -51.28265 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3398" Parameter: A <- "-80.3398" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0572" Parameter: B <- "-29.0572" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2827" Parameter: C <- "-51.2827" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3708 TOTAL ENERGY = -80.3398 RDTITL> * VAN DER WAALS = -29.0572 ELECTROSTATIC = -51.2827 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3708" Parameter: CONF_N -> "8002" Comparing "3708" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3709" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755842 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41793 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28695 from a total of 757009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3709 -78.34828 -1.99157 0.62485 INTE EXTERN> -30.00615 -48.34213 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3483" Parameter: A <- "-78.3483" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0061" Parameter: B <- "-30.0061" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3421" Parameter: C <- "-48.3421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3709 TOTAL ENERGY = -78.3483 RDTITL> * VAN DER WAALS = -30.0061 ELECTROSTATIC = -48.3421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3709" Parameter: CONF_N -> "8002" Comparing "3709" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3710" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765585 ATOM PAIRS WERE FOUND FOR ATOM LIST 42083 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28971 from a total of 765585 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3710 -78.81560 0.46733 0.75417 INTE EXTERN> -26.05604 -52.75957 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8156" Parameter: A <- "-78.8156" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.056" Parameter: B <- "-26.056" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.7596" Parameter: C <- "-52.7596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3710 TOTAL ENERGY = -78.8156 RDTITL> * VAN DER WAALS = -26.056 ELECTROSTATIC = -52.7596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3710" Parameter: CONF_N -> "8002" Comparing "3710" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3711" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765585 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763795 ATOM PAIRS WERE FOUND FOR ATOM LIST 42065 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28900 from a total of 763795 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3711 -82.36776 3.55215 0.63663 INTE EXTERN> -31.33155 -51.03621 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3678" Parameter: A <- "-82.3678" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3316" Parameter: B <- "-31.3316" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0362" Parameter: C <- "-51.0362" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3711 TOTAL ENERGY = -82.3678 RDTITL> * VAN DER WAALS = -31.3316 ELECTROSTATIC = -51.0362 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3711" Parameter: CONF_N -> "8002" Comparing "3711" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3712" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763795 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768090 ATOM PAIRS WERE FOUND FOR ATOM LIST 42033 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28952 from a total of 768090 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3712 -73.41377 -8.95399 0.58666 INTE EXTERN> -27.75686 -45.65690 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4138" Parameter: A <- "-73.4138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7569" Parameter: B <- "-27.7569" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6569" Parameter: C <- "-45.6569" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3712 TOTAL ENERGY = -73.4138 RDTITL> * VAN DER WAALS = -27.7569 ELECTROSTATIC = -45.6569 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3712" Parameter: CONF_N -> "8002" Comparing "3712" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3713" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768090 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764976 ATOM PAIRS WERE FOUND FOR ATOM LIST 42174 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28985 from a total of 764976 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3713 -75.80536 2.39159 0.66446 INTE EXTERN> -28.54517 -47.26019 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8054" Parameter: A <- "-75.8054" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5452" Parameter: B <- "-28.5452" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2602" Parameter: C <- "-47.2602" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3713 TOTAL ENERGY = -75.8054 RDTITL> * VAN DER WAALS = -28.5452 ELECTROSTATIC = -47.2602 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3713" Parameter: CONF_N -> "8002" Comparing "3713" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3714" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764976 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761602 ATOM PAIRS WERE FOUND FOR ATOM LIST 42252 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29617 from a total of 761602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3714 -76.70584 0.90048 0.66939 INTE EXTERN> -25.86484 -50.84101 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7058" Parameter: A <- "-76.7058" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8648" Parameter: B <- "-25.8648" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.841" Parameter: C <- "-50.841" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3714 TOTAL ENERGY = -76.7058 RDTITL> * VAN DER WAALS = -25.8648 ELECTROSTATIC = -50.841 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3714" Parameter: CONF_N -> "8002" Comparing "3714" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3715" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762067 ATOM PAIRS WERE FOUND FOR ATOM LIST 42121 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28773 from a total of 762067 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3715 -74.85745 -1.84839 0.56420 INTE EXTERN> -30.51241 -44.34504 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8575" Parameter: A <- "-74.8575" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5124" Parameter: B <- "-30.5124" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.345" Parameter: C <- "-44.345" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3715 TOTAL ENERGY = -74.8575 RDTITL> * VAN DER WAALS = -30.5124 ELECTROSTATIC = -44.345 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3715" Parameter: CONF_N -> "8002" Comparing "3715" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3716" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762067 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764418 ATOM PAIRS WERE FOUND FOR ATOM LIST 42204 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29268 from a total of 764418 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3716 -82.66739 7.80994 0.63490 INTE EXTERN> -28.84123 -53.82616 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.6674" Parameter: A <- "-82.6674" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8412" Parameter: B <- "-28.8412" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8262" Parameter: C <- "-53.8262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3716 TOTAL ENERGY = -82.6674 RDTITL> * VAN DER WAALS = -28.8412 ELECTROSTATIC = -53.8262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3716" Parameter: CONF_N -> "8002" Comparing "3716" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3717" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764418 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764550 ATOM PAIRS WERE FOUND FOR ATOM LIST 42209 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29569 from a total of 764550 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3717 -79.13077 -3.53662 0.65337 INTE EXTERN> -29.47250 -49.65827 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1308" Parameter: A <- "-79.1308" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4725" Parameter: B <- "-29.4725" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6583" Parameter: C <- "-49.6583" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3717 TOTAL ENERGY = -79.1308 RDTITL> * VAN DER WAALS = -29.4725 ELECTROSTATIC = -49.6583 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3717" Parameter: CONF_N -> "8002" Comparing "3717" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3718" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764550 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760871 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29320 from a total of 760871 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3718 -74.91413 -4.21664 0.70925 INTE EXTERN> -27.58253 -47.33160 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9141" Parameter: A <- "-74.9141" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5825" Parameter: B <- "-27.5825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3316" Parameter: C <- "-47.3316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3718 TOTAL ENERGY = -74.9141 RDTITL> * VAN DER WAALS = -27.5825 ELECTROSTATIC = -47.3316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3718" Parameter: CONF_N -> "8002" Comparing "3718" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3719" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760871 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759101 ATOM PAIRS WERE FOUND FOR ATOM LIST 41884 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29540 from a total of 759101 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3719 -84.07361 9.15948 0.60337 INTE EXTERN> -32.03986 -52.03375 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.0736" Parameter: A <- "-84.0736" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0399" Parameter: B <- "-32.0399" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0338" Parameter: C <- "-52.0338" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3719 TOTAL ENERGY = -84.0736 RDTITL> * VAN DER WAALS = -32.0399 ELECTROSTATIC = -52.0338 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3719" Parameter: CONF_N -> "8002" Comparing "3719" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3720" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759101 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757029 ATOM PAIRS WERE FOUND FOR ATOM LIST 41681 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29281 from a total of 757029 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3720 -78.57135 -5.50226 0.59163 INTE EXTERN> -31.37199 -47.19936 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5714" Parameter: A <- "-78.5714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.372" Parameter: B <- "-31.372" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1994" Parameter: C <- "-47.1994" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3720 TOTAL ENERGY = -78.5714 RDTITL> * VAN DER WAALS = -31.372 ELECTROSTATIC = -47.1994 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3720" Parameter: CONF_N -> "8002" Comparing "3720" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3721" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757029 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763796 ATOM PAIRS WERE FOUND FOR ATOM LIST 42073 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29453 from a total of 763796 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3721 -81.04295 2.47160 0.56669 INTE EXTERN> -35.18155 -45.86140 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.043" Parameter: A <- "-81.043" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.1816" Parameter: B <- "-35.1816" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8614" Parameter: C <- "-45.8614" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3721 TOTAL ENERGY = -81.043 RDTITL> * VAN DER WAALS = -35.1816 ELECTROSTATIC = -45.8614 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3721" Parameter: CONF_N -> "8002" Comparing "3721" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3722" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763796 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761702 ATOM PAIRS WERE FOUND FOR ATOM LIST 41969 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29278 from a total of 761702 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3722 -81.64934 0.60639 0.68963 INTE EXTERN> -29.26692 -52.38242 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6493" Parameter: A <- "-81.6493" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2669" Parameter: B <- "-29.2669" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3824" Parameter: C <- "-52.3824" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3722 TOTAL ENERGY = -81.6493 RDTITL> * VAN DER WAALS = -29.2669 ELECTROSTATIC = -52.3824 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3722" Parameter: CONF_N -> "8002" Comparing "3722" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3723" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761702 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760430 ATOM PAIRS WERE FOUND FOR ATOM LIST 41932 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29276 from a total of 760430 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3723 -86.07945 4.43011 0.69729 INTE EXTERN> -30.86334 -55.21610 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.0794" Parameter: A <- "-86.0794" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8633" Parameter: B <- "-30.8633" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.2161" Parameter: C <- "-55.2161" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3723 TOTAL ENERGY = -86.0794 RDTITL> * VAN DER WAALS = -30.8633 ELECTROSTATIC = -55.2161 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3723" Parameter: CONF_N -> "8002" Comparing "3723" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3724" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760430 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757615 ATOM PAIRS WERE FOUND FOR ATOM LIST 41839 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29197 from a total of 757615 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3724 -73.15489 -12.92455 0.55702 INTE EXTERN> -33.45437 -39.70052 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1549" Parameter: A <- "-73.1549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4544" Parameter: B <- "-33.4544" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7005" Parameter: C <- "-39.7005" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3724 TOTAL ENERGY = -73.1549 RDTITL> * VAN DER WAALS = -33.4544 ELECTROSTATIC = -39.7005 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3724" Parameter: CONF_N -> "8002" Comparing "3724" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3725" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757615 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767856 ATOM PAIRS WERE FOUND FOR ATOM LIST 42250 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29450 from a total of 767856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3725 -85.82503 12.67014 0.63412 INTE EXTERN> -30.97972 -54.84531 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.825" Parameter: A <- "-85.825" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9797" Parameter: B <- "-30.9797" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8453" Parameter: C <- "-54.8453" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3725 TOTAL ENERGY = -85.825 RDTITL> * VAN DER WAALS = -30.9797 ELECTROSTATIC = -54.8453 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3725" Parameter: CONF_N -> "8002" Comparing "3725" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3726" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771271 ATOM PAIRS WERE FOUND FOR ATOM LIST 42580 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30214 from a total of 771271 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3726 -75.66333 -10.16170 0.64586 INTE EXTERN> -31.28484 -44.37849 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6633" Parameter: A <- "-75.6633" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2848" Parameter: B <- "-31.2848" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3785" Parameter: C <- "-44.3785" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3726 TOTAL ENERGY = -75.6633 RDTITL> * VAN DER WAALS = -31.2848 ELECTROSTATIC = -44.3785 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3726" Parameter: CONF_N -> "8002" Comparing "3726" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3727" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771271 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764519 ATOM PAIRS WERE FOUND FOR ATOM LIST 42189 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29937 from a total of 764519 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3727 -71.26612 -4.39721 0.64004 INTE EXTERN> -28.77276 -42.49336 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2661" Parameter: A <- "-71.2661" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7728" Parameter: B <- "-28.7728" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4934" Parameter: C <- "-42.4934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3727 TOTAL ENERGY = -71.2661 RDTITL> * VAN DER WAALS = -28.7728 ELECTROSTATIC = -42.4934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3727" Parameter: CONF_N -> "8002" Comparing "3727" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3728" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764519 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763513 ATOM PAIRS WERE FOUND FOR ATOM LIST 42202 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29197 from a total of 763513 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3728 -78.88071 7.61459 0.55678 INTE EXTERN> -33.34020 -45.54051 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8807" Parameter: A <- "-78.8807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3402" Parameter: B <- "-33.3402" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5405" Parameter: C <- "-45.5405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3728 TOTAL ENERGY = -78.8807 RDTITL> * VAN DER WAALS = -33.3402 ELECTROSTATIC = -45.5405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3728" Parameter: CONF_N -> "8002" Comparing "3728" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3729" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763513 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761472 ATOM PAIRS WERE FOUND FOR ATOM LIST 41963 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29294 from a total of 761472 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3729 -74.27117 -4.60953 0.63412 INTE EXTERN> -27.97403 -46.29715 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2712" Parameter: A <- "-74.2712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.974" Parameter: B <- "-27.974" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2971" Parameter: C <- "-46.2971" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3729 TOTAL ENERGY = -74.2712 RDTITL> * VAN DER WAALS = -27.974 ELECTROSTATIC = -46.2971 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3729" Parameter: CONF_N -> "8002" Comparing "3729" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3730" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761472 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764689 ATOM PAIRS WERE FOUND FOR ATOM LIST 42152 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29464 from a total of 764689 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3730 -78.47071 4.19954 0.65465 INTE EXTERN> -29.73236 -48.73835 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4707" Parameter: A <- "-78.4707" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7324" Parameter: B <- "-29.7324" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7384" Parameter: C <- "-48.7384" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3730 TOTAL ENERGY = -78.4707 RDTITL> * VAN DER WAALS = -29.7324 ELECTROSTATIC = -48.7384 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3730" Parameter: CONF_N -> "8002" Comparing "3730" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3731" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764689 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761456 ATOM PAIRS WERE FOUND FOR ATOM LIST 42110 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29265 from a total of 761456 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3731 -74.82075 -3.64996 0.65355 INTE EXTERN> -29.33116 -45.48959 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8207" Parameter: A <- "-74.8207" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3312" Parameter: B <- "-29.3312" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4896" Parameter: C <- "-45.4896" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3731 TOTAL ENERGY = -74.8207 RDTITL> * VAN DER WAALS = -29.3312 ELECTROSTATIC = -45.4896 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3731" Parameter: CONF_N -> "8002" Comparing "3731" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3732" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761456 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759491 ATOM PAIRS WERE FOUND FOR ATOM LIST 41979 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29038 from a total of 759491 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3732 -75.15216 0.33141 0.54330 INTE EXTERN> -33.75955 -41.39261 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1522" Parameter: A <- "-75.1522" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7595" Parameter: B <- "-33.7595" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3926" Parameter: C <- "-41.3926" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3732 TOTAL ENERGY = -75.1522 RDTITL> * VAN DER WAALS = -33.7595 ELECTROSTATIC = -41.3926 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3732" Parameter: CONF_N -> "8002" Comparing "3732" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3733" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759491 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760706 ATOM PAIRS WERE FOUND FOR ATOM LIST 42094 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29051 from a total of 760706 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3733 -73.69064 -1.46151 0.54196 INTE EXTERN> -32.42115 -41.26949 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6906" Parameter: A <- "-73.6906" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4211" Parameter: B <- "-32.4211" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2695" Parameter: C <- "-41.2695" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3733 TOTAL ENERGY = -73.6906 RDTITL> * VAN DER WAALS = -32.4211 ELECTROSTATIC = -41.2695 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3733" Parameter: CONF_N -> "8002" Comparing "3733" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3734" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760706 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761297 ATOM PAIRS WERE FOUND FOR ATOM LIST 41779 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28933 from a total of 761297 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3734 -69.11440 -4.57624 0.47653 INTE EXTERN> -34.86733 -34.24707 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1144" Parameter: A <- "-69.1144" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.8673" Parameter: B <- "-34.8673" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2471" Parameter: C <- "-34.2471" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3734 TOTAL ENERGY = -69.1144 RDTITL> * VAN DER WAALS = -34.8673 ELECTROSTATIC = -34.2471 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3734" Parameter: CONF_N -> "8002" Comparing "3734" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3735" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761297 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758024 ATOM PAIRS WERE FOUND FOR ATOM LIST 41685 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28469 from a total of 758024 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3735 -78.94136 9.82696 0.61971 INTE EXTERN> -30.17770 -48.76366 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9414" Parameter: A <- "-78.9414" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1777" Parameter: B <- "-30.1777" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7637" Parameter: C <- "-48.7637" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3735 TOTAL ENERGY = -78.9414 RDTITL> * VAN DER WAALS = -30.1777 ELECTROSTATIC = -48.7637 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3735" Parameter: CONF_N -> "8002" Comparing "3735" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3736" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758024 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757906 ATOM PAIRS WERE FOUND FOR ATOM LIST 41749 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28638 from a total of 757906 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3736 -73.30891 -5.63246 0.70563 INTE EXTERN> -28.07553 -45.23338 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3089" Parameter: A <- "-73.3089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0755" Parameter: B <- "-28.0755" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2334" Parameter: C <- "-45.2334" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3736 TOTAL ENERGY = -73.3089 RDTITL> * VAN DER WAALS = -28.0755 ELECTROSTATIC = -45.2334 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3736" Parameter: CONF_N -> "8002" Comparing "3736" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3737" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757906 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41731 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28918 from a total of 757110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3737 -76.14486 2.83595 0.62371 INTE EXTERN> -29.97299 -46.17187 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1449" Parameter: A <- "-76.1449" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.973" Parameter: B <- "-29.973" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1719" Parameter: C <- "-46.1719" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3737 TOTAL ENERGY = -76.1449 RDTITL> * VAN DER WAALS = -29.973 ELECTROSTATIC = -46.1719 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3737" Parameter: CONF_N -> "8002" Comparing "3737" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3738" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758180 ATOM PAIRS WERE FOUND FOR ATOM LIST 41818 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28798 from a total of 758180 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3738 -77.66738 1.52253 0.60099 INTE EXTERN> -31.38866 -46.27873 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6674" Parameter: A <- "-77.6674" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3887" Parameter: B <- "-31.3887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2787" Parameter: C <- "-46.2787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3738 TOTAL ENERGY = -77.6674 RDTITL> * VAN DER WAALS = -31.3887 ELECTROSTATIC = -46.2787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3738" Parameter: CONF_N -> "8002" Comparing "3738" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3739" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758180 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758527 ATOM PAIRS WERE FOUND FOR ATOM LIST 41868 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28910 from a total of 758527 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3739 -75.99540 -1.67198 0.70751 INTE EXTERN> -28.79017 -47.20523 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9954" Parameter: A <- "-75.9954" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7902" Parameter: B <- "-28.7902" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2052" Parameter: C <- "-47.2052" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3739 TOTAL ENERGY = -75.9954 RDTITL> * VAN DER WAALS = -28.7902 ELECTROSTATIC = -47.2052 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3739" Parameter: CONF_N -> "8002" Comparing "3739" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3740" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758527 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766897 ATOM PAIRS WERE FOUND FOR ATOM LIST 42306 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29498 from a total of 766897 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3740 -74.49954 -1.49586 0.56721 INTE EXTERN> -33.03243 -41.46711 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4995" Parameter: A <- "-74.4995" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0324" Parameter: B <- "-33.0324" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4671" Parameter: C <- "-41.4671" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3740 TOTAL ENERGY = -74.4995 RDTITL> * VAN DER WAALS = -33.0324 ELECTROSTATIC = -41.4671 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3740" Parameter: CONF_N -> "8002" Comparing "3740" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3741" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766897 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757665 ATOM PAIRS WERE FOUND FOR ATOM LIST 41664 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28011 from a total of 757665 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3741 -79.57412 5.07458 0.71345 INTE EXTERN> -25.95212 -53.62200 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5741" Parameter: A <- "-79.5741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9521" Parameter: B <- "-25.9521" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.622" Parameter: C <- "-53.622" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3741 TOTAL ENERGY = -79.5741 RDTITL> * VAN DER WAALS = -25.9521 ELECTROSTATIC = -53.622 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3741" Parameter: CONF_N -> "8002" Comparing "3741" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3742" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757665 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756489 ATOM PAIRS WERE FOUND FOR ATOM LIST 41788 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28488 from a total of 756489 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3742 -75.20185 -4.37228 0.71191 INTE EXTERN> -26.75284 -48.44901 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2018" Parameter: A <- "-75.2018" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7528" Parameter: B <- "-26.7528" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.449" Parameter: C <- "-48.449" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3742 TOTAL ENERGY = -75.2018 RDTITL> * VAN DER WAALS = -26.7528 ELECTROSTATIC = -48.449 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3742" Parameter: CONF_N -> "8002" Comparing "3742" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3743" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756489 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757019 ATOM PAIRS WERE FOUND FOR ATOM LIST 41979 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28565 from a total of 757019 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3743 -75.32919 0.12734 0.59738 INTE EXTERN> -29.25743 -46.07176 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3292" Parameter: A <- "-75.3292" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2574" Parameter: B <- "-29.2574" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0718" Parameter: C <- "-46.0718" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3743 TOTAL ENERGY = -75.3292 RDTITL> * VAN DER WAALS = -29.2574 ELECTROSTATIC = -46.0718 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3743" Parameter: CONF_N -> "8002" Comparing "3743" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3744" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757019 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756754 ATOM PAIRS WERE FOUND FOR ATOM LIST 41686 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28421 from a total of 756754 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3744 -76.12963 0.80045 0.74834 INTE EXTERN> -24.88865 -51.24098 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1296" Parameter: A <- "-76.1296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8887" Parameter: B <- "-24.8887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.241" Parameter: C <- "-51.241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3744 TOTAL ENERGY = -76.1296 RDTITL> * VAN DER WAALS = -24.8887 ELECTROSTATIC = -51.241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3744" Parameter: CONF_N -> "8002" Comparing "3744" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3745" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756754 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761221 ATOM PAIRS WERE FOUND FOR ATOM LIST 42049 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28903 from a total of 761221 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3745 -75.88835 -0.24128 0.63311 INTE EXTERN> -29.08850 -46.79985 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8884" Parameter: A <- "-75.8884" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0885" Parameter: B <- "-29.0885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7999" Parameter: C <- "-46.7999" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3745 TOTAL ENERGY = -75.8884 RDTITL> * VAN DER WAALS = -29.0885 ELECTROSTATIC = -46.7999 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3745" Parameter: CONF_N -> "8002" Comparing "3745" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3746" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761221 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761473 ATOM PAIRS WERE FOUND FOR ATOM LIST 41986 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29056 from a total of 761473 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3746 -76.49180 0.60345 0.74417 INTE EXTERN> -26.08095 -50.41085 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4918" Parameter: A <- "-76.4918" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0809" Parameter: B <- "-26.0809" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4109" Parameter: C <- "-50.4109" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3746 TOTAL ENERGY = -76.4918 RDTITL> * VAN DER WAALS = -26.0809 ELECTROSTATIC = -50.4109 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3746" Parameter: CONF_N -> "8002" Comparing "3746" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3747" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761473 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759816 ATOM PAIRS WERE FOUND FOR ATOM LIST 41784 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28390 from a total of 759816 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3747 -77.68327 1.19147 0.66871 INTE EXTERN> -28.34618 -49.33709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6833" Parameter: A <- "-77.6833" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3462" Parameter: B <- "-28.3462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3371" Parameter: C <- "-49.3371" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3747 TOTAL ENERGY = -77.6833 RDTITL> * VAN DER WAALS = -28.3462 ELECTROSTATIC = -49.3371 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3747" Parameter: CONF_N -> "8002" Comparing "3747" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3748" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759816 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756206 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28518 from a total of 756206 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3748 -77.14568 -0.53759 0.65509 INTE EXTERN> -27.60574 -49.53995 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1457" Parameter: A <- "-77.1457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6057" Parameter: B <- "-27.6057" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5399" Parameter: C <- "-49.5399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3748 TOTAL ENERGY = -77.1457 RDTITL> * VAN DER WAALS = -27.6057 ELECTROSTATIC = -49.5399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3748" Parameter: CONF_N -> "8002" Comparing "3748" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3749" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756206 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760978 ATOM PAIRS WERE FOUND FOR ATOM LIST 42012 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28551 from a total of 760978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3749 -73.67398 -3.47170 0.60838 INTE EXTERN> -29.83855 -43.83544 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.674" Parameter: A <- "-73.674" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8385" Parameter: B <- "-29.8385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8354" Parameter: C <- "-43.8354" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3749 TOTAL ENERGY = -73.674 RDTITL> * VAN DER WAALS = -29.8385 ELECTROSTATIC = -43.8354 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3749" Parameter: CONF_N -> "8002" Comparing "3749" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3750" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758468 ATOM PAIRS WERE FOUND FOR ATOM LIST 41735 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29015 from a total of 758468 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3750 -73.07896 -0.59503 0.69579 INTE EXTERN> -23.93820 -49.14075 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.079" Parameter: A <- "-73.079" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9382" Parameter: B <- "-23.9382" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1408" Parameter: C <- "-49.1408" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3750 TOTAL ENERGY = -73.079 RDTITL> * VAN DER WAALS = -23.9382 ELECTROSTATIC = -49.1408 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3750" Parameter: CONF_N -> "8002" Comparing "3750" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3751" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758468 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763363 ATOM PAIRS WERE FOUND FOR ATOM LIST 42139 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27863 from a total of 763363 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3751 -79.56947 6.49051 0.76657 INTE EXTERN> -21.42497 -58.14451 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5695" Parameter: A <- "-79.5695" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.425" Parameter: B <- "-21.425" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.1445" Parameter: C <- "-58.1445" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3751 TOTAL ENERGY = -79.5695 RDTITL> * VAN DER WAALS = -21.425 ELECTROSTATIC = -58.1445 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3751" Parameter: CONF_N -> "8002" Comparing "3751" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3752" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763363 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764834 ATOM PAIRS WERE FOUND FOR ATOM LIST 42015 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28222 from a total of 764834 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3752 -75.01361 -4.55586 0.69384 INTE EXTERN> -26.19708 -48.81653 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0136" Parameter: A <- "-75.0136" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1971" Parameter: B <- "-26.1971" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8165" Parameter: C <- "-48.8165" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3752 TOTAL ENERGY = -75.0136 RDTITL> * VAN DER WAALS = -26.1971 ELECTROSTATIC = -48.8165 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3752" Parameter: CONF_N -> "8002" Comparing "3752" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3753" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764834 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756684 ATOM PAIRS WERE FOUND FOR ATOM LIST 41758 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28496 from a total of 756684 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3753 -74.31019 -0.70341 0.59954 INTE EXTERN> -30.61069 -43.69951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3102" Parameter: A <- "-74.3102" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6107" Parameter: B <- "-30.6107" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6995" Parameter: C <- "-43.6995" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3753 TOTAL ENERGY = -74.3102 RDTITL> * VAN DER WAALS = -30.6107 ELECTROSTATIC = -43.6995 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3753" Parameter: CONF_N -> "8002" Comparing "3753" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3754" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756684 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758844 ATOM PAIRS WERE FOUND FOR ATOM LIST 41886 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28140 from a total of 758844 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3754 -73.48543 -0.82477 0.87877 INTE EXTERN> -20.01104 -53.47439 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4854" Parameter: A <- "-73.4854" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.011" Parameter: B <- "-20.011" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4744" Parameter: C <- "-53.4744" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3754 TOTAL ENERGY = -73.4854 RDTITL> * VAN DER WAALS = -20.011 ELECTROSTATIC = -53.4744 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3754" Parameter: CONF_N -> "8002" Comparing "3754" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3755" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758844 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757633 ATOM PAIRS WERE FOUND FOR ATOM LIST 41783 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29349 from a total of 757633 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3755 -73.81924 0.33381 0.63019 INTE EXTERN> -30.59743 -43.22181 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8192" Parameter: A <- "-73.8192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5974" Parameter: B <- "-30.5974" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2218" Parameter: C <- "-43.2218" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3755 TOTAL ENERGY = -73.8192 RDTITL> * VAN DER WAALS = -30.5974 ELECTROSTATIC = -43.2218 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3755" Parameter: CONF_N -> "8002" Comparing "3755" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3756" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757633 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29102 from a total of 757110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3756 -71.61906 -2.20018 0.61820 INTE EXTERN> -30.22196 -41.39710 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6191" Parameter: A <- "-71.6191" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.222" Parameter: B <- "-30.222" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3971" Parameter: C <- "-41.3971" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3756 TOTAL ENERGY = -71.6191 RDTITL> * VAN DER WAALS = -30.222 ELECTROSTATIC = -41.3971 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3756" Parameter: CONF_N -> "8002" Comparing "3756" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3757" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758931 ATOM PAIRS WERE FOUND FOR ATOM LIST 41867 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29548 from a total of 758931 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3757 -74.83844 3.21939 0.63578 INTE EXTERN> -29.37958 -45.45887 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8384" Parameter: A <- "-74.8384" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3796" Parameter: B <- "-29.3796" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4589" Parameter: C <- "-45.4589" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3757 TOTAL ENERGY = -74.8384 RDTITL> * VAN DER WAALS = -29.3796 ELECTROSTATIC = -45.4589 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3757" Parameter: CONF_N -> "8002" Comparing "3757" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3758" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758931 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754999 ATOM PAIRS WERE FOUND FOR ATOM LIST 41516 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27822 from a total of 754999 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3758 -73.17991 -1.65853 0.64630 INTE EXTERN> -26.75779 -46.42212 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1799" Parameter: A <- "-73.1799" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7578" Parameter: B <- "-26.7578" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4221" Parameter: C <- "-46.4221" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3758 TOTAL ENERGY = -73.1799 RDTITL> * VAN DER WAALS = -26.7578 ELECTROSTATIC = -46.4221 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3758" Parameter: CONF_N -> "8002" Comparing "3758" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3759" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754999 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761065 ATOM PAIRS WERE FOUND FOR ATOM LIST 41980 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29008 from a total of 761065 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3759 -81.91362 8.73372 0.68571 INTE EXTERN> -30.76786 -51.14577 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9136" Parameter: A <- "-81.9136" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7679" Parameter: B <- "-30.7679" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1458" Parameter: C <- "-51.1458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3759 TOTAL ENERGY = -81.9136 RDTITL> * VAN DER WAALS = -30.7679 ELECTROSTATIC = -51.1458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3759" Parameter: CONF_N -> "8002" Comparing "3759" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3760" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761065 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765444 ATOM PAIRS WERE FOUND FOR ATOM LIST 42341 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29144 from a total of 765444 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3760 -75.07902 -6.83460 0.60816 INTE EXTERN> -31.07093 -44.00809 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.079" Parameter: A <- "-75.079" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0709" Parameter: B <- "-31.0709" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0081" Parameter: C <- "-44.0081" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3760 TOTAL ENERGY = -75.079 RDTITL> * VAN DER WAALS = -31.0709 ELECTROSTATIC = -44.0081 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3760" Parameter: CONF_N -> "8002" Comparing "3760" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3761" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765444 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760655 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29080 from a total of 760655 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3761 -69.28542 -5.79361 0.66328 INTE EXTERN> -29.43545 -39.84996 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2854" Parameter: A <- "-69.2854" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4355" Parameter: B <- "-29.4355" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.85" Parameter: C <- "-39.85" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3761 TOTAL ENERGY = -69.2854 RDTITL> * VAN DER WAALS = -29.4355 ELECTROSTATIC = -39.85 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3761" Parameter: CONF_N -> "8002" Comparing "3761" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3762" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760655 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758659 ATOM PAIRS WERE FOUND FOR ATOM LIST 41968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28438 from a total of 758659 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3762 -77.97120 8.68578 0.67726 INTE EXTERN> -28.34130 -49.62989 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9712" Parameter: A <- "-77.9712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3413" Parameter: B <- "-28.3413" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6299" Parameter: C <- "-49.6299" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3762 TOTAL ENERGY = -77.9712 RDTITL> * VAN DER WAALS = -28.3413 ELECTROSTATIC = -49.6299 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3762" Parameter: CONF_N -> "8002" Comparing "3762" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3763" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758659 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761765 ATOM PAIRS WERE FOUND FOR ATOM LIST 41871 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28212 from a total of 761765 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3763 -69.59891 -8.37229 0.67070 INTE EXTERN> -25.20755 -44.39135 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5989" Parameter: A <- "-69.5989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2076" Parameter: B <- "-25.2076" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3914" Parameter: C <- "-44.3914" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3763 TOTAL ENERGY = -69.5989 RDTITL> * VAN DER WAALS = -25.2076 ELECTROSTATIC = -44.3914 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3763" Parameter: CONF_N -> "8002" Comparing "3763" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3764" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761765 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755970 ATOM PAIRS WERE FOUND FOR ATOM LIST 41865 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28485 from a total of 755970 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3764 -73.66016 4.06125 0.74412 INTE EXTERN> -24.68739 -48.97277 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6602" Parameter: A <- "-73.6602" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6874" Parameter: B <- "-24.6874" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9728" Parameter: C <- "-48.9728" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3764 TOTAL ENERGY = -73.6602 RDTITL> * VAN DER WAALS = -24.6874 ELECTROSTATIC = -48.9728 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3764" Parameter: CONF_N -> "8002" Comparing "3764" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3765" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755970 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760186 ATOM PAIRS WERE FOUND FOR ATOM LIST 41953 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28027 from a total of 760186 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3765 -67.63280 -6.02736 0.48585 INTE EXTERN> -30.96287 -36.66993 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6328" Parameter: A <- "-67.6328" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9629" Parameter: B <- "-30.9629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6699" Parameter: C <- "-36.6699" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3765 TOTAL ENERGY = -67.6328 RDTITL> * VAN DER WAALS = -30.9629 ELECTROSTATIC = -36.6699 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3765" Parameter: CONF_N -> "8002" Comparing "3765" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3766" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760186 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761319 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28312 from a total of 761319 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3766 -66.27832 -1.35448 0.53331 INTE EXTERN> -30.78212 -35.49620 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2783" Parameter: A <- "-66.2783" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7821" Parameter: B <- "-30.7821" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4962" Parameter: C <- "-35.4962" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3766 TOTAL ENERGY = -66.2783 RDTITL> * VAN DER WAALS = -30.7821 ELECTROSTATIC = -35.4962 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3766" Parameter: CONF_N -> "8002" Comparing "3766" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3767" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761319 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763242 ATOM PAIRS WERE FOUND FOR ATOM LIST 42014 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29376 from a total of 763242 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3767 -66.88182 0.60350 0.59725 INTE EXTERN> -29.41043 -37.47138 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8818" Parameter: A <- "-66.8818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4104" Parameter: B <- "-29.4104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4714" Parameter: C <- "-37.4714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3767 TOTAL ENERGY = -66.8818 RDTITL> * VAN DER WAALS = -29.4104 ELECTROSTATIC = -37.4714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3767" Parameter: CONF_N -> "8002" Comparing "3767" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3768" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763242 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759983 ATOM PAIRS WERE FOUND FOR ATOM LIST 41941 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28900 from a total of 759983 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3768 -75.08583 8.20402 0.72562 INTE EXTERN> -24.79662 -50.28921 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0858" Parameter: A <- "-75.0858" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7966" Parameter: B <- "-24.7966" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2892" Parameter: C <- "-50.2892" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3768 TOTAL ENERGY = -75.0858 RDTITL> * VAN DER WAALS = -24.7966 ELECTROSTATIC = -50.2892 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3768" Parameter: CONF_N -> "8002" Comparing "3768" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3769" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759983 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758690 ATOM PAIRS WERE FOUND FOR ATOM LIST 41981 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29099 from a total of 758690 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3769 -75.96928 0.88344 0.68281 INTE EXTERN> -26.13634 -49.83294 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9693" Parameter: A <- "-75.9693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1363" Parameter: B <- "-26.1363" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8329" Parameter: C <- "-49.8329" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3769 TOTAL ENERGY = -75.9693 RDTITL> * VAN DER WAALS = -26.1363 ELECTROSTATIC = -49.8329 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3769" Parameter: CONF_N -> "8002" Comparing "3769" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3770" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758690 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759300 ATOM PAIRS WERE FOUND FOR ATOM LIST 41899 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29032 from a total of 759300 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3770 -72.70367 -3.26560 0.58768 INTE EXTERN> -29.01614 -43.68753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7037" Parameter: A <- "-72.7037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0161" Parameter: B <- "-29.0161" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6875" Parameter: C <- "-43.6875" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3770 TOTAL ENERGY = -72.7037 RDTITL> * VAN DER WAALS = -29.0161 ELECTROSTATIC = -43.6875 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3770" Parameter: CONF_N -> "8002" Comparing "3770" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3771" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759300 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759168 ATOM PAIRS WERE FOUND FOR ATOM LIST 41897 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29527 from a total of 759168 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3771 -75.02511 2.32144 0.63110 INTE EXTERN> -27.34937 -47.67574 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0251" Parameter: A <- "-75.0251" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3494" Parameter: B <- "-27.3494" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6757" Parameter: C <- "-47.6757" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3771 TOTAL ENERGY = -75.0251 RDTITL> * VAN DER WAALS = -27.3494 ELECTROSTATIC = -47.6757 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3771" Parameter: CONF_N -> "8002" Comparing "3771" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3772" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759168 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758843 ATOM PAIRS WERE FOUND FOR ATOM LIST 41791 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27898 from a total of 758843 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3772 -77.99194 2.96683 0.66221 INTE EXTERN> -28.42067 -49.57127 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9919" Parameter: A <- "-77.9919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4207" Parameter: B <- "-28.4207" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5713" Parameter: C <- "-49.5713" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3772 TOTAL ENERGY = -77.9919 RDTITL> * VAN DER WAALS = -28.4207 ELECTROSTATIC = -49.5713 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3772" Parameter: CONF_N -> "8002" Comparing "3772" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3773" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758843 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760864 ATOM PAIRS WERE FOUND FOR ATOM LIST 41985 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28719 from a total of 760864 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3773 -67.37559 -10.61636 0.55369 INTE EXTERN> -28.85166 -38.52393 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3756" Parameter: A <- "-67.3756" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8517" Parameter: B <- "-28.8517" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5239" Parameter: C <- "-38.5239" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3773 TOTAL ENERGY = -67.3756 RDTITL> * VAN DER WAALS = -28.8517 ELECTROSTATIC = -38.5239 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3773" Parameter: CONF_N -> "8002" Comparing "3773" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3774" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760864 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755574 ATOM PAIRS WERE FOUND FOR ATOM LIST 41635 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29112 from a total of 755574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3774 -76.96229 9.58670 0.67195 INTE EXTERN> -27.58925 -49.37304 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9623" Parameter: A <- "-76.9623" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5893" Parameter: B <- "-27.5893" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.373" Parameter: C <- "-49.373" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3774 TOTAL ENERGY = -76.9623 RDTITL> * VAN DER WAALS = -27.5893 ELECTROSTATIC = -49.373 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3774" Parameter: CONF_N -> "8002" Comparing "3774" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3775" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758530 ATOM PAIRS WERE FOUND FOR ATOM LIST 41969 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28289 from a total of 758530 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3775 -74.46535 -2.49694 0.57554 INTE EXTERN> -32.18538 -42.27997 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4654" Parameter: A <- "-74.4654" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1854" Parameter: B <- "-32.1854" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.28" Parameter: C <- "-42.28" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3775 TOTAL ENERGY = -74.4654 RDTITL> * VAN DER WAALS = -32.1854 ELECTROSTATIC = -42.28 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3775" Parameter: CONF_N -> "8002" Comparing "3775" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3776" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758530 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758284 ATOM PAIRS WERE FOUND FOR ATOM LIST 41721 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27947 from a total of 758284 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3776 -80.34306 5.87771 0.68974 INTE EXTERN> -28.65513 -51.68793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3431" Parameter: A <- "-80.3431" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6551" Parameter: B <- "-28.6551" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6879" Parameter: C <- "-51.6879" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3776 TOTAL ENERGY = -80.3431 RDTITL> * VAN DER WAALS = -28.6551 ELECTROSTATIC = -51.6879 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3776" Parameter: CONF_N -> "8002" Comparing "3776" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3777" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758284 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755780 ATOM PAIRS WERE FOUND FOR ATOM LIST 41583 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28027 from a total of 755780 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3777 -71.58056 -8.76249 0.71778 INTE EXTERN> -25.60790 -45.97266 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5806" Parameter: A <- "-71.5806" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6079" Parameter: B <- "-25.6079" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9727" Parameter: C <- "-45.9727" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3777 TOTAL ENERGY = -71.5806 RDTITL> * VAN DER WAALS = -25.6079 ELECTROSTATIC = -45.9727 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3777" Parameter: CONF_N -> "8002" Comparing "3777" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3778" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755780 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755021 ATOM PAIRS WERE FOUND FOR ATOM LIST 41570 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28488 from a total of 755021 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3778 -69.46394 -2.11662 0.68261 INTE EXTERN> -24.62668 -44.83726 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4639" Parameter: A <- "-69.4639" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6267" Parameter: B <- "-24.6267" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8373" Parameter: C <- "-44.8373" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3778 TOTAL ENERGY = -69.4639 RDTITL> * VAN DER WAALS = -24.6267 ELECTROSTATIC = -44.8373 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3778" Parameter: CONF_N -> "8002" Comparing "3778" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3779" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755021 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757290 ATOM PAIRS WERE FOUND FOR ATOM LIST 41739 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28926 from a total of 757290 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3779 -79.82859 10.36465 0.65526 INTE EXTERN> -27.77237 -52.05621 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8286" Parameter: A <- "-79.8286" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7724" Parameter: B <- "-27.7724" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0562" Parameter: C <- "-52.0562" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3779 TOTAL ENERGY = -79.8286 RDTITL> * VAN DER WAALS = -27.7724 ELECTROSTATIC = -52.0562 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3779" Parameter: CONF_N -> "8002" Comparing "3779" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3780" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757290 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758620 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29130 from a total of 758620 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3780 -78.86340 -0.96519 0.58840 INTE EXTERN> -31.13618 -47.72722 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8634" Parameter: A <- "-78.8634" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1362" Parameter: B <- "-31.1362" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7272" Parameter: C <- "-47.7272" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3780 TOTAL ENERGY = -78.8634 RDTITL> * VAN DER WAALS = -31.1362 ELECTROSTATIC = -47.7272 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3780" Parameter: CONF_N -> "8002" Comparing "3780" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3781" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758620 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759895 ATOM PAIRS WERE FOUND FOR ATOM LIST 42093 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28117 from a total of 759895 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3781 -71.16764 -7.69576 0.62720 INTE EXTERN> -27.55525 -43.61240 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1676" Parameter: A <- "-71.1676" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5552" Parameter: B <- "-27.5552" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6124" Parameter: C <- "-43.6124" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3781 TOTAL ENERGY = -71.1676 RDTITL> * VAN DER WAALS = -27.5552 ELECTROSTATIC = -43.6124 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3781" Parameter: CONF_N -> "8002" Comparing "3781" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3782" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759895 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759800 ATOM PAIRS WERE FOUND FOR ATOM LIST 41987 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28652 from a total of 759800 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3782 -55.34732 -15.82033 0.59934 INTE EXTERN> -27.33582 -28.01149 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.3473" Parameter: A <- "-55.3473" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3358" Parameter: B <- "-27.3358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.0115" Parameter: C <- "-28.0115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3782 TOTAL ENERGY = -55.3473 RDTITL> * VAN DER WAALS = -27.3358 ELECTROSTATIC = -28.0115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3782" Parameter: CONF_N -> "8002" Comparing "3782" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3783" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759800 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757083 ATOM PAIRS WERE FOUND FOR ATOM LIST 41847 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28370 from a total of 757083 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3783 -69.13911 13.79179 0.57693 INTE EXTERN> -26.99593 -42.14318 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1391" Parameter: A <- "-69.1391" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9959" Parameter: B <- "-26.9959" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1432" Parameter: C <- "-42.1432" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3783 TOTAL ENERGY = -69.1391 RDTITL> * VAN DER WAALS = -26.9959 ELECTROSTATIC = -42.1432 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3783" Parameter: CONF_N -> "8002" Comparing "3783" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3784" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757083 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753000 ATOM PAIRS WERE FOUND FOR ATOM LIST 41749 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27668 from a total of 753000 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3784 -70.20696 1.06785 0.55995 INTE EXTERN> -28.19839 -42.00857 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.207" Parameter: A <- "-70.207" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1984" Parameter: B <- "-28.1984" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0086" Parameter: C <- "-42.0086" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3784 TOTAL ENERGY = -70.207 RDTITL> * VAN DER WAALS = -28.1984 ELECTROSTATIC = -42.0086 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3784" Parameter: CONF_N -> "8002" Comparing "3784" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3785" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753000 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756640 ATOM PAIRS WERE FOUND FOR ATOM LIST 41729 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27780 from a total of 756640 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3785 -71.48162 1.27466 0.57033 INTE EXTERN> -28.31027 -43.17135 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4816" Parameter: A <- "-71.4816" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3103" Parameter: B <- "-28.3103" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1713" Parameter: C <- "-43.1713" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3785 TOTAL ENERGY = -71.4816 RDTITL> * VAN DER WAALS = -28.3103 ELECTROSTATIC = -43.1713 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3785" Parameter: CONF_N -> "8002" Comparing "3785" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3786" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756640 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755942 ATOM PAIRS WERE FOUND FOR ATOM LIST 41633 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27785 from a total of 755942 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3786 -73.83955 2.35793 0.61480 INTE EXTERN> -27.93017 -45.90937 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8395" Parameter: A <- "-73.8395" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9302" Parameter: B <- "-27.9302" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9094" Parameter: C <- "-45.9094" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3786 TOTAL ENERGY = -73.8395 RDTITL> * VAN DER WAALS = -27.9302 ELECTROSTATIC = -45.9094 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3786" Parameter: CONF_N -> "8002" Comparing "3786" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3787" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755942 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753650 ATOM PAIRS WERE FOUND FOR ATOM LIST 41448 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27816 from a total of 753650 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3787 -65.25700 -8.58254 0.54289 INTE EXTERN> -27.89531 -37.36170 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.257" Parameter: A <- "-65.257" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8953" Parameter: B <- "-27.8953" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3617" Parameter: C <- "-37.3617" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3787 TOTAL ENERGY = -65.257 RDTITL> * VAN DER WAALS = -27.8953 ELECTROSTATIC = -37.3617 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3787" Parameter: CONF_N -> "8002" Comparing "3787" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3788" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753650 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751548 ATOM PAIRS WERE FOUND FOR ATOM LIST 41358 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28436 from a total of 751548 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3788 -75.72402 10.46701 0.61248 INTE EXTERN> -27.52708 -48.19693 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.724" Parameter: A <- "-75.724" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5271" Parameter: B <- "-27.5271" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1969" Parameter: C <- "-48.1969" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3788 TOTAL ENERGY = -75.724 RDTITL> * VAN DER WAALS = -27.5271 ELECTROSTATIC = -48.1969 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3788" Parameter: CONF_N -> "8002" Comparing "3788" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3789" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751548 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746288 ATOM PAIRS WERE FOUND FOR ATOM LIST 41143 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27373 from a total of 746288 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3789 -70.57113 -5.15289 0.55900 INTE EXTERN> -30.42900 -40.14213 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5711" Parameter: A <- "-70.5711" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.429" Parameter: B <- "-30.429" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1421" Parameter: C <- "-40.1421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3789 TOTAL ENERGY = -70.5711 RDTITL> * VAN DER WAALS = -30.429 ELECTROSTATIC = -40.1421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3789" Parameter: CONF_N -> "8002" Comparing "3789" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3790" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746288 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748168 ATOM PAIRS WERE FOUND FOR ATOM LIST 41224 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 26928 from a total of 748168 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3790 -63.84158 -6.72955 0.59689 INTE EXTERN> -25.29630 -38.54528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.8416" Parameter: A <- "-63.8416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2963" Parameter: B <- "-25.2963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5453" Parameter: C <- "-38.5453" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3790 TOTAL ENERGY = -63.8416 RDTITL> * VAN DER WAALS = -25.2963 ELECTROSTATIC = -38.5453 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3790" Parameter: CONF_N -> "8002" Comparing "3790" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3791" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748168 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754880 ATOM PAIRS WERE FOUND FOR ATOM LIST 41592 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27977 from a total of 754880 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3791 -72.12377 8.28219 0.57117 INTE EXTERN> -29.80585 -42.31792 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1238" Parameter: A <- "-72.1238" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8058" Parameter: B <- "-29.8058" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3179" Parameter: C <- "-42.3179" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3791 TOTAL ENERGY = -72.1238 RDTITL> * VAN DER WAALS = -29.8058 ELECTROSTATIC = -42.3179 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3791" Parameter: CONF_N -> "8002" Comparing "3791" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3792" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754880 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754543 ATOM PAIRS WERE FOUND FOR ATOM LIST 41567 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27807 from a total of 754543 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3792 -76.20376 4.08000 0.70113 INTE EXTERN> -25.45906 -50.74471 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2038" Parameter: A <- "-76.2038" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4591" Parameter: B <- "-25.4591" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7447" Parameter: C <- "-50.7447" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3792 TOTAL ENERGY = -76.2038 RDTITL> * VAN DER WAALS = -25.4591 ELECTROSTATIC = -50.7447 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3792" Parameter: CONF_N -> "8002" Comparing "3792" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3793" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754543 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754281 ATOM PAIRS WERE FOUND FOR ATOM LIST 41576 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27900 from a total of 754281 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3793 -75.82153 -0.38224 0.67677 INTE EXTERN> -26.85380 -48.96772 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8215" Parameter: A <- "-75.8215" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8538" Parameter: B <- "-26.8538" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9677" Parameter: C <- "-48.9677" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3793 TOTAL ENERGY = -75.8215 RDTITL> * VAN DER WAALS = -26.8538 ELECTROSTATIC = -48.9677 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3793" Parameter: CONF_N -> "8002" Comparing "3793" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3794" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754281 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754258 ATOM PAIRS WERE FOUND FOR ATOM LIST 41497 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28071 from a total of 754258 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3794 -69.63383 -6.18770 0.59280 INTE EXTERN> -28.76142 -40.87240 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6338" Parameter: A <- "-69.6338" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7614" Parameter: B <- "-28.7614" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8724" Parameter: C <- "-40.8724" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3794 TOTAL ENERGY = -69.6338 RDTITL> * VAN DER WAALS = -28.7614 ELECTROSTATIC = -40.8724 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3794" Parameter: CONF_N -> "8002" Comparing "3794" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3795" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754258 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755438 ATOM PAIRS WERE FOUND FOR ATOM LIST 41502 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28043 from a total of 755438 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3795 -73.84385 4.21002 0.57877 INTE EXTERN> -28.53021 -45.31364 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8438" Parameter: A <- "-73.8438" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5302" Parameter: B <- "-28.5302" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3136" Parameter: C <- "-45.3136" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3795 TOTAL ENERGY = -73.8438 RDTITL> * VAN DER WAALS = -28.5302 ELECTROSTATIC = -45.3136 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3795" Parameter: CONF_N -> "8002" Comparing "3795" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3796" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755438 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753872 ATOM PAIRS WERE FOUND FOR ATOM LIST 41603 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27589 from a total of 753872 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3796 -73.39985 -0.44399 0.67749 INTE EXTERN> -24.01839 -49.38146 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3999" Parameter: A <- "-73.3999" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0184" Parameter: B <- "-24.0184" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3815" Parameter: C <- "-49.3815" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3796 TOTAL ENERGY = -73.3999 RDTITL> * VAN DER WAALS = -24.0184 ELECTROSTATIC = -49.3815 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3796" Parameter: CONF_N -> "8002" Comparing "3796" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3797" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753872 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755273 ATOM PAIRS WERE FOUND FOR ATOM LIST 41694 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27769 from a total of 755273 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3797 -69.39918 -4.00067 0.62473 INTE EXTERN> -28.76916 -40.63002 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3992" Parameter: A <- "-69.3992" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7692" Parameter: B <- "-28.7692" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.63" Parameter: C <- "-40.63" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3797 TOTAL ENERGY = -69.3992 RDTITL> * VAN DER WAALS = -28.7692 ELECTROSTATIC = -40.63 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3797" Parameter: CONF_N -> "8002" Comparing "3797" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3798" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755273 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754920 ATOM PAIRS WERE FOUND FOR ATOM LIST 41596 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27885 from a total of 754920 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3798 -72.17295 2.77377 0.48307 INTE EXTERN> -32.67377 -39.49918 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.173" Parameter: A <- "-72.173" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6738" Parameter: B <- "-32.6738" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4992" Parameter: C <- "-39.4992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3798 TOTAL ENERGY = -72.173 RDTITL> * VAN DER WAALS = -32.6738 ELECTROSTATIC = -39.4992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3798" Parameter: CONF_N -> "8002" Comparing "3798" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3799" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754920 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754022 ATOM PAIRS WERE FOUND FOR ATOM LIST 41686 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28034 from a total of 754022 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3799 -67.69929 -4.47366 0.62923 INTE EXTERN> -26.47442 -41.22487 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6993" Parameter: A <- "-67.6993" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4744" Parameter: B <- "-26.4744" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2249" Parameter: C <- "-41.2249" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3799 TOTAL ENERGY = -67.6993 RDTITL> * VAN DER WAALS = -26.4744 ELECTROSTATIC = -41.2249 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3799" Parameter: CONF_N -> "8002" Comparing "3799" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3800" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754022 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750673 ATOM PAIRS WERE FOUND FOR ATOM LIST 41537 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27869 from a total of 750673 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3800 -74.16460 6.46531 0.63876 INTE EXTERN> -26.77613 -47.38847 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1646" Parameter: A <- "-74.1646" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7761" Parameter: B <- "-26.7761" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3885" Parameter: C <- "-47.3885" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3800 TOTAL ENERGY = -74.1646 RDTITL> * VAN DER WAALS = -26.7761 ELECTROSTATIC = -47.3885 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3800" Parameter: CONF_N -> "8002" Comparing "3800" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3801" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750673 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761204 ATOM PAIRS WERE FOUND FOR ATOM LIST 41998 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28339 from a total of 761204 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3801 -69.34678 -4.81782 0.55926 INTE EXTERN> -30.35754 -38.98924 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3468" Parameter: A <- "-69.3468" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3575" Parameter: B <- "-30.3575" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9892" Parameter: C <- "-38.9892" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3801 TOTAL ENERGY = -69.3468 RDTITL> * VAN DER WAALS = -30.3575 ELECTROSTATIC = -38.9892 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3801" Parameter: CONF_N -> "8002" Comparing "3801" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3802" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761204 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756591 ATOM PAIRS WERE FOUND FOR ATOM LIST 41804 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28651 from a total of 756591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3802 -77.20239 7.85561 0.61534 INTE EXTERN> -29.09912 -48.10327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2024" Parameter: A <- "-77.2024" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0991" Parameter: B <- "-29.0991" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1033" Parameter: C <- "-48.1033" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3802 TOTAL ENERGY = -77.2024 RDTITL> * VAN DER WAALS = -29.0991 ELECTROSTATIC = -48.1033 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3802" Parameter: CONF_N -> "8002" Comparing "3802" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3803" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759573 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28702 from a total of 759573 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3803 -75.20779 -1.99460 0.59016 INTE EXTERN> -30.11531 -45.09248 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2078" Parameter: A <- "-75.2078" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1153" Parameter: B <- "-30.1153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0925" Parameter: C <- "-45.0925" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3803 TOTAL ENERGY = -75.2078 RDTITL> * VAN DER WAALS = -30.1153 ELECTROSTATIC = -45.0925 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3803" Parameter: CONF_N -> "8002" Comparing "3803" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3804" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759573 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757033 ATOM PAIRS WERE FOUND FOR ATOM LIST 41552 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27692 from a total of 757033 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3804 -69.26055 -5.94724 0.64854 INTE EXTERN> -24.14919 -45.11136 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2606" Parameter: A <- "-69.2606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1492" Parameter: B <- "-24.1492" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1114" Parameter: C <- "-45.1114" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3804 TOTAL ENERGY = -69.2606 RDTITL> * VAN DER WAALS = -24.1492 ELECTROSTATIC = -45.1114 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3804" Parameter: CONF_N -> "8002" Comparing "3804" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3805" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757033 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759119 ATOM PAIRS WERE FOUND FOR ATOM LIST 41757 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28425 from a total of 759119 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3805 -72.40343 3.14288 0.67326 INTE EXTERN> -26.37348 -46.02995 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4034" Parameter: A <- "-72.4034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3735" Parameter: B <- "-26.3735" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.03" Parameter: C <- "-46.03" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3805 TOTAL ENERGY = -72.4034 RDTITL> * VAN DER WAALS = -26.3735 ELECTROSTATIC = -46.03 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3805" Parameter: CONF_N -> "8002" Comparing "3805" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3806" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759119 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758915 ATOM PAIRS WERE FOUND FOR ATOM LIST 41757 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29013 from a total of 758915 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3806 -71.21579 -1.18764 0.65958 INTE EXTERN> -26.69054 -44.52525 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2158" Parameter: A <- "-71.2158" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6905" Parameter: B <- "-26.6905" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5252" Parameter: C <- "-44.5252" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3806 TOTAL ENERGY = -71.2158 RDTITL> * VAN DER WAALS = -26.6905 ELECTROSTATIC = -44.5252 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3806" Parameter: CONF_N -> "8002" Comparing "3806" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3807" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758915 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754060 ATOM PAIRS WERE FOUND FOR ATOM LIST 41630 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28288 from a total of 754060 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3807 -72.94130 1.72550 0.54750 INTE EXTERN> -29.68141 -43.25989 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9413" Parameter: A <- "-72.9413" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6814" Parameter: B <- "-29.6814" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2599" Parameter: C <- "-43.2599" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3807 TOTAL ENERGY = -72.9413 RDTITL> * VAN DER WAALS = -29.6814 ELECTROSTATIC = -43.2599 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3807" Parameter: CONF_N -> "8002" Comparing "3807" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3808" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754060 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762594 ATOM PAIRS WERE FOUND FOR ATOM LIST 42086 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28212 from a total of 762594 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3808 -73.08413 0.14284 0.50043 INTE EXTERN> -30.61365 -42.47048 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0841" Parameter: A <- "-73.0841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6136" Parameter: B <- "-30.6136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4705" Parameter: C <- "-42.4705" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3808 TOTAL ENERGY = -73.0841 RDTITL> * VAN DER WAALS = -30.6136 ELECTROSTATIC = -42.4705 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3808" Parameter: CONF_N -> "8002" Comparing "3808" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3809" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762594 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755877 ATOM PAIRS WERE FOUND FOR ATOM LIST 41748 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27837 from a total of 755877 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3809 -69.24818 -3.83595 0.56856 INTE EXTERN> -28.57686 -40.67132 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2482" Parameter: A <- "-69.2482" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5769" Parameter: B <- "-28.5769" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6713" Parameter: C <- "-40.6713" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3809 TOTAL ENERGY = -69.2482 RDTITL> * VAN DER WAALS = -28.5769 ELECTROSTATIC = -40.6713 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3809" Parameter: CONF_N -> "8002" Comparing "3809" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3810" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755877 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757272 ATOM PAIRS WERE FOUND FOR ATOM LIST 41978 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28664 from a total of 757272 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3810 -67.98482 -1.26336 0.63375 INTE EXTERN> -26.03115 -41.95367 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9848" Parameter: A <- "-67.9848" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0312" Parameter: B <- "-26.0312" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9537" Parameter: C <- "-41.9537" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3810 TOTAL ENERGY = -67.9848 RDTITL> * VAN DER WAALS = -26.0312 ELECTROSTATIC = -41.9537 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3810" Parameter: CONF_N -> "8002" Comparing "3810" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3811" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757272 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759478 ATOM PAIRS WERE FOUND FOR ATOM LIST 41914 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28654 from a total of 759478 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3811 -61.47163 -6.51320 0.55063 INTE EXTERN> -30.59188 -30.87975 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.4716" Parameter: A <- "-61.4716" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5919" Parameter: B <- "-30.5919" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.8797" Parameter: C <- "-30.8797" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3811 TOTAL ENERGY = -61.4716 RDTITL> * VAN DER WAALS = -30.5919 ELECTROSTATIC = -30.8797 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3811" Parameter: CONF_N -> "8002" Comparing "3811" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3812" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759478 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752952 ATOM PAIRS WERE FOUND FOR ATOM LIST 41729 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28435 from a total of 752952 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3812 -78.23399 16.76236 0.59627 INTE EXTERN> -30.62305 -47.61094 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.234" Parameter: A <- "-78.234" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.623" Parameter: B <- "-30.623" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6109" Parameter: C <- "-47.6109" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3812 TOTAL ENERGY = -78.234 RDTITL> * VAN DER WAALS = -30.623 ELECTROSTATIC = -47.6109 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3812" Parameter: CONF_N -> "8002" Comparing "3812" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3813" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752952 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759653 ATOM PAIRS WERE FOUND FOR ATOM LIST 41804 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28574 from a total of 759653 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3813 -74.85526 -3.37872 0.69729 INTE EXTERN> -25.76479 -49.09047 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8553" Parameter: A <- "-74.8553" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7648" Parameter: B <- "-25.7648" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0905" Parameter: C <- "-49.0905" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3813 TOTAL ENERGY = -74.8553 RDTITL> * VAN DER WAALS = -25.7648 ELECTROSTATIC = -49.0905 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3813" Parameter: CONF_N -> "8002" Comparing "3813" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3814" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759653 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761710 ATOM PAIRS WERE FOUND FOR ATOM LIST 41950 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28751 from a total of 761710 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3814 -66.18650 -8.66876 0.54385 INTE EXTERN> -31.39046 -34.79604 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1865" Parameter: A <- "-66.1865" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3905" Parameter: B <- "-31.3905" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.796" Parameter: C <- "-34.796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3814 TOTAL ENERGY = -66.1865 RDTITL> * VAN DER WAALS = -31.3905 ELECTROSTATIC = -34.796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3814" Parameter: CONF_N -> "8002" Comparing "3814" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3815" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761710 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758054 ATOM PAIRS WERE FOUND FOR ATOM LIST 41763 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28551 from a total of 758054 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3815 -69.57687 3.39036 0.55056 INTE EXTERN> -32.92809 -36.64878 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5769" Parameter: A <- "-69.5769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9281" Parameter: B <- "-32.9281" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6488" Parameter: C <- "-36.6488" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3815 TOTAL ENERGY = -69.5769 RDTITL> * VAN DER WAALS = -32.9281 ELECTROSTATIC = -36.6488 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3815" Parameter: CONF_N -> "8002" Comparing "3815" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3816" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758054 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756606 ATOM PAIRS WERE FOUND FOR ATOM LIST 41599 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27698 from a total of 756606 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3816 -58.28177 -11.29510 0.57912 INTE EXTERN> -28.23987 -30.04189 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.2818" Parameter: A <- "-58.2818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2399" Parameter: B <- "-28.2399" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.0419" Parameter: C <- "-30.0419" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3816 TOTAL ENERGY = -58.2818 RDTITL> * VAN DER WAALS = -28.2399 ELECTROSTATIC = -30.0419 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3816" Parameter: CONF_N -> "8002" Comparing "3816" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3817" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756606 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754855 ATOM PAIRS WERE FOUND FOR ATOM LIST 41673 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27817 from a total of 754855 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3817 -71.04039 12.75862 0.57127 INTE EXTERN> -31.24029 -39.80010 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0404" Parameter: A <- "-71.0404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2403" Parameter: B <- "-31.2403" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8001" Parameter: C <- "-39.8001" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3817 TOTAL ENERGY = -71.0404 RDTITL> * VAN DER WAALS = -31.2403 ELECTROSTATIC = -39.8001 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3817" Parameter: CONF_N -> "8002" Comparing "3817" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3818" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754855 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756870 ATOM PAIRS WERE FOUND FOR ATOM LIST 41755 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28062 from a total of 756870 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3818 -67.72933 -3.31106 0.58992 INTE EXTERN> -29.06700 -38.66233 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7293" Parameter: A <- "-67.7293" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.067" Parameter: B <- "-29.067" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6623" Parameter: C <- "-38.6623" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3818 TOTAL ENERGY = -67.7293 RDTITL> * VAN DER WAALS = -29.067 ELECTROSTATIC = -38.6623 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3818" Parameter: CONF_N -> "8002" Comparing "3818" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3819" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756870 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753672 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27933 from a total of 753672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3819 -65.81166 -1.91768 0.63484 INTE EXTERN> -23.98421 -41.82744 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8117" Parameter: A <- "-65.8117" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9842" Parameter: B <- "-23.9842" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8274" Parameter: C <- "-41.8274" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3819 TOTAL ENERGY = -65.8117 RDTITL> * VAN DER WAALS = -23.9842 ELECTROSTATIC = -41.8274 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3819" Parameter: CONF_N -> "8002" Comparing "3819" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3820" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753029 ATOM PAIRS WERE FOUND FOR ATOM LIST 41515 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27860 from a total of 753029 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3820 -70.30767 4.49601 0.63130 INTE EXTERN> -28.45010 -41.85756 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3077" Parameter: A <- "-70.3077" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4501" Parameter: B <- "-28.4501" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8576" Parameter: C <- "-41.8576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3820 TOTAL ENERGY = -70.3077 RDTITL> * VAN DER WAALS = -28.4501 ELECTROSTATIC = -41.8576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3820" Parameter: CONF_N -> "8002" Comparing "3820" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3821" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753029 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754459 ATOM PAIRS WERE FOUND FOR ATOM LIST 41684 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27896 from a total of 754459 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3821 -69.48676 -0.82091 0.59631 INTE EXTERN> -30.93426 -38.55250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4868" Parameter: A <- "-69.4868" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9343" Parameter: B <- "-30.9343" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5525" Parameter: C <- "-38.5525" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3821 TOTAL ENERGY = -69.4868 RDTITL> * VAN DER WAALS = -30.9343 ELECTROSTATIC = -38.5525 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3821" Parameter: CONF_N -> "8002" Comparing "3821" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3822" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754459 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754198 ATOM PAIRS WERE FOUND FOR ATOM LIST 41513 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28274 from a total of 754198 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3822 -65.08147 -4.40529 0.50165 INTE EXTERN> -32.36843 -32.71303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0815" Parameter: A <- "-65.0815" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3684" Parameter: B <- "-32.3684" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.713" Parameter: C <- "-32.713" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3822 TOTAL ENERGY = -65.0815 RDTITL> * VAN DER WAALS = -32.3684 ELECTROSTATIC = -32.713 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3822" Parameter: CONF_N -> "8002" Comparing "3822" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3823" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754198 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760926 ATOM PAIRS WERE FOUND FOR ATOM LIST 42074 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27928 from a total of 760926 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3823 -70.13632 5.05485 0.63646 INTE EXTERN> -28.03225 -42.10407 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1363" Parameter: A <- "-70.1363" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0322" Parameter: B <- "-28.0322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1041" Parameter: C <- "-42.1041" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3823 TOTAL ENERGY = -70.1363 RDTITL> * VAN DER WAALS = -28.0322 ELECTROSTATIC = -42.1041 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3823" Parameter: CONF_N -> "8002" Comparing "3823" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3824" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760926 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756840 ATOM PAIRS WERE FOUND FOR ATOM LIST 41515 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27973 from a total of 756840 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3824 -67.13214 -3.00418 0.59854 INTE EXTERN> -29.74687 -37.38527 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1321" Parameter: A <- "-67.1321" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7469" Parameter: B <- "-29.7469" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3853" Parameter: C <- "-37.3853" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3824 TOTAL ENERGY = -67.1321 RDTITL> * VAN DER WAALS = -29.7469 ELECTROSTATIC = -37.3853 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3824" Parameter: CONF_N -> "8002" Comparing "3824" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3825" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756840 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753139 ATOM PAIRS WERE FOUND FOR ATOM LIST 41485 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27975 from a total of 753139 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3825 -72.10790 4.97576 0.64272 INTE EXTERN> -28.37815 -43.72976 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1079" Parameter: A <- "-72.1079" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3781" Parameter: B <- "-28.3781" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7298" Parameter: C <- "-43.7298" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3825 TOTAL ENERGY = -72.1079 RDTITL> * VAN DER WAALS = -28.3781 ELECTROSTATIC = -43.7298 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3825" Parameter: CONF_N -> "8002" Comparing "3825" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3826" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753139 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760728 ATOM PAIRS WERE FOUND FOR ATOM LIST 41737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27643 from a total of 760728 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3826 -67.95200 -4.15590 0.61598 INTE EXTERN> -27.44992 -40.50209 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.952" Parameter: A <- "-67.952" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4499" Parameter: B <- "-27.4499" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5021" Parameter: C <- "-40.5021" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3826 TOTAL ENERGY = -67.952 RDTITL> * VAN DER WAALS = -27.4499 ELECTROSTATIC = -40.5021 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3826" Parameter: CONF_N -> "8002" Comparing "3826" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3827" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760728 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751725 ATOM PAIRS WERE FOUND FOR ATOM LIST 41441 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27800 from a total of 751725 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3827 -69.94810 1.99610 0.57904 INTE EXTERN> -29.55870 -40.38940 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9481" Parameter: A <- "-69.9481" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5587" Parameter: B <- "-29.5587" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3894" Parameter: C <- "-40.3894" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3827 TOTAL ENERGY = -69.9481 RDTITL> * VAN DER WAALS = -29.5587 ELECTROSTATIC = -40.3894 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3827" Parameter: CONF_N -> "8002" Comparing "3827" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3828" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751725 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753894 ATOM PAIRS WERE FOUND FOR ATOM LIST 41656 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27947 from a total of 753894 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3828 -68.94146 -1.00665 0.53407 INTE EXTERN> -30.81865 -38.12280 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9415" Parameter: A <- "-68.9415" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8187" Parameter: B <- "-30.8187" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1228" Parameter: C <- "-38.1228" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3828 TOTAL ENERGY = -68.9415 RDTITL> * VAN DER WAALS = -30.8187 ELECTROSTATIC = -38.1228 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3828" Parameter: CONF_N -> "8002" Comparing "3828" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3829" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753894 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758121 ATOM PAIRS WERE FOUND FOR ATOM LIST 41867 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28643 from a total of 758121 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3829 -69.76518 0.82372 0.70615 INTE EXTERN> -25.69819 -44.06699 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7652" Parameter: A <- "-69.7652" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6982" Parameter: B <- "-25.6982" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.067" Parameter: C <- "-44.067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3829 TOTAL ENERGY = -69.7652 RDTITL> * VAN DER WAALS = -25.6982 ELECTROSTATIC = -44.067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3829" Parameter: CONF_N -> "8002" Comparing "3829" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3830" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758121 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767001 ATOM PAIRS WERE FOUND FOR ATOM LIST 42162 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28402 from a total of 767001 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3830 -64.81464 -4.95054 0.55476 INTE EXTERN> -30.55326 -34.26139 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8146" Parameter: A <- "-64.8146" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5533" Parameter: B <- "-30.5533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2614" Parameter: C <- "-34.2614" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3830 TOTAL ENERGY = -64.8146 RDTITL> * VAN DER WAALS = -30.5533 ELECTROSTATIC = -34.2614 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3830" Parameter: CONF_N -> "8002" Comparing "3830" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3831" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767001 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757276 ATOM PAIRS WERE FOUND FOR ATOM LIST 41825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27708 from a total of 757276 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3831 -65.62436 0.80971 0.74125 INTE EXTERN> -21.49709 -44.12727 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6244" Parameter: A <- "-65.6244" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.4971" Parameter: B <- "-21.4971" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1273" Parameter: C <- "-44.1273" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3831 TOTAL ENERGY = -65.6244 RDTITL> * VAN DER WAALS = -21.4971 ELECTROSTATIC = -44.1273 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3831" Parameter: CONF_N -> "8002" Comparing "3831" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3832" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757276 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755217 ATOM PAIRS WERE FOUND FOR ATOM LIST 41666 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28199 from a total of 755217 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3832 -64.21448 -1.40988 0.55770 INTE EXTERN> -29.68655 -34.52793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2145" Parameter: A <- "-64.2145" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6866" Parameter: B <- "-29.6866" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5279" Parameter: C <- "-34.5279" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3832 TOTAL ENERGY = -64.2145 RDTITL> * VAN DER WAALS = -29.6866 ELECTROSTATIC = -34.5279 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3832" Parameter: CONF_N -> "8002" Comparing "3832" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3833" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755217 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762237 ATOM PAIRS WERE FOUND FOR ATOM LIST 41976 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28205 from a total of 762237 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3833 -64.43714 0.22267 0.58948 INTE EXTERN> -28.23840 -36.19874 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.4371" Parameter: A <- "-64.4371" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2384" Parameter: B <- "-28.2384" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1987" Parameter: C <- "-36.1987" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3833 TOTAL ENERGY = -64.4371 RDTITL> * VAN DER WAALS = -28.2384 ELECTROSTATIC = -36.1987 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3833" Parameter: CONF_N -> "8002" Comparing "3833" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3834" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762237 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760115 ATOM PAIRS WERE FOUND FOR ATOM LIST 41973 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28133 from a total of 760115 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3834 -67.15612 2.71897 0.63240 INTE EXTERN> -29.15709 -37.99902 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1561" Parameter: A <- "-67.1561" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1571" Parameter: B <- "-29.1571" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.999" Parameter: C <- "-37.999" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3834 TOTAL ENERGY = -67.1561 RDTITL> * VAN DER WAALS = -29.1571 ELECTROSTATIC = -37.999 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3834" Parameter: CONF_N -> "8002" Comparing "3834" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3835" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760115 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763290 ATOM PAIRS WERE FOUND FOR ATOM LIST 42082 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28111 from a total of 763290 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3835 -74.66663 7.51052 0.57086 INTE EXTERN> -31.09570 -43.57094 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6666" Parameter: A <- "-74.6666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0957" Parameter: B <- "-31.0957" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5709" Parameter: C <- "-43.5709" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3835 TOTAL ENERGY = -74.6666 RDTITL> * VAN DER WAALS = -31.0957 ELECTROSTATIC = -43.5709 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3835" Parameter: CONF_N -> "8002" Comparing "3835" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3836" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763290 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761263 ATOM PAIRS WERE FOUND FOR ATOM LIST 41793 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27944 from a total of 761263 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3836 -66.68436 -7.98227 0.67401 INTE EXTERN> -24.90473 -41.77964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6844" Parameter: A <- "-66.6844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9047" Parameter: B <- "-24.9047" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7796" Parameter: C <- "-41.7796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3836 TOTAL ENERGY = -66.6844 RDTITL> * VAN DER WAALS = -24.9047 ELECTROSTATIC = -41.7796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3836" Parameter: CONF_N -> "8002" Comparing "3836" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3837" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761263 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762724 ATOM PAIRS WERE FOUND FOR ATOM LIST 42037 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28048 from a total of 762724 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3837 -65.15949 -1.52488 0.75891 INTE EXTERN> -22.08155 -43.07794 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1595" Parameter: A <- "-65.1595" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.0815" Parameter: B <- "-22.0815" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0779" Parameter: C <- "-43.0779" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3837 TOTAL ENERGY = -65.1595 RDTITL> * VAN DER WAALS = -22.0815 ELECTROSTATIC = -43.0779 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3837" Parameter: CONF_N -> "8002" Comparing "3837" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3838" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762724 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760091 ATOM PAIRS WERE FOUND FOR ATOM LIST 41829 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27965 from a total of 760091 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3838 -62.30493 -2.85456 0.56491 INTE EXTERN> -30.92180 -31.38313 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3049" Parameter: A <- "-62.3049" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9218" Parameter: B <- "-30.9218" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.3831" Parameter: C <- "-31.3831" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3838 TOTAL ENERGY = -62.3049 RDTITL> * VAN DER WAALS = -30.9218 ELECTROSTATIC = -31.3831 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3838" Parameter: CONF_N -> "8002" Comparing "3838" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3839" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760091 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758332 ATOM PAIRS WERE FOUND FOR ATOM LIST 41809 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28160 from a total of 758332 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3839 -59.28561 -3.01932 0.56030 INTE EXTERN> -29.10280 -30.18281 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.2856" Parameter: A <- "-59.2856" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1028" Parameter: B <- "-29.1028" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.1828" Parameter: C <- "-30.1828" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3839 TOTAL ENERGY = -59.2856 RDTITL> * VAN DER WAALS = -29.1028 ELECTROSTATIC = -30.1828 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3839" Parameter: CONF_N -> "8002" Comparing "3839" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3840" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758332 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760102 ATOM PAIRS WERE FOUND FOR ATOM LIST 42037 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27759 from a total of 760102 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3840 -63.28209 3.99648 0.61014 INTE EXTERN> -26.00811 -37.27398 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.2821" Parameter: A <- "-63.2821" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0081" Parameter: B <- "-26.0081" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.274" Parameter: C <- "-37.274" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3840 TOTAL ENERGY = -63.2821 RDTITL> * VAN DER WAALS = -26.0081 ELECTROSTATIC = -37.274 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3840" Parameter: CONF_N -> "8002" Comparing "3840" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3841" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760102 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761222 ATOM PAIRS WERE FOUND FOR ATOM LIST 42217 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28458 from a total of 761222 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3841 -74.91648 11.63440 0.66836 INTE EXTERN> -27.99951 -46.91697 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9165" Parameter: A <- "-74.9165" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9995" Parameter: B <- "-27.9995" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.917" Parameter: C <- "-46.917" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3841 TOTAL ENERGY = -74.9165 RDTITL> * VAN DER WAALS = -27.9995 ELECTROSTATIC = -46.917 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3841" Parameter: CONF_N -> "8002" Comparing "3841" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3842" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761222 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759530 ATOM PAIRS WERE FOUND FOR ATOM LIST 42009 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28643 from a total of 759530 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3842 -67.34197 -7.57451 0.62080 INTE EXTERN> -26.27927 -41.06269 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.342" Parameter: A <- "-67.342" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2793" Parameter: B <- "-26.2793" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0627" Parameter: C <- "-41.0627" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3842 TOTAL ENERGY = -67.342 RDTITL> * VAN DER WAALS = -26.2793 ELECTROSTATIC = -41.0627 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3842" Parameter: CONF_N -> "8002" Comparing "3842" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3843" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759530 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756757 ATOM PAIRS WERE FOUND FOR ATOM LIST 41746 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27749 from a total of 756757 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3843 -67.04666 -0.29531 0.53690 INTE EXTERN> -30.36740 -36.67926 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0467" Parameter: A <- "-67.0467" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3674" Parameter: B <- "-30.3674" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6793" Parameter: C <- "-36.6793" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3843 TOTAL ENERGY = -67.0467 RDTITL> * VAN DER WAALS = -30.3674 ELECTROSTATIC = -36.6793 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3843" Parameter: CONF_N -> "8002" Comparing "3843" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3844" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756757 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759733 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28350 from a total of 759733 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3844 -66.92868 -0.11797 0.55882 INTE EXTERN> -30.73978 -36.18890 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9287" Parameter: A <- "-66.9287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7398" Parameter: B <- "-30.7398" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1889" Parameter: C <- "-36.1889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3844 TOTAL ENERGY = -66.9287 RDTITL> * VAN DER WAALS = -30.7398 ELECTROSTATIC = -36.1889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3844" Parameter: CONF_N -> "8002" Comparing "3844" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3845" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759733 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763611 ATOM PAIRS WERE FOUND FOR ATOM LIST 42139 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29355 from a total of 763611 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3845 -59.47281 -7.45588 0.49564 INTE EXTERN> -33.15265 -26.32016 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.4728" Parameter: A <- "-59.4728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1526" Parameter: B <- "-33.1526" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-26.3202" Parameter: C <- "-26.3202" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3845 TOTAL ENERGY = -59.4728 RDTITL> * VAN DER WAALS = -33.1526 ELECTROSTATIC = -26.3202 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3845" Parameter: CONF_N -> "8002" Comparing "3845" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3846" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763611 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757595 ATOM PAIRS WERE FOUND FOR ATOM LIST 41735 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27959 from a total of 757595 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3846 -55.06504 -4.40777 0.46032 INTE EXTERN> -31.77684 -23.28820 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.065" Parameter: A <- "-55.065" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7768" Parameter: B <- "-31.7768" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-23.2882" Parameter: C <- "-23.2882" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3846 TOTAL ENERGY = -55.065 RDTITL> * VAN DER WAALS = -31.7768 ELECTROSTATIC = -23.2882 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3846" Parameter: CONF_N -> "8002" Comparing "3846" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3847" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757595 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763560 ATOM PAIRS WERE FOUND FOR ATOM LIST 42239 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29026 from a total of 763560 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3847 -63.79331 8.72827 0.58272 INTE EXTERN> -28.93392 -34.85939 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7933" Parameter: A <- "-63.7933" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9339" Parameter: B <- "-28.9339" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8594" Parameter: C <- "-34.8594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3847 TOTAL ENERGY = -63.7933 RDTITL> * VAN DER WAALS = -28.9339 ELECTROSTATIC = -34.8594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3847" Parameter: CONF_N -> "8002" Comparing "3847" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3848" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763560 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764078 ATOM PAIRS WERE FOUND FOR ATOM LIST 42206 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28897 from a total of 764078 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3848 -65.72462 1.93130 0.60661 INTE EXTERN> -28.69668 -37.02793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7246" Parameter: A <- "-65.7246" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6967" Parameter: B <- "-28.6967" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0279" Parameter: C <- "-37.0279" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3848 TOTAL ENERGY = -65.7246 RDTITL> * VAN DER WAALS = -28.6967 ELECTROSTATIC = -37.0279 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3848" Parameter: CONF_N -> "8002" Comparing "3848" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3849" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764078 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762264 ATOM PAIRS WERE FOUND FOR ATOM LIST 42019 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28866 from a total of 762264 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3849 -55.51607 -10.20855 0.62201 INTE EXTERN> -27.97462 -27.54144 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.5161" Parameter: A <- "-55.5161" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9746" Parameter: B <- "-27.9746" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.5414" Parameter: C <- "-27.5414" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3849 TOTAL ENERGY = -55.5161 RDTITL> * VAN DER WAALS = -27.9746 ELECTROSTATIC = -27.5414 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3849" Parameter: CONF_N -> "8002" Comparing "3849" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3850" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762264 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759936 ATOM PAIRS WERE FOUND FOR ATOM LIST 42019 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28815 from a total of 759936 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3850 -58.73838 3.22232 0.60910 INTE EXTERN> -24.43285 -34.30554 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.7384" Parameter: A <- "-58.7384" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4328" Parameter: B <- "-24.4328" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3055" Parameter: C <- "-34.3055" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3850 TOTAL ENERGY = -58.7384 RDTITL> * VAN DER WAALS = -24.4328 ELECTROSTATIC = -34.3055 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3850" Parameter: CONF_N -> "8002" Comparing "3850" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3851" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759936 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760914 ATOM PAIRS WERE FOUND FOR ATOM LIST 42144 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28576 from a total of 760914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3851 -58.10066 -0.63773 0.53900 INTE EXTERN> -28.45384 -29.64682 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.1007" Parameter: A <- "-58.1007" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4538" Parameter: B <- "-28.4538" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.6468" Parameter: C <- "-29.6468" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3851 TOTAL ENERGY = -58.1007 RDTITL> * VAN DER WAALS = -28.4538 ELECTROSTATIC = -29.6468 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3851" Parameter: CONF_N -> "8002" Comparing "3851" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3852" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761435 ATOM PAIRS WERE FOUND FOR ATOM LIST 41823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28304 from a total of 761435 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3852 -59.64616 1.54550 0.60163 INTE EXTERN> -27.70352 -31.94264 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.6462" Parameter: A <- "-59.6462" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7035" Parameter: B <- "-27.7035" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.9426" Parameter: C <- "-31.9426" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3852 TOTAL ENERGY = -59.6462 RDTITL> * VAN DER WAALS = -27.7035 ELECTROSTATIC = -31.9426 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3852" Parameter: CONF_N -> "8002" Comparing "3852" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3853" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761435 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759810 ATOM PAIRS WERE FOUND FOR ATOM LIST 41925 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29017 from a total of 759810 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3853 -62.34582 2.69967 0.57044 INTE EXTERN> -27.92417 -34.42165 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3458" Parameter: A <- "-62.3458" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9242" Parameter: B <- "-27.9242" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4217" Parameter: C <- "-34.4217" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3853 TOTAL ENERGY = -62.3458 RDTITL> * VAN DER WAALS = -27.9242 ELECTROSTATIC = -34.4217 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3853" Parameter: CONF_N -> "8002" Comparing "3853" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3854" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759810 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768035 ATOM PAIRS WERE FOUND FOR ATOM LIST 42625 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28804 from a total of 768035 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3854 -56.51855 -5.82727 0.68982 INTE EXTERN> -22.95666 -33.56189 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-56.5186" Parameter: A <- "-56.5186" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.9567" Parameter: B <- "-22.9567" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.5619" Parameter: C <- "-33.5619" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3854 TOTAL ENERGY = -56.5186 RDTITL> * VAN DER WAALS = -22.9567 ELECTROSTATIC = -33.5619 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3854" Parameter: CONF_N -> "8002" Comparing "3854" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3855" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768035 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764453 ATOM PAIRS WERE FOUND FOR ATOM LIST 42069 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29333 from a total of 764453 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3855 -61.72599 5.20744 0.62131 INTE EXTERN> -27.81565 -33.91034 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.726" Parameter: A <- "-61.726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8157" Parameter: B <- "-27.8157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9103" Parameter: C <- "-33.9103" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3855 TOTAL ENERGY = -61.726 RDTITL> * VAN DER WAALS = -27.8157 ELECTROSTATIC = -33.9103 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3855" Parameter: CONF_N -> "8002" Comparing "3855" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3856" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764453 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763536 ATOM PAIRS WERE FOUND FOR ATOM LIST 42080 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29543 from a total of 763536 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3856 -57.90128 -3.82472 0.66482 INTE EXTERN> -26.83537 -31.06591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.9013" Parameter: A <- "-57.9013" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8354" Parameter: B <- "-26.8354" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.0659" Parameter: C <- "-31.0659" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3856 TOTAL ENERGY = -57.9013 RDTITL> * VAN DER WAALS = -26.8354 ELECTROSTATIC = -31.0659 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3856" Parameter: CONF_N -> "8002" Comparing "3856" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3857" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763536 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762592 ATOM PAIRS WERE FOUND FOR ATOM LIST 41984 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28721 from a total of 762592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3857 -55.20018 -2.70110 0.60246 INTE EXTERN> -26.27001 -28.93016 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.2002" Parameter: A <- "-55.2002" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.27" Parameter: B <- "-26.27" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.9302" Parameter: C <- "-28.9302" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3857 TOTAL ENERGY = -55.2002 RDTITL> * VAN DER WAALS = -26.27 ELECTROSTATIC = -28.9302 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3857" Parameter: CONF_N -> "8002" Comparing "3857" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3858" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758846 ATOM PAIRS WERE FOUND FOR ATOM LIST 41785 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28866 from a total of 758846 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3858 -55.12205 -0.07813 0.60436 INTE EXTERN> -27.97272 -27.14932 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.122" Parameter: A <- "-55.122" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9727" Parameter: B <- "-27.9727" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.1493" Parameter: C <- "-27.1493" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3858 TOTAL ENERGY = -55.122 RDTITL> * VAN DER WAALS = -27.9727 ELECTROSTATIC = -27.1493 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3858" Parameter: CONF_N -> "8002" Comparing "3858" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3859" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758846 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763521 ATOM PAIRS WERE FOUND FOR ATOM LIST 42034 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28771 from a total of 763521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3859 -58.53110 3.40906 0.54162 INTE EXTERN> -30.22409 -28.30701 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.5311" Parameter: A <- "-58.5311" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2241" Parameter: B <- "-30.2241" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.307" Parameter: C <- "-28.307" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3859 TOTAL ENERGY = -58.5311 RDTITL> * VAN DER WAALS = -30.2241 ELECTROSTATIC = -28.307 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3859" Parameter: CONF_N -> "8002" Comparing "3859" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3860" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759095 ATOM PAIRS WERE FOUND FOR ATOM LIST 42052 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28795 from a total of 759095 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3860 -57.25687 -1.27423 0.46755 INTE EXTERN> -31.22596 -26.03091 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.2569" Parameter: A <- "-57.2569" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.226" Parameter: B <- "-31.226" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-26.0309" Parameter: C <- "-26.0309" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3860 TOTAL ENERGY = -57.2569 RDTITL> * VAN DER WAALS = -31.226 ELECTROSTATIC = -26.0309 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3860" Parameter: CONF_N -> "8002" Comparing "3860" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3861" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759095 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761178 ATOM PAIRS WERE FOUND FOR ATOM LIST 41860 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28925 from a total of 761178 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3861 -56.66042 -0.59645 0.57608 INTE EXTERN> -28.95269 -27.70773 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-56.6604" Parameter: A <- "-56.6604" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9527" Parameter: B <- "-28.9527" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.7077" Parameter: C <- "-27.7077" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3861 TOTAL ENERGY = -56.6604 RDTITL> * VAN DER WAALS = -28.9527 ELECTROSTATIC = -27.7077 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3861" Parameter: CONF_N -> "8002" Comparing "3861" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3862" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761178 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754455 ATOM PAIRS WERE FOUND FOR ATOM LIST 41522 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29063 from a total of 754455 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3862 -64.47966 7.81924 0.59339 INTE EXTERN> -27.12045 -37.35921 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.4797" Parameter: A <- "-64.4797" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1205" Parameter: B <- "-27.1205" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3592" Parameter: C <- "-37.3592" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3862 TOTAL ENERGY = -64.4797 RDTITL> * VAN DER WAALS = -27.1205 ELECTROSTATIC = -37.3592 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3862" Parameter: CONF_N -> "8002" Comparing "3862" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3863" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754455 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755657 ATOM PAIRS WERE FOUND FOR ATOM LIST 41661 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28158 from a total of 755657 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3863 -63.37446 -1.10520 0.64063 INTE EXTERN> -24.49409 -38.88037 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3745" Parameter: A <- "-63.3745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4941" Parameter: B <- "-24.4941" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8804" Parameter: C <- "-38.8804" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3863 TOTAL ENERGY = -63.3745 RDTITL> * VAN DER WAALS = -24.4941 ELECTROSTATIC = -38.8804 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3863" Parameter: CONF_N -> "8002" Comparing "3863" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3864" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755657 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763793 ATOM PAIRS WERE FOUND FOR ATOM LIST 41927 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29170 from a total of 763793 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3864 -69.20137 5.82691 0.60630 INTE EXTERN> -28.99696 -40.20441 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2014" Parameter: A <- "-69.2014" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.997" Parameter: B <- "-28.997" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2044" Parameter: C <- "-40.2044" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3864 TOTAL ENERGY = -69.2014 RDTITL> * VAN DER WAALS = -28.997 ELECTROSTATIC = -40.2044 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3864" Parameter: CONF_N -> "8002" Comparing "3864" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3865" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763793 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760485 ATOM PAIRS WERE FOUND FOR ATOM LIST 42022 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29277 from a total of 760485 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3865 -77.32476 8.12339 0.58453 INTE EXTERN> -31.55012 -45.77464 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3248" Parameter: A <- "-77.3248" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5501" Parameter: B <- "-31.5501" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7746" Parameter: C <- "-45.7746" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3865 TOTAL ENERGY = -77.3248 RDTITL> * VAN DER WAALS = -31.5501 ELECTROSTATIC = -45.7746 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3865" Parameter: CONF_N -> "8002" Comparing "3865" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3866" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760485 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757588 ATOM PAIRS WERE FOUND FOR ATOM LIST 41826 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29294 from a total of 757588 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3866 -73.26955 -4.05521 0.78566 INTE EXTERN> -24.26048 -49.00907 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2695" Parameter: A <- "-73.2695" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2605" Parameter: B <- "-24.2605" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0091" Parameter: C <- "-49.0091" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3866 TOTAL ENERGY = -73.2695 RDTITL> * VAN DER WAALS = -24.2605 ELECTROSTATIC = -49.0091 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3866" Parameter: CONF_N -> "8002" Comparing "3866" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3867" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757588 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755116 ATOM PAIRS WERE FOUND FOR ATOM LIST 41624 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29155 from a total of 755116 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3867 -67.52796 -5.74159 0.59814 INTE EXTERN> -29.42235 -38.10561 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.528" Parameter: A <- "-67.528" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4223" Parameter: B <- "-29.4223" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1056" Parameter: C <- "-38.1056" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3867 TOTAL ENERGY = -67.528 RDTITL> * VAN DER WAALS = -29.4223 ELECTROSTATIC = -38.1056 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3867" Parameter: CONF_N -> "8002" Comparing "3867" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3868" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755116 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759489 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29185 from a total of 759489 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3868 -78.56997 11.04201 0.63910 INTE EXTERN> -30.12643 -48.44354 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.57" Parameter: A <- "-78.57" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1264" Parameter: B <- "-30.1264" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4435" Parameter: C <- "-48.4435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3868 TOTAL ENERGY = -78.57 RDTITL> * VAN DER WAALS = -30.1264 ELECTROSTATIC = -48.4435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3868" Parameter: CONF_N -> "8002" Comparing "3868" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3869" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759489 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759912 ATOM PAIRS WERE FOUND FOR ATOM LIST 42049 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29230 from a total of 759912 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3869 -65.20993 -13.36005 0.52560 INTE EXTERN> -30.22873 -34.98119 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2099" Parameter: A <- "-65.2099" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2287" Parameter: B <- "-30.2287" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9812" Parameter: C <- "-34.9812" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3869 TOTAL ENERGY = -65.2099 RDTITL> * VAN DER WAALS = -30.2287 ELECTROSTATIC = -34.9812 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3869" Parameter: CONF_N -> "8002" Comparing "3869" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3870" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759912 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753084 ATOM PAIRS WERE FOUND FOR ATOM LIST 41509 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28893 from a total of 753084 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3870 -74.40602 9.19609 0.58774 INTE EXTERN> -28.25335 -46.15267 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.406" Parameter: A <- "-74.406" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2533" Parameter: B <- "-28.2533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1527" Parameter: C <- "-46.1527" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3870 TOTAL ENERGY = -74.406 RDTITL> * VAN DER WAALS = -28.2533 ELECTROSTATIC = -46.1527 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3870" Parameter: CONF_N -> "8002" Comparing "3870" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3871" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753084 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762322 ATOM PAIRS WERE FOUND FOR ATOM LIST 42058 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29844 from a total of 762322 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3871 -76.98662 2.58060 0.61249 INTE EXTERN> -29.58476 -47.40186 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9866" Parameter: A <- "-76.9866" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5848" Parameter: B <- "-29.5848" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4019" Parameter: C <- "-47.4019" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3871 TOTAL ENERGY = -76.9866 RDTITL> * VAN DER WAALS = -29.5848 ELECTROSTATIC = -47.4019 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3871" Parameter: CONF_N -> "8002" Comparing "3871" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3872" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762322 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761103 ATOM PAIRS WERE FOUND FOR ATOM LIST 41852 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29316 from a total of 761103 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3872 -67.67288 -9.31374 0.54546 INTE EXTERN> -30.39043 -37.28245 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6729" Parameter: A <- "-67.6729" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3904" Parameter: B <- "-30.3904" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2825" Parameter: C <- "-37.2825" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3872 TOTAL ENERGY = -67.6729 RDTITL> * VAN DER WAALS = -30.3904 ELECTROSTATIC = -37.2825 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3872" Parameter: CONF_N -> "8002" Comparing "3872" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3873" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761103 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762555 ATOM PAIRS WERE FOUND FOR ATOM LIST 41878 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29294 from a total of 762555 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3873 -67.26266 -0.41022 0.47326 INTE EXTERN> -34.71059 -32.55207 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2627" Parameter: A <- "-67.2627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.7106" Parameter: B <- "-34.7106" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5521" Parameter: C <- "-32.5521" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3873 TOTAL ENERGY = -67.2627 RDTITL> * VAN DER WAALS = -34.7106 ELECTROSTATIC = -32.5521 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3873" Parameter: CONF_N -> "8002" Comparing "3873" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3874" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762555 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757592 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28374 from a total of 757592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3874 -66.44383 -0.81883 0.55214 INTE EXTERN> -30.07293 -36.37090 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4438" Parameter: A <- "-66.4438" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0729" Parameter: B <- "-30.0729" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3709" Parameter: C <- "-36.3709" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3874 TOTAL ENERGY = -66.4438 RDTITL> * VAN DER WAALS = -30.0729 ELECTROSTATIC = -36.3709 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3874" Parameter: CONF_N -> "8002" Comparing "3874" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3875" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757575 ATOM PAIRS WERE FOUND FOR ATOM LIST 41872 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29071 from a total of 757575 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3875 -71.35476 4.91093 0.56313 INTE EXTERN> -32.23925 -39.11551 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3548" Parameter: A <- "-71.3548" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2392" Parameter: B <- "-32.2392" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1155" Parameter: C <- "-39.1155" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3875 TOTAL ENERGY = -71.3548 RDTITL> * VAN DER WAALS = -32.2392 ELECTROSTATIC = -39.1155 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3875" Parameter: CONF_N -> "8002" Comparing "3875" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3876" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757575 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761959 ATOM PAIRS WERE FOUND FOR ATOM LIST 41986 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28883 from a total of 761959 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3876 -70.79891 -0.55585 0.55634 INTE EXTERN> -31.59549 -39.20342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7989" Parameter: A <- "-70.7989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5955" Parameter: B <- "-31.5955" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2034" Parameter: C <- "-39.2034" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3876 TOTAL ENERGY = -70.7989 RDTITL> * VAN DER WAALS = -31.5955 ELECTROSTATIC = -39.2034 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3876" Parameter: CONF_N -> "8002" Comparing "3876" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3877" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761959 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758042 ATOM PAIRS WERE FOUND FOR ATOM LIST 41687 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28806 from a total of 758042 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3877 -68.13228 -2.66663 0.64280 INTE EXTERN> -27.74290 -40.38939 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1323" Parameter: A <- "-68.1323" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7429" Parameter: B <- "-27.7429" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3894" Parameter: C <- "-40.3894" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3877 TOTAL ENERGY = -68.1323 RDTITL> * VAN DER WAALS = -27.7429 ELECTROSTATIC = -40.3894 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3877" Parameter: CONF_N -> "8002" Comparing "3877" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3878" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758042 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754502 ATOM PAIRS WERE FOUND FOR ATOM LIST 41560 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29144 from a total of 754502 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3878 -76.68641 8.55412 0.56788 INTE EXTERN> -29.89911 -46.78730 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6864" Parameter: A <- "-76.6864" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8991" Parameter: B <- "-29.8991" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7873" Parameter: C <- "-46.7873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3878 TOTAL ENERGY = -76.6864 RDTITL> * VAN DER WAALS = -29.8991 ELECTROSTATIC = -46.7873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3878" Parameter: CONF_N -> "8002" Comparing "3878" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3879" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754502 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758133 ATOM PAIRS WERE FOUND FOR ATOM LIST 41918 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29274 from a total of 758133 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3879 -76.24608 -0.44033 0.62676 INTE EXTERN> -26.02483 -50.22125 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2461" Parameter: A <- "-76.2461" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0248" Parameter: B <- "-26.0248" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2212" Parameter: C <- "-50.2212" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3879 TOTAL ENERGY = -76.2461 RDTITL> * VAN DER WAALS = -26.0248 ELECTROSTATIC = -50.2212 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3879" Parameter: CONF_N -> "8002" Comparing "3879" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3880" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758133 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756853 ATOM PAIRS WERE FOUND FOR ATOM LIST 41711 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28449 from a total of 756853 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3880 -67.77680 -8.46927 0.70356 INTE EXTERN> -23.43290 -44.34390 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7768" Parameter: A <- "-67.7768" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4329" Parameter: B <- "-23.4329" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3439" Parameter: C <- "-44.3439" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3880 TOTAL ENERGY = -67.7768 RDTITL> * VAN DER WAALS = -23.4329 ELECTROSTATIC = -44.3439 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3880" Parameter: CONF_N -> "8002" Comparing "3880" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3881" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756853 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754863 ATOM PAIRS WERE FOUND FOR ATOM LIST 41517 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28176 from a total of 754863 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3881 -66.71435 -1.06245 0.78149 INTE EXTERN> -21.23453 -45.47982 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7144" Parameter: A <- "-66.7144" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.2345" Parameter: B <- "-21.2345" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4798" Parameter: C <- "-45.4798" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3881 TOTAL ENERGY = -66.7144 RDTITL> * VAN DER WAALS = -21.2345 ELECTROSTATIC = -45.4798 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3881" Parameter: CONF_N -> "8002" Comparing "3881" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3882" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754863 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758836 ATOM PAIRS WERE FOUND FOR ATOM LIST 41903 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28765 from a total of 758836 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3882 -75.70800 8.99365 0.54196 INTE EXTERN> -31.80755 -43.90046 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.708" Parameter: A <- "-75.708" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8075" Parameter: B <- "-31.8075" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9005" Parameter: C <- "-43.9005" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3882 TOTAL ENERGY = -75.708 RDTITL> * VAN DER WAALS = -31.8075 ELECTROSTATIC = -43.9005 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3882" Parameter: CONF_N -> "8002" Comparing "3882" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3883" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758836 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758996 ATOM PAIRS WERE FOUND FOR ATOM LIST 41843 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28765 from a total of 758996 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3883 -70.73022 -4.97778 0.63944 INTE EXTERN> -26.54617 -44.18405 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7302" Parameter: A <- "-70.7302" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5462" Parameter: B <- "-26.5462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1841" Parameter: C <- "-44.1841" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3883 TOTAL ENERGY = -70.7302 RDTITL> * VAN DER WAALS = -26.5462 ELECTROSTATIC = -44.1841 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3883" Parameter: CONF_N -> "8002" Comparing "3883" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3884" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758996 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757778 ATOM PAIRS WERE FOUND FOR ATOM LIST 41872 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29115 from a total of 757778 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3884 -77.76202 7.03180 0.70728 INTE EXTERN> -26.88466 -50.87735 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.762" Parameter: A <- "-77.762" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8847" Parameter: B <- "-26.8847" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8774" Parameter: C <- "-50.8774" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3884 TOTAL ENERGY = -77.762 RDTITL> * VAN DER WAALS = -26.8847 ELECTROSTATIC = -50.8774 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3884" Parameter: CONF_N -> "8002" Comparing "3884" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3885" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757778 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768409 ATOM PAIRS WERE FOUND FOR ATOM LIST 42431 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29687 from a total of 768409 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3885 -72.94765 -4.81436 0.61782 INTE EXTERN> -29.47126 -43.47639 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9477" Parameter: A <- "-72.9477" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4713" Parameter: B <- "-29.4713" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4764" Parameter: C <- "-43.4764" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3885 TOTAL ENERGY = -72.9477 RDTITL> * VAN DER WAALS = -29.4713 ELECTROSTATIC = -43.4764 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3885" Parameter: CONF_N -> "8002" Comparing "3885" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3886" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768409 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759656 ATOM PAIRS WERE FOUND FOR ATOM LIST 41931 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28575 from a total of 759656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3886 -71.05416 -1.89349 0.59785 INTE EXTERN> -27.87506 -43.17910 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0542" Parameter: A <- "-71.0542" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8751" Parameter: B <- "-27.8751" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1791" Parameter: C <- "-43.1791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3886 TOTAL ENERGY = -71.0542 RDTITL> * VAN DER WAALS = -27.8751 ELECTROSTATIC = -43.1791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3886" Parameter: CONF_N -> "8002" Comparing "3886" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3887" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758386 ATOM PAIRS WERE FOUND FOR ATOM LIST 41994 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28233 from a total of 758386 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3887 -69.18182 -1.87234 0.63709 INTE EXTERN> -26.89964 -42.28218 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1818" Parameter: A <- "-69.1818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8996" Parameter: B <- "-26.8996" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2822" Parameter: C <- "-42.2822" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3887 TOTAL ENERGY = -69.1818 RDTITL> * VAN DER WAALS = -26.8996 ELECTROSTATIC = -42.2822 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3887" Parameter: CONF_N -> "8002" Comparing "3887" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3888" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758386 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764744 ATOM PAIRS WERE FOUND FOR ATOM LIST 42246 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29134 from a total of 764744 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3888 -69.86652 0.68469 0.71777 INTE EXTERN> -27.89353 -41.97298 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8665" Parameter: A <- "-69.8665" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8935" Parameter: B <- "-27.8935" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.973" Parameter: C <- "-41.973" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3888 TOTAL ENERGY = -69.8665 RDTITL> * VAN DER WAALS = -27.8935 ELECTROSTATIC = -41.973 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3888" Parameter: CONF_N -> "8002" Comparing "3888" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3889" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764744 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756857 ATOM PAIRS WERE FOUND FOR ATOM LIST 41728 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28374 from a total of 756857 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3889 -82.10915 12.24263 0.77705 INTE EXTERN> -26.25248 -55.85667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.1091" Parameter: A <- "-82.1091" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2525" Parameter: B <- "-26.2525" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.8567" Parameter: C <- "-55.8567" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3889 TOTAL ENERGY = -82.1091 RDTITL> * VAN DER WAALS = -26.2525 ELECTROSTATIC = -55.8567 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3889" Parameter: CONF_N -> "8002" Comparing "3889" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3890" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756857 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756662 ATOM PAIRS WERE FOUND FOR ATOM LIST 41781 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28816 from a total of 756662 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3890 -75.73602 -6.37313 0.65177 INTE EXTERN> -28.84299 -46.89302 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.736" Parameter: A <- "-75.736" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.843" Parameter: B <- "-28.843" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.893" Parameter: C <- "-46.893" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3890 TOTAL ENERGY = -75.736 RDTITL> * VAN DER WAALS = -28.843 ELECTROSTATIC = -46.893 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3890" Parameter: CONF_N -> "8002" Comparing "3890" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3891" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756662 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762628 ATOM PAIRS WERE FOUND FOR ATOM LIST 42164 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28647 from a total of 762628 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3891 -72.38027 -3.35575 0.64529 INTE EXTERN> -26.66184 -45.71843 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3803" Parameter: A <- "-72.3803" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6618" Parameter: B <- "-26.6618" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7184" Parameter: C <- "-45.7184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3891 TOTAL ENERGY = -72.3803 RDTITL> * VAN DER WAALS = -26.6618 ELECTROSTATIC = -45.7184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3891" Parameter: CONF_N -> "8002" Comparing "3891" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3892" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762628 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759032 ATOM PAIRS WERE FOUND FOR ATOM LIST 41900 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28555 from a total of 759032 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3892 -68.85633 -3.52393 0.58541 INTE EXTERN> -30.21137 -38.64497 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8563" Parameter: A <- "-68.8563" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2114" Parameter: B <- "-30.2114" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.645" Parameter: C <- "-38.645" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3892 TOTAL ENERGY = -68.8563 RDTITL> * VAN DER WAALS = -30.2114 ELECTROSTATIC = -38.645 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3892" Parameter: CONF_N -> "8002" Comparing "3892" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3893" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759032 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760283 ATOM PAIRS WERE FOUND FOR ATOM LIST 41786 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28592 from a total of 760283 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3893 -78.59666 9.74033 0.60123 INTE EXTERN> -29.34720 -49.24946 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5967" Parameter: A <- "-78.5967" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3472" Parameter: B <- "-29.3472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2495" Parameter: C <- "-49.2495" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3893 TOTAL ENERGY = -78.5967 RDTITL> * VAN DER WAALS = -29.3472 ELECTROSTATIC = -49.2495 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3893" Parameter: CONF_N -> "8002" Comparing "3893" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3894" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760283 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761780 ATOM PAIRS WERE FOUND FOR ATOM LIST 42038 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28346 from a total of 761780 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3894 -81.36244 2.76578 0.65451 INTE EXTERN> -26.47284 -54.88959 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.3624" Parameter: A <- "-81.3624" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4728" Parameter: B <- "-26.4728" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8896" Parameter: C <- "-54.8896" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3894 TOTAL ENERGY = -81.3624 RDTITL> * VAN DER WAALS = -26.4728 ELECTROSTATIC = -54.8896 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3894" Parameter: CONF_N -> "8002" Comparing "3894" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3895" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761780 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756039 ATOM PAIRS WERE FOUND FOR ATOM LIST 41592 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28180 from a total of 756039 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3895 -78.50063 -2.86181 0.57720 INTE EXTERN> -28.54738 -49.95325 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5006" Parameter: A <- "-78.5006" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5474" Parameter: B <- "-28.5474" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9532" Parameter: C <- "-49.9532" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3895 TOTAL ENERGY = -78.5006 RDTITL> * VAN DER WAALS = -28.5474 ELECTROSTATIC = -49.9532 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3895" Parameter: CONF_N -> "8002" Comparing "3895" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3896" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756039 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41727 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28785 from a total of 756958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3896 -71.83092 -6.66971 0.69938 INTE EXTERN> -24.80696 -47.02396 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8309" Parameter: A <- "-71.8309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.807" Parameter: B <- "-24.807" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.024" Parameter: C <- "-47.024" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3896 TOTAL ENERGY = -71.8309 RDTITL> * VAN DER WAALS = -24.807 ELECTROSTATIC = -47.024 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3896" Parameter: CONF_N -> "8002" Comparing "3896" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3897" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758109 ATOM PAIRS WERE FOUND FOR ATOM LIST 41889 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27843 from a total of 758109 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3897 -72.69865 0.86773 0.69416 INTE EXTERN> -24.43052 -48.26812 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6986" Parameter: A <- "-72.6986" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4305" Parameter: B <- "-24.4305" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2681" Parameter: C <- "-48.2681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3897 TOTAL ENERGY = -72.6986 RDTITL> * VAN DER WAALS = -24.4305 ELECTROSTATIC = -48.2681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3897" Parameter: CONF_N -> "8002" Comparing "3897" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3898" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758109 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41443 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28278 from a total of 755794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3898 -74.24940 1.55075 0.61054 INTE EXTERN> -29.19424 -45.05516 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2494" Parameter: A <- "-74.2494" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1942" Parameter: B <- "-29.1942" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0552" Parameter: C <- "-45.0552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3898 TOTAL ENERGY = -74.2494 RDTITL> * VAN DER WAALS = -29.1942 ELECTROSTATIC = -45.0552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3898" Parameter: CONF_N -> "8002" Comparing "3898" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3899" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758882 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28595 from a total of 758882 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3899 -76.75525 2.50585 0.59034 INTE EXTERN> -29.81384 -46.94141 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7552" Parameter: A <- "-76.7552" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8138" Parameter: B <- "-29.8138" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9414" Parameter: C <- "-46.9414" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3899 TOTAL ENERGY = -76.7552 RDTITL> * VAN DER WAALS = -29.8138 ELECTROSTATIC = -46.9414 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3899" Parameter: CONF_N -> "8002" Comparing "3899" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3900" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758882 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760556 ATOM PAIRS WERE FOUND FOR ATOM LIST 41785 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28303 from a total of 760556 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3900 -81.15936 4.40411 0.65423 INTE EXTERN> -28.22057 -52.93879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1594" Parameter: A <- "-81.1594" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2206" Parameter: B <- "-28.2206" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9388" Parameter: C <- "-52.9388" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3900 TOTAL ENERGY = -81.1594 RDTITL> * VAN DER WAALS = -28.2206 ELECTROSTATIC = -52.9388 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3900" Parameter: CONF_N -> "8002" Comparing "3900" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3901" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760556 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764755 ATOM PAIRS WERE FOUND FOR ATOM LIST 42016 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28711 from a total of 764755 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3901 -76.86173 -4.29763 0.76300 INTE EXTERN> -23.69005 -53.17168 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8617" Parameter: A <- "-76.8617" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.69" Parameter: B <- "-23.69" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.1717" Parameter: C <- "-53.1717" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3901 TOTAL ENERGY = -76.8617 RDTITL> * VAN DER WAALS = -23.69 ELECTROSTATIC = -53.1717 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3901" Parameter: CONF_N -> "8002" Comparing "3901" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3902" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764755 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764340 ATOM PAIRS WERE FOUND FOR ATOM LIST 42053 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28941 from a total of 764340 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3902 -77.97119 1.10947 0.65727 INTE EXTERN> -27.95275 -50.01844 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9712" Parameter: A <- "-77.9712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9528" Parameter: B <- "-27.9528" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0184" Parameter: C <- "-50.0184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3902 TOTAL ENERGY = -77.9712 RDTITL> * VAN DER WAALS = -27.9528 ELECTROSTATIC = -50.0184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3902" Parameter: CONF_N -> "8002" Comparing "3902" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3903" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764340 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766053 ATOM PAIRS WERE FOUND FOR ATOM LIST 42274 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28266 from a total of 766053 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3903 -73.51121 -4.45998 0.68771 INTE EXTERN> -27.34326 -46.16795 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5112" Parameter: A <- "-73.5112" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3433" Parameter: B <- "-27.3433" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1679" Parameter: C <- "-46.1679" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3903 TOTAL ENERGY = -73.5112 RDTITL> * VAN DER WAALS = -27.3433 ELECTROSTATIC = -46.1679 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3903" Parameter: CONF_N -> "8002" Comparing "3903" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3904" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766053 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764873 ATOM PAIRS WERE FOUND FOR ATOM LIST 41859 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28274 from a total of 764873 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3904 -79.20181 5.69059 0.59280 INTE EXTERN> -28.80606 -50.39575 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2018" Parameter: A <- "-79.2018" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8061" Parameter: B <- "-28.8061" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3957" Parameter: C <- "-50.3957" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3904 TOTAL ENERGY = -79.2018 RDTITL> * VAN DER WAALS = -28.8061 ELECTROSTATIC = -50.3957 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3904" Parameter: CONF_N -> "8002" Comparing "3904" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3905" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764873 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763769 ATOM PAIRS WERE FOUND FOR ATOM LIST 42061 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28535 from a total of 763769 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3905 -71.84259 -7.35922 0.52484 INTE EXTERN> -29.52647 -42.31612 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8426" Parameter: A <- "-71.8426" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5265" Parameter: B <- "-29.5265" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3161" Parameter: C <- "-42.3161" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3905 TOTAL ENERGY = -71.8426 RDTITL> * VAN DER WAALS = -29.5265 ELECTROSTATIC = -42.3161 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3905" Parameter: CONF_N -> "8002" Comparing "3905" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3906" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763769 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764188 ATOM PAIRS WERE FOUND FOR ATOM LIST 41929 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28797 from a total of 764188 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3906 -75.66177 3.81918 0.65457 INTE EXTERN> -26.80089 -48.86088 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6618" Parameter: A <- "-75.6618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8009" Parameter: B <- "-26.8009" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8609" Parameter: C <- "-48.8609" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3906 TOTAL ENERGY = -75.6618 RDTITL> * VAN DER WAALS = -26.8009 ELECTROSTATIC = -48.8609 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3906" Parameter: CONF_N -> "8002" Comparing "3906" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3907" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764188 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764280 ATOM PAIRS WERE FOUND FOR ATOM LIST 41989 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28954 from a total of 764280 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3907 -77.24744 1.58567 0.64281 INTE EXTERN> -27.40479 -49.84265 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2474" Parameter: A <- "-77.2474" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4048" Parameter: B <- "-27.4048" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8426" Parameter: C <- "-49.8426" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3907 TOTAL ENERGY = -77.2474 RDTITL> * VAN DER WAALS = -27.4048 ELECTROSTATIC = -49.8426 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3907" Parameter: CONF_N -> "8002" Comparing "3907" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3908" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764280 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761952 ATOM PAIRS WERE FOUND FOR ATOM LIST 41947 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28189 from a total of 761952 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3908 -70.13969 -7.10774 0.56000 INTE EXTERN> -31.24428 -38.89542 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1397" Parameter: A <- "-70.1397" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2443" Parameter: B <- "-31.2443" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8954" Parameter: C <- "-38.8954" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3908 TOTAL ENERGY = -70.1397 RDTITL> * VAN DER WAALS = -31.2443 ELECTROSTATIC = -38.8954 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3908" Parameter: CONF_N -> "8002" Comparing "3908" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3909" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761952 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768805 ATOM PAIRS WERE FOUND FOR ATOM LIST 42181 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28758 from a total of 768805 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3909 -78.37912 8.23943 0.76130 INTE EXTERN> -24.82938 -53.54975 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3791" Parameter: A <- "-78.3791" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8294" Parameter: B <- "-24.8294" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.5497" Parameter: C <- "-53.5497" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3909 TOTAL ENERGY = -78.3791 RDTITL> * VAN DER WAALS = -24.8294 ELECTROSTATIC = -53.5497 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3909" Parameter: CONF_N -> "8002" Comparing "3909" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3910" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768805 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761568 ATOM PAIRS WERE FOUND FOR ATOM LIST 41940 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28354 from a total of 761568 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3910 -70.90093 -7.47819 0.52736 INTE EXTERN> -31.53234 -39.36859 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9009" Parameter: A <- "-70.9009" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5323" Parameter: B <- "-31.5323" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3686" Parameter: C <- "-39.3686" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3910 TOTAL ENERGY = -70.9009 RDTITL> * VAN DER WAALS = -31.5323 ELECTROSTATIC = -39.3686 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3910" Parameter: CONF_N -> "8002" Comparing "3910" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3911" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761568 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761870 ATOM PAIRS WERE FOUND FOR ATOM LIST 42011 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29073 from a total of 761870 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3911 -69.52842 -1.37251 0.66208 INTE EXTERN> -26.44096 -43.08745 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5284" Parameter: A <- "-69.5284" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.441" Parameter: B <- "-26.441" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0875" Parameter: C <- "-43.0875" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3911 TOTAL ENERGY = -69.5284 RDTITL> * VAN DER WAALS = -26.441 ELECTROSTATIC = -43.0875 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3911" Parameter: CONF_N -> "8002" Comparing "3911" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3912" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761870 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763256 ATOM PAIRS WERE FOUND FOR ATOM LIST 41934 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28705 from a total of 763256 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3912 -68.57200 -0.95641 0.55703 INTE EXTERN> -29.24177 -39.33023 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.572" Parameter: A <- "-68.572" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2418" Parameter: B <- "-29.2418" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3302" Parameter: C <- "-39.3302" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3912 TOTAL ENERGY = -68.572 RDTITL> * VAN DER WAALS = -29.2418 ELECTROSTATIC = -39.3302 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3912" Parameter: CONF_N -> "8002" Comparing "3912" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3913" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763256 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761223 ATOM PAIRS WERE FOUND FOR ATOM LIST 41959 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28482 from a total of 761223 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3913 -72.28942 3.71741 0.63515 INTE EXTERN> -29.25278 -43.03664 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2894" Parameter: A <- "-72.2894" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2528" Parameter: B <- "-29.2528" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0366" Parameter: C <- "-43.0366" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3913 TOTAL ENERGY = -72.2894 RDTITL> * VAN DER WAALS = -29.2528 ELECTROSTATIC = -43.0366 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3913" Parameter: CONF_N -> "8002" Comparing "3913" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3914" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761223 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761491 ATOM PAIRS WERE FOUND FOR ATOM LIST 41837 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28190 from a total of 761491 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3914 -70.83550 -1.45392 0.66299 INTE EXTERN> -26.69567 -44.13983 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8355" Parameter: A <- "-70.8355" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6957" Parameter: B <- "-26.6957" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1398" Parameter: C <- "-44.1398" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3914 TOTAL ENERGY = -70.8355 RDTITL> * VAN DER WAALS = -26.6957 ELECTROSTATIC = -44.1398 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3914" Parameter: CONF_N -> "8002" Comparing "3914" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3915" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761491 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765430 ATOM PAIRS WERE FOUND FOR ATOM LIST 42118 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28768 from a total of 765430 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3915 -77.02756 6.19206 0.60540 INTE EXTERN> -29.38351 -47.64405 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0276" Parameter: A <- "-77.0276" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3835" Parameter: B <- "-29.3835" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6441" Parameter: C <- "-47.6441" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3915 TOTAL ENERGY = -77.0276 RDTITL> * VAN DER WAALS = -29.3835 ELECTROSTATIC = -47.6441 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3915" Parameter: CONF_N -> "8002" Comparing "3915" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3916" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765430 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765353 ATOM PAIRS WERE FOUND FOR ATOM LIST 42315 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29078 from a total of 765353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3916 -78.90162 1.87406 0.62653 INTE EXTERN> -29.69478 -49.20685 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9016" Parameter: A <- "-78.9016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6948" Parameter: B <- "-29.6948" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2068" Parameter: C <- "-49.2068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3916 TOTAL ENERGY = -78.9016 RDTITL> * VAN DER WAALS = -29.6948 ELECTROSTATIC = -49.2068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3916" Parameter: CONF_N -> "8002" Comparing "3916" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3917" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768895 ATOM PAIRS WERE FOUND FOR ATOM LIST 42115 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28977 from a total of 768895 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3917 -76.14151 -2.76011 0.55571 INTE EXTERN> -32.96774 -43.17377 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1415" Parameter: A <- "-76.1415" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9677" Parameter: B <- "-32.9677" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1738" Parameter: C <- "-43.1738" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3917 TOTAL ENERGY = -76.1415 RDTITL> * VAN DER WAALS = -32.9677 ELECTROSTATIC = -43.1738 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3917" Parameter: CONF_N -> "8002" Comparing "3917" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3918" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768895 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768322 ATOM PAIRS WERE FOUND FOR ATOM LIST 42302 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29349 from a total of 768322 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3918 -81.81787 5.67636 0.65895 INTE EXTERN> -29.76213 -52.05574 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8179" Parameter: A <- "-81.8179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7621" Parameter: B <- "-29.7621" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0557" Parameter: C <- "-52.0557" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3918 TOTAL ENERGY = -81.8179 RDTITL> * VAN DER WAALS = -29.7621 ELECTROSTATIC = -52.0557 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3918" Parameter: CONF_N -> "8002" Comparing "3918" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3919" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768322 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765964 ATOM PAIRS WERE FOUND FOR ATOM LIST 42155 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28183 from a total of 765964 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3919 -74.31339 -7.50448 0.66795 INTE EXTERN> -28.22672 -46.08667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3134" Parameter: A <- "-74.3134" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2267" Parameter: B <- "-28.2267" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0867" Parameter: C <- "-46.0867" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3919 TOTAL ENERGY = -74.3134 RDTITL> * VAN DER WAALS = -28.2267 ELECTROSTATIC = -46.0867 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3919" Parameter: CONF_N -> "8002" Comparing "3919" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3920" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765964 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760905 ATOM PAIRS WERE FOUND FOR ATOM LIST 41936 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28159 from a total of 760905 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3920 -72.86378 -1.44961 0.66181 INTE EXTERN> -28.19604 -44.66774 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8638" Parameter: A <- "-72.8638" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.196" Parameter: B <- "-28.196" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6677" Parameter: C <- "-44.6677" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3920 TOTAL ENERGY = -72.8638 RDTITL> * VAN DER WAALS = -28.196 ELECTROSTATIC = -44.6677 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3920" Parameter: CONF_N -> "8002" Comparing "3920" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3921" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760905 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759507 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28652 from a total of 759507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3921 -72.42645 -0.43733 0.66216 INTE EXTERN> -27.14119 -45.28526 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4265" Parameter: A <- "-72.4265" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1412" Parameter: B <- "-27.1412" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2853" Parameter: C <- "-45.2853" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3921 TOTAL ENERGY = -72.4265 RDTITL> * VAN DER WAALS = -27.1412 ELECTROSTATIC = -45.2853 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3921" Parameter: CONF_N -> "8002" Comparing "3921" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3922" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758048 ATOM PAIRS WERE FOUND FOR ATOM LIST 41764 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28517 from a total of 758048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3922 -75.49944 3.07299 0.53917 INTE EXTERN> -30.54894 -44.95050 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4994" Parameter: A <- "-75.4994" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5489" Parameter: B <- "-30.5489" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9505" Parameter: C <- "-44.9505" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3922 TOTAL ENERGY = -75.4994 RDTITL> * VAN DER WAALS = -30.5489 ELECTROSTATIC = -44.9505 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3922" Parameter: CONF_N -> "8002" Comparing "3922" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3923" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762697 ATOM PAIRS WERE FOUND FOR ATOM LIST 41863 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28565 from a total of 762697 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3923 -79.01500 3.51556 0.67388 INTE EXTERN> -27.29136 -51.72365 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.015" Parameter: A <- "-79.015" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2914" Parameter: B <- "-27.2914" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7236" Parameter: C <- "-51.7236" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3923 TOTAL ENERGY = -79.015 RDTITL> * VAN DER WAALS = -27.2914 ELECTROSTATIC = -51.7236 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3923" Parameter: CONF_N -> "8002" Comparing "3923" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3924" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762697 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763992 ATOM PAIRS WERE FOUND FOR ATOM LIST 42022 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28424 from a total of 763992 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3924 -78.21786 -0.79714 0.69004 INTE EXTERN> -27.69828 -50.51958 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2179" Parameter: A <- "-78.2179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6983" Parameter: B <- "-27.6983" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5196" Parameter: C <- "-50.5196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3924 TOTAL ENERGY = -78.2179 RDTITL> * VAN DER WAALS = -27.6983 ELECTROSTATIC = -50.5196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3924" Parameter: CONF_N -> "8002" Comparing "3924" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3925" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763992 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759717 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28321 from a total of 759717 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3925 -61.11329 -17.10457 0.59925 INTE EXTERN> -27.67111 -33.44218 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.1133" Parameter: A <- "-61.1133" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6711" Parameter: B <- "-27.6711" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.4422" Parameter: C <- "-33.4422" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3925 TOTAL ENERGY = -61.1133 RDTITL> * VAN DER WAALS = -27.6711 ELECTROSTATIC = -33.4422 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3925" Parameter: CONF_N -> "8002" Comparing "3925" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3926" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759717 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756182 ATOM PAIRS WERE FOUND FOR ATOM LIST 41739 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28783 from a total of 756182 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3926 -69.05568 7.94238 0.50634 INTE EXTERN> -30.16004 -38.89564 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0557" Parameter: A <- "-69.0557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.16" Parameter: B <- "-30.16" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8956" Parameter: C <- "-38.8956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3926 TOTAL ENERGY = -69.0557 RDTITL> * VAN DER WAALS = -30.16 ELECTROSTATIC = -38.8956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3926" Parameter: CONF_N -> "8002" Comparing "3926" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3927" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756182 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754655 ATOM PAIRS WERE FOUND FOR ATOM LIST 41507 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28413 from a total of 754655 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3927 -70.32797 1.27229 0.55286 INTE EXTERN> -29.70604 -40.62193 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.328" Parameter: A <- "-70.328" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.706" Parameter: B <- "-29.706" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6219" Parameter: C <- "-40.6219" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3927 TOTAL ENERGY = -70.328 RDTITL> * VAN DER WAALS = -29.706 ELECTROSTATIC = -40.6219 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3927" Parameter: CONF_N -> "8002" Comparing "3927" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3928" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754655 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762994 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28762 from a total of 762994 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3928 -67.66826 -2.65971 0.59180 INTE EXTERN> -28.56314 -39.10512 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6683" Parameter: A <- "-67.6683" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5631" Parameter: B <- "-28.5631" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1051" Parameter: C <- "-39.1051" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3928 TOTAL ENERGY = -67.6683 RDTITL> * VAN DER WAALS = -28.5631 ELECTROSTATIC = -39.1051 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3928" Parameter: CONF_N -> "8002" Comparing "3928" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3929" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762994 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761911 ATOM PAIRS WERE FOUND FOR ATOM LIST 41970 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29030 from a total of 761911 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3929 -76.87143 9.20317 0.57396 INTE EXTERN> -29.63128 -47.24015 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8714" Parameter: A <- "-76.8714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6313" Parameter: B <- "-29.6313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2401" Parameter: C <- "-47.2401" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3929 TOTAL ENERGY = -76.8714 RDTITL> * VAN DER WAALS = -29.6313 ELECTROSTATIC = -47.2401 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3929" Parameter: CONF_N -> "8002" Comparing "3929" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3930" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761911 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762046 ATOM PAIRS WERE FOUND FOR ATOM LIST 42157 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29006 from a total of 762046 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3930 -70.28362 -6.58781 0.58274 INTE EXTERN> -27.79028 -42.49334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2836" Parameter: A <- "-70.2836" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7903" Parameter: B <- "-27.7903" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4933" Parameter: C <- "-42.4933" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3930 TOTAL ENERGY = -70.2836 RDTITL> * VAN DER WAALS = -27.7903 ELECTROSTATIC = -42.4933 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3930" Parameter: CONF_N -> "8002" Comparing "3930" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3931" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762046 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764329 ATOM PAIRS WERE FOUND FOR ATOM LIST 42228 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28503 from a total of 764329 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3931 -75.21428 4.93066 0.55528 INTE EXTERN> -32.12916 -43.08512 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2143" Parameter: A <- "-75.2143" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1292" Parameter: B <- "-32.1292" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0851" Parameter: C <- "-43.0851" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3931 TOTAL ENERGY = -75.2143 RDTITL> * VAN DER WAALS = -32.1292 ELECTROSTATIC = -43.0851 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3931" Parameter: CONF_N -> "8002" Comparing "3931" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3932" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764329 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759816 ATOM PAIRS WERE FOUND FOR ATOM LIST 42010 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28321 from a total of 759816 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3932 -71.82635 -3.38793 0.58353 INTE EXTERN> -28.60066 -43.22569 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8263" Parameter: A <- "-71.8263" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6007" Parameter: B <- "-28.6007" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2257" Parameter: C <- "-43.2257" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3932 TOTAL ENERGY = -71.8263 RDTITL> * VAN DER WAALS = -28.6007 ELECTROSTATIC = -43.2257 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3932" Parameter: CONF_N -> "8002" Comparing "3932" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3933" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759816 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763986 ATOM PAIRS WERE FOUND FOR ATOM LIST 41946 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29000 from a total of 763986 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3933 -71.42279 -0.40356 0.53103 INTE EXTERN> -32.35880 -39.06398 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4228" Parameter: A <- "-71.4228" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3588" Parameter: B <- "-32.3588" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.064" Parameter: C <- "-39.064" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3933 TOTAL ENERGY = -71.4228 RDTITL> * VAN DER WAALS = -32.3588 ELECTROSTATIC = -39.064 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3933" Parameter: CONF_N -> "8002" Comparing "3933" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3934" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763986 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763664 ATOM PAIRS WERE FOUND FOR ATOM LIST 41999 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28451 from a total of 763664 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3934 -67.83555 -3.58724 0.50396 INTE EXTERN> -29.50365 -38.33189 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8355" Parameter: A <- "-67.8355" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5037" Parameter: B <- "-29.5037" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3319" Parameter: C <- "-38.3319" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3934 TOTAL ENERGY = -67.8355 RDTITL> * VAN DER WAALS = -29.5037 ELECTROSTATIC = -38.3319 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3934" Parameter: CONF_N -> "8002" Comparing "3934" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3935" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763664 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767507 ATOM PAIRS WERE FOUND FOR ATOM LIST 42333 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28622 from a total of 767507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3935 -67.76795 -0.06759 0.51331 INTE EXTERN> -31.77501 -35.99294 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.768" Parameter: A <- "-67.768" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.775" Parameter: B <- "-31.775" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9929" Parameter: C <- "-35.9929" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3935 TOTAL ENERGY = -67.768 RDTITL> * VAN DER WAALS = -31.775 ELECTROSTATIC = -35.9929 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3935" Parameter: CONF_N -> "8002" Comparing "3935" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3936" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758171 ATOM PAIRS WERE FOUND FOR ATOM LIST 41989 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27996 from a total of 758171 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3936 -71.16533 3.39738 0.61436 INTE EXTERN> -28.36091 -42.80442 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1653" Parameter: A <- "-71.1653" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3609" Parameter: B <- "-28.3609" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8044" Parameter: C <- "-42.8044" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3936 TOTAL ENERGY = -71.1653 RDTITL> * VAN DER WAALS = -28.3609 ELECTROSTATIC = -42.8044 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3936" Parameter: CONF_N -> "8002" Comparing "3936" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3937" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758171 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763621 ATOM PAIRS WERE FOUND FOR ATOM LIST 42141 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28592 from a total of 763621 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3937 -65.70796 -5.45737 0.48963 INTE EXTERN> -29.88992 -35.81804 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.708" Parameter: A <- "-65.708" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8899" Parameter: B <- "-29.8899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.818" Parameter: C <- "-35.818" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3937 TOTAL ENERGY = -65.708 RDTITL> * VAN DER WAALS = -29.8899 ELECTROSTATIC = -35.818 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3937" Parameter: CONF_N -> "8002" Comparing "3937" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3938" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763621 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767669 ATOM PAIRS WERE FOUND FOR ATOM LIST 42375 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28849 from a total of 767669 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3938 -68.20251 2.49454 0.65480 INTE EXTERN> -28.33104 -39.87147 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2025" Parameter: A <- "-68.2025" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.331" Parameter: B <- "-28.331" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8715" Parameter: C <- "-39.8715" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3938 TOTAL ENERGY = -68.2025 RDTITL> * VAN DER WAALS = -28.331 ELECTROSTATIC = -39.8715 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3938" Parameter: CONF_N -> "8002" Comparing "3938" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3939" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767669 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765085 ATOM PAIRS WERE FOUND FOR ATOM LIST 42266 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28754 from a total of 765085 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3939 -71.72031 3.51781 0.75259 INTE EXTERN> -25.22436 -46.49595 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7203" Parameter: A <- "-71.7203" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2244" Parameter: B <- "-25.2244" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.496" Parameter: C <- "-46.496" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3939 TOTAL ENERGY = -71.7203 RDTITL> * VAN DER WAALS = -25.2244 ELECTROSTATIC = -46.496 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3939" Parameter: CONF_N -> "8002" Comparing "3939" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3940" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765085 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758764 ATOM PAIRS WERE FOUND FOR ATOM LIST 41793 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28700 from a total of 758764 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3940 -70.04082 -1.67949 0.69000 INTE EXTERN> -24.28120 -45.75963 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0408" Parameter: A <- "-70.0408" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2812" Parameter: B <- "-24.2812" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7596" Parameter: C <- "-45.7596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3940 TOTAL ENERGY = -70.0408 RDTITL> * VAN DER WAALS = -24.2812 ELECTROSTATIC = -45.7596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3940" Parameter: CONF_N -> "8002" Comparing "3940" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3941" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758764 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760980 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28910 from a total of 760980 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3941 -66.29873 -3.74209 0.52941 INTE EXTERN> -30.61478 -35.68395 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2987" Parameter: A <- "-66.2987" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6148" Parameter: B <- "-30.6148" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6839" Parameter: C <- "-35.6839" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3941 TOTAL ENERGY = -66.2987 RDTITL> * VAN DER WAALS = -30.6148 ELECTROSTATIC = -35.6839 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3941" Parameter: CONF_N -> "8002" Comparing "3941" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3942" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760980 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764716 ATOM PAIRS WERE FOUND FOR ATOM LIST 42197 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28720 from a total of 764716 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3942 -67.37458 1.07586 0.59091 INTE EXTERN> -29.36097 -38.01361 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3746" Parameter: A <- "-67.3746" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.361" Parameter: B <- "-29.361" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0136" Parameter: C <- "-38.0136" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3942 TOTAL ENERGY = -67.3746 RDTITL> * VAN DER WAALS = -29.361 ELECTROSTATIC = -38.0136 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3942" Parameter: CONF_N -> "8002" Comparing "3942" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3943" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764716 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766339 ATOM PAIRS WERE FOUND FOR ATOM LIST 42191 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29042 from a total of 766339 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3943 -67.33437 -0.04021 0.61219 INTE EXTERN> -29.40008 -37.93429 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3344" Parameter: A <- "-67.3344" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4001" Parameter: B <- "-29.4001" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9343" Parameter: C <- "-37.9343" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3943 TOTAL ENERGY = -67.3344 RDTITL> * VAN DER WAALS = -29.4001 ELECTROSTATIC = -37.9343 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3943" Parameter: CONF_N -> "8002" Comparing "3943" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3944" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766339 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764948 ATOM PAIRS WERE FOUND FOR ATOM LIST 42355 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29360 from a total of 764948 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3944 -76.82944 9.49507 0.47077 INTE EXTERN> -35.25716 -41.57228 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8294" Parameter: A <- "-76.8294" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.2572" Parameter: B <- "-35.2572" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5723" Parameter: C <- "-41.5723" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3944 TOTAL ENERGY = -76.8294 RDTITL> * VAN DER WAALS = -35.2572 ELECTROSTATIC = -41.5723 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3944" Parameter: CONF_N -> "8002" Comparing "3944" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3945" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764948 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758788 ATOM PAIRS WERE FOUND FOR ATOM LIST 41821 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28932 from a total of 758788 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3945 -69.63041 -7.19903 0.59783 INTE EXTERN> -28.32703 -41.30339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6304" Parameter: A <- "-69.6304" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.327" Parameter: B <- "-28.327" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3034" Parameter: C <- "-41.3034" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3945 TOTAL ENERGY = -69.6304 RDTITL> * VAN DER WAALS = -28.327 ELECTROSTATIC = -41.3034 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3945" Parameter: CONF_N -> "8002" Comparing "3945" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3946" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758788 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762912 ATOM PAIRS WERE FOUND FOR ATOM LIST 41935 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29496 from a total of 762912 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3946 -70.91839 1.28797 0.67767 INTE EXTERN> -27.50906 -43.40933 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9184" Parameter: A <- "-70.9184" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5091" Parameter: B <- "-27.5091" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4093" Parameter: C <- "-43.4093" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3946 TOTAL ENERGY = -70.9184 RDTITL> * VAN DER WAALS = -27.5091 ELECTROSTATIC = -43.4093 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3946" Parameter: CONF_N -> "8002" Comparing "3946" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3947" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762912 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764375 ATOM PAIRS WERE FOUND FOR ATOM LIST 42093 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28998 from a total of 764375 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3947 -68.89931 -2.01908 0.66445 INTE EXTERN> -25.39811 -43.50120 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8993" Parameter: A <- "-68.8993" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3981" Parameter: B <- "-25.3981" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5012" Parameter: C <- "-43.5012" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3947 TOTAL ENERGY = -68.8993 RDTITL> * VAN DER WAALS = -25.3981 ELECTROSTATIC = -43.5012 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3947" Parameter: CONF_N -> "8002" Comparing "3947" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3948" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764375 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759534 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29172 from a total of 759534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3948 -70.48287 1.58356 0.50827 INTE EXTERN> -31.93093 -38.55194 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4829" Parameter: A <- "-70.4829" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9309" Parameter: B <- "-31.9309" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5519" Parameter: C <- "-38.5519" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3948 TOTAL ENERGY = -70.4829 RDTITL> * VAN DER WAALS = -31.9309 ELECTROSTATIC = -38.5519 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3948" Parameter: CONF_N -> "8002" Comparing "3948" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3949" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761680 ATOM PAIRS WERE FOUND FOR ATOM LIST 41905 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29082 from a total of 761680 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3949 -64.58359 -5.89928 0.48665 INTE EXTERN> -31.16368 -33.41992 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5836" Parameter: A <- "-64.5836" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1637" Parameter: B <- "-31.1637" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.4199" Parameter: C <- "-33.4199" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3949 TOTAL ENERGY = -64.5836 RDTITL> * VAN DER WAALS = -31.1637 ELECTROSTATIC = -33.4199 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3949" Parameter: CONF_N -> "8002" Comparing "3949" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3950" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761680 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756989 ATOM PAIRS WERE FOUND FOR ATOM LIST 41721 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28606 from a total of 756989 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3950 -69.57643 4.99283 0.58845 INTE EXTERN> -28.29523 -41.28119 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5764" Parameter: A <- "-69.5764" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2952" Parameter: B <- "-28.2952" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2812" Parameter: C <- "-41.2812" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3950 TOTAL ENERGY = -69.5764 RDTITL> * VAN DER WAALS = -28.2952 ELECTROSTATIC = -41.2812 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3950" Parameter: CONF_N -> "8002" Comparing "3950" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3951" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756989 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765021 ATOM PAIRS WERE FOUND FOR ATOM LIST 42092 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28682 from a total of 765021 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3951 -68.58997 -0.98646 0.67511 INTE EXTERN> -27.20307 -41.38690 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.59" Parameter: A <- "-68.59" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2031" Parameter: B <- "-27.2031" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3869" Parameter: C <- "-41.3869" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3951 TOTAL ENERGY = -68.59 RDTITL> * VAN DER WAALS = -27.2031 ELECTROSTATIC = -41.3869 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3951" Parameter: CONF_N -> "8002" Comparing "3951" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3952" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765021 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760530 ATOM PAIRS WERE FOUND FOR ATOM LIST 41812 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29104 from a total of 760530 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3952 -68.23711 -0.35286 0.61355 INTE EXTERN> -27.73872 -40.49838 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2371" Parameter: A <- "-68.2371" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7387" Parameter: B <- "-27.7387" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4984" Parameter: C <- "-40.4984" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3952 TOTAL ENERGY = -68.2371 RDTITL> * VAN DER WAALS = -27.7387 ELECTROSTATIC = -40.4984 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3952" Parameter: CONF_N -> "8002" Comparing "3952" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3953" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760530 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767104 ATOM PAIRS WERE FOUND FOR ATOM LIST 42247 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29901 from a total of 767104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3953 -70.43760 2.20049 0.53754 INTE EXTERN> -31.33203 -39.10557 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4376" Parameter: A <- "-70.4376" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.332" Parameter: B <- "-31.332" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1056" Parameter: C <- "-39.1056" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3953 TOTAL ENERGY = -70.4376 RDTITL> * VAN DER WAALS = -31.332 ELECTROSTATIC = -39.1056 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3953" Parameter: CONF_N -> "8002" Comparing "3953" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3954" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764644 ATOM PAIRS WERE FOUND FOR ATOM LIST 42217 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29656 from a total of 764644 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3954 -69.36267 -1.07493 0.60324 INTE EXTERN> -28.88019 -40.48247 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3627" Parameter: A <- "-69.3627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8802" Parameter: B <- "-28.8802" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4825" Parameter: C <- "-40.4825" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3954 TOTAL ENERGY = -69.3627 RDTITL> * VAN DER WAALS = -28.8802 ELECTROSTATIC = -40.4825 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3954" Parameter: CONF_N -> "8002" Comparing "3954" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3955" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764644 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755517 ATOM PAIRS WERE FOUND FOR ATOM LIST 41601 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29705 from a total of 755517 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3955 -68.30041 -1.06225 0.55810 INTE EXTERN> -29.24621 -39.05421 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3004" Parameter: A <- "-68.3004" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2462" Parameter: B <- "-29.2462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0542" Parameter: C <- "-39.0542" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3955 TOTAL ENERGY = -68.3004 RDTITL> * VAN DER WAALS = -29.2462 ELECTROSTATIC = -39.0542 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3955" Parameter: CONF_N -> "8002" Comparing "3955" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3956" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755517 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762924 ATOM PAIRS WERE FOUND FOR ATOM LIST 41948 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29434 from a total of 762924 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3956 -70.76336 2.46295 0.61281 INTE EXTERN> -29.27988 -41.48348 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7634" Parameter: A <- "-70.7634" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2799" Parameter: B <- "-29.2799" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4835" Parameter: C <- "-41.4835" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3956 TOTAL ENERGY = -70.7634 RDTITL> * VAN DER WAALS = -29.2799 ELECTROSTATIC = -41.4835 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3956" Parameter: CONF_N -> "8002" Comparing "3956" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3957" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762924 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764143 ATOM PAIRS WERE FOUND FOR ATOM LIST 42088 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29453 from a total of 764143 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3957 -64.05848 -6.70488 0.54606 INTE EXTERN> -30.03153 -34.02695 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0585" Parameter: A <- "-64.0585" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0315" Parameter: B <- "-30.0315" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.027" Parameter: C <- "-34.027" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3957 TOTAL ENERGY = -64.0585 RDTITL> * VAN DER WAALS = -30.0315 ELECTROSTATIC = -34.027 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3957" Parameter: CONF_N -> "8002" Comparing "3957" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3958" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764143 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764464 ATOM PAIRS WERE FOUND FOR ATOM LIST 42235 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29376 from a total of 764464 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3958 -71.71263 7.65414 0.61738 INTE EXTERN> -29.88011 -41.83252 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7126" Parameter: A <- "-71.7126" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8801" Parameter: B <- "-29.8801" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8325" Parameter: C <- "-41.8325" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3958 TOTAL ENERGY = -71.7126 RDTITL> * VAN DER WAALS = -29.8801 ELECTROSTATIC = -41.8325 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3958" Parameter: CONF_N -> "8002" Comparing "3958" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3959" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764464 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764902 ATOM PAIRS WERE FOUND FOR ATOM LIST 42268 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30232 from a total of 764902 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3959 -74.27079 2.55816 0.59350 INTE EXTERN> -30.30517 -43.96563 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2708" Parameter: A <- "-74.2708" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3052" Parameter: B <- "-30.3052" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9656" Parameter: C <- "-43.9656" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3959 TOTAL ENERGY = -74.2708 RDTITL> * VAN DER WAALS = -30.3052 ELECTROSTATIC = -43.9656 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3959" Parameter: CONF_N -> "8002" Comparing "3959" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3960" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764902 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767003 ATOM PAIRS WERE FOUND FOR ATOM LIST 42404 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30304 from a total of 767003 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3960 -69.70255 -4.56824 0.63225 INTE EXTERN> -30.63224 -39.07031 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7025" Parameter: A <- "-69.7025" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6322" Parameter: B <- "-30.6322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0703" Parameter: C <- "-39.0703" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3960 TOTAL ENERGY = -69.7025 RDTITL> * VAN DER WAALS = -30.6322 ELECTROSTATIC = -39.0703 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3960" Parameter: CONF_N -> "8002" Comparing "3960" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3961" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767003 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757943 ATOM PAIRS WERE FOUND FOR ATOM LIST 41973 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29193 from a total of 757943 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3961 -71.35646 1.65391 0.63057 INTE EXTERN> -29.98506 -41.37140 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3565" Parameter: A <- "-71.3565" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9851" Parameter: B <- "-29.9851" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3714" Parameter: C <- "-41.3714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3961 TOTAL ENERGY = -71.3565 RDTITL> * VAN DER WAALS = -29.9851 ELECTROSTATIC = -41.3714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3961" Parameter: CONF_N -> "8002" Comparing "3961" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3962" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757943 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760767 ATOM PAIRS WERE FOUND FOR ATOM LIST 42040 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28952 from a total of 760767 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3962 -65.48294 -5.87352 0.57875 INTE EXTERN> -27.08391 -38.39904 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4829" Parameter: A <- "-65.4829" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0839" Parameter: B <- "-27.0839" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.399" Parameter: C <- "-38.399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3962 TOTAL ENERGY = -65.4829 RDTITL> * VAN DER WAALS = -27.0839 ELECTROSTATIC = -38.399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3962" Parameter: CONF_N -> "8002" Comparing "3962" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3963" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760767 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766155 ATOM PAIRS WERE FOUND FOR ATOM LIST 42310 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29804 from a total of 766155 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3963 -67.94380 2.46085 0.64780 INTE EXTERN> -25.74747 -42.19633 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9438" Parameter: A <- "-67.9438" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7475" Parameter: B <- "-25.7475" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1963" Parameter: C <- "-42.1963" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3963 TOTAL ENERGY = -67.9438 RDTITL> * VAN DER WAALS = -25.7475 ELECTROSTATIC = -42.1963 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3963" Parameter: CONF_N -> "8002" Comparing "3963" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3964" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766155 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763389 ATOM PAIRS WERE FOUND FOR ATOM LIST 42078 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29133 from a total of 763389 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3964 -61.81153 -6.13226 0.50219 INTE EXTERN> -30.48106 -31.33047 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.8115" Parameter: A <- "-61.8115" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4811" Parameter: B <- "-30.4811" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.3305" Parameter: C <- "-31.3305" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3964 TOTAL ENERGY = -61.8115 RDTITL> * VAN DER WAALS = -30.4811 ELECTROSTATIC = -31.3305 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3964" Parameter: CONF_N -> "8002" Comparing "3964" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3965" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763389 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764488 ATOM PAIRS WERE FOUND FOR ATOM LIST 42112 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29083 from a total of 764488 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3965 -62.52419 0.71266 0.58106 INTE EXTERN> -29.34083 -33.18337 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5242" Parameter: A <- "-62.5242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3408" Parameter: B <- "-29.3408" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1834" Parameter: C <- "-33.1834" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3965 TOTAL ENERGY = -62.5242 RDTITL> * VAN DER WAALS = -29.3408 ELECTROSTATIC = -33.1834 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3965" Parameter: CONF_N -> "8002" Comparing "3965" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3966" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764488 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764490 ATOM PAIRS WERE FOUND FOR ATOM LIST 42132 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29562 from a total of 764490 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3966 -51.00871 -11.51549 0.59691 INTE EXTERN> -28.92476 -22.08395 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-51.0087" Parameter: A <- "-51.0087" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9248" Parameter: B <- "-28.9248" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-22.084" Parameter: C <- "-22.084" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3966 TOTAL ENERGY = -51.0087 RDTITL> * VAN DER WAALS = -28.9248 ELECTROSTATIC = -22.084 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3966" Parameter: CONF_N -> "8002" Comparing "3966" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3967" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764490 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761557 ATOM PAIRS WERE FOUND FOR ATOM LIST 41934 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29394 from a total of 761557 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3967 -53.45210 2.44339 0.49601 INTE EXTERN> -30.63474 -22.81736 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-53.4521" Parameter: A <- "-53.4521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6347" Parameter: B <- "-30.6347" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-22.8174" Parameter: C <- "-22.8174" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3967 TOTAL ENERGY = -53.4521 RDTITL> * VAN DER WAALS = -30.6347 ELECTROSTATIC = -22.8174 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3967" Parameter: CONF_N -> "8002" Comparing "3967" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3968" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761557 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767022 ATOM PAIRS WERE FOUND FOR ATOM LIST 42317 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29692 from a total of 767022 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3968 -58.78097 5.32887 0.51421 INTE EXTERN> -31.30862 -27.47236 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.781" Parameter: A <- "-58.781" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3086" Parameter: B <- "-31.3086" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.4724" Parameter: C <- "-27.4724" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3968 TOTAL ENERGY = -58.781 RDTITL> * VAN DER WAALS = -31.3086 ELECTROSTATIC = -27.4724 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3968" Parameter: CONF_N -> "8002" Comparing "3968" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3969" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767022 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759162 ATOM PAIRS WERE FOUND FOR ATOM LIST 41978 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28874 from a total of 759162 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3969 -54.93338 -3.84759 0.45223 INTE EXTERN> -32.05760 -22.87578 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-54.9334" Parameter: A <- "-54.9334" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0576" Parameter: B <- "-32.0576" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-22.8758" Parameter: C <- "-22.8758" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3969 TOTAL ENERGY = -54.9334 RDTITL> * VAN DER WAALS = -32.0576 ELECTROSTATIC = -22.8758 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3969" Parameter: CONF_N -> "8002" Comparing "3969" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3970" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759162 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758756 ATOM PAIRS WERE FOUND FOR ATOM LIST 41754 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30057 from a total of 758756 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3970 -72.01399 17.08061 0.52225 INTE EXTERN> -32.05943 -39.95455 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.014" Parameter: A <- "-72.014" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0594" Parameter: B <- "-32.0594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9546" Parameter: C <- "-39.9546" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3970 TOTAL ENERGY = -72.014 RDTITL> * VAN DER WAALS = -32.0594 ELECTROSTATIC = -39.9546 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3970" Parameter: CONF_N -> "8002" Comparing "3970" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3971" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758756 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760461 ATOM PAIRS WERE FOUND FOR ATOM LIST 41790 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29256 from a total of 760461 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3971 -74.01211 1.99812 0.70972 INTE EXTERN> -26.50130 -47.51081 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0121" Parameter: A <- "-74.0121" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5013" Parameter: B <- "-26.5013" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5108" Parameter: C <- "-47.5108" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3971 TOTAL ENERGY = -74.0121 RDTITL> * VAN DER WAALS = -26.5013 ELECTROSTATIC = -47.5108 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3971" Parameter: CONF_N -> "8002" Comparing "3971" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3972" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760461 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761014 ATOM PAIRS WERE FOUND FOR ATOM LIST 42117 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29764 from a total of 761014 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3972 -73.03557 -0.97654 0.60338 INTE EXTERN> -29.85012 -43.18544 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0356" Parameter: A <- "-73.0356" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8501" Parameter: B <- "-29.8501" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1854" Parameter: C <- "-43.1854" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3972 TOTAL ENERGY = -73.0356 RDTITL> * VAN DER WAALS = -29.8501 ELECTROSTATIC = -43.1854 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3972" Parameter: CONF_N -> "8002" Comparing "3972" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3973" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761014 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766474 ATOM PAIRS WERE FOUND FOR ATOM LIST 42256 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30179 from a total of 766474 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3973 -73.35445 0.31889 0.50512 INTE EXTERN> -33.21554 -40.13892 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3545" Parameter: A <- "-73.3545" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2155" Parameter: B <- "-33.2155" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1389" Parameter: C <- "-40.1389" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3973 TOTAL ENERGY = -73.3545 RDTITL> * VAN DER WAALS = -33.2155 ELECTROSTATIC = -40.1389 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3973" Parameter: CONF_N -> "8002" Comparing "3973" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3974" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766474 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768466 ATOM PAIRS WERE FOUND FOR ATOM LIST 42449 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29384 from a total of 768466 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3974 -74.52658 1.17213 0.64885 INTE EXTERN> -29.44244 -45.08414 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5266" Parameter: A <- "-74.5266" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4424" Parameter: B <- "-29.4424" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0841" Parameter: C <- "-45.0841" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3974 TOTAL ENERGY = -74.5266 RDTITL> * VAN DER WAALS = -29.4424 ELECTROSTATIC = -45.0841 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3974" Parameter: CONF_N -> "8002" Comparing "3974" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3975" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768466 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761091 ATOM PAIRS WERE FOUND FOR ATOM LIST 41941 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29108 from a total of 761091 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3975 -70.07648 -4.45010 0.60143 INTE EXTERN> -28.19536 -41.88113 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0765" Parameter: A <- "-70.0765" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1954" Parameter: B <- "-28.1954" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8811" Parameter: C <- "-41.8811" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3975 TOTAL ENERGY = -70.0765 RDTITL> * VAN DER WAALS = -28.1954 ELECTROSTATIC = -41.8811 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3975" Parameter: CONF_N -> "8002" Comparing "3975" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3976" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761091 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758519 ATOM PAIRS WERE FOUND FOR ATOM LIST 42122 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29054 from a total of 758519 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3976 -67.37505 -2.70143 0.55818 INTE EXTERN> -30.35024 -37.02481 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3751" Parameter: A <- "-67.3751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3502" Parameter: B <- "-30.3502" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0248" Parameter: C <- "-37.0248" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3976 TOTAL ENERGY = -67.3751 RDTITL> * VAN DER WAALS = -30.3502 ELECTROSTATIC = -37.0248 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3976" Parameter: CONF_N -> "8002" Comparing "3976" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3977" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758519 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763195 ATOM PAIRS WERE FOUND FOR ATOM LIST 42114 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29144 from a total of 763195 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3977 -69.97717 2.60212 0.57278 INTE EXTERN> -29.49570 -40.48148 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9772" Parameter: A <- "-69.9772" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4957" Parameter: B <- "-29.4957" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4815" Parameter: C <- "-40.4815" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3977 TOTAL ENERGY = -69.9772 RDTITL> * VAN DER WAALS = -29.4957 ELECTROSTATIC = -40.4815 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3977" Parameter: CONF_N -> "8002" Comparing "3977" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3978" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763195 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762112 ATOM PAIRS WERE FOUND FOR ATOM LIST 42085 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29138 from a total of 762112 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3978 -66.07088 -3.90630 0.51584 INTE EXTERN> -32.03127 -34.03961 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0709" Parameter: A <- "-66.0709" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0313" Parameter: B <- "-32.0313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.0396" Parameter: C <- "-34.0396" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3978 TOTAL ENERGY = -66.0709 RDTITL> * VAN DER WAALS = -32.0313 ELECTROSTATIC = -34.0396 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3978" Parameter: CONF_N -> "8002" Comparing "3978" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3979" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762112 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758312 ATOM PAIRS WERE FOUND FOR ATOM LIST 42072 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29373 from a total of 758312 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3979 -69.88004 3.80916 0.54638 INTE EXTERN> -32.83012 -37.04992 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.88" Parameter: A <- "-69.88" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8301" Parameter: B <- "-32.8301" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0499" Parameter: C <- "-37.0499" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3979 TOTAL ENERGY = -69.88 RDTITL> * VAN DER WAALS = -32.8301 ELECTROSTATIC = -37.0499 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3979" Parameter: CONF_N -> "8002" Comparing "3979" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3980" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758312 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759014 ATOM PAIRS WERE FOUND FOR ATOM LIST 41940 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29436 from a total of 759014 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3980 -64.57371 -5.30633 0.52057 INTE EXTERN> -33.09771 -31.47600 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5737" Parameter: A <- "-64.5737" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0977" Parameter: B <- "-33.0977" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.476" Parameter: C <- "-31.476" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3980 TOTAL ENERGY = -64.5737 RDTITL> * VAN DER WAALS = -33.0977 ELECTROSTATIC = -31.476 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3980" Parameter: CONF_N -> "8002" Comparing "3980" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3981" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759014 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756848 ATOM PAIRS WERE FOUND FOR ATOM LIST 42185 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29234 from a total of 756848 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3981 -61.31505 -3.25866 0.64667 INTE EXTERN> -28.68564 -32.62941 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.315" Parameter: A <- "-61.315" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6856" Parameter: B <- "-28.6856" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.6294" Parameter: C <- "-32.6294" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3981 TOTAL ENERGY = -61.315 RDTITL> * VAN DER WAALS = -28.6856 ELECTROSTATIC = -32.6294 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3981" Parameter: CONF_N -> "8002" Comparing "3981" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3982" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756848 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762236 ATOM PAIRS WERE FOUND FOR ATOM LIST 42108 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29404 from a total of 762236 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3982 -68.71714 7.40209 0.56403 INTE EXTERN> -32.86225 -35.85490 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7171" Parameter: A <- "-68.7171" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8622" Parameter: B <- "-32.8622" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8549" Parameter: C <- "-35.8549" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3982 TOTAL ENERGY = -68.7171 RDTITL> * VAN DER WAALS = -32.8622 ELECTROSTATIC = -35.8549 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3982" Parameter: CONF_N -> "8002" Comparing "3982" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3983" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762236 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764666 ATOM PAIRS WERE FOUND FOR ATOM LIST 42136 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29635 from a total of 764666 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3983 -72.77299 4.05585 0.57711 INTE EXTERN> -28.14042 -44.63257 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.773" Parameter: A <- "-72.773" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1404" Parameter: B <- "-28.1404" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6326" Parameter: C <- "-44.6326" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3983 TOTAL ENERGY = -72.773 RDTITL> * VAN DER WAALS = -28.1404 ELECTROSTATIC = -44.6326 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3983" Parameter: CONF_N -> "8002" Comparing "3983" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3984" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764666 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759403 ATOM PAIRS WERE FOUND FOR ATOM LIST 42016 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29705 from a total of 759403 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3984 -70.83302 -1.93997 0.53934 INTE EXTERN> -32.30374 -38.52928 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.833" Parameter: A <- "-70.833" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3037" Parameter: B <- "-32.3037" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5293" Parameter: C <- "-38.5293" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3984 TOTAL ENERGY = -70.833 RDTITL> * VAN DER WAALS = -32.3037 ELECTROSTATIC = -38.5293 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3984" Parameter: CONF_N -> "8002" Comparing "3984" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3985" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759403 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765353 ATOM PAIRS WERE FOUND FOR ATOM LIST 42367 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30049 from a total of 765353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3985 -73.95158 3.11856 0.58748 INTE EXTERN> -32.82061 -41.13096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9516" Parameter: A <- "-73.9516" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8206" Parameter: B <- "-32.8206" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.131" Parameter: C <- "-41.131" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3985 TOTAL ENERGY = -73.9516 RDTITL> * VAN DER WAALS = -32.8206 ELECTROSTATIC = -41.131 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3985" Parameter: CONF_N -> "8002" Comparing "3985" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3986" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763298 ATOM PAIRS WERE FOUND FOR ATOM LIST 42125 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30056 from a total of 763298 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3986 -77.43267 3.48109 0.60377 INTE EXTERN> -30.08978 -47.34289 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4327" Parameter: A <- "-77.4327" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0898" Parameter: B <- "-30.0898" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3429" Parameter: C <- "-47.3429" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3986 TOTAL ENERGY = -77.4327 RDTITL> * VAN DER WAALS = -30.0898 ELECTROSTATIC = -47.3429 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3986" Parameter: CONF_N -> "8002" Comparing "3986" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3987" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763298 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764732 ATOM PAIRS WERE FOUND FOR ATOM LIST 42401 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30057 from a total of 764732 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3987 -69.53879 -7.89389 0.56661 INTE EXTERN> -31.01817 -38.52062 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5388" Parameter: A <- "-69.5388" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0182" Parameter: B <- "-31.0182" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5206" Parameter: C <- "-38.5206" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3987 TOTAL ENERGY = -69.5388 RDTITL> * VAN DER WAALS = -31.0182 ELECTROSTATIC = -38.5206 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3987" Parameter: CONF_N -> "8002" Comparing "3987" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3988" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764732 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762978 ATOM PAIRS WERE FOUND FOR ATOM LIST 42276 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29389 from a total of 762978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3988 -66.57263 -2.96616 0.61819 INTE EXTERN> -28.30550 -38.26713 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5726" Parameter: A <- "-66.5726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3055" Parameter: B <- "-28.3055" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2671" Parameter: C <- "-38.2671" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3988 TOTAL ENERGY = -66.5726 RDTITL> * VAN DER WAALS = -28.3055 ELECTROSTATIC = -38.2671 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3988" Parameter: CONF_N -> "8002" Comparing "3988" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3989" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758505 ATOM PAIRS WERE FOUND FOR ATOM LIST 42068 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29167 from a total of 758505 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3989 -75.97450 9.40187 0.67224 INTE EXTERN> -27.08722 -48.88728 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9745" Parameter: A <- "-75.9745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0872" Parameter: B <- "-27.0872" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8873" Parameter: C <- "-48.8873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3989 TOTAL ENERGY = -75.9745 RDTITL> * VAN DER WAALS = -27.0872 ELECTROSTATIC = -48.8873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3989" Parameter: CONF_N -> "8002" Comparing "3989" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3990" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758505 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756959 ATOM PAIRS WERE FOUND FOR ATOM LIST 41795 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29393 from a total of 756959 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3990 -76.27029 0.29579 0.70925 INTE EXTERN> -26.82655 -49.44374 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2703" Parameter: A <- "-76.2703" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8265" Parameter: B <- "-26.8265" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4437" Parameter: C <- "-49.4437" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3990 TOTAL ENERGY = -76.2703 RDTITL> * VAN DER WAALS = -26.8265 ELECTROSTATIC = -49.4437 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3990" Parameter: CONF_N -> "8002" Comparing "3990" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3991" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756959 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754396 ATOM PAIRS WERE FOUND FOR ATOM LIST 41837 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29030 from a total of 754396 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3991 -74.38241 -1.88787 0.53984 INTE EXTERN> -29.96478 -44.41763 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3824" Parameter: A <- "-74.3824" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9648" Parameter: B <- "-29.9648" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4176" Parameter: C <- "-44.4176" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3991 TOTAL ENERGY = -74.3824 RDTITL> * VAN DER WAALS = -29.9648 ELECTROSTATIC = -44.4176 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3991" Parameter: CONF_N -> "8002" Comparing "3991" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3992" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754396 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759340 ATOM PAIRS WERE FOUND FOR ATOM LIST 41867 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29227 from a total of 759340 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3992 -65.38313 -8.99928 0.48132 INTE EXTERN> -31.79634 -33.58679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3831" Parameter: A <- "-65.3831" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7963" Parameter: B <- "-31.7963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.5868" Parameter: C <- "-33.5868" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3992 TOTAL ENERGY = -65.3831 RDTITL> * VAN DER WAALS = -31.7963 ELECTROSTATIC = -33.5868 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3992" Parameter: CONF_N -> "8002" Comparing "3992" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3993" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759340 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756249 ATOM PAIRS WERE FOUND FOR ATOM LIST 41827 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29121 from a total of 756249 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3993 -73.61887 8.23574 0.61578 INTE EXTERN> -28.73427 -44.88460 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6189" Parameter: A <- "-73.6189" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7343" Parameter: B <- "-28.7343" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8846" Parameter: C <- "-44.8846" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3993 TOTAL ENERGY = -73.6189 RDTITL> * VAN DER WAALS = -28.7343 ELECTROSTATIC = -44.8846 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3993" Parameter: CONF_N -> "8002" Comparing "3993" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3994" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756249 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757832 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28901 from a total of 757832 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3994 -61.77649 -11.84238 0.55957 INTE EXTERN> -29.37026 -32.40623 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.7765" Parameter: A <- "-61.7765" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3703" Parameter: B <- "-29.3703" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.4062" Parameter: C <- "-32.4062" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3994 TOTAL ENERGY = -61.7765 RDTITL> * VAN DER WAALS = -29.3703 ELECTROSTATIC = -32.4062 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3994" Parameter: CONF_N -> "8002" Comparing "3994" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3995" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757832 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760321 ATOM PAIRS WERE FOUND FOR ATOM LIST 41991 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29144 from a total of 760321 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3995 -72.35037 10.57388 0.57133 INTE EXTERN> -31.75839 -40.59198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3504" Parameter: A <- "-72.3504" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7584" Parameter: B <- "-31.7584" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.592" Parameter: C <- "-40.592" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3995 TOTAL ENERGY = -72.3504 RDTITL> * VAN DER WAALS = -31.7584 ELECTROSTATIC = -40.592 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3995" Parameter: CONF_N -> "8002" Comparing "3995" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3996" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760321 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766883 ATOM PAIRS WERE FOUND FOR ATOM LIST 42339 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29532 from a total of 766883 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3996 -69.38896 -2.96141 0.59115 INTE EXTERN> -30.66154 -38.72742 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.389" Parameter: A <- "-69.389" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6615" Parameter: B <- "-30.6615" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7274" Parameter: C <- "-38.7274" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3996 TOTAL ENERGY = -69.389 RDTITL> * VAN DER WAALS = -30.6615 ELECTROSTATIC = -38.7274 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3996" Parameter: CONF_N -> "8002" Comparing "3996" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3997" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766883 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762149 ATOM PAIRS WERE FOUND FOR ATOM LIST 42019 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29684 from a total of 762149 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3997 -71.05176 1.66280 0.54496 INTE EXTERN> -29.90182 -41.14993 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0518" Parameter: A <- "-71.0518" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9018" Parameter: B <- "-29.9018" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1499" Parameter: C <- "-41.1499" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3997 TOTAL ENERGY = -71.0518 RDTITL> * VAN DER WAALS = -29.9018 ELECTROSTATIC = -41.1499 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3997" Parameter: CONF_N -> "8002" Comparing "3997" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3998" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762149 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755592 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29571 from a total of 755592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3998 -70.07279 -0.97897 0.47335 INTE EXTERN> -33.41215 -36.66064 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0728" Parameter: A <- "-70.0728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4121" Parameter: B <- "-33.4121" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6606" Parameter: C <- "-36.6606" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3998 TOTAL ENERGY = -70.0728 RDTITL> * VAN DER WAALS = -33.4121 ELECTROSTATIC = -36.6606 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3998" Parameter: CONF_N -> "8002" Comparing "3998" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "3999" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761167 ATOM PAIRS WERE FOUND FOR ATOM LIST 42040 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29518 from a total of 761167 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 3999 -68.86264 -1.21015 0.56204 INTE EXTERN> -28.77978 -40.08286 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8626" Parameter: A <- "-68.8626" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7798" Parameter: B <- "-28.7798" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0829" Parameter: C <- "-40.0829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 3999 TOTAL ENERGY = -68.8626 RDTITL> * VAN DER WAALS = -28.7798 ELECTROSTATIC = -40.0829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "3999" Parameter: CONF_N -> "8002" Comparing "3999" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4000" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761167 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759111 ATOM PAIRS WERE FOUND FOR ATOM LIST 42114 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29152 from a total of 759111 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4000 -59.26290 -9.59975 0.44489 INTE EXTERN> -30.49744 -28.76546 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.2629" Parameter: A <- "-59.2629" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4974" Parameter: B <- "-30.4974" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.7655" Parameter: C <- "-28.7655" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4000 TOTAL ENERGY = -59.2629 RDTITL> * VAN DER WAALS = -30.4974 ELECTROSTATIC = -28.7655 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4000" Parameter: CONF_N -> "8002" Comparing "4000" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4001" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759111 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760974 ATOM PAIRS WERE FOUND FOR ATOM LIST 42145 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28754 from a total of 760974 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4001 -59.14132 -0.12158 0.61178 INTE EXTERN> -27.64515 -31.49617 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.1413" Parameter: A <- "-59.1413" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6452" Parameter: B <- "-27.6452" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4962" Parameter: C <- "-31.4962" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4001 TOTAL ENERGY = -59.1413 RDTITL> * VAN DER WAALS = -27.6452 ELECTROSTATIC = -31.4962 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4001" Parameter: CONF_N -> "8002" Comparing "4001" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4002" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760974 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760518 ATOM PAIRS WERE FOUND FOR ATOM LIST 41766 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30068 from a total of 760518 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4002 -66.54485 7.40353 0.55094 INTE EXTERN> -29.77762 -36.76723 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5448" Parameter: A <- "-66.5448" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7776" Parameter: B <- "-29.7776" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7672" Parameter: C <- "-36.7672" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4002 TOTAL ENERGY = -66.5448 RDTITL> * VAN DER WAALS = -29.7776 ELECTROSTATIC = -36.7672 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4002" Parameter: CONF_N -> "8002" Comparing "4002" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4003" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760518 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764613 ATOM PAIRS WERE FOUND FOR ATOM LIST 41806 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29875 from a total of 764613 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4003 -68.91966 2.37482 0.67034 INTE EXTERN> -29.08871 -39.83096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9197" Parameter: A <- "-68.9197" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0887" Parameter: B <- "-29.0887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.831" Parameter: C <- "-39.831" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4003 TOTAL ENERGY = -68.9197 RDTITL> * VAN DER WAALS = -29.0887 ELECTROSTATIC = -39.831 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4003" Parameter: CONF_N -> "8002" Comparing "4003" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4004" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764613 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761686 ATOM PAIRS WERE FOUND FOR ATOM LIST 41804 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29903 from a total of 761686 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4004 -77.75159 8.83193 0.74873 INTE EXTERN> -25.90407 -51.84752 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7516" Parameter: A <- "-77.7516" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9041" Parameter: B <- "-25.9041" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8475" Parameter: C <- "-51.8475" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4004 TOTAL ENERGY = -77.7516 RDTITL> * VAN DER WAALS = -25.9041 ELECTROSTATIC = -51.8475 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4004" Parameter: CONF_N -> "8002" Comparing "4004" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4005" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761686 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763701 ATOM PAIRS WERE FOUND FOR ATOM LIST 41885 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29759 from a total of 763701 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4005 -74.77693 -2.97467 0.70884 INTE EXTERN> -30.63159 -44.14533 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7769" Parameter: A <- "-74.7769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6316" Parameter: B <- "-30.6316" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1453" Parameter: C <- "-44.1453" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4005 TOTAL ENERGY = -74.7769 RDTITL> * VAN DER WAALS = -30.6316 ELECTROSTATIC = -44.1453 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4005" Parameter: CONF_N -> "8002" Comparing "4005" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4006" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763701 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763970 ATOM PAIRS WERE FOUND FOR ATOM LIST 41926 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30200 from a total of 763970 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4006 -70.48373 -4.29320 0.69258 INTE EXTERN> -27.60752 -42.87621 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4837" Parameter: A <- "-70.4837" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6075" Parameter: B <- "-27.6075" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8762" Parameter: C <- "-42.8762" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4006 TOTAL ENERGY = -70.4837 RDTITL> * VAN DER WAALS = -27.6075 ELECTROSTATIC = -42.8762 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4006" Parameter: CONF_N -> "8002" Comparing "4006" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4007" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763970 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760376 ATOM PAIRS WERE FOUND FOR ATOM LIST 41810 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29816 from a total of 760376 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4007 -70.78144 0.29771 0.65389 INTE EXTERN> -30.74116 -40.04028 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7814" Parameter: A <- "-70.7814" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7412" Parameter: B <- "-30.7412" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0403" Parameter: C <- "-40.0403" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4007 TOTAL ENERGY = -70.7814 RDTITL> * VAN DER WAALS = -30.7412 ELECTROSTATIC = -40.0403 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4007" Parameter: CONF_N -> "8002" Comparing "4007" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4008" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760376 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762147 ATOM PAIRS WERE FOUND FOR ATOM LIST 41787 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29716 from a total of 762147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4008 -68.31100 -2.47044 0.61265 INTE EXTERN> -29.20038 -39.11062 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.311" Parameter: A <- "-68.311" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2004" Parameter: B <- "-29.2004" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1106" Parameter: C <- "-39.1106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4008 TOTAL ENERGY = -68.311 RDTITL> * VAN DER WAALS = -29.2004 ELECTROSTATIC = -39.1106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4008" Parameter: CONF_N -> "8002" Comparing "4008" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4009" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762929 ATOM PAIRS WERE FOUND FOR ATOM LIST 41843 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30008 from a total of 762929 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4009 -70.06800 1.75700 0.57515 INTE EXTERN> -31.80682 -38.26117 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.068" Parameter: A <- "-70.068" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8068" Parameter: B <- "-31.8068" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2612" Parameter: C <- "-38.2612" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4009 TOTAL ENERGY = -70.068 RDTITL> * VAN DER WAALS = -31.8068 ELECTROSTATIC = -38.2612 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4009" Parameter: CONF_N -> "8002" Comparing "4009" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4010" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762929 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759349 ATOM PAIRS WERE FOUND FOR ATOM LIST 41639 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29685 from a total of 759349 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4010 -55.85079 -14.21720 0.47416 INTE EXTERN> -32.29531 -23.55549 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-55.8508" Parameter: A <- "-55.8508" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2953" Parameter: B <- "-32.2953" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-23.5555" Parameter: C <- "-23.5555" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4010 TOTAL ENERGY = -55.8508 RDTITL> * VAN DER WAALS = -32.2953 ELECTROSTATIC = -23.5555 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4010" Parameter: CONF_N -> "8002" Comparing "4010" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4011" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759349 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755292 ATOM PAIRS WERE FOUND FOR ATOM LIST 41654 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29357 from a total of 755292 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4011 -69.10308 13.25228 0.50523 INTE EXTERN> -34.17162 -34.93146 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1031" Parameter: A <- "-69.1031" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1716" Parameter: B <- "-34.1716" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9315" Parameter: C <- "-34.9315" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4011 TOTAL ENERGY = -69.1031 RDTITL> * VAN DER WAALS = -34.1716 ELECTROSTATIC = -34.9315 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4011" Parameter: CONF_N -> "8002" Comparing "4011" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4012" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755292 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762757 ATOM PAIRS WERE FOUND FOR ATOM LIST 41813 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29957 from a total of 762757 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4012 -71.44599 2.34291 0.69624 INTE EXTERN> -27.11538 -44.33061 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.446" Parameter: A <- "-71.446" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1154" Parameter: B <- "-27.1154" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3306" Parameter: C <- "-44.3306" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4012 TOTAL ENERGY = -71.446 RDTITL> * VAN DER WAALS = -27.1154 ELECTROSTATIC = -44.3306 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4012" Parameter: CONF_N -> "8002" Comparing "4012" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4013" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762757 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41685 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29053 from a total of 758422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4013 -62.57076 -8.87524 0.59396 INTE EXTERN> -26.08863 -36.48212 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5708" Parameter: A <- "-62.5708" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0886" Parameter: B <- "-26.0886" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4821" Parameter: C <- "-36.4821" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4013 TOTAL ENERGY = -62.5708 RDTITL> * VAN DER WAALS = -26.0886 ELECTROSTATIC = -36.4821 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4013" Parameter: CONF_N -> "8002" Comparing "4013" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4014" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756592 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29083 from a total of 756592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4014 -60.19924 -2.37151 0.48268 INTE EXTERN> -34.02761 -26.17164 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.1992" Parameter: A <- "-60.1992" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0276" Parameter: B <- "-34.0276" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-26.1716" Parameter: C <- "-26.1716" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4014 TOTAL ENERGY = -60.1992 RDTITL> * VAN DER WAALS = -34.0276 ELECTROSTATIC = -26.1716 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4014" Parameter: CONF_N -> "8002" Comparing "4014" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4015" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746066 ATOM PAIRS WERE FOUND FOR ATOM LIST 41111 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28869 from a total of 746066 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4015 -64.47380 4.27456 0.51120 INTE EXTERN> -32.24781 -32.22599 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.4738" Parameter: A <- "-64.4738" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2478" Parameter: B <- "-32.2478" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.226" Parameter: C <- "-32.226" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4015 TOTAL ENERGY = -64.4738 RDTITL> * VAN DER WAALS = -32.2478 ELECTROSTATIC = -32.226 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4015" Parameter: CONF_N -> "8002" Comparing "4015" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4016" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746066 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755154 ATOM PAIRS WERE FOUND FOR ATOM LIST 41658 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29505 from a total of 755154 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4016 -65.16883 0.69503 0.61747 INTE EXTERN> -26.50306 -38.66577 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1688" Parameter: A <- "-65.1688" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5031" Parameter: B <- "-26.5031" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6658" Parameter: C <- "-38.6658" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4016 TOTAL ENERGY = -65.1688 RDTITL> * VAN DER WAALS = -26.5031 ELECTROSTATIC = -38.6658 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4016" Parameter: CONF_N -> "8002" Comparing "4016" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4017" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755154 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760109 ATOM PAIRS WERE FOUND FOR ATOM LIST 41673 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29859 from a total of 760109 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4017 -65.54950 0.38067 0.57783 INTE EXTERN> -29.94714 -35.60236 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5495" Parameter: A <- "-65.5495" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9471" Parameter: B <- "-29.9471" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6024" Parameter: C <- "-35.6024" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4017 TOTAL ENERGY = -65.5495 RDTITL> * VAN DER WAALS = -29.9471 ELECTROSTATIC = -35.6024 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4017" Parameter: CONF_N -> "8002" Comparing "4017" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4018" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760109 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759071 ATOM PAIRS WERE FOUND FOR ATOM LIST 41616 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29822 from a total of 759071 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4018 -65.07695 -0.47255 0.59692 INTE EXTERN> -30.72156 -34.35539 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.077" Parameter: A <- "-65.077" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7216" Parameter: B <- "-30.7216" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3554" Parameter: C <- "-34.3554" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4018 TOTAL ENERGY = -65.077 RDTITL> * VAN DER WAALS = -30.7216 ELECTROSTATIC = -34.3554 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4018" Parameter: CONF_N -> "8002" Comparing "4018" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4019" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759071 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751944 ATOM PAIRS WERE FOUND FOR ATOM LIST 41287 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28935 from a total of 751944 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4019 -69.55190 4.47495 0.64958 INTE EXTERN> -27.88784 -41.66406 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5519" Parameter: A <- "-69.5519" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8878" Parameter: B <- "-27.8878" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6641" Parameter: C <- "-41.6641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4019 TOTAL ENERGY = -69.5519 RDTITL> * VAN DER WAALS = -27.8878 ELECTROSTATIC = -41.6641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4019" Parameter: CONF_N -> "8002" Comparing "4019" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4020" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751944 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761012 ATOM PAIRS WERE FOUND FOR ATOM LIST 41708 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29875 from a total of 761012 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4020 -70.62016 1.06826 0.54160 INTE EXTERN> -32.51419 -38.10596 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6202" Parameter: A <- "-70.6202" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5142" Parameter: B <- "-32.5142" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.106" Parameter: C <- "-38.106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4020 TOTAL ENERGY = -70.6202 RDTITL> * VAN DER WAALS = -32.5142 ELECTROSTATIC = -38.106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4020" Parameter: CONF_N -> "8002" Comparing "4020" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4021" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761012 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761895 ATOM PAIRS WERE FOUND FOR ATOM LIST 41962 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29660 from a total of 761895 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4021 -61.67054 -8.94962 0.63359 INTE EXTERN> -28.00402 -33.66652 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.6705" Parameter: A <- "-61.6705" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.004" Parameter: B <- "-28.004" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6665" Parameter: C <- "-33.6665" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4021 TOTAL ENERGY = -61.6705 RDTITL> * VAN DER WAALS = -28.004 ELECTROSTATIC = -33.6665 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4021" Parameter: CONF_N -> "8002" Comparing "4021" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4022" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761895 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764727 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29649 from a total of 764727 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4022 -67.81412 6.14357 0.72453 INTE EXTERN> -25.68686 -42.12726 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8141" Parameter: A <- "-67.8141" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6869" Parameter: B <- "-25.6869" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1273" Parameter: C <- "-42.1273" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4022 TOTAL ENERGY = -67.8141 RDTITL> * VAN DER WAALS = -25.6869 ELECTROSTATIC = -42.1273 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4022" Parameter: CONF_N -> "8002" Comparing "4022" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4023" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764727 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758719 ATOM PAIRS WERE FOUND FOR ATOM LIST 41849 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29301 from a total of 758719 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4023 -69.02832 1.21420 0.57706 INTE EXTERN> -30.58904 -38.43928 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0283" Parameter: A <- "-69.0283" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.589" Parameter: B <- "-30.589" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4393" Parameter: C <- "-38.4393" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4023 TOTAL ENERGY = -69.0283 RDTITL> * VAN DER WAALS = -30.589 ELECTROSTATIC = -38.4393 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4023" Parameter: CONF_N -> "8002" Comparing "4023" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4024" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758719 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751461 ATOM PAIRS WERE FOUND FOR ATOM LIST 41430 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28804 from a total of 751461 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4024 -69.53868 0.51036 0.57607 INTE EXTERN> -32.05590 -37.48278 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5387" Parameter: A <- "-69.5387" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0559" Parameter: B <- "-32.0559" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4828" Parameter: C <- "-37.4828" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4024 TOTAL ENERGY = -69.5387 RDTITL> * VAN DER WAALS = -32.0559 ELECTROSTATIC = -37.4828 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4024" Parameter: CONF_N -> "8002" Comparing "4024" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4025" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751461 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760698 ATOM PAIRS WERE FOUND FOR ATOM LIST 41767 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29946 from a total of 760698 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4025 -65.35702 -4.18165 0.51783 INTE EXTERN> -33.41364 -31.94338 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.357" Parameter: A <- "-65.357" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4136" Parameter: B <- "-33.4136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.9434" Parameter: C <- "-31.9434" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4025 TOTAL ENERGY = -65.357 RDTITL> * VAN DER WAALS = -33.4136 ELECTROSTATIC = -31.9434 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4025" Parameter: CONF_N -> "8002" Comparing "4025" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4026" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760698 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755371 ATOM PAIRS WERE FOUND FOR ATOM LIST 41527 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29396 from a total of 755371 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4026 -62.09717 -3.25986 0.50252 INTE EXTERN> -32.35880 -29.73837 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.0972" Parameter: A <- "-62.0972" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3588" Parameter: B <- "-32.3588" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.7384" Parameter: C <- "-29.7384" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4026 TOTAL ENERGY = -62.0972 RDTITL> * VAN DER WAALS = -32.3588 ELECTROSTATIC = -29.7384 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4026" Parameter: CONF_N -> "8002" Comparing "4026" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4027" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755371 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759431 ATOM PAIRS WERE FOUND FOR ATOM LIST 41677 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29473 from a total of 759431 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4027 -64.54368 2.44651 0.49955 INTE EXTERN> -32.05473 -32.48894 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5437" Parameter: A <- "-64.5437" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0547" Parameter: B <- "-32.0547" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.4889" Parameter: C <- "-32.4889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4027 TOTAL ENERGY = -64.5437 RDTITL> * VAN DER WAALS = -32.0547 ELECTROSTATIC = -32.4889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4027" Parameter: CONF_N -> "8002" Comparing "4027" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4028" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759431 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757251 ATOM PAIRS WERE FOUND FOR ATOM LIST 41630 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29260 from a total of 757251 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4028 -68.84437 4.30069 0.51563 INTE EXTERN> -31.26901 -37.57535 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8444" Parameter: A <- "-68.8444" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.269" Parameter: B <- "-31.269" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5754" Parameter: C <- "-37.5754" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4028 TOTAL ENERGY = -68.8444 RDTITL> * VAN DER WAALS = -31.269 ELECTROSTATIC = -37.5754 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4028" Parameter: CONF_N -> "8002" Comparing "4028" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4029" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757251 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757938 ATOM PAIRS WERE FOUND FOR ATOM LIST 41697 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29506 from a total of 757938 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4029 -74.13770 5.29334 0.58374 INTE EXTERN> -31.35455 -42.78315 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1377" Parameter: A <- "-74.1377" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3546" Parameter: B <- "-31.3546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7832" Parameter: C <- "-42.7832" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4029 TOTAL ENERGY = -74.1377 RDTITL> * VAN DER WAALS = -31.3546 ELECTROSTATIC = -42.7832 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4029" Parameter: CONF_N -> "8002" Comparing "4029" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4030" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757938 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755498 ATOM PAIRS WERE FOUND FOR ATOM LIST 41315 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29167 from a total of 755498 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4030 -80.33801 6.20031 0.55409 INTE EXTERN> -31.49255 -48.84546 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.338" Parameter: A <- "-80.338" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4926" Parameter: B <- "-31.4926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8455" Parameter: C <- "-48.8455" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4030 TOTAL ENERGY = -80.338 RDTITL> * VAN DER WAALS = -31.4926 ELECTROSTATIC = -48.8455 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4030" Parameter: CONF_N -> "8002" Comparing "4030" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4031" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755498 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762356 ATOM PAIRS WERE FOUND FOR ATOM LIST 41811 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29308 from a total of 762356 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4031 -78.03416 -2.30386 0.57629 INTE EXTERN> -32.86825 -45.16591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0342" Parameter: A <- "-78.0342" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8682" Parameter: B <- "-32.8682" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1659" Parameter: C <- "-45.1659" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4031 TOTAL ENERGY = -78.0342 RDTITL> * VAN DER WAALS = -32.8682 ELECTROSTATIC = -45.1659 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4031" Parameter: CONF_N -> "8002" Comparing "4031" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4032" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762356 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760716 ATOM PAIRS WERE FOUND FOR ATOM LIST 41843 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30126 from a total of 760716 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4032 -73.47904 -4.55512 0.58290 INTE EXTERN> -32.20377 -41.27527 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.479" Parameter: A <- "-73.479" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2038" Parameter: B <- "-32.2038" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2753" Parameter: C <- "-41.2753" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4032 TOTAL ENERGY = -73.479 RDTITL> * VAN DER WAALS = -32.2038 ELECTROSTATIC = -41.2753 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4032" Parameter: CONF_N -> "8002" Comparing "4032" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4033" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760716 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758348 ATOM PAIRS WERE FOUND FOR ATOM LIST 41417 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29776 from a total of 758348 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4033 -72.31139 -1.16765 0.69007 INTE EXTERN> -25.10929 -47.20209 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3114" Parameter: A <- "-72.3114" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1093" Parameter: B <- "-25.1093" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2021" Parameter: C <- "-47.2021" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4033 TOTAL ENERGY = -72.3114 RDTITL> * VAN DER WAALS = -25.1093 ELECTROSTATIC = -47.2021 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4033" Parameter: CONF_N -> "8002" Comparing "4033" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4034" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758348 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757884 ATOM PAIRS WERE FOUND FOR ATOM LIST 41524 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29433 from a total of 757884 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4034 -78.10055 5.78916 0.58931 INTE EXTERN> -32.95339 -45.14716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1006" Parameter: A <- "-78.1006" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9534" Parameter: B <- "-32.9534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1472" Parameter: C <- "-45.1472" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4034 TOTAL ENERGY = -78.1006 RDTITL> * VAN DER WAALS = -32.9534 ELECTROSTATIC = -45.1472 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4034" Parameter: CONF_N -> "8002" Comparing "4034" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4035" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757884 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757433 ATOM PAIRS WERE FOUND FOR ATOM LIST 41591 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29949 from a total of 757433 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4035 -73.82839 -4.27216 0.56556 INTE EXTERN> -31.30283 -42.52556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8284" Parameter: A <- "-73.8284" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3028" Parameter: B <- "-31.3028" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5256" Parameter: C <- "-42.5256" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4035 TOTAL ENERGY = -73.8284 RDTITL> * VAN DER WAALS = -31.3028 ELECTROSTATIC = -42.5256 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4035" Parameter: CONF_N -> "8002" Comparing "4035" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4036" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757433 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762715 ATOM PAIRS WERE FOUND FOR ATOM LIST 41878 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30280 from a total of 762715 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4036 -75.52463 1.69624 0.65406 INTE EXTERN> -30.22227 -45.30236 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5246" Parameter: A <- "-75.5246" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2223" Parameter: B <- "-30.2223" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3024" Parameter: C <- "-45.3024" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4036 TOTAL ENERGY = -75.5246 RDTITL> * VAN DER WAALS = -30.2223 ELECTROSTATIC = -45.3024 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4036" Parameter: CONF_N -> "8002" Comparing "4036" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4037" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762715 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757186 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29054 from a total of 757186 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4037 -75.69618 0.17155 0.57053 INTE EXTERN> -32.48890 -43.20728 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6962" Parameter: A <- "-75.6962" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4889" Parameter: B <- "-32.4889" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2073" Parameter: C <- "-43.2073" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4037 TOTAL ENERGY = -75.6962 RDTITL> * VAN DER WAALS = -32.4889 ELECTROSTATIC = -43.2073 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4037" Parameter: CONF_N -> "8002" Comparing "4037" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4038" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757186 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756981 ATOM PAIRS WERE FOUND FOR ATOM LIST 41502 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29508 from a total of 756981 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4038 -68.76072 -6.93546 0.58197 INTE EXTERN> -31.59222 -37.16850 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7607" Parameter: A <- "-68.7607" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5922" Parameter: B <- "-31.5922" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1685" Parameter: C <- "-37.1685" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4038 TOTAL ENERGY = -68.7607 RDTITL> * VAN DER WAALS = -31.5922 ELECTROSTATIC = -37.1685 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4038" Parameter: CONF_N -> "8002" Comparing "4038" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4039" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756981 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761554 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29860 from a total of 761554 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4039 -80.79086 12.03013 0.64357 INTE EXTERN> -30.47061 -50.32025 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7909" Parameter: A <- "-80.7909" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4706" Parameter: B <- "-30.4706" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3202" Parameter: C <- "-50.3202" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4039 TOTAL ENERGY = -80.7909 RDTITL> * VAN DER WAALS = -30.4706 ELECTROSTATIC = -50.3202 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4039" Parameter: CONF_N -> "8002" Comparing "4039" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4040" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761554 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760071 ATOM PAIRS WERE FOUND FOR ATOM LIST 41766 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29460 from a total of 760071 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4040 -73.08354 -7.70732 0.65893 INTE EXTERN> -29.68954 -43.39399 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0835" Parameter: A <- "-73.0835" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6895" Parameter: B <- "-29.6895" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.394" Parameter: C <- "-43.394" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4040 TOTAL ENERGY = -73.0835 RDTITL> * VAN DER WAALS = -29.6895 ELECTROSTATIC = -43.394 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4040" Parameter: CONF_N -> "8002" Comparing "4040" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4041" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760071 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762416 ATOM PAIRS WERE FOUND FOR ATOM LIST 41784 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30201 from a total of 762416 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4041 -65.82120 -7.26234 0.69213 INTE EXTERN> -28.90237 -36.91883 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8212" Parameter: A <- "-65.8212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9024" Parameter: B <- "-28.9024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9188" Parameter: C <- "-36.9188" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4041 TOTAL ENERGY = -65.8212 RDTITL> * VAN DER WAALS = -28.9024 ELECTROSTATIC = -36.9188 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4041" Parameter: CONF_N -> "8002" Comparing "4041" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4042" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762416 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762666 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29661 from a total of 762666 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4042 -75.41784 9.59665 0.64332 INTE EXTERN> -27.66869 -47.74915 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4178" Parameter: A <- "-75.4178" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6687" Parameter: B <- "-27.6687" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7492" Parameter: C <- "-47.7492" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4042 TOTAL ENERGY = -75.4178 RDTITL> * VAN DER WAALS = -27.6687 ELECTROSTATIC = -47.7492 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4042" Parameter: CONF_N -> "8002" Comparing "4042" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4043" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762666 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756127 ATOM PAIRS WERE FOUND FOR ATOM LIST 41568 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29419 from a total of 756127 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4043 -77.36749 1.94964 0.58676 INTE EXTERN> -32.26255 -45.10494 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3675" Parameter: A <- "-77.3675" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2626" Parameter: B <- "-32.2626" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1049" Parameter: C <- "-45.1049" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4043 TOTAL ENERGY = -77.3675 RDTITL> * VAN DER WAALS = -32.2626 ELECTROSTATIC = -45.1049 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4043" Parameter: CONF_N -> "8002" Comparing "4043" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4044" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756127 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756568 ATOM PAIRS WERE FOUND FOR ATOM LIST 41469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29148 from a total of 756568 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4044 -75.98017 -1.38731 0.71727 INTE EXTERN> -26.75293 -49.22724 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9802" Parameter: A <- "-75.9802" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7529" Parameter: B <- "-26.7529" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2272" Parameter: C <- "-49.2272" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4044 TOTAL ENERGY = -75.9802 RDTITL> * VAN DER WAALS = -26.7529 ELECTROSTATIC = -49.2272 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4044" Parameter: CONF_N -> "8002" Comparing "4044" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4045" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756568 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759046 ATOM PAIRS WERE FOUND FOR ATOM LIST 41522 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29559 from a total of 759046 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4045 -74.72524 -1.25493 0.58206 INTE EXTERN> -31.80240 -42.92284 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7252" Parameter: A <- "-74.7252" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8024" Parameter: B <- "-31.8024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9228" Parameter: C <- "-42.9228" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4045 TOTAL ENERGY = -74.7252 RDTITL> * VAN DER WAALS = -31.8024 ELECTROSTATIC = -42.9228 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4045" Parameter: CONF_N -> "8002" Comparing "4045" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4046" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759046 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753416 ATOM PAIRS WERE FOUND FOR ATOM LIST 41323 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29557 from a total of 753416 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4046 -71.20621 -3.51903 0.63900 INTE EXTERN> -28.72213 -42.48408 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2062" Parameter: A <- "-71.2062" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7221" Parameter: B <- "-28.7221" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4841" Parameter: C <- "-42.4841" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4046 TOTAL ENERGY = -71.2062 RDTITL> * VAN DER WAALS = -28.7221 ELECTROSTATIC = -42.4841 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4046" Parameter: CONF_N -> "8002" Comparing "4046" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4047" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753416 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759053 ATOM PAIRS WERE FOUND FOR ATOM LIST 41605 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30020 from a total of 759053 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4047 -73.97914 2.77293 0.66253 INTE EXTERN> -31.28357 -42.69557 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9791" Parameter: A <- "-73.9791" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2836" Parameter: B <- "-31.2836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6956" Parameter: C <- "-42.6956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4047 TOTAL ENERGY = -73.9791 RDTITL> * VAN DER WAALS = -31.2836 ELECTROSTATIC = -42.6956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4047" Parameter: CONF_N -> "8002" Comparing "4047" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4048" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759053 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757860 ATOM PAIRS WERE FOUND FOR ATOM LIST 41895 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29703 from a total of 757860 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4048 -76.18632 2.20718 0.65189 INTE EXTERN> -29.11074 -47.07558 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1863" Parameter: A <- "-76.1863" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1107" Parameter: B <- "-29.1107" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0756" Parameter: C <- "-47.0756" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4048 TOTAL ENERGY = -76.1863 RDTITL> * VAN DER WAALS = -29.1107 ELECTROSTATIC = -47.0756 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4048" Parameter: CONF_N -> "8002" Comparing "4048" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4049" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757860 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762036 ATOM PAIRS WERE FOUND FOR ATOM LIST 41782 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29788 from a total of 762036 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4049 -72.97836 -3.20796 0.58175 INTE EXTERN> -31.81036 -41.16800 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9784" Parameter: A <- "-72.9784" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8104" Parameter: B <- "-31.8104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.168" Parameter: C <- "-41.168" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4049 TOTAL ENERGY = -72.9784 RDTITL> * VAN DER WAALS = -31.8104 ELECTROSTATIC = -41.168 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4049" Parameter: CONF_N -> "8002" Comparing "4049" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4050" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762036 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760111 ATOM PAIRS WERE FOUND FOR ATOM LIST 41627 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29355 from a total of 760111 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4050 -71.72144 -1.25692 0.59404 INTE EXTERN> -28.02889 -43.69254 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7214" Parameter: A <- "-71.7214" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0289" Parameter: B <- "-28.0289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6925" Parameter: C <- "-43.6925" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4050 TOTAL ENERGY = -71.7214 RDTITL> * VAN DER WAALS = -28.0289 ELECTROSTATIC = -43.6925 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4050" Parameter: CONF_N -> "8002" Comparing "4050" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4051" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760111 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760889 ATOM PAIRS WERE FOUND FOR ATOM LIST 41771 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30464 from a total of 760889 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4051 -76.42180 4.70036 0.74402 INTE EXTERN> -27.41433 -49.00746 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4218" Parameter: A <- "-76.4218" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4143" Parameter: B <- "-27.4143" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0075" Parameter: C <- "-49.0075" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4051 TOTAL ENERGY = -76.4218 RDTITL> * VAN DER WAALS = -27.4143 ELECTROSTATIC = -49.0075 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4051" Parameter: CONF_N -> "8002" Comparing "4051" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4052" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760889 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763904 ATOM PAIRS WERE FOUND FOR ATOM LIST 41922 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29383 from a total of 763904 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4052 -74.53576 -1.88603 0.55191 INTE EXTERN> -33.90967 -40.62609 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5358" Parameter: A <- "-74.5358" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9097" Parameter: B <- "-33.9097" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6261" Parameter: C <- "-40.6261" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4052 TOTAL ENERGY = -74.5358 RDTITL> * VAN DER WAALS = -33.9097 ELECTROSTATIC = -40.6261 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4052" Parameter: CONF_N -> "8002" Comparing "4052" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4053" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763904 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761667 ATOM PAIRS WERE FOUND FOR ATOM LIST 41845 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29629 from a total of 761667 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4053 -69.50625 -5.02951 0.49956 INTE EXTERN> -33.24144 -36.26481 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5062" Parameter: A <- "-69.5062" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2414" Parameter: B <- "-33.2414" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2648" Parameter: C <- "-36.2648" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4053 TOTAL ENERGY = -69.5062 RDTITL> * VAN DER WAALS = -33.2414 ELECTROSTATIC = -36.2648 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4053" Parameter: CONF_N -> "8002" Comparing "4053" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4054" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761667 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760657 ATOM PAIRS WERE FOUND FOR ATOM LIST 41872 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29912 from a total of 760657 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4054 -74.54759 5.04135 0.57412 INTE EXTERN> -32.57058 -41.97701 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5476" Parameter: A <- "-74.5476" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5706" Parameter: B <- "-32.5706" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.977" Parameter: C <- "-41.977" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4054 TOTAL ENERGY = -74.5476 RDTITL> * VAN DER WAALS = -32.5706 ELECTROSTATIC = -41.977 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4054" Parameter: CONF_N -> "8002" Comparing "4054" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4055" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760657 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763347 ATOM PAIRS WERE FOUND FOR ATOM LIST 41913 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29773 from a total of 763347 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4055 -64.75417 -9.79342 0.57671 INTE EXTERN> -28.97616 -35.77801 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7542" Parameter: A <- "-64.7542" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9762" Parameter: B <- "-28.9762" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.778" Parameter: C <- "-35.778" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4055 TOTAL ENERGY = -64.7542 RDTITL> * VAN DER WAALS = -28.9762 ELECTROSTATIC = -35.778 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4055" Parameter: CONF_N -> "8002" Comparing "4055" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4056" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763347 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766037 ATOM PAIRS WERE FOUND FOR ATOM LIST 42306 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29799 from a total of 766037 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4056 -76.58073 11.82656 0.78892 INTE EXTERN> -25.32740 -51.25333 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5807" Parameter: A <- "-76.5807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3274" Parameter: B <- "-25.3274" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2533" Parameter: C <- "-51.2533" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4056 TOTAL ENERGY = -76.5807 RDTITL> * VAN DER WAALS = -25.3274 ELECTROSTATIC = -51.2533 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4056" Parameter: CONF_N -> "8002" Comparing "4056" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4057" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766037 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762395 ATOM PAIRS WERE FOUND FOR ATOM LIST 41832 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29606 from a total of 762395 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4057 -72.88895 -3.69178 0.72772 INTE EXTERN> -24.95088 -47.93807 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8889" Parameter: A <- "-72.8889" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9509" Parameter: B <- "-24.9509" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9381" Parameter: C <- "-47.9381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4057 TOTAL ENERGY = -72.8889 RDTITL> * VAN DER WAALS = -24.9509 ELECTROSTATIC = -47.9381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4057" Parameter: CONF_N -> "8002" Comparing "4057" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4058" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762395 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757616 ATOM PAIRS WERE FOUND FOR ATOM LIST 41624 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29402 from a total of 757616 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4058 -68.39672 -4.49223 0.61425 INTE EXTERN> -28.32621 -40.07051 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3967" Parameter: A <- "-68.3967" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3262" Parameter: B <- "-28.3262" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0705" Parameter: C <- "-40.0705" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4058 TOTAL ENERGY = -68.3967 RDTITL> * VAN DER WAALS = -28.3262 ELECTROSTATIC = -40.0705 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4058" Parameter: CONF_N -> "8002" Comparing "4058" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4059" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757616 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762668 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30164 from a total of 762668 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4059 -80.01648 11.61976 0.72259 INTE EXTERN> -28.18714 -51.82934 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0165" Parameter: A <- "-80.0165" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1871" Parameter: B <- "-28.1871" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8293" Parameter: C <- "-51.8293" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4059 TOTAL ENERGY = -80.0165 RDTITL> * VAN DER WAALS = -28.1871 ELECTROSTATIC = -51.8293 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4059" Parameter: CONF_N -> "8002" Comparing "4059" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4060" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762668 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763699 ATOM PAIRS WERE FOUND FOR ATOM LIST 41936 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29953 from a total of 763699 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4060 -69.17997 -10.83651 0.59856 INTE EXTERN> -30.15344 -39.02653 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.18" Parameter: A <- "-69.18" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1534" Parameter: B <- "-30.1534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0265" Parameter: C <- "-39.0265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4060 TOTAL ENERGY = -69.18 RDTITL> * VAN DER WAALS = -30.1534 ELECTROSTATIC = -39.0265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4060" Parameter: CONF_N -> "8002" Comparing "4060" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4061" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763699 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764273 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30078 from a total of 764273 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4061 -73.38596 4.20599 0.67607 INTE EXTERN> -27.61702 -45.76894 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.386" Parameter: A <- "-73.386" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.617" Parameter: B <- "-27.617" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7689" Parameter: C <- "-45.7689" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4061 TOTAL ENERGY = -73.386 RDTITL> * VAN DER WAALS = -27.617 ELECTROSTATIC = -45.7689 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4061" Parameter: CONF_N -> "8002" Comparing "4061" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4062" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764273 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762456 ATOM PAIRS WERE FOUND FOR ATOM LIST 41895 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29856 from a total of 762456 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4062 -69.68176 -3.70420 0.59378 INTE EXTERN> -31.92354 -37.75822 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6818" Parameter: A <- "-69.6818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9235" Parameter: B <- "-31.9235" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7582" Parameter: C <- "-37.7582" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4062 TOTAL ENERGY = -69.6818 RDTITL> * VAN DER WAALS = -31.9235 ELECTROSTATIC = -37.7582 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4062" Parameter: CONF_N -> "8002" Comparing "4062" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4063" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762456 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760773 ATOM PAIRS WERE FOUND FOR ATOM LIST 41845 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29713 from a total of 760773 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4063 -68.08659 -1.59517 0.70306 INTE EXTERN> -25.86408 -42.22251 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0866" Parameter: A <- "-68.0866" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8641" Parameter: B <- "-25.8641" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2225" Parameter: C <- "-42.2225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4063 TOTAL ENERGY = -68.0866 RDTITL> * VAN DER WAALS = -25.8641 ELECTROSTATIC = -42.2225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4063" Parameter: CONF_N -> "8002" Comparing "4063" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4064" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760773 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765500 ATOM PAIRS WERE FOUND FOR ATOM LIST 42065 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29885 from a total of 765500 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4064 -70.72037 2.63378 0.72361 INTE EXTERN> -28.54842 -42.17196 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7204" Parameter: A <- "-70.7204" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5484" Parameter: B <- "-28.5484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.172" Parameter: C <- "-42.172" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4064 TOTAL ENERGY = -70.7204 RDTITL> * VAN DER WAALS = -28.5484 ELECTROSTATIC = -42.172 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4064" Parameter: CONF_N -> "8002" Comparing "4064" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4065" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765500 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767098 ATOM PAIRS WERE FOUND FOR ATOM LIST 42167 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30387 from a total of 767098 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4065 -79.46296 8.74258 0.74804 INTE EXTERN> -25.78490 -53.67806 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.463" Parameter: A <- "-79.463" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7849" Parameter: B <- "-25.7849" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6781" Parameter: C <- "-53.6781" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4065 TOTAL ENERGY = -79.463 RDTITL> * VAN DER WAALS = -25.7849 ELECTROSTATIC = -53.6781 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4065" Parameter: CONF_N -> "8002" Comparing "4065" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4066" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767098 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758934 ATOM PAIRS WERE FOUND FOR ATOM LIST 41499 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29880 from a total of 758934 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4066 -74.51459 -4.94837 0.60498 INTE EXTERN> -31.70090 -42.81369 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5146" Parameter: A <- "-74.5146" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7009" Parameter: B <- "-31.7009" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8137" Parameter: C <- "-42.8137" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4066 TOTAL ENERGY = -74.5146 RDTITL> * VAN DER WAALS = -31.7009 ELECTROSTATIC = -42.8137 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4066" Parameter: CONF_N -> "8002" Comparing "4066" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4067" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758934 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757195 ATOM PAIRS WERE FOUND FOR ATOM LIST 41440 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29922 from a total of 757195 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4067 -77.04107 2.52648 0.58727 INTE EXTERN> -31.96139 -45.07968 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0411" Parameter: A <- "-77.0411" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9614" Parameter: B <- "-31.9614" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0797" Parameter: C <- "-45.0797" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4067 TOTAL ENERGY = -77.0411 RDTITL> * VAN DER WAALS = -31.9614 ELECTROSTATIC = -45.0797 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4067" Parameter: CONF_N -> "8002" Comparing "4067" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4068" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757195 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755827 ATOM PAIRS WERE FOUND FOR ATOM LIST 41544 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29105 from a total of 755827 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4068 -74.85678 -2.18428 0.67553 INTE EXTERN> -25.92370 -48.93309 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8568" Parameter: A <- "-74.8568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9237" Parameter: B <- "-25.9237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9331" Parameter: C <- "-48.9331" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4068 TOTAL ENERGY = -74.8568 RDTITL> * VAN DER WAALS = -25.9237 ELECTROSTATIC = -48.9331 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4068" Parameter: CONF_N -> "8002" Comparing "4068" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4069" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755827 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761219 ATOM PAIRS WERE FOUND FOR ATOM LIST 41839 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29814 from a total of 761219 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4069 -68.85429 -6.00250 0.63285 INTE EXTERN> -28.05569 -40.79860 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8543" Parameter: A <- "-68.8543" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0557" Parameter: B <- "-28.0557" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7986" Parameter: C <- "-40.7986" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4069 TOTAL ENERGY = -68.8543 RDTITL> * VAN DER WAALS = -28.0557 ELECTROSTATIC = -40.7986 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4069" Parameter: CONF_N -> "8002" Comparing "4069" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4070" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761219 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757767 ATOM PAIRS WERE FOUND FOR ATOM LIST 41780 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29899 from a total of 757767 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4070 -70.42593 1.57164 0.59304 INTE EXTERN> -28.91405 -41.51188 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4259" Parameter: A <- "-70.4259" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.914" Parameter: B <- "-28.914" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5119" Parameter: C <- "-41.5119" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4070 TOTAL ENERGY = -70.4259 RDTITL> * VAN DER WAALS = -28.914 ELECTROSTATIC = -41.5119 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4070" Parameter: CONF_N -> "8002" Comparing "4070" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4071" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757767 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755378 ATOM PAIRS WERE FOUND FOR ATOM LIST 41613 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28989 from a total of 755378 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4071 -68.60133 -1.82460 0.69756 INTE EXTERN> -25.51933 -43.08200 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6013" Parameter: A <- "-68.6013" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5193" Parameter: B <- "-25.5193" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.082" Parameter: C <- "-43.082" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4071 TOTAL ENERGY = -68.6013 RDTITL> * VAN DER WAALS = -25.5193 ELECTROSTATIC = -43.082 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4071" Parameter: CONF_N -> "8002" Comparing "4071" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4072" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755378 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758953 ATOM PAIRS WERE FOUND FOR ATOM LIST 41857 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29724 from a total of 758953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4072 -73.46811 4.86677 0.64099 INTE EXTERN> -28.64184 -44.82626 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4681" Parameter: A <- "-73.4681" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6418" Parameter: B <- "-28.6418" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8263" Parameter: C <- "-44.8263" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4072 TOTAL ENERGY = -73.4681 RDTITL> * VAN DER WAALS = -28.6418 ELECTROSTATIC = -44.8263 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4072" Parameter: CONF_N -> "8002" Comparing "4072" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4073" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753479 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29375 from a total of 753479 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4073 -71.73017 -1.73794 0.58484 INTE EXTERN> -29.37310 -42.35707 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7302" Parameter: A <- "-71.7302" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3731" Parameter: B <- "-29.3731" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3571" Parameter: C <- "-42.3571" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4073 TOTAL ENERGY = -71.7302 RDTITL> * VAN DER WAALS = -29.3731 ELECTROSTATIC = -42.3571 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4073" Parameter: CONF_N -> "8002" Comparing "4073" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4074" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753479 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757157 ATOM PAIRS WERE FOUND FOR ATOM LIST 41536 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30054 from a total of 757157 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4074 -78.09329 6.36313 0.64779 INTE EXTERN> -28.31036 -49.78294 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0933" Parameter: A <- "-78.0933" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3104" Parameter: B <- "-28.3104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7829" Parameter: C <- "-49.7829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4074 TOTAL ENERGY = -78.0933 RDTITL> * VAN DER WAALS = -28.3104 ELECTROSTATIC = -49.7829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4074" Parameter: CONF_N -> "8002" Comparing "4074" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4075" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757157 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761076 ATOM PAIRS WERE FOUND FOR ATOM LIST 41806 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30165 from a total of 761076 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4075 -81.20748 3.11418 0.77418 INTE EXTERN> -25.48418 -55.72330 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.2075" Parameter: A <- "-81.2075" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4842" Parameter: B <- "-25.4842" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.7233" Parameter: C <- "-55.7233" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4075 TOTAL ENERGY = -81.2075 RDTITL> * VAN DER WAALS = -25.4842 ELECTROSTATIC = -55.7233 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4075" Parameter: CONF_N -> "8002" Comparing "4075" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4076" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761076 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757727 ATOM PAIRS WERE FOUND FOR ATOM LIST 41661 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29511 from a total of 757727 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4076 -77.42731 -3.78016 0.71144 INTE EXTERN> -26.59437 -50.83295 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4273" Parameter: A <- "-77.4273" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5944" Parameter: B <- "-26.5944" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8329" Parameter: C <- "-50.8329" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4076 TOTAL ENERGY = -77.4273 RDTITL> * VAN DER WAALS = -26.5944 ELECTROSTATIC = -50.8329 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4076" Parameter: CONF_N -> "8002" Comparing "4076" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4077" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757727 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753430 ATOM PAIRS WERE FOUND FOR ATOM LIST 41392 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29238 from a total of 753430 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4077 -73.44349 -3.98382 0.58572 INTE EXTERN> -30.94860 -42.49490 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4435" Parameter: A <- "-73.4435" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9486" Parameter: B <- "-30.9486" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4949" Parameter: C <- "-42.4949" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4077 TOTAL ENERGY = -73.4435 RDTITL> * VAN DER WAALS = -30.9486 ELECTROSTATIC = -42.4949 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4077" Parameter: CONF_N -> "8002" Comparing "4077" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4078" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753430 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756920 ATOM PAIRS WERE FOUND FOR ATOM LIST 41574 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29566 from a total of 756920 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4078 -74.01694 0.57344 0.66573 INTE EXTERN> -26.14760 -47.86934 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0169" Parameter: A <- "-74.0169" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1476" Parameter: B <- "-26.1476" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8693" Parameter: C <- "-47.8693" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4078 TOTAL ENERGY = -74.0169 RDTITL> * VAN DER WAALS = -26.1476 ELECTROSTATIC = -47.8693 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4078" Parameter: CONF_N -> "8002" Comparing "4078" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4079" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756920 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761382 ATOM PAIRS WERE FOUND FOR ATOM LIST 41738 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30099 from a total of 761382 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4079 -73.36083 -0.65611 0.72350 INTE EXTERN> -27.72723 -45.63359 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3608" Parameter: A <- "-73.3608" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7272" Parameter: B <- "-27.7272" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6336" Parameter: C <- "-45.6336" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4079 TOTAL ENERGY = -73.3608 RDTITL> * VAN DER WAALS = -27.7272 ELECTROSTATIC = -45.6336 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4079" Parameter: CONF_N -> "8002" Comparing "4079" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4080" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761382 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761312 ATOM PAIRS WERE FOUND FOR ATOM LIST 41780 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30162 from a total of 761312 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4080 -75.27219 1.91136 0.64478 INTE EXTERN> -29.34842 -45.92377 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2722" Parameter: A <- "-75.2722" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3484" Parameter: B <- "-29.3484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9238" Parameter: C <- "-45.9238" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4080 TOTAL ENERGY = -75.2722 RDTITL> * VAN DER WAALS = -29.3484 ELECTROSTATIC = -45.9238 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4080" Parameter: CONF_N -> "8002" Comparing "4080" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4081" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761312 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761452 ATOM PAIRS WERE FOUND FOR ATOM LIST 41909 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30245 from a total of 761452 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4081 -78.44332 3.17113 0.65284 INTE EXTERN> -30.03297 -48.41036 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4433" Parameter: A <- "-78.4433" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.033" Parameter: B <- "-30.033" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4104" Parameter: C <- "-48.4104" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4081 TOTAL ENERGY = -78.4433 RDTITL> * VAN DER WAALS = -30.033 ELECTROSTATIC = -48.4104 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4081" Parameter: CONF_N -> "8002" Comparing "4081" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4082" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761452 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758516 ATOM PAIRS WERE FOUND FOR ATOM LIST 41652 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29559 from a total of 758516 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4082 -71.72342 -6.71991 0.68275 INTE EXTERN> -28.19521 -43.52821 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7234" Parameter: A <- "-71.7234" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1952" Parameter: B <- "-28.1952" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5282" Parameter: C <- "-43.5282" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4082 TOTAL ENERGY = -71.7234 RDTITL> * VAN DER WAALS = -28.1952 ELECTROSTATIC = -43.5282 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4082" Parameter: CONF_N -> "8002" Comparing "4082" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4083" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758516 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765077 ATOM PAIRS WERE FOUND FOR ATOM LIST 41973 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29919 from a total of 765077 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4083 -70.26881 -1.45461 0.54682 INTE EXTERN> -31.88981 -38.37901 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2688" Parameter: A <- "-70.2688" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8898" Parameter: B <- "-31.8898" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.379" Parameter: C <- "-38.379" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4083 TOTAL ENERGY = -70.2688 RDTITL> * VAN DER WAALS = -31.8898 ELECTROSTATIC = -38.379 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4083" Parameter: CONF_N -> "8002" Comparing "4083" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4084" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765077 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763052 ATOM PAIRS WERE FOUND FOR ATOM LIST 41733 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29663 from a total of 763052 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4084 -73.01507 2.74626 0.58303 INTE EXTERN> -32.33239 -40.68268 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0151" Parameter: A <- "-73.0151" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3324" Parameter: B <- "-32.3324" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6827" Parameter: C <- "-40.6827" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4084 TOTAL ENERGY = -73.0151 RDTITL> * VAN DER WAALS = -32.3324 ELECTROSTATIC = -40.6827 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4084" Parameter: CONF_N -> "8002" Comparing "4084" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4085" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763052 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756449 ATOM PAIRS WERE FOUND FOR ATOM LIST 41670 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29297 from a total of 756449 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4085 -69.19144 -3.82363 0.48258 INTE EXTERN> -33.82847 -35.36297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1914" Parameter: A <- "-69.1914" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8285" Parameter: B <- "-33.8285" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.363" Parameter: C <- "-35.363" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4085 TOTAL ENERGY = -69.1914 RDTITL> * VAN DER WAALS = -33.8285 ELECTROSTATIC = -35.363 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4085" Parameter: CONF_N -> "8002" Comparing "4085" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4086" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756449 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756278 ATOM PAIRS WERE FOUND FOR ATOM LIST 41468 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29612 from a total of 756278 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4086 -74.33421 5.14277 0.54773 INTE EXTERN> -32.67911 -41.65510 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3342" Parameter: A <- "-74.3342" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6791" Parameter: B <- "-32.6791" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6551" Parameter: C <- "-41.6551" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4086 TOTAL ENERGY = -74.3342 RDTITL> * VAN DER WAALS = -32.6791 ELECTROSTATIC = -41.6551 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4086" Parameter: CONF_N -> "8002" Comparing "4086" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4087" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756278 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756838 ATOM PAIRS WERE FOUND FOR ATOM LIST 41482 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29665 from a total of 756838 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4087 -78.31536 3.98114 0.58954 INTE EXTERN> -33.48289 -44.83247 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3154" Parameter: A <- "-78.3154" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4829" Parameter: B <- "-33.4829" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8325" Parameter: C <- "-44.8325" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4087 TOTAL ENERGY = -78.3154 RDTITL> * VAN DER WAALS = -33.4829 ELECTROSTATIC = -44.8325 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4087" Parameter: CONF_N -> "8002" Comparing "4087" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4088" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756838 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761241 ATOM PAIRS WERE FOUND FOR ATOM LIST 41881 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30296 from a total of 761241 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4088 -75.39496 -2.92040 0.72138 INTE EXTERN> -27.35542 -48.03954 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.395" Parameter: A <- "-75.395" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3554" Parameter: B <- "-27.3554" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0395" Parameter: C <- "-48.0395" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4088 TOTAL ENERGY = -75.395 RDTITL> * VAN DER WAALS = -27.3554 ELECTROSTATIC = -48.0395 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4088" Parameter: CONF_N -> "8002" Comparing "4088" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4089" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761241 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756850 ATOM PAIRS WERE FOUND FOR ATOM LIST 41429 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29863 from a total of 756850 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4089 -74.41678 -0.97818 0.57040 INTE EXTERN> -33.10838 -41.30840 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4168" Parameter: A <- "-74.4168" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1084" Parameter: B <- "-33.1084" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3084" Parameter: C <- "-41.3084" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4089 TOTAL ENERGY = -74.4168 RDTITL> * VAN DER WAALS = -33.1084 ELECTROSTATIC = -41.3084 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4089" Parameter: CONF_N -> "8002" Comparing "4089" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4090" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756850 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757346 ATOM PAIRS WERE FOUND FOR ATOM LIST 41399 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29823 from a total of 757346 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4090 -69.39938 -5.01740 0.53933 INTE EXTERN> -33.40727 -35.99211 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3994" Parameter: A <- "-69.3994" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4073" Parameter: B <- "-33.4073" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9921" Parameter: C <- "-35.9921" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4090 TOTAL ENERGY = -69.3994 RDTITL> * VAN DER WAALS = -33.4073 ELECTROSTATIC = -35.9921 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4090" Parameter: CONF_N -> "8002" Comparing "4090" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4091" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757346 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762403 ATOM PAIRS WERE FOUND FOR ATOM LIST 41842 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29931 from a total of 762403 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4091 -75.40714 6.00776 0.60666 INTE EXTERN> -31.09980 -44.30734 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4071" Parameter: A <- "-75.4071" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0998" Parameter: B <- "-31.0998" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3073" Parameter: C <- "-44.3073" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4091 TOTAL ENERGY = -75.4071 RDTITL> * VAN DER WAALS = -31.0998 ELECTROSTATIC = -44.3073 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4091" Parameter: CONF_N -> "8002" Comparing "4091" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4092" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762403 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761491 ATOM PAIRS WERE FOUND FOR ATOM LIST 41829 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30012 from a total of 761491 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4092 -73.97550 -1.43164 0.61724 INTE EXTERN> -31.59424 -42.38126 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9755" Parameter: A <- "-73.9755" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5942" Parameter: B <- "-31.5942" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3813" Parameter: C <- "-42.3813" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4092 TOTAL ENERGY = -73.9755 RDTITL> * VAN DER WAALS = -31.5942 ELECTROSTATIC = -42.3813 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4092" Parameter: CONF_N -> "8002" Comparing "4092" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4093" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761491 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758743 ATOM PAIRS WERE FOUND FOR ATOM LIST 41601 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29665 from a total of 758743 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4093 -83.66776 9.69226 0.67664 INTE EXTERN> -30.57350 -53.09426 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.6678" Parameter: A <- "-83.6678" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5735" Parameter: B <- "-30.5735" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0943" Parameter: C <- "-53.0943" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4093 TOTAL ENERGY = -83.6678 RDTITL> * VAN DER WAALS = -30.5735 ELECTROSTATIC = -53.0943 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4093" Parameter: CONF_N -> "8002" Comparing "4093" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4094" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758743 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41799 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30501 from a total of 766009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4094 -71.08021 -12.58755 0.68138 INTE EXTERN> -27.24357 -43.83664 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0802" Parameter: A <- "-71.0802" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2436" Parameter: B <- "-27.2436" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8366" Parameter: C <- "-43.8366" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4094 TOTAL ENERGY = -71.0802 RDTITL> * VAN DER WAALS = -27.2436 ELECTROSTATIC = -43.8366 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4094" Parameter: CONF_N -> "8002" Comparing "4094" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4095" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760018 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29720 from a total of 760018 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4095 -79.98334 8.90313 0.63351 INTE EXTERN> -29.83608 -50.14726 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9833" Parameter: A <- "-79.9833" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8361" Parameter: B <- "-29.8361" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1473" Parameter: C <- "-50.1473" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4095 TOTAL ENERGY = -79.9833 RDTITL> * VAN DER WAALS = -29.8361 ELECTROSTATIC = -50.1473 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4095" Parameter: CONF_N -> "8002" Comparing "4095" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4096" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760018 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761151 ATOM PAIRS WERE FOUND FOR ATOM LIST 41768 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30174 from a total of 761151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4096 -75.53624 -4.44710 0.68165 INTE EXTERN> -30.67719 -44.85905 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5362" Parameter: A <- "-75.5362" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6772" Parameter: B <- "-30.6772" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.859" Parameter: C <- "-44.859" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4096 TOTAL ENERGY = -75.5362 RDTITL> * VAN DER WAALS = -30.6772 ELECTROSTATIC = -44.859 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4096" Parameter: CONF_N -> "8002" Comparing "4096" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4097" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759716 ATOM PAIRS WERE FOUND FOR ATOM LIST 41804 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29695 from a total of 759716 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4097 -62.47564 -13.06060 0.82277 INTE EXTERN> -25.71826 -36.75738 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.4756" Parameter: A <- "-62.4756" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7183" Parameter: B <- "-25.7183" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7574" Parameter: C <- "-36.7574" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4097 TOTAL ENERGY = -62.4756 RDTITL> * VAN DER WAALS = -25.7183 ELECTROSTATIC = -36.7574 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4097" Parameter: CONF_N -> "8002" Comparing "4097" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4098" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759716 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763287 ATOM PAIRS WERE FOUND FOR ATOM LIST 41930 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29625 from a total of 763287 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4098 -73.50160 11.02597 0.59695 INTE EXTERN> -33.42771 -40.07390 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5016" Parameter: A <- "-73.5016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4277" Parameter: B <- "-33.4277" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0739" Parameter: C <- "-40.0739" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4098 TOTAL ENERGY = -73.5016 RDTITL> * VAN DER WAALS = -33.4277 ELECTROSTATIC = -40.0739 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4098" Parameter: CONF_N -> "8002" Comparing "4098" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4099" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763287 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760581 ATOM PAIRS WERE FOUND FOR ATOM LIST 41799 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29574 from a total of 760581 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4099 -75.45375 1.95215 0.68723 INTE EXTERN> -28.88339 -46.57036 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4538" Parameter: A <- "-75.4538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8834" Parameter: B <- "-28.8834" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5704" Parameter: C <- "-46.5704" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4099 TOTAL ENERGY = -75.4538 RDTITL> * VAN DER WAALS = -28.8834 ELECTROSTATIC = -46.5704 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4099" Parameter: CONF_N -> "8002" Comparing "4099" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4100" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760581 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765403 ATOM PAIRS WERE FOUND FOR ATOM LIST 42044 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29192 from a total of 765403 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4100 -80.74690 5.29315 0.64392 INTE EXTERN> -31.88932 -48.85758 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7469" Parameter: A <- "-80.7469" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8893" Parameter: B <- "-31.8893" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8576" Parameter: C <- "-48.8576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4100 TOTAL ENERGY = -80.7469 RDTITL> * VAN DER WAALS = -31.8893 ELECTROSTATIC = -48.8576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4100" Parameter: CONF_N -> "8002" Comparing "4100" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4101" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765403 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761433 ATOM PAIRS WERE FOUND FOR ATOM LIST 41957 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29703 from a total of 761433 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4101 -79.47747 -1.26943 0.64487 INTE EXTERN> -29.84618 -49.63128 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4775" Parameter: A <- "-79.4775" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8462" Parameter: B <- "-29.8462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6313" Parameter: C <- "-49.6313" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4101 TOTAL ENERGY = -79.4775 RDTITL> * VAN DER WAALS = -29.8462 ELECTROSTATIC = -49.6313 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4101" Parameter: CONF_N -> "8002" Comparing "4101" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4102" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761433 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762978 ATOM PAIRS WERE FOUND FOR ATOM LIST 41877 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29248 from a total of 762978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4102 -74.37257 -5.10489 0.64743 INTE EXTERN> -29.34874 -45.02384 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3726" Parameter: A <- "-74.3726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3487" Parameter: B <- "-29.3487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0238" Parameter: C <- "-45.0238" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4102 TOTAL ENERGY = -74.3726 RDTITL> * VAN DER WAALS = -29.3487 ELECTROSTATIC = -45.0238 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4102" Parameter: CONF_N -> "8002" Comparing "4102" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4103" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763106 ATOM PAIRS WERE FOUND FOR ATOM LIST 41889 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29609 from a total of 763106 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4103 -79.40902 5.03645 0.67041 INTE EXTERN> -28.05575 -51.35327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.409" Parameter: A <- "-79.409" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0558" Parameter: B <- "-28.0558" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3533" Parameter: C <- "-51.3533" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4103 TOTAL ENERGY = -79.409 RDTITL> * VAN DER WAALS = -28.0558 ELECTROSTATIC = -51.3533 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4103" Parameter: CONF_N -> "8002" Comparing "4103" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4104" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763106 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763982 ATOM PAIRS WERE FOUND FOR ATOM LIST 41904 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29174 from a total of 763982 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4104 -76.14466 -3.26436 0.67281 INTE EXTERN> -29.25497 -46.88969 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1447" Parameter: A <- "-76.1447" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.255" Parameter: B <- "-29.255" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8897" Parameter: C <- "-46.8897" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4104 TOTAL ENERGY = -76.1447 RDTITL> * VAN DER WAALS = -29.255 ELECTROSTATIC = -46.8897 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4104" Parameter: CONF_N -> "8002" Comparing "4104" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4105" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763982 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765459 ATOM PAIRS WERE FOUND FOR ATOM LIST 42070 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29780 from a total of 765459 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4105 -76.15416 0.00950 0.66288 INTE EXTERN> -29.37414 -46.78002 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1542" Parameter: A <- "-76.1542" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3741" Parameter: B <- "-29.3741" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.78" Parameter: C <- "-46.78" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4105 TOTAL ENERGY = -76.1542 RDTITL> * VAN DER WAALS = -29.3741 ELECTROSTATIC = -46.78 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4105" Parameter: CONF_N -> "8002" Comparing "4105" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4106" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765459 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766319 ATOM PAIRS WERE FOUND FOR ATOM LIST 42174 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29107 from a total of 766319 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4106 -77.71184 1.55768 0.58944 INTE EXTERN> -31.26405 -46.44778 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7118" Parameter: A <- "-77.7118" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2641" Parameter: B <- "-31.2641" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4478" Parameter: C <- "-46.4478" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4106 TOTAL ENERGY = -77.7118 RDTITL> * VAN DER WAALS = -31.2641 ELECTROSTATIC = -46.4478 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4106" Parameter: CONF_N -> "8002" Comparing "4106" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4107" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766319 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765598 ATOM PAIRS WERE FOUND FOR ATOM LIST 41875 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29608 from a total of 765598 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4107 -75.12307 -2.58877 0.64211 INTE EXTERN> -27.17353 -47.94954 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1231" Parameter: A <- "-75.1231" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1735" Parameter: B <- "-27.1735" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9495" Parameter: C <- "-47.9495" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4107 TOTAL ENERGY = -75.1231 RDTITL> * VAN DER WAALS = -27.1735 ELECTROSTATIC = -47.9495 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4107" Parameter: CONF_N -> "8002" Comparing "4107" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4108" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765598 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758419 ATOM PAIRS WERE FOUND FOR ATOM LIST 41662 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29249 from a total of 758419 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4108 -70.53906 -4.58401 0.55948 INTE EXTERN> -31.18705 -39.35202 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5391" Parameter: A <- "-70.5391" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.187" Parameter: B <- "-31.187" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.352" Parameter: C <- "-39.352" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4108 TOTAL ENERGY = -70.5391 RDTITL> * VAN DER WAALS = -31.187 ELECTROSTATIC = -39.352 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4108" Parameter: CONF_N -> "8002" Comparing "4108" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4109" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758419 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764895 ATOM PAIRS WERE FOUND FOR ATOM LIST 42063 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29481 from a total of 764895 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4109 -72.61951 2.08045 0.54593 INTE EXTERN> -31.93769 -40.68182 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6195" Parameter: A <- "-72.6195" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9377" Parameter: B <- "-31.9377" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6818" Parameter: C <- "-40.6818" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4109 TOTAL ENERGY = -72.6195 RDTITL> * VAN DER WAALS = -31.9377 ELECTROSTATIC = -40.6818 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4109" Parameter: CONF_N -> "8002" Comparing "4109" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4110" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764895 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761903 ATOM PAIRS WERE FOUND FOR ATOM LIST 41736 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29722 from a total of 761903 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4110 -70.97025 -1.64927 0.65575 INTE EXTERN> -27.72017 -43.25007 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9702" Parameter: A <- "-70.9702" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7202" Parameter: B <- "-27.7202" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2501" Parameter: C <- "-43.2501" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4110 TOTAL ENERGY = -70.9702 RDTITL> * VAN DER WAALS = -27.7202 ELECTROSTATIC = -43.2501 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4110" Parameter: CONF_N -> "8002" Comparing "4110" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4111" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761903 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759542 ATOM PAIRS WERE FOUND FOR ATOM LIST 41751 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29148 from a total of 759542 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4111 -68.95924 -2.01100 0.49820 INTE EXTERN> -31.22446 -37.73478 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9592" Parameter: A <- "-68.9592" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2245" Parameter: B <- "-31.2245" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7348" Parameter: C <- "-37.7348" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4111 TOTAL ENERGY = -68.9592 RDTITL> * VAN DER WAALS = -31.2245 ELECTROSTATIC = -37.7348 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4111" Parameter: CONF_N -> "8002" Comparing "4111" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4112" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759542 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759781 ATOM PAIRS WERE FOUND FOR ATOM LIST 41649 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30130 from a total of 759781 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4112 -73.50428 4.54503 0.64655 INTE EXTERN> -30.42959 -43.07469 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5043" Parameter: A <- "-73.5043" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4296" Parameter: B <- "-30.4296" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0747" Parameter: C <- "-43.0747" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4112 TOTAL ENERGY = -73.5043 RDTITL> * VAN DER WAALS = -30.4296 ELECTROSTATIC = -43.0747 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4112" Parameter: CONF_N -> "8002" Comparing "4112" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4113" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759781 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756066 ATOM PAIRS WERE FOUND FOR ATOM LIST 41462 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29429 from a total of 756066 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4113 -71.20711 -2.29717 0.60027 INTE EXTERN> -28.79588 -42.41123 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2071" Parameter: A <- "-71.2071" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7959" Parameter: B <- "-28.7959" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4112" Parameter: C <- "-42.4112" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4113 TOTAL ENERGY = -71.2071 RDTITL> * VAN DER WAALS = -28.7959 ELECTROSTATIC = -42.4112 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4113" Parameter: CONF_N -> "8002" Comparing "4113" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4114" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756066 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763812 ATOM PAIRS WERE FOUND FOR ATOM LIST 41758 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30154 from a total of 763812 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4114 -68.03391 -3.17320 0.76772 INTE EXTERN> -22.24191 -45.79201 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0339" Parameter: A <- "-68.0339" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.2419" Parameter: B <- "-22.2419" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.792" Parameter: C <- "-45.792" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4114 TOTAL ENERGY = -68.0339 RDTITL> * VAN DER WAALS = -22.2419 ELECTROSTATIC = -45.792 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4114" Parameter: CONF_N -> "8002" Comparing "4114" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4115" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763812 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761559 ATOM PAIRS WERE FOUND FOR ATOM LIST 41621 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29310 from a total of 761559 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4115 -68.58066 0.54675 0.70202 INTE EXTERN> -24.70330 -43.87737 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5807" Parameter: A <- "-68.5807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7033" Parameter: B <- "-24.7033" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8774" Parameter: C <- "-43.8774" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4115 TOTAL ENERGY = -68.5807 RDTITL> * VAN DER WAALS = -24.7033 ELECTROSTATIC = -43.8774 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4115" Parameter: CONF_N -> "8002" Comparing "4115" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4116" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761559 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762231 ATOM PAIRS WERE FOUND FOR ATOM LIST 41654 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29557 from a total of 762231 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4116 -74.79437 6.21371 0.63432 INTE EXTERN> -27.28084 -47.51353 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7944" Parameter: A <- "-74.7944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2808" Parameter: B <- "-27.2808" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5135" Parameter: C <- "-47.5135" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4116 TOTAL ENERGY = -74.7944 RDTITL> * VAN DER WAALS = -27.2808 ELECTROSTATIC = -47.5135 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4116" Parameter: CONF_N -> "8002" Comparing "4116" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4117" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762231 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759619 ATOM PAIRS WERE FOUND FOR ATOM LIST 41523 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29406 from a total of 759619 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4117 -71.81526 -2.97911 0.64457 INTE EXTERN> -27.35041 -44.46485 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8153" Parameter: A <- "-71.8153" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3504" Parameter: B <- "-27.3504" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4649" Parameter: C <- "-44.4649" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4117 TOTAL ENERGY = -71.8153 RDTITL> * VAN DER WAALS = -27.3504 ELECTROSTATIC = -44.4649 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4117" Parameter: CONF_N -> "8002" Comparing "4117" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4118" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759619 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759690 ATOM PAIRS WERE FOUND FOR ATOM LIST 41712 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29768 from a total of 759690 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4118 -73.93817 2.12291 0.58859 INTE EXTERN> -30.55050 -43.38767 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9382" Parameter: A <- "-73.9382" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5505" Parameter: B <- "-30.5505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3877" Parameter: C <- "-43.3877" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4118 TOTAL ENERGY = -73.9382 RDTITL> * VAN DER WAALS = -30.5505 ELECTROSTATIC = -43.3877 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4118" Parameter: CONF_N -> "8002" Comparing "4118" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4119" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759690 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764046 ATOM PAIRS WERE FOUND FOR ATOM LIST 41918 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29417 from a total of 764046 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4119 -79.30451 5.36634 0.68537 INTE EXTERN> -29.15928 -50.14523 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.3045" Parameter: A <- "-79.3045" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1593" Parameter: B <- "-29.1593" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1452" Parameter: C <- "-50.1452" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4119 TOTAL ENERGY = -79.3045 RDTITL> * VAN DER WAALS = -29.1593 ELECTROSTATIC = -50.1452 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4119" Parameter: CONF_N -> "8002" Comparing "4119" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4120" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764046 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762219 ATOM PAIRS WERE FOUND FOR ATOM LIST 41864 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29509 from a total of 762219 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4120 -74.58295 -4.72155 0.67962 INTE EXTERN> -26.98608 -47.59687 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.583" Parameter: A <- "-74.583" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9861" Parameter: B <- "-26.9861" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5969" Parameter: C <- "-47.5969" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4120 TOTAL ENERGY = -74.583 RDTITL> * VAN DER WAALS = -26.9861 ELECTROSTATIC = -47.5969 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4120" Parameter: CONF_N -> "8002" Comparing "4120" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4121" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762219 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759750 ATOM PAIRS WERE FOUND FOR ATOM LIST 41782 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29468 from a total of 759750 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4121 -71.79695 -2.78601 0.53720 INTE EXTERN> -32.53430 -39.26265 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7969" Parameter: A <- "-71.7969" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5343" Parameter: B <- "-32.5343" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2626" Parameter: C <- "-39.2626" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4121 TOTAL ENERGY = -71.7969 RDTITL> * VAN DER WAALS = -32.5343 ELECTROSTATIC = -39.2626 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4121" Parameter: CONF_N -> "8002" Comparing "4121" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4122" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759750 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754274 ATOM PAIRS WERE FOUND FOR ATOM LIST 41427 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29726 from a total of 754274 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4122 -74.48078 2.68383 0.60267 INTE EXTERN> -28.42729 -46.05349 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4808" Parameter: A <- "-74.4808" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4273" Parameter: B <- "-28.4273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0535" Parameter: C <- "-46.0535" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4122 TOTAL ENERGY = -74.4808 RDTITL> * VAN DER WAALS = -28.4273 ELECTROSTATIC = -46.0535 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4122" Parameter: CONF_N -> "8002" Comparing "4122" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4123" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754274 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754256 ATOM PAIRS WERE FOUND FOR ATOM LIST 41511 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29166 from a total of 754256 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4123 -77.34256 2.86178 0.59113 INTE EXTERN> -30.40153 -46.94103 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3426" Parameter: A <- "-77.3426" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4015" Parameter: B <- "-30.4015" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.941" Parameter: C <- "-46.941" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4123 TOTAL ENERGY = -77.3426 RDTITL> * VAN DER WAALS = -30.4015 ELECTROSTATIC = -46.941 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4123" Parameter: CONF_N -> "8002" Comparing "4123" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4124" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754256 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760185 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29691 from a total of 760185 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4124 -81.17469 3.83213 0.67105 INTE EXTERN> -28.08521 -53.08948 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1747" Parameter: A <- "-81.1747" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0852" Parameter: B <- "-28.0852" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0895" Parameter: C <- "-53.0895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4124 TOTAL ENERGY = -81.1747 RDTITL> * VAN DER WAALS = -28.0852 ELECTROSTATIC = -53.0895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4124" Parameter: CONF_N -> "8002" Comparing "4124" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4125" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760185 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764978 ATOM PAIRS WERE FOUND FOR ATOM LIST 41923 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29694 from a total of 764978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4125 -67.00028 -14.17442 0.60921 INTE EXTERN> -28.43489 -38.56539 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0003" Parameter: A <- "-67.0003" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4349" Parameter: B <- "-28.4349" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5654" Parameter: C <- "-38.5654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4125 TOTAL ENERGY = -67.0003 RDTITL> * VAN DER WAALS = -28.4349 ELECTROSTATIC = -38.5654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4125" Parameter: CONF_N -> "8002" Comparing "4125" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4126" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764316 ATOM PAIRS WERE FOUND FOR ATOM LIST 42102 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30696 from a total of 764316 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4126 -79.01229 12.01201 0.69344 INTE EXTERN> -29.90337 -49.10893 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0123" Parameter: A <- "-79.0123" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9034" Parameter: B <- "-29.9034" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1089" Parameter: C <- "-49.1089" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4126 TOTAL ENERGY = -79.0123 RDTITL> * VAN DER WAALS = -29.9034 ELECTROSTATIC = -49.1089 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4126" Parameter: CONF_N -> "8002" Comparing "4126" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4127" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764316 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761105 ATOM PAIRS WERE FOUND FOR ATOM LIST 41733 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30144 from a total of 761105 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4127 -75.05908 -3.95321 0.67449 INTE EXTERN> -28.79462 -46.26447 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0591" Parameter: A <- "-75.0591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7946" Parameter: B <- "-28.7946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2645" Parameter: C <- "-46.2645" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4127 TOTAL ENERGY = -75.0591 RDTITL> * VAN DER WAALS = -28.7946 ELECTROSTATIC = -46.2645 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4127" Parameter: CONF_N -> "8002" Comparing "4127" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4128" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761105 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759081 ATOM PAIRS WERE FOUND FOR ATOM LIST 41705 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29934 from a total of 759081 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4128 -72.54745 -2.51163 0.68664 INTE EXTERN> -28.11427 -44.43318 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5475" Parameter: A <- "-72.5475" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1143" Parameter: B <- "-28.1143" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4332" Parameter: C <- "-44.4332" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4128 TOTAL ENERGY = -72.5475 RDTITL> * VAN DER WAALS = -28.1143 ELECTROSTATIC = -44.4332 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4128" Parameter: CONF_N -> "8002" Comparing "4128" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4129" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759081 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765867 ATOM PAIRS WERE FOUND FOR ATOM LIST 41882 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30057 from a total of 765867 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4129 -74.19801 1.65056 0.60726 INTE EXTERN> -31.62320 -42.57482 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.198" Parameter: A <- "-74.198" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6232" Parameter: B <- "-31.6232" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5748" Parameter: C <- "-42.5748" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4129 TOTAL ENERGY = -74.198 RDTITL> * VAN DER WAALS = -31.6232 ELECTROSTATIC = -42.5748 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4129" Parameter: CONF_N -> "8002" Comparing "4129" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4130" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765867 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757939 ATOM PAIRS WERE FOUND FOR ATOM LIST 41595 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29443 from a total of 757939 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4130 -70.20177 -3.99624 0.53505 INTE EXTERN> -30.87160 -39.33017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2018" Parameter: A <- "-70.2018" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8716" Parameter: B <- "-30.8716" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3302" Parameter: C <- "-39.3302" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4130 TOTAL ENERGY = -70.2018 RDTITL> * VAN DER WAALS = -30.8716 ELECTROSTATIC = -39.3302 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4130" Parameter: CONF_N -> "8002" Comparing "4130" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4131" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757939 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763919 ATOM PAIRS WERE FOUND FOR ATOM LIST 42003 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30314 from a total of 763919 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4131 -83.49385 13.29207 0.72569 INTE EXTERN> -27.72249 -55.77136 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.4938" Parameter: A <- "-83.4938" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7225" Parameter: B <- "-27.7225" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.7714" Parameter: C <- "-55.7714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4131 TOTAL ENERGY = -83.4938 RDTITL> * VAN DER WAALS = -27.7225 ELECTROSTATIC = -55.7714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4131" Parameter: CONF_N -> "8002" Comparing "4131" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4132" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763919 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760901 ATOM PAIRS WERE FOUND FOR ATOM LIST 41727 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29380 from a total of 760901 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4132 -72.25447 -11.23938 0.67427 INTE EXTERN> -26.20462 -46.04985 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2545" Parameter: A <- "-72.2545" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2046" Parameter: B <- "-26.2046" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0498" Parameter: C <- "-46.0498" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4132 TOTAL ENERGY = -72.2545 RDTITL> * VAN DER WAALS = -26.2046 ELECTROSTATIC = -46.0498 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4132" Parameter: CONF_N -> "8002" Comparing "4132" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4133" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760901 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763353 ATOM PAIRS WERE FOUND FOR ATOM LIST 41979 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29594 from a total of 763353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4133 -76.36401 4.10954 0.75393 INTE EXTERN> -27.58510 -48.77891 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.364" Parameter: A <- "-76.364" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5851" Parameter: B <- "-27.5851" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7789" Parameter: C <- "-48.7789" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4133 TOTAL ENERGY = -76.364 RDTITL> * VAN DER WAALS = -27.5851 ELECTROSTATIC = -48.7789 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4133" Parameter: CONF_N -> "8002" Comparing "4133" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4134" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759267 ATOM PAIRS WERE FOUND FOR ATOM LIST 41790 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29822 from a total of 759267 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4134 -70.19935 -6.16466 0.70467 INTE EXTERN> -28.73024 -41.46911 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1994" Parameter: A <- "-70.1994" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7302" Parameter: B <- "-28.7302" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4691" Parameter: C <- "-41.4691" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4134 TOTAL ENERGY = -70.1994 RDTITL> * VAN DER WAALS = -28.7302 ELECTROSTATIC = -41.4691 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4134" Parameter: CONF_N -> "8002" Comparing "4134" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4135" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759267 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763367 ATOM PAIRS WERE FOUND FOR ATOM LIST 42046 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30928 from a total of 763367 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4135 -71.96646 1.76711 0.68227 INTE EXTERN> -28.73335 -43.23310 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9665" Parameter: A <- "-71.9665" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7334" Parameter: B <- "-28.7334" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2331" Parameter: C <- "-43.2331" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4135 TOTAL ENERGY = -71.9665 RDTITL> * VAN DER WAALS = -28.7334 ELECTROSTATIC = -43.2331 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4135" Parameter: CONF_N -> "8002" Comparing "4135" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4136" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763367 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762394 ATOM PAIRS WERE FOUND FOR ATOM LIST 41751 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29813 from a total of 762394 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4136 -69.81488 -2.15157 0.53223 INTE EXTERN> -31.96482 -37.85006 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8149" Parameter: A <- "-69.8149" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9648" Parameter: B <- "-31.9648" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8501" Parameter: C <- "-37.8501" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4136 TOTAL ENERGY = -69.8149 RDTITL> * VAN DER WAALS = -31.9648 ELECTROSTATIC = -37.8501 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4136" Parameter: CONF_N -> "8002" Comparing "4136" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4137" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762394 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758409 ATOM PAIRS WERE FOUND FOR ATOM LIST 41767 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29386 from a total of 758409 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4137 -75.28408 5.46919 0.61226 INTE EXTERN> -29.55061 -45.73347 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2841" Parameter: A <- "-75.2841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5506" Parameter: B <- "-29.5506" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7335" Parameter: C <- "-45.7335" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4137 TOTAL ENERGY = -75.2841 RDTITL> * VAN DER WAALS = -29.5506 ELECTROSTATIC = -45.7335 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4137" Parameter: CONF_N -> "8002" Comparing "4137" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4138" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758409 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759746 ATOM PAIRS WERE FOUND FOR ATOM LIST 41698 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29251 from a total of 759746 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4138 -73.69479 -1.58928 0.64104 INTE EXTERN> -27.53846 -46.15634 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6948" Parameter: A <- "-73.6948" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5385" Parameter: B <- "-27.5385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1563" Parameter: C <- "-46.1563" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4138 TOTAL ENERGY = -73.6948 RDTITL> * VAN DER WAALS = -27.5385 ELECTROSTATIC = -46.1563 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4138" Parameter: CONF_N -> "8002" Comparing "4138" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4139" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759746 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760604 ATOM PAIRS WERE FOUND FOR ATOM LIST 41858 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29496 from a total of 760604 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4139 -74.30237 0.60758 0.65481 INTE EXTERN> -27.84447 -46.45790 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3024" Parameter: A <- "-74.3024" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8445" Parameter: B <- "-27.8445" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4579" Parameter: C <- "-46.4579" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4139 TOTAL ENERGY = -74.3024 RDTITL> * VAN DER WAALS = -27.8445 ELECTROSTATIC = -46.4579 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4139" Parameter: CONF_N -> "8002" Comparing "4139" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4140" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760604 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767048 ATOM PAIRS WERE FOUND FOR ATOM LIST 41975 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29701 from a total of 767048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4140 -81.20571 6.90334 0.68690 INTE EXTERN> -28.48167 -52.72403 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.2057" Parameter: A <- "-81.2057" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4817" Parameter: B <- "-28.4817" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.724" Parameter: C <- "-52.724" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4140 TOTAL ENERGY = -81.2057 RDTITL> * VAN DER WAALS = -28.4817 ELECTROSTATIC = -52.724 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4140" Parameter: CONF_N -> "8002" Comparing "4140" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4141" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762147 ATOM PAIRS WERE FOUND FOR ATOM LIST 41755 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29504 from a total of 762147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4141 -70.45434 -10.75136 0.52418 INTE EXTERN> -33.38714 -37.06721 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4543" Parameter: A <- "-70.4543" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3871" Parameter: B <- "-33.3871" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0672" Parameter: C <- "-37.0672" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4141 TOTAL ENERGY = -70.4543 RDTITL> * VAN DER WAALS = -33.3871 ELECTROSTATIC = -37.0672 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4141" Parameter: CONF_N -> "8002" Comparing "4141" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4142" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761840 ATOM PAIRS WERE FOUND FOR ATOM LIST 41811 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29481 from a total of 761840 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4142 -73.56362 3.10928 0.65477 INTE EXTERN> -28.82663 -44.73699 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5636" Parameter: A <- "-73.5636" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8266" Parameter: B <- "-28.8266" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.737" Parameter: C <- "-44.737" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4142 TOTAL ENERGY = -73.5636 RDTITL> * VAN DER WAALS = -28.8266 ELECTROSTATIC = -44.737 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4142" Parameter: CONF_N -> "8002" Comparing "4142" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4143" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761840 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762432 ATOM PAIRS WERE FOUND FOR ATOM LIST 41625 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29648 from a total of 762432 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4143 -66.03760 -7.52602 0.68301 INTE EXTERN> -25.74880 -40.28880 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0376" Parameter: A <- "-66.0376" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7488" Parameter: B <- "-25.7488" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2888" Parameter: C <- "-40.2888" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4143 TOTAL ENERGY = -66.0376 RDTITL> * VAN DER WAALS = -25.7488 ELECTROSTATIC = -40.2888 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4143" Parameter: CONF_N -> "8002" Comparing "4143" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4144" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762432 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764935 ATOM PAIRS WERE FOUND FOR ATOM LIST 41842 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29873 from a total of 764935 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4144 -73.08966 7.05206 0.64407 INTE EXTERN> -29.65536 -43.43431 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0897" Parameter: A <- "-73.0897" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6554" Parameter: B <- "-29.6554" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4343" Parameter: C <- "-43.4343" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4144 TOTAL ENERGY = -73.0897 RDTITL> * VAN DER WAALS = -29.6554 ELECTROSTATIC = -43.4343 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4144" Parameter: CONF_N -> "8002" Comparing "4144" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4145" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764935 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765216 ATOM PAIRS WERE FOUND FOR ATOM LIST 42103 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30042 from a total of 765216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4145 -73.30502 0.21536 0.64199 INTE EXTERN> -29.02462 -44.28040 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.305" Parameter: A <- "-73.305" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0246" Parameter: B <- "-29.0246" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2804" Parameter: C <- "-44.2804" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4145 TOTAL ENERGY = -73.305 RDTITL> * VAN DER WAALS = -29.0246 ELECTROSTATIC = -44.2804 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4145" Parameter: CONF_N -> "8002" Comparing "4145" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4146" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762411 ATOM PAIRS WERE FOUND FOR ATOM LIST 41872 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29650 from a total of 762411 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4146 -66.38539 -6.91963 0.61881 INTE EXTERN> -29.83860 -36.54679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3854" Parameter: A <- "-66.3854" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8386" Parameter: B <- "-29.8386" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5468" Parameter: C <- "-36.5468" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4146 TOTAL ENERGY = -66.3854 RDTITL> * VAN DER WAALS = -29.8386 ELECTROSTATIC = -36.5468 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4146" Parameter: CONF_N -> "8002" Comparing "4146" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4147" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762411 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760109 ATOM PAIRS WERE FOUND FOR ATOM LIST 41682 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28827 from a total of 760109 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4147 -76.88016 10.49477 0.66404 INTE EXTERN> -28.44732 -48.43285 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8802" Parameter: A <- "-76.8802" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4473" Parameter: B <- "-28.4473" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4328" Parameter: C <- "-48.4328" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4147 TOTAL ENERGY = -76.8802 RDTITL> * VAN DER WAALS = -28.4473 ELECTROSTATIC = -48.4328 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4147" Parameter: CONF_N -> "8002" Comparing "4147" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4148" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760109 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765617 ATOM PAIRS WERE FOUND FOR ATOM LIST 42206 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29640 from a total of 765617 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4148 -74.41052 -2.46965 0.63851 INTE EXTERN> -30.89203 -43.51849 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4105" Parameter: A <- "-74.4105" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.892" Parameter: B <- "-30.892" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5185" Parameter: C <- "-43.5185" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4148 TOTAL ENERGY = -74.4105 RDTITL> * VAN DER WAALS = -30.892 ELECTROSTATIC = -43.5185 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4148" Parameter: CONF_N -> "8002" Comparing "4148" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4149" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765617 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761463 ATOM PAIRS WERE FOUND FOR ATOM LIST 41718 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28690 from a total of 761463 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4149 -70.11138 -4.29914 0.58925 INTE EXTERN> -30.50705 -39.60433 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1114" Parameter: A <- "-70.1114" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5071" Parameter: B <- "-30.5071" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6043" Parameter: C <- "-39.6043" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4149 TOTAL ENERGY = -70.1114 RDTITL> * VAN DER WAALS = -30.5071 ELECTROSTATIC = -39.6043 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4149" Parameter: CONF_N -> "8002" Comparing "4149" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4150" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761463 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759278 ATOM PAIRS WERE FOUND FOR ATOM LIST 41748 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29384 from a total of 759278 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4150 -68.28018 -1.83120 0.52943 INTE EXTERN> -30.75156 -37.52862 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2802" Parameter: A <- "-68.2802" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7516" Parameter: B <- "-30.7516" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5286" Parameter: C <- "-37.5286" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4150 TOTAL ENERGY = -68.2802 RDTITL> * VAN DER WAALS = -30.7516 ELECTROSTATIC = -37.5286 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4150" Parameter: CONF_N -> "8002" Comparing "4150" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4151" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759278 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761392 ATOM PAIRS WERE FOUND FOR ATOM LIST 41881 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29708 from a total of 761392 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4151 -65.59456 -2.68563 0.55120 INTE EXTERN> -31.90969 -33.68487 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5946" Parameter: A <- "-65.5946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9097" Parameter: B <- "-31.9097" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6849" Parameter: C <- "-33.6849" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4151 TOTAL ENERGY = -65.5946 RDTITL> * VAN DER WAALS = -31.9097 ELECTROSTATIC = -33.6849 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4151" Parameter: CONF_N -> "8002" Comparing "4151" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4152" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761392 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763602 ATOM PAIRS WERE FOUND FOR ATOM LIST 42229 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29444 from a total of 763602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4152 -69.91493 4.32037 0.66946 INTE EXTERN> -28.65769 -41.25724 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9149" Parameter: A <- "-69.9149" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6577" Parameter: B <- "-28.6577" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2572" Parameter: C <- "-41.2572" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4152 TOTAL ENERGY = -69.9149 RDTITL> * VAN DER WAALS = -28.6577 ELECTROSTATIC = -41.2572 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4152" Parameter: CONF_N -> "8002" Comparing "4152" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4153" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757856 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29165 from a total of 757856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4153 -67.61752 -2.29741 0.44774 INTE EXTERN> -32.46048 -35.15703 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6175" Parameter: A <- "-67.6175" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4605" Parameter: B <- "-32.4605" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.157" Parameter: C <- "-35.157" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4153 TOTAL ENERGY = -67.6175 RDTITL> * VAN DER WAALS = -32.4605 ELECTROSTATIC = -35.157 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4153" Parameter: CONF_N -> "8002" Comparing "4153" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4154" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759361 ATOM PAIRS WERE FOUND FOR ATOM LIST 41802 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29796 from a total of 759361 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4154 -75.82624 8.20872 0.68331 INTE EXTERN> -28.79446 -47.03177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8262" Parameter: A <- "-75.8262" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7945" Parameter: B <- "-28.7945" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0318" Parameter: C <- "-47.0318" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4154 TOTAL ENERGY = -75.8262 RDTITL> * VAN DER WAALS = -28.7945 ELECTROSTATIC = -47.0318 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4154" Parameter: CONF_N -> "8002" Comparing "4154" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4155" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759361 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760512 ATOM PAIRS WERE FOUND FOR ATOM LIST 41752 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29085 from a total of 760512 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4155 -69.48016 -6.34607 0.74761 INTE EXTERN> -25.84679 -43.63337 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4802" Parameter: A <- "-69.4802" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8468" Parameter: B <- "-25.8468" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6334" Parameter: C <- "-43.6334" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4155 TOTAL ENERGY = -69.4802 RDTITL> * VAN DER WAALS = -25.8468 ELECTROSTATIC = -43.6334 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4155" Parameter: CONF_N -> "8002" Comparing "4155" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4156" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760512 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764308 ATOM PAIRS WERE FOUND FOR ATOM LIST 42064 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30161 from a total of 764308 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4156 -68.68805 -0.79211 0.65516 INTE EXTERN> -30.50255 -38.18550 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6881" Parameter: A <- "-68.6881" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5025" Parameter: B <- "-30.5025" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1855" Parameter: C <- "-38.1855" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4156 TOTAL ENERGY = -68.6881 RDTITL> * VAN DER WAALS = -30.5025 ELECTROSTATIC = -38.1855 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4156" Parameter: CONF_N -> "8002" Comparing "4156" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4157" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764308 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756351 ATOM PAIRS WERE FOUND FOR ATOM LIST 41781 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29716 from a total of 756351 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4157 -65.78373 -2.90432 0.54263 INTE EXTERN> -32.28972 -33.49401 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7837" Parameter: A <- "-65.7837" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2897" Parameter: B <- "-32.2897" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.494" Parameter: C <- "-33.494" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4157 TOTAL ENERGY = -65.7837 RDTITL> * VAN DER WAALS = -32.2897 ELECTROSTATIC = -33.494 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4157" Parameter: CONF_N -> "8002" Comparing "4157" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4158" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756351 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753547 ATOM PAIRS WERE FOUND FOR ATOM LIST 41452 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28850 from a total of 753547 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4158 -57.55072 -8.23301 0.62605 INTE EXTERN> -29.10720 -28.44352 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.5507" Parameter: A <- "-57.5507" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1072" Parameter: B <- "-29.1072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.4435" Parameter: C <- "-28.4435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4158 TOTAL ENERGY = -57.5507 RDTITL> * VAN DER WAALS = -29.1072 ELECTROSTATIC = -28.4435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4158" Parameter: CONF_N -> "8002" Comparing "4158" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4159" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753547 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761097 ATOM PAIRS WERE FOUND FOR ATOM LIST 41816 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29836 from a total of 761097 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4159 -72.21048 14.65976 0.72720 INTE EXTERN> -25.52416 -46.68633 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2105" Parameter: A <- "-72.2105" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5242" Parameter: B <- "-25.5242" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6863" Parameter: C <- "-46.6863" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4159 TOTAL ENERGY = -72.2105 RDTITL> * VAN DER WAALS = -25.5242 ELECTROSTATIC = -46.6863 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4159" Parameter: CONF_N -> "8002" Comparing "4159" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4160" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761097 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757937 ATOM PAIRS WERE FOUND FOR ATOM LIST 41736 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29573 from a total of 757937 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4160 -64.52996 -7.68052 0.64262 INTE EXTERN> -28.10060 -36.42936 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.53" Parameter: A <- "-64.53" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1006" Parameter: B <- "-28.1006" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4294" Parameter: C <- "-36.4294" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4160 TOTAL ENERGY = -64.53 RDTITL> * VAN DER WAALS = -28.1006 ELECTROSTATIC = -36.4294 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4160" Parameter: CONF_N -> "8002" Comparing "4160" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4161" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757937 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762196 ATOM PAIRS WERE FOUND FOR ATOM LIST 41843 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29795 from a total of 762196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4161 -70.11798 5.58802 0.70785 INTE EXTERN> -28.11360 -42.00438 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.118" Parameter: A <- "-70.118" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1136" Parameter: B <- "-28.1136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0044" Parameter: C <- "-42.0044" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4161 TOTAL ENERGY = -70.118 RDTITL> * VAN DER WAALS = -28.1136 ELECTROSTATIC = -42.0044 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4161" Parameter: CONF_N -> "8002" Comparing "4161" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4162" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767491 ATOM PAIRS WERE FOUND FOR ATOM LIST 42126 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30280 from a total of 767491 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4162 -60.63460 -9.48338 0.53330 INTE EXTERN> -33.12345 -27.51115 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.6346" Parameter: A <- "-60.6346" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1234" Parameter: B <- "-33.1234" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.5112" Parameter: C <- "-27.5112" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4162 TOTAL ENERGY = -60.6346 RDTITL> * VAN DER WAALS = -33.1234 ELECTROSTATIC = -27.5112 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4162" Parameter: CONF_N -> "8002" Comparing "4162" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4163" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767491 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758648 ATOM PAIRS WERE FOUND FOR ATOM LIST 41659 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29907 from a total of 758648 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4163 -77.27886 16.64426 0.71875 INTE EXTERN> -28.75965 -48.51922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2789" Parameter: A <- "-77.2789" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7596" Parameter: B <- "-28.7596" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5192" Parameter: C <- "-48.5192" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4163 TOTAL ENERGY = -77.2789 RDTITL> * VAN DER WAALS = -28.7596 ELECTROSTATIC = -48.5192 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4163" Parameter: CONF_N -> "8002" Comparing "4163" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4164" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758648 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761147 ATOM PAIRS WERE FOUND FOR ATOM LIST 41808 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30271 from a total of 761147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4164 -69.07590 -8.20296 0.61244 INTE EXTERN> -31.03468 -38.04123 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0759" Parameter: A <- "-69.0759" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0347" Parameter: B <- "-31.0347" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0412" Parameter: C <- "-38.0412" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4164 TOTAL ENERGY = -69.0759 RDTITL> * VAN DER WAALS = -31.0347 ELECTROSTATIC = -38.0412 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4164" Parameter: CONF_N -> "8002" Comparing "4164" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4165" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760848 ATOM PAIRS WERE FOUND FOR ATOM LIST 41608 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29958 from a total of 760848 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4165 -73.53348 4.45758 0.63017 INTE EXTERN> -31.23318 -42.30030 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5335" Parameter: A <- "-73.5335" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2332" Parameter: B <- "-31.2332" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3003" Parameter: C <- "-42.3003" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4165 TOTAL ENERGY = -73.5335 RDTITL> * VAN DER WAALS = -31.2332 ELECTROSTATIC = -42.3003 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4165" Parameter: CONF_N -> "8002" Comparing "4165" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4166" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760848 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763972 ATOM PAIRS WERE FOUND FOR ATOM LIST 41905 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30513 from a total of 763972 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4166 -71.32313 -2.21035 0.69002 INTE EXTERN> -27.61157 -43.71157 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3231" Parameter: A <- "-71.3231" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6116" Parameter: B <- "-27.6116" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7116" Parameter: C <- "-43.7116" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4166 TOTAL ENERGY = -71.3231 RDTITL> * VAN DER WAALS = -27.6116 ELECTROSTATIC = -43.7116 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4166" Parameter: CONF_N -> "8002" Comparing "4166" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4167" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763972 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763419 ATOM PAIRS WERE FOUND FOR ATOM LIST 41742 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30338 from a total of 763419 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4167 -70.78049 -0.54264 0.58303 INTE EXTERN> -33.46247 -37.31802 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7805" Parameter: A <- "-70.7805" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4625" Parameter: B <- "-33.4625" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.318" Parameter: C <- "-37.318" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4167 TOTAL ENERGY = -70.7805 RDTITL> * VAN DER WAALS = -33.4625 ELECTROSTATIC = -37.318 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4167" Parameter: CONF_N -> "8002" Comparing "4167" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4168" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763419 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758463 ATOM PAIRS WERE FOUND FOR ATOM LIST 41655 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30146 from a total of 758463 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4168 -70.63532 -0.14518 0.57117 INTE EXTERN> -33.41974 -37.21558 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6353" Parameter: A <- "-70.6353" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4197" Parameter: B <- "-33.4197" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2156" Parameter: C <- "-37.2156" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4168 TOTAL ENERGY = -70.6353 RDTITL> * VAN DER WAALS = -33.4197 ELECTROSTATIC = -37.2156 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4168" Parameter: CONF_N -> "8002" Comparing "4168" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4169" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758463 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758804 ATOM PAIRS WERE FOUND FOR ATOM LIST 41617 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30667 from a total of 758804 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4169 -71.30506 0.66974 0.67264 INTE EXTERN> -29.37868 -41.92637 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3051" Parameter: A <- "-71.3051" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3787" Parameter: B <- "-29.3787" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9264" Parameter: C <- "-41.9264" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4169 TOTAL ENERGY = -71.3051 RDTITL> * VAN DER WAALS = -29.3787 ELECTROSTATIC = -41.9264 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4169" Parameter: CONF_N -> "8002" Comparing "4169" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4170" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758804 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763684 ATOM PAIRS WERE FOUND FOR ATOM LIST 41962 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30819 from a total of 763684 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4170 -72.55070 1.24564 0.63034 INTE EXTERN> -31.83241 -40.71829 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5507" Parameter: A <- "-72.5507" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8324" Parameter: B <- "-31.8324" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7183" Parameter: C <- "-40.7183" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4170 TOTAL ENERGY = -72.5507 RDTITL> * VAN DER WAALS = -31.8324 ELECTROSTATIC = -40.7183 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4170" Parameter: CONF_N -> "8002" Comparing "4170" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4171" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763684 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758004 ATOM PAIRS WERE FOUND FOR ATOM LIST 41752 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30529 from a total of 758004 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4171 -73.27097 0.72027 0.64835 INTE EXTERN> -30.91332 -42.35765 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.271" Parameter: A <- "-73.271" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9133" Parameter: B <- "-30.9133" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3577" Parameter: C <- "-42.3577" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4171 TOTAL ENERGY = -73.271 RDTITL> * VAN DER WAALS = -30.9133 ELECTROSTATIC = -42.3577 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4171" Parameter: CONF_N -> "8002" Comparing "4171" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4172" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758004 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750783 ATOM PAIRS WERE FOUND FOR ATOM LIST 41346 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30363 from a total of 750783 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4172 -65.53722 -7.73375 0.61092 INTE EXTERN> -27.21695 -38.32027 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5372" Parameter: A <- "-65.5372" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.217" Parameter: B <- "-27.217" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3203" Parameter: C <- "-38.3203" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4172 TOTAL ENERGY = -65.5372 RDTITL> * VAN DER WAALS = -27.217 ELECTROSTATIC = -38.3203 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4172" Parameter: CONF_N -> "8002" Comparing "4172" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4173" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750783 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761210 ATOM PAIRS WERE FOUND FOR ATOM LIST 41764 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30229 from a total of 761210 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4173 -71.33389 5.79666 0.79288 INTE EXTERN> -25.31772 -46.01617 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3339" Parameter: A <- "-71.3339" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3177" Parameter: B <- "-25.3177" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0162" Parameter: C <- "-46.0162" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4173 TOTAL ENERGY = -71.3339 RDTITL> * VAN DER WAALS = -25.3177 ELECTROSTATIC = -46.0162 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4173" Parameter: CONF_N -> "8002" Comparing "4173" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4174" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761210 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762219 ATOM PAIRS WERE FOUND FOR ATOM LIST 41789 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30103 from a total of 762219 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4174 -70.63478 -0.69911 0.62987 INTE EXTERN> -29.88529 -40.74949 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6348" Parameter: A <- "-70.6348" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8853" Parameter: B <- "-29.8853" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7495" Parameter: C <- "-40.7495" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4174 TOTAL ENERGY = -70.6348 RDTITL> * VAN DER WAALS = -29.8853 ELECTROSTATIC = -40.7495 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4174" Parameter: CONF_N -> "8002" Comparing "4174" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4175" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762219 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757990 ATOM PAIRS WERE FOUND FOR ATOM LIST 41622 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29641 from a total of 757990 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4175 -69.52656 -1.10822 0.66506 INTE EXTERN> -28.09500 -41.43156 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5266" Parameter: A <- "-69.5266" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.095" Parameter: B <- "-28.095" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4316" Parameter: C <- "-41.4316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4175 TOTAL ENERGY = -69.5266 RDTITL> * VAN DER WAALS = -28.095 ELECTROSTATIC = -41.4316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4175" Parameter: CONF_N -> "8002" Comparing "4175" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4176" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757990 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764287 ATOM PAIRS WERE FOUND FOR ATOM LIST 42266 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29705 from a total of 764287 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4176 -66.43722 -3.08935 0.59966 INTE EXTERN> -31.24361 -35.19361 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4372" Parameter: A <- "-66.4372" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2436" Parameter: B <- "-31.2436" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1936" Parameter: C <- "-35.1936" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4176 TOTAL ENERGY = -66.4372 RDTITL> * VAN DER WAALS = -31.2436 ELECTROSTATIC = -35.1936 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4176" Parameter: CONF_N -> "8002" Comparing "4176" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4177" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764287 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764946 ATOM PAIRS WERE FOUND FOR ATOM LIST 41912 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30222 from a total of 764946 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4177 -69.27590 2.83869 0.68377 INTE EXTERN> -28.27843 -40.99747 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2759" Parameter: A <- "-69.2759" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2784" Parameter: B <- "-28.2784" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9975" Parameter: C <- "-40.9975" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4177 TOTAL ENERGY = -69.2759 RDTITL> * VAN DER WAALS = -28.2784 ELECTROSTATIC = -40.9975 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4177" Parameter: CONF_N -> "8002" Comparing "4177" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4178" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764946 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761761 ATOM PAIRS WERE FOUND FOR ATOM LIST 41844 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29608 from a total of 761761 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4178 -73.49951 4.22361 0.62557 INTE EXTERN> -31.83370 -41.66581 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4995" Parameter: A <- "-73.4995" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8337" Parameter: B <- "-31.8337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6658" Parameter: C <- "-41.6658" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4178 TOTAL ENERGY = -73.4995 RDTITL> * VAN DER WAALS = -31.8337 ELECTROSTATIC = -41.6658 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4178" Parameter: CONF_N -> "8002" Comparing "4178" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4179" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761761 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763744 ATOM PAIRS WERE FOUND FOR ATOM LIST 41980 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30199 from a total of 763744 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4179 -78.84956 5.35005 0.68448 INTE EXTERN> -29.88360 -48.96596 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8496" Parameter: A <- "-78.8496" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8836" Parameter: B <- "-29.8836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.966" Parameter: C <- "-48.966" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4179 TOTAL ENERGY = -78.8496 RDTITL> * VAN DER WAALS = -29.8836 ELECTROSTATIC = -48.966 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4179" Parameter: CONF_N -> "8002" Comparing "4179" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4180" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763744 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764947 ATOM PAIRS WERE FOUND FOR ATOM LIST 42225 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30105 from a total of 764947 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4180 -63.97379 -14.87577 0.59911 INTE EXTERN> -30.89468 -33.07911 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.9738" Parameter: A <- "-63.9738" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8947" Parameter: B <- "-30.8947" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.0791" Parameter: C <- "-33.0791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4180 TOTAL ENERGY = -63.9738 RDTITL> * VAN DER WAALS = -30.8947 ELECTROSTATIC = -33.0791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4180" Parameter: CONF_N -> "8002" Comparing "4180" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4181" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764947 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770123 ATOM PAIRS WERE FOUND FOR ATOM LIST 42208 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30177 from a total of 770123 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4181 -68.50992 4.53614 0.53743 INTE EXTERN> -32.46259 -36.04733 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5099" Parameter: A <- "-68.5099" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4626" Parameter: B <- "-32.4626" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0473" Parameter: C <- "-36.0473" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4181 TOTAL ENERGY = -68.5099 RDTITL> * VAN DER WAALS = -32.4626 ELECTROSTATIC = -36.0473 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4181" Parameter: CONF_N -> "8002" Comparing "4181" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4182" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770123 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761226 ATOM PAIRS WERE FOUND FOR ATOM LIST 41969 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29387 from a total of 761226 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4182 -73.52899 5.01906 0.66100 INTE EXTERN> -29.54104 -43.98794 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.529" Parameter: A <- "-73.529" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.541" Parameter: B <- "-29.541" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9879" Parameter: C <- "-43.9879" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4182 TOTAL ENERGY = -73.529 RDTITL> * VAN DER WAALS = -29.541 ELECTROSTATIC = -43.9879 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4182" Parameter: CONF_N -> "8002" Comparing "4182" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4183" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761226 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756975 ATOM PAIRS WERE FOUND FOR ATOM LIST 41602 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29313 from a total of 756975 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4183 -62.69024 -10.83875 0.62045 INTE EXTERN> -26.73366 -35.95658 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.6902" Parameter: A <- "-62.6902" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7337" Parameter: B <- "-26.7337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9566" Parameter: C <- "-35.9566" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4183 TOTAL ENERGY = -62.6902 RDTITL> * VAN DER WAALS = -26.7337 ELECTROSTATIC = -35.9566 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4183" Parameter: CONF_N -> "8002" Comparing "4183" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4184" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756975 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768116 ATOM PAIRS WERE FOUND FOR ATOM LIST 42295 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29723 from a total of 768116 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4184 -74.78756 12.09732 0.65388 INTE EXTERN> -29.73659 -45.05097 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7876" Parameter: A <- "-74.7876" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7366" Parameter: B <- "-29.7366" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.051" Parameter: C <- "-45.051" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4184 TOTAL ENERGY = -74.7876 RDTITL> * VAN DER WAALS = -29.7366 ELECTROSTATIC = -45.051 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4184" Parameter: CONF_N -> "8002" Comparing "4184" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4185" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768116 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767264 ATOM PAIRS WERE FOUND FOR ATOM LIST 42404 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30155 from a total of 767264 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4185 -74.64269 -0.14487 0.66208 INTE EXTERN> -29.01790 -45.62479 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6427" Parameter: A <- "-74.6427" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0179" Parameter: B <- "-29.0179" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6248" Parameter: C <- "-45.6248" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4185 TOTAL ENERGY = -74.6427 RDTITL> * VAN DER WAALS = -29.0179 ELECTROSTATIC = -45.6248 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4185" Parameter: CONF_N -> "8002" Comparing "4185" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4186" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767264 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761812 ATOM PAIRS WERE FOUND FOR ATOM LIST 41887 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30521 from a total of 761812 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4186 -71.34014 -3.30255 0.62741 INTE EXTERN> -28.34905 -42.99109 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3401" Parameter: A <- "-71.3401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.349" Parameter: B <- "-28.349" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9911" Parameter: C <- "-42.9911" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4186 TOTAL ENERGY = -71.3401 RDTITL> * VAN DER WAALS = -28.349 ELECTROSTATIC = -42.9911 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4186" Parameter: CONF_N -> "8002" Comparing "4186" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4187" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761812 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763424 ATOM PAIRS WERE FOUND FOR ATOM LIST 42052 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29318 from a total of 763424 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4187 -69.77778 -1.56236 0.57270 INTE EXTERN> -29.35923 -40.41855 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7778" Parameter: A <- "-69.7778" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3592" Parameter: B <- "-29.3592" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4186" Parameter: C <- "-40.4186" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4187 TOTAL ENERGY = -69.7778 RDTITL> * VAN DER WAALS = -29.3592 ELECTROSTATIC = -40.4186 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4187" Parameter: CONF_N -> "8002" Comparing "4187" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4188" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763424 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759543 ATOM PAIRS WERE FOUND FOR ATOM LIST 41767 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29900 from a total of 759543 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4188 -73.00972 3.23194 0.74003 INTE EXTERN> -25.49071 -47.51900 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0097" Parameter: A <- "-73.0097" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4907" Parameter: B <- "-25.4907" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.519" Parameter: C <- "-47.519" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4188 TOTAL ENERGY = -73.0097 RDTITL> * VAN DER WAALS = -25.4907 ELECTROSTATIC = -47.519 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4188" Parameter: CONF_N -> "8002" Comparing "4188" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4189" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759543 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764095 ATOM PAIRS WERE FOUND FOR ATOM LIST 41859 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29733 from a total of 764095 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4189 -69.16171 -3.84801 0.61746 INTE EXTERN> -27.89692 -41.26479 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1617" Parameter: A <- "-69.1617" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8969" Parameter: B <- "-27.8969" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2648" Parameter: C <- "-41.2648" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4189 TOTAL ENERGY = -69.1617 RDTITL> * VAN DER WAALS = -27.8969 ELECTROSTATIC = -41.2648 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4189" Parameter: CONF_N -> "8002" Comparing "4189" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4190" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764095 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758093 ATOM PAIRS WERE FOUND FOR ATOM LIST 41635 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29918 from a total of 758093 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4190 -70.89619 1.73448 0.71301 INTE EXTERN> -25.80669 -45.08949 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8962" Parameter: A <- "-70.8962" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8067" Parameter: B <- "-25.8067" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0895" Parameter: C <- "-45.0895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4190 TOTAL ENERGY = -70.8962 RDTITL> * VAN DER WAALS = -25.8067 ELECTROSTATIC = -45.0895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4190" Parameter: CONF_N -> "8002" Comparing "4190" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4191" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758093 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760223 ATOM PAIRS WERE FOUND FOR ATOM LIST 41827 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29922 from a total of 760223 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4191 -68.64504 -2.25114 0.67234 INTE EXTERN> -27.76036 -40.88469 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.645" Parameter: A <- "-68.645" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7604" Parameter: B <- "-27.7604" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8847" Parameter: C <- "-40.8847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4191 TOTAL ENERGY = -68.645 RDTITL> * VAN DER WAALS = -27.7604 ELECTROSTATIC = -40.8847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4191" Parameter: CONF_N -> "8002" Comparing "4191" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4192" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760223 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763390 ATOM PAIRS WERE FOUND FOR ATOM LIST 41782 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30232 from a total of 763390 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4192 -70.14185 1.49681 0.60210 INTE EXTERN> -30.31906 -39.82280 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1419" Parameter: A <- "-70.1419" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3191" Parameter: B <- "-30.3191" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8228" Parameter: C <- "-39.8228" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4192 TOTAL ENERGY = -70.1419 RDTITL> * VAN DER WAALS = -30.3191 ELECTROSTATIC = -39.8228 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4192" Parameter: CONF_N -> "8002" Comparing "4192" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4193" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763390 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763506 ATOM PAIRS WERE FOUND FOR ATOM LIST 41935 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29418 from a total of 763506 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4193 -70.05572 -0.08614 0.52140 INTE EXTERN> -32.35771 -37.69801 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0557" Parameter: A <- "-70.0557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3577" Parameter: B <- "-32.3577" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.698" Parameter: C <- "-37.698" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4193 TOTAL ENERGY = -70.0557 RDTITL> * VAN DER WAALS = -32.3577 ELECTROSTATIC = -37.698 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4193" Parameter: CONF_N -> "8002" Comparing "4193" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4194" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763506 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758568 ATOM PAIRS WERE FOUND FOR ATOM LIST 41567 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30347 from a total of 758568 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4194 -71.76559 1.70988 0.58061 INTE EXTERN> -32.24665 -39.51894 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7656" Parameter: A <- "-71.7656" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2467" Parameter: B <- "-32.2467" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5189" Parameter: C <- "-39.5189" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4194 TOTAL ENERGY = -71.7656 RDTITL> * VAN DER WAALS = -32.2467 ELECTROSTATIC = -39.5189 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4194" Parameter: CONF_N -> "8002" Comparing "4194" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4195" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758568 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753418 ATOM PAIRS WERE FOUND FOR ATOM LIST 41506 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28908 from a total of 753418 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4195 -75.66531 3.89971 0.61368 INTE EXTERN> -28.28774 -47.37757 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6653" Parameter: A <- "-75.6653" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2877" Parameter: B <- "-28.2877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3776" Parameter: C <- "-47.3776" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4195 TOTAL ENERGY = -75.6653 RDTITL> * VAN DER WAALS = -28.2877 ELECTROSTATIC = -47.3776 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4195" Parameter: CONF_N -> "8002" Comparing "4195" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4196" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753418 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757910 ATOM PAIRS WERE FOUND FOR ATOM LIST 41577 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29912 from a total of 757910 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4196 -74.90573 -0.75958 0.60562 INTE EXTERN> -29.99427 -44.91146 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9057" Parameter: A <- "-74.9057" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9943" Parameter: B <- "-29.9943" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9115" Parameter: C <- "-44.9115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4196 TOTAL ENERGY = -74.9057 RDTITL> * VAN DER WAALS = -29.9943 ELECTROSTATIC = -44.9115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4196" Parameter: CONF_N -> "8002" Comparing "4196" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4197" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757910 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765127 ATOM PAIRS WERE FOUND FOR ATOM LIST 41823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30131 from a total of 765127 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4197 -69.92358 -4.98215 0.74130 INTE EXTERN> -22.37553 -47.54805 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9236" Parameter: A <- "-69.9236" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.3755" Parameter: B <- "-22.3755" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5481" Parameter: C <- "-47.5481" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4197 TOTAL ENERGY = -69.9236 RDTITL> * VAN DER WAALS = -22.3755 ELECTROSTATIC = -47.5481 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4197" Parameter: CONF_N -> "8002" Comparing "4197" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4198" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765127 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761212 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28927 from a total of 761212 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4198 -79.68696 9.76338 0.62359 INTE EXTERN> -30.33903 -49.34793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.687" Parameter: A <- "-79.687" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.339" Parameter: B <- "-30.339" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3479" Parameter: C <- "-49.3479" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4198 TOTAL ENERGY = -79.687 RDTITL> * VAN DER WAALS = -30.339 ELECTROSTATIC = -49.3479 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4198" Parameter: CONF_N -> "8002" Comparing "4198" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4199" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761212 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766107 ATOM PAIRS WERE FOUND FOR ATOM LIST 41784 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30032 from a total of 766107 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4199 -69.32787 -10.35909 0.70221 INTE EXTERN> -26.33033 -42.99754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3279" Parameter: A <- "-69.3279" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3303" Parameter: B <- "-26.3303" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9975" Parameter: C <- "-42.9975" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4199 TOTAL ENERGY = -69.3279 RDTITL> * VAN DER WAALS = -26.3303 ELECTROSTATIC = -42.9975 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4199" Parameter: CONF_N -> "8002" Comparing "4199" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4200" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766107 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760319 ATOM PAIRS WERE FOUND FOR ATOM LIST 41632 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29875 from a total of 760319 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4200 -73.65941 4.33154 0.62869 INTE EXTERN> -29.26786 -44.39155 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6594" Parameter: A <- "-73.6594" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2679" Parameter: B <- "-29.2679" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3916" Parameter: C <- "-44.3916" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4200 TOTAL ENERGY = -73.6594 RDTITL> * VAN DER WAALS = -29.2679 ELECTROSTATIC = -44.3916 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4200" Parameter: CONF_N -> "8002" Comparing "4200" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4201" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760319 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756501 ATOM PAIRS WERE FOUND FOR ATOM LIST 41599 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29848 from a total of 756501 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4201 -71.61266 -2.04675 0.76393 INTE EXTERN> -25.42237 -46.19030 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6127" Parameter: A <- "-71.6127" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4224" Parameter: B <- "-25.4224" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1903" Parameter: C <- "-46.1903" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4201 TOTAL ENERGY = -71.6127 RDTITL> * VAN DER WAALS = -25.4224 ELECTROSTATIC = -46.1903 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4201" Parameter: CONF_N -> "8002" Comparing "4201" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4202" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756501 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762219 ATOM PAIRS WERE FOUND FOR ATOM LIST 41737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30114 from a total of 762219 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4202 -67.48240 -4.13026 0.64847 INTE EXTERN> -27.26255 -40.21986 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4824" Parameter: A <- "-67.4824" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2625" Parameter: B <- "-27.2625" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2199" Parameter: C <- "-40.2199" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4202 TOTAL ENERGY = -67.4824 RDTITL> * VAN DER WAALS = -27.2625 ELECTROSTATIC = -40.2199 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4202" Parameter: CONF_N -> "8002" Comparing "4202" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4203" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762219 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764623 ATOM PAIRS WERE FOUND FOR ATOM LIST 42012 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29934 from a total of 764623 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4203 -74.63160 7.14919 0.62933 INTE EXTERN> -28.54824 -46.08335 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6316" Parameter: A <- "-74.6316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5482" Parameter: B <- "-28.5482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0834" Parameter: C <- "-46.0834" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4203 TOTAL ENERGY = -74.6316 RDTITL> * VAN DER WAALS = -28.5482 ELECTROSTATIC = -46.0834 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4203" Parameter: CONF_N -> "8002" Comparing "4203" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4204" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764623 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765773 ATOM PAIRS WERE FOUND FOR ATOM LIST 41975 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30556 from a total of 765773 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4204 -72.14716 -2.48443 0.79535 INTE EXTERN> -22.62366 -49.52350 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1472" Parameter: A <- "-72.1472" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.6237" Parameter: B <- "-22.6237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5235" Parameter: C <- "-49.5235" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4204 TOTAL ENERGY = -72.1472 RDTITL> * VAN DER WAALS = -22.6237 ELECTROSTATIC = -49.5235 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4204" Parameter: CONF_N -> "8002" Comparing "4204" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4205" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765773 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753450 ATOM PAIRS WERE FOUND FOR ATOM LIST 41398 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29464 from a total of 753450 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4205 -67.39161 -4.75556 0.78760 INTE EXTERN> -21.39581 -45.99580 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3916" Parameter: A <- "-67.3916" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.3958" Parameter: B <- "-21.3958" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9958" Parameter: C <- "-45.9958" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4205 TOTAL ENERGY = -67.3916 RDTITL> * VAN DER WAALS = -21.3958 ELECTROSTATIC = -45.9958 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4205" Parameter: CONF_N -> "8002" Comparing "4205" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4206" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753450 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758466 ATOM PAIRS WERE FOUND FOR ATOM LIST 41560 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29668 from a total of 758466 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4206 -73.35955 5.96795 0.68761 INTE EXTERN> -27.47198 -45.88758 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3596" Parameter: A <- "-73.3596" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.472" Parameter: B <- "-27.472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8876" Parameter: C <- "-45.8876" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4206 TOTAL ENERGY = -73.3596 RDTITL> * VAN DER WAALS = -27.472 ELECTROSTATIC = -45.8876 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4206" Parameter: CONF_N -> "8002" Comparing "4206" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4207" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758466 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762911 ATOM PAIRS WERE FOUND FOR ATOM LIST 42002 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29973 from a total of 762911 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4207 -78.64847 5.28891 0.73404 INTE EXTERN> -26.65637 -51.99209 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6485" Parameter: A <- "-78.6485" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6564" Parameter: B <- "-26.6564" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.9921" Parameter: C <- "-51.9921" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4207 TOTAL ENERGY = -78.6485 RDTITL> * VAN DER WAALS = -26.6564 ELECTROSTATIC = -51.9921 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4207" Parameter: CONF_N -> "8002" Comparing "4207" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4208" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762911 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757711 ATOM PAIRS WERE FOUND FOR ATOM LIST 41631 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29232 from a total of 757711 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4208 -72.71184 -5.93662 0.61257 INTE EXTERN> -31.20031 -41.51153 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7118" Parameter: A <- "-72.7118" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2003" Parameter: B <- "-31.2003" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5115" Parameter: C <- "-41.5115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4208 TOTAL ENERGY = -72.7118 RDTITL> * VAN DER WAALS = -31.2003 ELECTROSTATIC = -41.5115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4208" Parameter: CONF_N -> "8002" Comparing "4208" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4209" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757711 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758568 ATOM PAIRS WERE FOUND FOR ATOM LIST 41559 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29132 from a total of 758568 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4209 -74.07363 1.36179 0.76586 INTE EXTERN> -25.28214 -48.79149 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0736" Parameter: A <- "-74.0736" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2821" Parameter: B <- "-25.2821" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7915" Parameter: C <- "-48.7915" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4209 TOTAL ENERGY = -74.0736 RDTITL> * VAN DER WAALS = -25.2821 ELECTROSTATIC = -48.7915 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4209" Parameter: CONF_N -> "8002" Comparing "4209" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4210" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758568 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763282 ATOM PAIRS WERE FOUND FOR ATOM LIST 41856 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29070 from a total of 763282 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4210 -74.72141 0.64778 0.70114 INTE EXTERN> -24.27383 -50.44759 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7214" Parameter: A <- "-74.7214" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2738" Parameter: B <- "-24.2738" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4476" Parameter: C <- "-50.4476" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4210 TOTAL ENERGY = -74.7214 RDTITL> * VAN DER WAALS = -24.2738 ELECTROSTATIC = -50.4476 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4210" Parameter: CONF_N -> "8002" Comparing "4210" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4211" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763282 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760540 ATOM PAIRS WERE FOUND FOR ATOM LIST 41891 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28945 from a total of 760540 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4211 -70.42318 -4.29823 0.65032 INTE EXTERN> -26.05602 -44.36715 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4232" Parameter: A <- "-70.4232" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.056" Parameter: B <- "-26.056" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3672" Parameter: C <- "-44.3672" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4211 TOTAL ENERGY = -70.4232 RDTITL> * VAN DER WAALS = -26.056 ELECTROSTATIC = -44.3672 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4211" Parameter: CONF_N -> "8002" Comparing "4211" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4212" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760540 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762052 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29814 from a total of 762052 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4212 -67.89923 -2.52395 0.54167 INTE EXTERN> -33.06612 -34.83311 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8992" Parameter: A <- "-67.8992" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0661" Parameter: B <- "-33.0661" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8331" Parameter: C <- "-34.8331" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4212 TOTAL ENERGY = -67.8992 RDTITL> * VAN DER WAALS = -33.0661 ELECTROSTATIC = -34.8331 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4212" Parameter: CONF_N -> "8002" Comparing "4212" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4213" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762052 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762740 ATOM PAIRS WERE FOUND FOR ATOM LIST 41590 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29937 from a total of 762740 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4213 -64.39936 -3.49987 0.60547 INTE EXTERN> -28.78373 -35.61563 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3994" Parameter: A <- "-64.3994" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7837" Parameter: B <- "-28.7837" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6156" Parameter: C <- "-35.6156" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4213 TOTAL ENERGY = -64.3994 RDTITL> * VAN DER WAALS = -28.7837 ELECTROSTATIC = -35.6156 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4213" Parameter: CONF_N -> "8002" Comparing "4213" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4214" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762740 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759489 ATOM PAIRS WERE FOUND FOR ATOM LIST 41725 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30005 from a total of 759489 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4214 -60.09846 -4.30090 0.53498 INTE EXTERN> -30.84117 -29.25729 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.0985" Parameter: A <- "-60.0985" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8412" Parameter: B <- "-30.8412" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.2573" Parameter: C <- "-29.2573" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4214 TOTAL ENERGY = -60.0985 RDTITL> * VAN DER WAALS = -30.8412 ELECTROSTATIC = -29.2573 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4214" Parameter: CONF_N -> "8002" Comparing "4214" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4215" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759489 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753921 ATOM PAIRS WERE FOUND FOR ATOM LIST 41400 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29154 from a total of 753921 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4215 -65.59716 5.49870 0.54292 INTE EXTERN> -31.74752 -33.84964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5972" Parameter: A <- "-65.5972" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7475" Parameter: B <- "-31.7475" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8496" Parameter: C <- "-33.8496" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4215 TOTAL ENERGY = -65.5972 RDTITL> * VAN DER WAALS = -31.7475 ELECTROSTATIC = -33.8496 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4215" Parameter: CONF_N -> "8002" Comparing "4215" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4216" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753921 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41762 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29885 from a total of 761794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4216 -70.83412 5.23696 0.65219 INTE EXTERN> -29.19289 -41.64123 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8341" Parameter: A <- "-70.8341" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1929" Parameter: B <- "-29.1929" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6412" Parameter: C <- "-41.6412" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4216 TOTAL ENERGY = -70.8341 RDTITL> * VAN DER WAALS = -29.1929 ELECTROSTATIC = -41.6412 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4216" Parameter: CONF_N -> "8002" Comparing "4216" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4217" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766075 ATOM PAIRS WERE FOUND FOR ATOM LIST 42172 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29699 from a total of 766075 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4217 -73.12121 2.28709 0.60196 INTE EXTERN> -30.12558 -42.99563 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1212" Parameter: A <- "-73.1212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1256" Parameter: B <- "-30.1256" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9956" Parameter: C <- "-42.9956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4217 TOTAL ENERGY = -73.1212 RDTITL> * VAN DER WAALS = -30.1256 ELECTROSTATIC = -42.9956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4217" Parameter: CONF_N -> "8002" Comparing "4217" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4218" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766075 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760425 ATOM PAIRS WERE FOUND FOR ATOM LIST 41920 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29971 from a total of 760425 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4218 -73.35264 0.23143 0.69885 INTE EXTERN> -26.01409 -47.33855 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3526" Parameter: A <- "-73.3526" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0141" Parameter: B <- "-26.0141" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3385" Parameter: C <- "-47.3385" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4218 TOTAL ENERGY = -73.3526 RDTITL> * VAN DER WAALS = -26.0141 ELECTROSTATIC = -47.3385 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4218" Parameter: CONF_N -> "8002" Comparing "4218" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4219" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760425 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763768 ATOM PAIRS WERE FOUND FOR ATOM LIST 41663 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29679 from a total of 763768 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4219 -68.08665 -5.26599 0.78912 INTE EXTERN> -23.56324 -44.52341 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0867" Parameter: A <- "-68.0867" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.5632" Parameter: B <- "-23.5632" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5234" Parameter: C <- "-44.5234" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4219 TOTAL ENERGY = -68.0867 RDTITL> * VAN DER WAALS = -23.5632 ELECTROSTATIC = -44.5234 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4219" Parameter: CONF_N -> "8002" Comparing "4219" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4220" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763768 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766353 ATOM PAIRS WERE FOUND FOR ATOM LIST 42050 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29635 from a total of 766353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4220 -72.65429 4.56764 0.63479 INTE EXTERN> -27.74849 -44.90580 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6543" Parameter: A <- "-72.6543" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7485" Parameter: B <- "-27.7485" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9058" Parameter: C <- "-44.9058" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4220 TOTAL ENERGY = -72.6543 RDTITL> * VAN DER WAALS = -27.7485 ELECTROSTATIC = -44.9058 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4220" Parameter: CONF_N -> "8002" Comparing "4220" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4221" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756228 ATOM PAIRS WERE FOUND FOR ATOM LIST 41318 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29429 from a total of 756228 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4221 -73.54438 0.89009 0.77823 INTE EXTERN> -25.54890 -47.99548 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5444" Parameter: A <- "-73.5444" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5489" Parameter: B <- "-25.5489" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9955" Parameter: C <- "-47.9955" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4221 TOTAL ENERGY = -73.5444 RDTITL> * VAN DER WAALS = -25.5489 ELECTROSTATIC = -47.9955 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4221" Parameter: CONF_N -> "8002" Comparing "4221" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4222" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756228 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756584 ATOM PAIRS WERE FOUND FOR ATOM LIST 41511 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28961 from a total of 756584 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4222 -64.28487 -9.25951 0.64190 INTE EXTERN> -27.07721 -37.20766 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2849" Parameter: A <- "-64.2849" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0772" Parameter: B <- "-27.0772" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2077" Parameter: C <- "-37.2077" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4222 TOTAL ENERGY = -64.2849 RDTITL> * VAN DER WAALS = -27.0772 ELECTROSTATIC = -37.2077 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4222" Parameter: CONF_N -> "8002" Comparing "4222" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4223" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756584 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759525 ATOM PAIRS WERE FOUND FOR ATOM LIST 41715 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28644 from a total of 759525 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4223 -75.00712 10.72225 0.63059 INTE EXTERN> -26.89207 -48.11505 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0071" Parameter: A <- "-75.0071" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8921" Parameter: B <- "-26.8921" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.115" Parameter: C <- "-48.115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4223 TOTAL ENERGY = -75.0071 RDTITL> * VAN DER WAALS = -26.8921 ELECTROSTATIC = -48.115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4223" Parameter: CONF_N -> "8002" Comparing "4223" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4224" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759525 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761830 ATOM PAIRS WERE FOUND FOR ATOM LIST 41709 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28927 from a total of 761830 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4224 -78.19323 3.18611 0.67694 INTE EXTERN> -27.06430 -51.12893 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1932" Parameter: A <- "-78.1932" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0643" Parameter: B <- "-27.0643" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1289" Parameter: C <- "-51.1289" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4224 TOTAL ENERGY = -78.1932 RDTITL> * VAN DER WAALS = -27.0643 ELECTROSTATIC = -51.1289 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4224" Parameter: CONF_N -> "8002" Comparing "4224" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4225" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761830 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759933 ATOM PAIRS WERE FOUND FOR ATOM LIST 41976 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29109 from a total of 759933 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4225 -70.93420 -7.25903 0.82671 INTE EXTERN> -23.88607 -47.04813 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9342" Parameter: A <- "-70.9342" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8861" Parameter: B <- "-23.8861" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0481" Parameter: C <- "-47.0481" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4225 TOTAL ENERGY = -70.9342 RDTITL> * VAN DER WAALS = -23.8861 ELECTROSTATIC = -47.0481 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4225" Parameter: CONF_N -> "8002" Comparing "4225" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4226" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759933 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761217 ATOM PAIRS WERE FOUND FOR ATOM LIST 41752 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29441 from a total of 761217 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4226 -67.73964 -3.19456 0.60882 INTE EXTERN> -27.49365 -40.24599 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7396" Parameter: A <- "-67.7396" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4936" Parameter: B <- "-27.4936" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.246" Parameter: C <- "-40.246" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4226 TOTAL ENERGY = -67.7396 RDTITL> * VAN DER WAALS = -27.4936 ELECTROSTATIC = -40.246 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4226" Parameter: CONF_N -> "8002" Comparing "4226" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4227" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761217 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768201 ATOM PAIRS WERE FOUND FOR ATOM LIST 42009 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29450 from a total of 768201 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4227 -61.35707 -6.38257 0.62413 INTE EXTERN> -24.86655 -36.49052 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.3571" Parameter: A <- "-61.3571" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8665" Parameter: B <- "-24.8665" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4905" Parameter: C <- "-36.4905" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4227 TOTAL ENERGY = -61.3571 RDTITL> * VAN DER WAALS = -24.8665 ELECTROSTATIC = -36.4905 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4227" Parameter: CONF_N -> "8002" Comparing "4227" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4228" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768201 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765850 ATOM PAIRS WERE FOUND FOR ATOM LIST 41952 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29543 from a total of 765850 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4228 -68.02747 6.67040 0.69067 INTE EXTERN> -25.06600 -42.96147 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0275" Parameter: A <- "-68.0275" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.066" Parameter: B <- "-25.066" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9615" Parameter: C <- "-42.9615" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4228 TOTAL ENERGY = -68.0275 RDTITL> * VAN DER WAALS = -25.066 ELECTROSTATIC = -42.9615 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4228" Parameter: CONF_N -> "8002" Comparing "4228" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4229" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765850 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765753 ATOM PAIRS WERE FOUND FOR ATOM LIST 42008 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29558 from a total of 765753 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4229 -71.02508 2.99761 0.61629 INTE EXTERN> -31.85335 -39.17173 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0251" Parameter: A <- "-71.0251" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8533" Parameter: B <- "-31.8533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1717" Parameter: C <- "-39.1717" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4229 TOTAL ENERGY = -71.0251 RDTITL> * VAN DER WAALS = -31.8533 ELECTROSTATIC = -39.1717 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4229" Parameter: CONF_N -> "8002" Comparing "4229" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4230" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765753 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763985 ATOM PAIRS WERE FOUND FOR ATOM LIST 41927 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29879 from a total of 763985 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4230 -70.44067 -0.58441 0.67928 INTE EXTERN> -27.15050 -43.29016 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4407" Parameter: A <- "-70.4407" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1505" Parameter: B <- "-27.1505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2902" Parameter: C <- "-43.2902" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4230 TOTAL ENERGY = -70.4407 RDTITL> * VAN DER WAALS = -27.1505 ELECTROSTATIC = -43.2902 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4230" Parameter: CONF_N -> "8002" Comparing "4230" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4231" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763985 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761447 ATOM PAIRS WERE FOUND FOR ATOM LIST 41913 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30337 from a total of 761447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4231 -79.12992 8.68925 0.82335 INTE EXTERN> -22.85541 -56.27450 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1299" Parameter: A <- "-79.1299" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.8554" Parameter: B <- "-22.8554" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.2745" Parameter: C <- "-56.2745" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4231 TOTAL ENERGY = -79.1299 RDTITL> * VAN DER WAALS = -22.8554 ELECTROSTATIC = -56.2745 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4231" Parameter: CONF_N -> "8002" Comparing "4231" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4232" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760453 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30080 from a total of 760453 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4232 -65.53502 -13.59490 0.65539 INTE EXTERN> -29.71972 -35.81530 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.535" Parameter: A <- "-65.535" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7197" Parameter: B <- "-29.7197" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8153" Parameter: C <- "-35.8153" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4232 TOTAL ENERGY = -65.535 RDTITL> * VAN DER WAALS = -29.7197 ELECTROSTATIC = -35.8153 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4232" Parameter: CONF_N -> "8002" Comparing "4232" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4233" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760453 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760139 ATOM PAIRS WERE FOUND FOR ATOM LIST 41763 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29831 from a total of 760139 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4233 -64.48110 -1.05392 0.72677 INTE EXTERN> -24.18546 -40.29564 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.4811" Parameter: A <- "-64.4811" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1855" Parameter: B <- "-24.1855" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2956" Parameter: C <- "-40.2956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4233 TOTAL ENERGY = -64.4811 RDTITL> * VAN DER WAALS = -24.1855 ELECTROSTATIC = -40.2956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4233" Parameter: CONF_N -> "8002" Comparing "4233" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4234" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760139 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764780 ATOM PAIRS WERE FOUND FOR ATOM LIST 41737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30244 from a total of 764780 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4234 -63.10729 -1.37381 0.58033 INTE EXTERN> -30.11747 -32.98982 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1073" Parameter: A <- "-63.1073" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1175" Parameter: B <- "-30.1175" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.9898" Parameter: C <- "-32.9898" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4234 TOTAL ENERGY = -63.1073 RDTITL> * VAN DER WAALS = -30.1175 ELECTROSTATIC = -32.9898 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4234" Parameter: CONF_N -> "8002" Comparing "4234" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4235" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764780 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756464 ATOM PAIRS WERE FOUND FOR ATOM LIST 41705 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30159 from a total of 756464 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4235 -73.99389 10.88659 0.71430 INTE EXTERN> -28.72867 -45.26522 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9939" Parameter: A <- "-73.9939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7287" Parameter: B <- "-28.7287" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2652" Parameter: C <- "-45.2652" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4235 TOTAL ENERGY = -73.9939 RDTITL> * VAN DER WAALS = -28.7287 ELECTROSTATIC = -45.2652 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4235" Parameter: CONF_N -> "8002" Comparing "4235" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4236" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756464 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754649 ATOM PAIRS WERE FOUND FOR ATOM LIST 41487 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29851 from a total of 754649 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4236 -71.43342 -2.56046 0.72456 INTE EXTERN> -27.67835 -43.75507 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4334" Parameter: A <- "-71.4334" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6784" Parameter: B <- "-27.6784" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7551" Parameter: C <- "-43.7551" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4236 TOTAL ENERGY = -71.4334 RDTITL> * VAN DER WAALS = -27.6784 ELECTROSTATIC = -43.7551 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4236" Parameter: CONF_N -> "8002" Comparing "4236" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4237" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754649 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762841 ATOM PAIRS WERE FOUND FOR ATOM LIST 41909 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29719 from a total of 762841 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4237 -73.85911 2.42569 0.65508 INTE EXTERN> -30.64650 -43.21261 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8591" Parameter: A <- "-73.8591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6465" Parameter: B <- "-30.6465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2126" Parameter: C <- "-43.2126" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4237 TOTAL ENERGY = -73.8591 RDTITL> * VAN DER WAALS = -30.6465 ELECTROSTATIC = -43.2126 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4237" Parameter: CONF_N -> "8002" Comparing "4237" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4238" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762841 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759990 ATOM PAIRS WERE FOUND FOR ATOM LIST 41850 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29456 from a total of 759990 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4238 -70.90856 -2.95055 0.71918 INTE EXTERN> -27.46294 -43.44562 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9086" Parameter: A <- "-70.9086" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4629" Parameter: B <- "-27.4629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4456" Parameter: C <- "-43.4456" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4238 TOTAL ENERGY = -70.9086 RDTITL> * VAN DER WAALS = -27.4629 ELECTROSTATIC = -43.4456 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4238" Parameter: CONF_N -> "8002" Comparing "4238" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4239" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759990 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763114 ATOM PAIRS WERE FOUND FOR ATOM LIST 41942 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29296 from a total of 763114 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4239 -67.90858 -2.99998 0.62017 INTE EXTERN> -28.52361 -39.38496 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9086" Parameter: A <- "-67.9086" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5236" Parameter: B <- "-28.5236" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.385" Parameter: C <- "-39.385" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4239 TOTAL ENERGY = -67.9086 RDTITL> * VAN DER WAALS = -28.5236 ELECTROSTATIC = -39.385 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4239" Parameter: CONF_N -> "8002" Comparing "4239" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4240" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763114 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760480 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29938 from a total of 760480 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4240 -70.36485 2.45628 0.63355 INTE EXTERN> -29.17086 -41.19399 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3649" Parameter: A <- "-70.3649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1709" Parameter: B <- "-29.1709" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.194" Parameter: C <- "-41.194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4240 TOTAL ENERGY = -70.3649 RDTITL> * VAN DER WAALS = -29.1709 ELECTROSTATIC = -41.194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4240" Parameter: CONF_N -> "8002" Comparing "4240" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4241" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760480 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763811 ATOM PAIRS WERE FOUND FOR ATOM LIST 42029 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29746 from a total of 763811 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4241 -73.81301 3.44816 0.62692 INTE EXTERN> -31.38234 -42.43067 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.813" Parameter: A <- "-73.813" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3823" Parameter: B <- "-31.3823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4307" Parameter: C <- "-42.4307" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4241 TOTAL ENERGY = -73.813 RDTITL> * VAN DER WAALS = -31.3823 ELECTROSTATIC = -42.4307 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4241" Parameter: CONF_N -> "8002" Comparing "4241" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4242" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763811 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764859 ATOM PAIRS WERE FOUND FOR ATOM LIST 42001 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29814 from a total of 764859 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4242 -72.05183 -1.76119 0.59160 INTE EXTERN> -32.93868 -39.11314 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0518" Parameter: A <- "-72.0518" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9387" Parameter: B <- "-32.9387" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1131" Parameter: C <- "-39.1131" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4242 TOTAL ENERGY = -72.0518 RDTITL> * VAN DER WAALS = -32.9387 ELECTROSTATIC = -39.1131 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4242" Parameter: CONF_N -> "8002" Comparing "4242" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4243" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764859 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767235 ATOM PAIRS WERE FOUND FOR ATOM LIST 42056 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30402 from a total of 767235 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4243 -74.16071 2.10889 0.69268 INTE EXTERN> -28.43232 -45.72840 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1607" Parameter: A <- "-74.1607" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4323" Parameter: B <- "-28.4323" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7284" Parameter: C <- "-45.7284" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4243 TOTAL ENERGY = -74.1607 RDTITL> * VAN DER WAALS = -28.4323 ELECTROSTATIC = -45.7284 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4243" Parameter: CONF_N -> "8002" Comparing "4243" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4244" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767235 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762559 ATOM PAIRS WERE FOUND FOR ATOM LIST 41737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29354 from a total of 762559 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4244 -69.60966 -4.55105 0.68746 INTE EXTERN> -29.21262 -40.39704 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6097" Parameter: A <- "-69.6097" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2126" Parameter: B <- "-29.2126" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.397" Parameter: C <- "-40.397" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4244 TOTAL ENERGY = -69.6097 RDTITL> * VAN DER WAALS = -29.2126 ELECTROSTATIC = -40.397 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4244" Parameter: CONF_N -> "8002" Comparing "4244" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4245" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762559 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763572 ATOM PAIRS WERE FOUND FOR ATOM LIST 42015 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29371 from a total of 763572 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4245 -69.91227 0.30261 0.61928 INTE EXTERN> -29.40696 -40.50532 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9123" Parameter: A <- "-69.9123" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.407" Parameter: B <- "-29.407" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5053" Parameter: C <- "-40.5053" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4245 TOTAL ENERGY = -69.9123 RDTITL> * VAN DER WAALS = -29.407 ELECTROSTATIC = -40.5053 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4245" Parameter: CONF_N -> "8002" Comparing "4245" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4246" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763572 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759475 ATOM PAIRS WERE FOUND FOR ATOM LIST 41708 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29243 from a total of 759475 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4246 -73.84426 3.93198 0.71352 INTE EXTERN> -29.70692 -44.13733 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8443" Parameter: A <- "-73.8443" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7069" Parameter: B <- "-29.7069" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1373" Parameter: C <- "-44.1373" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4246 TOTAL ENERGY = -73.8443 RDTITL> * VAN DER WAALS = -29.7069 ELECTROSTATIC = -44.1373 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4246" Parameter: CONF_N -> "8002" Comparing "4246" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4247" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759475 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764132 ATOM PAIRS WERE FOUND FOR ATOM LIST 41984 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29654 from a total of 764132 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4247 -65.71215 -8.13210 0.58281 INTE EXTERN> -31.86161 -33.85054 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7122" Parameter: A <- "-65.7122" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8616" Parameter: B <- "-31.8616" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8505" Parameter: C <- "-33.8505" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4247 TOTAL ENERGY = -65.7122 RDTITL> * VAN DER WAALS = -31.8616 ELECTROSTATIC = -33.8505 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4247" Parameter: CONF_N -> "8002" Comparing "4247" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4248" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764132 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767532 ATOM PAIRS WERE FOUND FOR ATOM LIST 41827 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29682 from a total of 767532 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4248 -67.76163 2.04947 0.65610 INTE EXTERN> -29.46603 -38.29559 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7616" Parameter: A <- "-67.7616" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.466" Parameter: B <- "-29.466" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2956" Parameter: C <- "-38.2956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4248 TOTAL ENERGY = -67.7616 RDTITL> * VAN DER WAALS = -29.466 ELECTROSTATIC = -38.2956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4248" Parameter: CONF_N -> "8002" Comparing "4248" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4249" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767532 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757389 ATOM PAIRS WERE FOUND FOR ATOM LIST 41594 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29012 from a total of 757389 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4249 -67.08698 -0.67465 0.81423 INTE EXTERN> -28.39748 -38.68949 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.087" Parameter: A <- "-67.087" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3975" Parameter: B <- "-28.3975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6895" Parameter: C <- "-38.6895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4249 TOTAL ENERGY = -67.087 RDTITL> * VAN DER WAALS = -28.3975 ELECTROSTATIC = -38.6895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4249" Parameter: CONF_N -> "8002" Comparing "4249" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4250" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757389 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760123 ATOM PAIRS WERE FOUND FOR ATOM LIST 41616 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29011 from a total of 760123 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4250 -70.23732 3.15034 0.75353 INTE EXTERN> -25.13897 -45.09835 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2373" Parameter: A <- "-70.2373" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.139" Parameter: B <- "-25.139" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0983" Parameter: C <- "-45.0983" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4250 TOTAL ENERGY = -70.2373 RDTITL> * VAN DER WAALS = -25.139 ELECTROSTATIC = -45.0983 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4250" Parameter: CONF_N -> "8002" Comparing "4250" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4251" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760123 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762153 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29274 from a total of 762153 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4251 -69.72089 -0.51643 0.63054 INTE EXTERN> -31.21788 -38.50301 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7209" Parameter: A <- "-69.7209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2179" Parameter: B <- "-31.2179" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.503" Parameter: C <- "-38.503" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4251 TOTAL ENERGY = -69.7209 RDTITL> * VAN DER WAALS = -31.2179 ELECTROSTATIC = -38.503 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4251" Parameter: CONF_N -> "8002" Comparing "4251" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4252" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762153 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764122 ATOM PAIRS WERE FOUND FOR ATOM LIST 41754 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29332 from a total of 764122 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4252 -74.16721 4.44632 0.68583 INTE EXTERN> -31.25898 -42.90823 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1672" Parameter: A <- "-74.1672" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.259" Parameter: B <- "-31.259" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9082" Parameter: C <- "-42.9082" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4252 TOTAL ENERGY = -74.1672 RDTITL> * VAN DER WAALS = -31.259 ELECTROSTATIC = -42.9082 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4252" Parameter: CONF_N -> "8002" Comparing "4252" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4253" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764122 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761934 ATOM PAIRS WERE FOUND FOR ATOM LIST 41886 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29013 from a total of 761934 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4253 -69.72602 -4.44119 0.71436 INTE EXTERN> -27.05651 -42.66951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.726" Parameter: A <- "-69.726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0565" Parameter: B <- "-27.0565" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6695" Parameter: C <- "-42.6695" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4253 TOTAL ENERGY = -69.726 RDTITL> * VAN DER WAALS = -27.0565 ELECTROSTATIC = -42.6695 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4253" Parameter: CONF_N -> "8002" Comparing "4253" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4254" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761934 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759656 ATOM PAIRS WERE FOUND FOR ATOM LIST 41809 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29477 from a total of 759656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4254 -73.07835 3.35233 0.59362 INTE EXTERN> -29.97834 -43.10001 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0783" Parameter: A <- "-73.0783" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9783" Parameter: B <- "-29.9783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1" Parameter: C <- "-43.1" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4254 TOTAL ENERGY = -73.0783 RDTITL> * VAN DER WAALS = -29.9783 ELECTROSTATIC = -43.1 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4254" Parameter: CONF_N -> "8002" Comparing "4254" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4255" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755125 ATOM PAIRS WERE FOUND FOR ATOM LIST 41401 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29285 from a total of 755125 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4255 -71.46537 -1.61298 0.80613 INTE EXTERN> -23.86374 -47.60163 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4654" Parameter: A <- "-71.4654" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8637" Parameter: B <- "-23.8637" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6016" Parameter: C <- "-47.6016" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4255 TOTAL ENERGY = -71.4654 RDTITL> * VAN DER WAALS = -23.8637 ELECTROSTATIC = -47.6016 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4255" Parameter: CONF_N -> "8002" Comparing "4255" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4256" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755125 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759639 ATOM PAIRS WERE FOUND FOR ATOM LIST 41740 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29532 from a total of 759639 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4256 -71.83036 0.36500 0.69610 INTE EXTERN> -28.43976 -43.39061 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8304" Parameter: A <- "-71.8304" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4398" Parameter: B <- "-28.4398" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3906" Parameter: C <- "-43.3906" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4256 TOTAL ENERGY = -71.8304 RDTITL> * VAN DER WAALS = -28.4398 ELECTROSTATIC = -43.3906 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4256" Parameter: CONF_N -> "8002" Comparing "4256" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4257" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759639 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761918 ATOM PAIRS WERE FOUND FOR ATOM LIST 41664 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29841 from a total of 761918 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4257 -71.80564 -0.02472 0.83794 INTE EXTERN> -23.73001 -48.07564 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8056" Parameter: A <- "-71.8056" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.73" Parameter: B <- "-23.73" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0756" Parameter: C <- "-48.0756" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4257 TOTAL ENERGY = -71.8056 RDTITL> * VAN DER WAALS = -23.73 ELECTROSTATIC = -48.0756 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4257" Parameter: CONF_N -> "8002" Comparing "4257" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4258" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761918 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759353 ATOM PAIRS WERE FOUND FOR ATOM LIST 41549 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29679 from a total of 759353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4258 -77.05674 5.25110 0.76689 INTE EXTERN> -26.08258 -50.97417 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0567" Parameter: A <- "-77.0567" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0826" Parameter: B <- "-26.0826" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9742" Parameter: C <- "-50.9742" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4258 TOTAL ENERGY = -77.0567 RDTITL> * VAN DER WAALS = -26.0826 ELECTROSTATIC = -50.9742 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4258" Parameter: CONF_N -> "8002" Comparing "4258" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4259" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764789 ATOM PAIRS WERE FOUND FOR ATOM LIST 42133 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29567 from a total of 764789 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4259 -74.09278 -2.96396 0.71400 INTE EXTERN> -27.30256 -46.79022 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0928" Parameter: A <- "-74.0928" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3026" Parameter: B <- "-27.3026" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7902" Parameter: C <- "-46.7902" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4259 TOTAL ENERGY = -74.0928 RDTITL> * VAN DER WAALS = -27.3026 ELECTROSTATIC = -46.7902 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4259" Parameter: CONF_N -> "8002" Comparing "4259" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4260" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764789 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757126 ATOM PAIRS WERE FOUND FOR ATOM LIST 41546 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29590 from a total of 757126 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4260 -71.30861 -2.78417 0.65446 INTE EXTERN> -28.96801 -42.34060 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3086" Parameter: A <- "-71.3086" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.968" Parameter: B <- "-28.968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3406" Parameter: C <- "-42.3406" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4260 TOTAL ENERGY = -71.3086 RDTITL> * VAN DER WAALS = -28.968 ELECTROSTATIC = -42.3406 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4260" Parameter: CONF_N -> "8002" Comparing "4260" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4261" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757126 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759925 ATOM PAIRS WERE FOUND FOR ATOM LIST 41586 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29752 from a total of 759925 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4261 -71.28403 -0.02458 0.67118 INTE EXTERN> -30.18600 -41.09803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.284" Parameter: A <- "-71.284" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.186" Parameter: B <- "-30.186" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.098" Parameter: C <- "-41.098" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4261 TOTAL ENERGY = -71.284 RDTITL> * VAN DER WAALS = -30.186 ELECTROSTATIC = -41.098 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4261" Parameter: CONF_N -> "8002" Comparing "4261" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4262" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759925 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765251 ATOM PAIRS WERE FOUND FOR ATOM LIST 41833 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29934 from a total of 765251 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4262 -68.27689 -3.00715 0.71675 INTE EXTERN> -28.54909 -39.72780 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2769" Parameter: A <- "-68.2769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5491" Parameter: B <- "-28.5491" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7278" Parameter: C <- "-39.7278" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4262 TOTAL ENERGY = -68.2769 RDTITL> * VAN DER WAALS = -28.5491 ELECTROSTATIC = -39.7278 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4262" Parameter: CONF_N -> "8002" Comparing "4262" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4263" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765251 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762498 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29443 from a total of 762498 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4263 -76.71356 8.43668 0.66940 INTE EXTERN> -29.45174 -47.26182 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7136" Parameter: A <- "-76.7136" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4517" Parameter: B <- "-29.4517" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2618" Parameter: C <- "-47.2618" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4263 TOTAL ENERGY = -76.7136 RDTITL> * VAN DER WAALS = -29.4517 ELECTROSTATIC = -47.2618 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4263" Parameter: CONF_N -> "8002" Comparing "4263" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4264" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762498 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756311 ATOM PAIRS WERE FOUND FOR ATOM LIST 41536 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29723 from a total of 756311 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4264 -75.29922 -1.41434 0.73933 INTE EXTERN> -30.40105 -44.89817 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2992" Parameter: A <- "-75.2992" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4011" Parameter: B <- "-30.4011" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8982" Parameter: C <- "-44.8982" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4264 TOTAL ENERGY = -75.2992 RDTITL> * VAN DER WAALS = -30.4011 ELECTROSTATIC = -44.8982 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4264" Parameter: CONF_N -> "8002" Comparing "4264" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4265" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756311 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759682 ATOM PAIRS WERE FOUND FOR ATOM LIST 41869 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29751 from a total of 759682 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4265 -72.50725 -2.79197 0.61504 INTE EXTERN> -32.58957 -39.91768 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5073" Parameter: A <- "-72.5073" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5896" Parameter: B <- "-32.5896" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9177" Parameter: C <- "-39.9177" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4265 TOTAL ENERGY = -72.5073 RDTITL> * VAN DER WAALS = -32.5896 ELECTROSTATIC = -39.9177 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4265" Parameter: CONF_N -> "8002" Comparing "4265" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4266" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759682 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761174 ATOM PAIRS WERE FOUND FOR ATOM LIST 41786 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29709 from a total of 761174 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4266 -76.69672 4.18946 0.70763 INTE EXTERN> -28.14837 -48.54835 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6967" Parameter: A <- "-76.6967" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1484" Parameter: B <- "-28.1484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5483" Parameter: C <- "-48.5483" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4266 TOTAL ENERGY = -76.6967 RDTITL> * VAN DER WAALS = -28.1484 ELECTROSTATIC = -48.5483 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4266" Parameter: CONF_N -> "8002" Comparing "4266" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4267" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761174 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770095 ATOM PAIRS WERE FOUND FOR ATOM LIST 42253 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30382 from a total of 770095 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4267 -68.18253 -8.51419 0.70107 INTE EXTERN> -25.93503 -42.24750 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1825" Parameter: A <- "-68.1825" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.935" Parameter: B <- "-25.935" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2475" Parameter: C <- "-42.2475" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4267 TOTAL ENERGY = -68.1825 RDTITL> * VAN DER WAALS = -25.935 ELECTROSTATIC = -42.2475 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4267" Parameter: CONF_N -> "8002" Comparing "4267" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4268" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770095 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761729 ATOM PAIRS WERE FOUND FOR ATOM LIST 41724 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29187 from a total of 761729 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4268 -63.70164 -4.48089 0.53961 INTE EXTERN> -29.45060 -34.25104 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7016" Parameter: A <- "-63.7016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4506" Parameter: B <- "-29.4506" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.251" Parameter: C <- "-34.251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4268 TOTAL ENERGY = -63.7016 RDTITL> * VAN DER WAALS = -29.4506 ELECTROSTATIC = -34.251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4268" Parameter: CONF_N -> "8002" Comparing "4268" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4269" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761729 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761477 ATOM PAIRS WERE FOUND FOR ATOM LIST 41692 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29908 from a total of 761477 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4269 -73.30216 9.60052 0.54832 INTE EXTERN> -33.47226 -39.82990 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3022" Parameter: A <- "-73.3022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4723" Parameter: B <- "-33.4723" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8299" Parameter: C <- "-39.8299" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4269 TOTAL ENERGY = -73.3022 RDTITL> * VAN DER WAALS = -33.4723 ELECTROSTATIC = -39.8299 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4269" Parameter: CONF_N -> "8002" Comparing "4269" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4270" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761477 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760452 ATOM PAIRS WERE FOUND FOR ATOM LIST 41594 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 760452 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4270 -61.69982 -11.60234 0.63151 INTE EXTERN> -27.87783 -33.82199 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.6998" Parameter: A <- "-61.6998" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8778" Parameter: B <- "-27.8778" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.822" Parameter: C <- "-33.822" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4270 TOTAL ENERGY = -61.6998 RDTITL> * VAN DER WAALS = -27.8778 ELECTROSTATIC = -33.822 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4270" Parameter: CONF_N -> "8002" Comparing "4270" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4271" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760452 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756947 ATOM PAIRS WERE FOUND FOR ATOM LIST 41672 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29216 from a total of 756947 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4271 -65.79801 4.09819 0.58190 INTE EXTERN> -29.56573 -36.23228 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.798" Parameter: A <- "-65.798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5657" Parameter: B <- "-29.5657" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2323" Parameter: C <- "-36.2323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4271 TOTAL ENERGY = -65.798 RDTITL> * VAN DER WAALS = -29.5657 ELECTROSTATIC = -36.2323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4271" Parameter: CONF_N -> "8002" Comparing "4271" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4272" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756947 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761921 ATOM PAIRS WERE FOUND FOR ATOM LIST 41970 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29345 from a total of 761921 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4272 -70.96128 5.16328 0.64004 INTE EXTERN> -30.88793 -40.07336 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9613" Parameter: A <- "-70.9613" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8879" Parameter: B <- "-30.8879" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0734" Parameter: C <- "-40.0734" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4272 TOTAL ENERGY = -70.9613 RDTITL> * VAN DER WAALS = -30.8879 ELECTROSTATIC = -40.0734 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4272" Parameter: CONF_N -> "8002" Comparing "4272" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4273" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761921 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761223 ATOM PAIRS WERE FOUND FOR ATOM LIST 41738 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29884 from a total of 761223 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4273 -74.40108 3.43979 0.69833 INTE EXTERN> -28.09694 -46.30414 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4011" Parameter: A <- "-74.4011" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0969" Parameter: B <- "-28.0969" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3041" Parameter: C <- "-46.3041" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4273 TOTAL ENERGY = -74.4011 RDTITL> * VAN DER WAALS = -28.0969 ELECTROSTATIC = -46.3041 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4273" Parameter: CONF_N -> "8002" Comparing "4273" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4274" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761223 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763666 ATOM PAIRS WERE FOUND FOR ATOM LIST 41886 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30082 from a total of 763666 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4274 -66.55015 -7.85093 0.70990 INTE EXTERN> -24.84648 -41.70367 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5502" Parameter: A <- "-66.5502" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8465" Parameter: B <- "-24.8465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7037" Parameter: C <- "-41.7037" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4274 TOTAL ENERGY = -66.5502 RDTITL> * VAN DER WAALS = -24.8465 ELECTROSTATIC = -41.7037 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4274" Parameter: CONF_N -> "8002" Comparing "4274" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4275" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763666 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757485 ATOM PAIRS WERE FOUND FOR ATOM LIST 41737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29452 from a total of 757485 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4275 -72.85076 6.30061 0.56879 INTE EXTERN> -29.78697 -43.06379 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8508" Parameter: A <- "-72.8508" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.787" Parameter: B <- "-29.787" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0638" Parameter: C <- "-43.0638" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4275 TOTAL ENERGY = -72.8508 RDTITL> * VAN DER WAALS = -29.787 ELECTROSTATIC = -43.0638 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4275" Parameter: CONF_N -> "8002" Comparing "4275" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4276" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757485 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761922 ATOM PAIRS WERE FOUND FOR ATOM LIST 41953 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29970 from a total of 761922 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4276 -74.57137 1.72062 0.68525 INTE EXTERN> -28.72555 -45.84583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5714" Parameter: A <- "-74.5714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7255" Parameter: B <- "-28.7255" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8458" Parameter: C <- "-45.8458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4276 TOTAL ENERGY = -74.5714 RDTITL> * VAN DER WAALS = -28.7255 ELECTROSTATIC = -45.8458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4276" Parameter: CONF_N -> "8002" Comparing "4276" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4277" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761922 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764930 ATOM PAIRS WERE FOUND FOR ATOM LIST 42135 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29872 from a total of 764930 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4277 -67.42650 -7.14487 0.70484 INTE EXTERN> -26.38346 -41.04305 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4265" Parameter: A <- "-67.4265" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3835" Parameter: B <- "-26.3835" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.043" Parameter: C <- "-41.043" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4277 TOTAL ENERGY = -67.4265 RDTITL> * VAN DER WAALS = -26.3835 ELECTROSTATIC = -41.043 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4277" Parameter: CONF_N -> "8002" Comparing "4277" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4278" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764930 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765767 ATOM PAIRS WERE FOUND FOR ATOM LIST 42019 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30149 from a total of 765767 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4278 -78.69447 11.26796 0.65131 INTE EXTERN> -31.25370 -47.44076 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6945" Parameter: A <- "-78.6945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2537" Parameter: B <- "-31.2537" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4408" Parameter: C <- "-47.4408" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4278 TOTAL ENERGY = -78.6945 RDTITL> * VAN DER WAALS = -31.2537 ELECTROSTATIC = -47.4408 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4278" Parameter: CONF_N -> "8002" Comparing "4278" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4279" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765767 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761263 ATOM PAIRS WERE FOUND FOR ATOM LIST 41878 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30455 from a total of 761263 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4279 -78.64406 -0.05040 0.70151 INTE EXTERN> -28.21938 -50.42468 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6441" Parameter: A <- "-78.6441" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2194" Parameter: B <- "-28.2194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4247" Parameter: C <- "-50.4247" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4279 TOTAL ENERGY = -78.6441 RDTITL> * VAN DER WAALS = -28.2194 ELECTROSTATIC = -50.4247 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4279" Parameter: CONF_N -> "8002" Comparing "4279" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4280" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761263 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761486 ATOM PAIRS WERE FOUND FOR ATOM LIST 41875 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30868 from a total of 761486 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4280 -74.59498 -4.04909 0.67657 INTE EXTERN> -28.21832 -46.37666 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.595" Parameter: A <- "-74.595" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2183" Parameter: B <- "-28.2183" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3767" Parameter: C <- "-46.3767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4280 TOTAL ENERGY = -74.595 RDTITL> * VAN DER WAALS = -28.2183 ELECTROSTATIC = -46.3767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4280" Parameter: CONF_N -> "8002" Comparing "4280" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4281" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761486 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759898 ATOM PAIRS WERE FOUND FOR ATOM LIST 41734 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30534 from a total of 759898 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4281 -71.54539 -3.04958 0.70781 INTE EXTERN> -27.89871 -43.64668 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5454" Parameter: A <- "-71.5454" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8987" Parameter: B <- "-27.8987" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6467" Parameter: C <- "-43.6467" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4281 TOTAL ENERGY = -71.5454 RDTITL> * VAN DER WAALS = -27.8987 ELECTROSTATIC = -43.6467 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4281" Parameter: CONF_N -> "8002" Comparing "4281" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4282" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759898 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762622 ATOM PAIRS WERE FOUND FOR ATOM LIST 41916 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30275 from a total of 762622 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4282 -73.03825 1.49286 0.72855 INTE EXTERN> -26.04486 -46.99340 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0383" Parameter: A <- "-73.0383" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0449" Parameter: B <- "-26.0449" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9934" Parameter: C <- "-46.9934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4282 TOTAL ENERGY = -73.0383 RDTITL> * VAN DER WAALS = -26.0449 ELECTROSTATIC = -46.9934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4282" Parameter: CONF_N -> "8002" Comparing "4282" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4283" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762622 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763343 ATOM PAIRS WERE FOUND FOR ATOM LIST 41907 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30433 from a total of 763343 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4283 -71.11146 -1.92679 0.85009 INTE EXTERN> -22.41040 -48.70106 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1115" Parameter: A <- "-71.1115" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.4104" Parameter: B <- "-22.4104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7011" Parameter: C <- "-48.7011" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4283 TOTAL ENERGY = -71.1115 RDTITL> * VAN DER WAALS = -22.4104 ELECTROSTATIC = -48.7011 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4283" Parameter: CONF_N -> "8002" Comparing "4283" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4284" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763343 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761841 ATOM PAIRS WERE FOUND FOR ATOM LIST 41888 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30063 from a total of 761841 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4284 -75.03040 3.91894 0.62965 INTE EXTERN> -29.35284 -45.67757 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0304" Parameter: A <- "-75.0304" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3528" Parameter: B <- "-29.3528" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6776" Parameter: C <- "-45.6776" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4284 TOTAL ENERGY = -75.0304 RDTITL> * VAN DER WAALS = -29.3528 ELECTROSTATIC = -45.6776 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4284" Parameter: CONF_N -> "8002" Comparing "4284" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4285" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761841 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767123 ATOM PAIRS WERE FOUND FOR ATOM LIST 41890 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30286 from a total of 767123 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4285 -78.94846 3.91806 0.75121 INTE EXTERN> -26.74633 -52.20213 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9485" Parameter: A <- "-78.9485" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7463" Parameter: B <- "-26.7463" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2021" Parameter: C <- "-52.2021" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4285 TOTAL ENERGY = -78.9485 RDTITL> * VAN DER WAALS = -26.7463 ELECTROSTATIC = -52.2021 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4285" Parameter: CONF_N -> "8002" Comparing "4285" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4286" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767123 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762578 ATOM PAIRS WERE FOUND FOR ATOM LIST 41698 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30304 from a total of 762578 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4286 -72.34990 -6.59856 0.66464 INTE EXTERN> -27.69482 -44.65509 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3499" Parameter: A <- "-72.3499" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6948" Parameter: B <- "-27.6948" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6551" Parameter: C <- "-44.6551" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4286 TOTAL ENERGY = -72.3499 RDTITL> * VAN DER WAALS = -27.6948 ELECTROSTATIC = -44.6551 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4286" Parameter: CONF_N -> "8002" Comparing "4286" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4287" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762578 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41656 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30349 from a total of 760958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4287 -76.08086 3.73096 0.74507 INTE EXTERN> -24.91516 -51.16570 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0809" Parameter: A <- "-76.0809" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9152" Parameter: B <- "-24.9152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1657" Parameter: C <- "-51.1657" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4287 TOTAL ENERGY = -76.0809 RDTITL> * VAN DER WAALS = -24.9152 ELECTROSTATIC = -51.1657 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4287" Parameter: CONF_N -> "8002" Comparing "4287" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4288" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759038 ATOM PAIRS WERE FOUND FOR ATOM LIST 41850 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30374 from a total of 759038 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4288 -84.63349 8.55263 0.64966 INTE EXTERN> -30.24403 -54.38946 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.6335" Parameter: A <- "-84.6335" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.244" Parameter: B <- "-30.244" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.3895" Parameter: C <- "-54.3895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4288 TOTAL ENERGY = -84.6335 RDTITL> * VAN DER WAALS = -30.244 ELECTROSTATIC = -54.3895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4288" Parameter: CONF_N -> "8002" Comparing "4288" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4289" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759038 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761208 ATOM PAIRS WERE FOUND FOR ATOM LIST 41761 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30248 from a total of 761208 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4289 -77.58794 -7.04555 0.69903 INTE EXTERN> -28.54225 -49.04568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5879" Parameter: A <- "-77.5879" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5423" Parameter: B <- "-28.5423" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0457" Parameter: C <- "-49.0457" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4289 TOTAL ENERGY = -77.5879 RDTITL> * VAN DER WAALS = -28.5423 ELECTROSTATIC = -49.0457 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4289" Parameter: CONF_N -> "8002" Comparing "4289" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4290" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761208 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765054 ATOM PAIRS WERE FOUND FOR ATOM LIST 41989 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30725 from a total of 765054 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4290 -71.76265 -5.82529 0.60123 INTE EXTERN> -29.63098 -42.13167 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7627" Parameter: A <- "-71.7627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.631" Parameter: B <- "-29.631" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1317" Parameter: C <- "-42.1317" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4290 TOTAL ENERGY = -71.7627 RDTITL> * VAN DER WAALS = -29.631 ELECTROSTATIC = -42.1317 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4290" Parameter: CONF_N -> "8002" Comparing "4290" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4291" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765054 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762781 ATOM PAIRS WERE FOUND FOR ATOM LIST 41867 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30281 from a total of 762781 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4291 -73.12681 1.36416 0.58386 INTE EXTERN> -31.45040 -41.67642 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1268" Parameter: A <- "-73.1268" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4504" Parameter: B <- "-31.4504" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6764" Parameter: C <- "-41.6764" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4291 TOTAL ENERGY = -73.1268 RDTITL> * VAN DER WAALS = -31.4504 ELECTROSTATIC = -41.6764 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4291" Parameter: CONF_N -> "8002" Comparing "4291" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4292" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762781 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762723 ATOM PAIRS WERE FOUND FOR ATOM LIST 41831 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30069 from a total of 762723 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4292 -70.06702 -3.05980 0.58723 INTE EXTERN> -31.18418 -38.88284 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.067" Parameter: A <- "-70.067" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1842" Parameter: B <- "-31.1842" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8828" Parameter: C <- "-38.8828" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4292 TOTAL ENERGY = -70.067 RDTITL> * VAN DER WAALS = -31.1842 ELECTROSTATIC = -38.8828 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4292" Parameter: CONF_N -> "8002" Comparing "4292" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4293" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762723 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756238 ATOM PAIRS WERE FOUND FOR ATOM LIST 41482 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29674 from a total of 756238 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4293 -68.78680 -1.28021 0.70260 INTE EXTERN> -26.68059 -42.10622 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7868" Parameter: A <- "-68.7868" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6806" Parameter: B <- "-26.6806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1062" Parameter: C <- "-42.1062" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4293 TOTAL ENERGY = -68.7868 RDTITL> * VAN DER WAALS = -26.6806 ELECTROSTATIC = -42.1062 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4293" Parameter: CONF_N -> "8002" Comparing "4293" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4294" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756238 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764242 ATOM PAIRS WERE FOUND FOR ATOM LIST 41958 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29703 from a total of 764242 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4294 -71.32334 2.53653 0.69415 INTE EXTERN> -26.99326 -44.33008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3233" Parameter: A <- "-71.3233" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9933" Parameter: B <- "-26.9933" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3301" Parameter: C <- "-44.3301" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4294 TOTAL ENERGY = -71.3233 RDTITL> * VAN DER WAALS = -26.9933 ELECTROSTATIC = -44.3301 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4294" Parameter: CONF_N -> "8002" Comparing "4294" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4295" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764242 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756812 ATOM PAIRS WERE FOUND FOR ATOM LIST 41624 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30145 from a total of 756812 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4295 -78.50223 7.17889 0.64470 INTE EXTERN> -30.33829 -48.16393 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5022" Parameter: A <- "-78.5022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3383" Parameter: B <- "-30.3383" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1639" Parameter: C <- "-48.1639" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4295 TOTAL ENERGY = -78.5022 RDTITL> * VAN DER WAALS = -30.3383 ELECTROSTATIC = -48.1639 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4295" Parameter: CONF_N -> "8002" Comparing "4295" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4296" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756812 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761084 ATOM PAIRS WERE FOUND FOR ATOM LIST 41860 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 761084 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4296 -70.28648 -8.21575 0.60345 INTE EXTERN> -31.28576 -39.00072 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2865" Parameter: A <- "-70.2865" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2858" Parameter: B <- "-31.2858" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0007" Parameter: C <- "-39.0007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4296 TOTAL ENERGY = -70.2865 RDTITL> * VAN DER WAALS = -31.2858 ELECTROSTATIC = -39.0007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4296" Parameter: CONF_N -> "8002" Comparing "4296" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4297" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761084 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755203 ATOM PAIRS WERE FOUND FOR ATOM LIST 41611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29639 from a total of 755203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4297 -69.80955 -0.47693 0.65012 INTE EXTERN> -26.65041 -43.15915 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8096" Parameter: A <- "-69.8096" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6504" Parameter: B <- "-26.6504" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1591" Parameter: C <- "-43.1591" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4297 TOTAL ENERGY = -69.8096 RDTITL> * VAN DER WAALS = -26.6504 ELECTROSTATIC = -43.1591 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4297" Parameter: CONF_N -> "8002" Comparing "4297" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4298" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753378 ATOM PAIRS WERE FOUND FOR ATOM LIST 41505 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29496 from a total of 753378 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4298 -76.93264 7.12309 0.61601 INTE EXTERN> -31.41422 -45.51843 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9326" Parameter: A <- "-76.9326" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4142" Parameter: B <- "-31.4142" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5184" Parameter: C <- "-45.5184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4298 TOTAL ENERGY = -76.9326 RDTITL> * VAN DER WAALS = -31.4142 ELECTROSTATIC = -45.5184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4298" Parameter: CONF_N -> "8002" Comparing "4298" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4299" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753378 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756914 ATOM PAIRS WERE FOUND FOR ATOM LIST 41522 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29715 from a total of 756914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4299 -74.18834 -2.74430 0.70794 INTE EXTERN> -26.88495 -47.30339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1883" Parameter: A <- "-74.1883" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.885" Parameter: B <- "-26.885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3034" Parameter: C <- "-47.3034" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4299 TOTAL ENERGY = -74.1883 RDTITL> * VAN DER WAALS = -26.885 ELECTROSTATIC = -47.3034 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4299" Parameter: CONF_N -> "8002" Comparing "4299" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4300" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754669 ATOM PAIRS WERE FOUND FOR ATOM LIST 41507 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29695 from a total of 754669 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4300 -67.69194 -6.49640 0.55889 INTE EXTERN> -32.03305 -35.65889 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6919" Parameter: A <- "-67.6919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0331" Parameter: B <- "-32.0331" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6589" Parameter: C <- "-35.6589" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4300 TOTAL ENERGY = -67.6919 RDTITL> * VAN DER WAALS = -32.0331 ELECTROSTATIC = -35.6589 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4300" Parameter: CONF_N -> "8002" Comparing "4300" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4301" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754669 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758194 ATOM PAIRS WERE FOUND FOR ATOM LIST 41681 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29635 from a total of 758194 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4301 -74.79883 7.10689 0.65929 INTE EXTERN> -29.61947 -45.17936 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7988" Parameter: A <- "-74.7988" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6195" Parameter: B <- "-29.6195" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1794" Parameter: C <- "-45.1794" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4301 TOTAL ENERGY = -74.7988 RDTITL> * VAN DER WAALS = -29.6195 ELECTROSTATIC = -45.1794 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4301" Parameter: CONF_N -> "8002" Comparing "4301" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4302" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758194 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762787 ATOM PAIRS WERE FOUND FOR ATOM LIST 41851 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30325 from a total of 762787 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4302 -74.91982 0.12099 0.66906 INTE EXTERN> -28.38257 -46.53725 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9198" Parameter: A <- "-74.9198" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3826" Parameter: B <- "-28.3826" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5372" Parameter: C <- "-46.5372" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4302 TOTAL ENERGY = -74.9198 RDTITL> * VAN DER WAALS = -28.3826 ELECTROSTATIC = -46.5372 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4302" Parameter: CONF_N -> "8002" Comparing "4302" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4303" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762787 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753899 ATOM PAIRS WERE FOUND FOR ATOM LIST 41189 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29393 from a total of 753899 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4303 -77.16250 2.24268 0.59285 INTE EXTERN> -30.23462 -46.92788 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1625" Parameter: A <- "-77.1625" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2346" Parameter: B <- "-30.2346" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9279" Parameter: C <- "-46.9279" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4303 TOTAL ENERGY = -77.1625 RDTITL> * VAN DER WAALS = -30.2346 ELECTROSTATIC = -46.9279 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4303" Parameter: CONF_N -> "8002" Comparing "4303" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4304" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753899 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756213 ATOM PAIRS WERE FOUND FOR ATOM LIST 41450 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29655 from a total of 756213 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4304 -78.67866 1.51617 0.71764 INTE EXTERN> -25.30873 -53.36993 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6787" Parameter: A <- "-78.6787" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3087" Parameter: B <- "-25.3087" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3699" Parameter: C <- "-53.3699" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4304 TOTAL ENERGY = -78.6787 RDTITL> * VAN DER WAALS = -25.3087 ELECTROSTATIC = -53.3699 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4304" Parameter: CONF_N -> "8002" Comparing "4304" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4305" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756213 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750997 ATOM PAIRS WERE FOUND FOR ATOM LIST 41263 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29497 from a total of 750997 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4305 -68.02427 -10.65440 0.57936 INTE EXTERN> -27.55063 -40.47363 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0243" Parameter: A <- "-68.0243" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5506" Parameter: B <- "-27.5506" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4736" Parameter: C <- "-40.4736" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4305 TOTAL ENERGY = -68.0243 RDTITL> * VAN DER WAALS = -27.5506 ELECTROSTATIC = -40.4736 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4305" Parameter: CONF_N -> "8002" Comparing "4305" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4306" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750997 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755984 ATOM PAIRS WERE FOUND FOR ATOM LIST 41739 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30041 from a total of 755984 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4306 -72.33483 4.31057 0.61664 INTE EXTERN> -28.30416 -44.03067 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3348" Parameter: A <- "-72.3348" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3042" Parameter: B <- "-28.3042" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0307" Parameter: C <- "-44.0307" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4306 TOTAL ENERGY = -72.3348 RDTITL> * VAN DER WAALS = -28.3042 ELECTROSTATIC = -44.0307 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4306" Parameter: CONF_N -> "8002" Comparing "4306" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4307" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755984 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759385 ATOM PAIRS WERE FOUND FOR ATOM LIST 41743 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29513 from a total of 759385 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4307 -74.42361 2.08878 0.69172 INTE EXTERN> -27.51537 -46.90825 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4236" Parameter: A <- "-74.4236" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5154" Parameter: B <- "-27.5154" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9082" Parameter: C <- "-46.9082" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4307 TOTAL ENERGY = -74.4236 RDTITL> * VAN DER WAALS = -27.5154 ELECTROSTATIC = -46.9082 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4307" Parameter: CONF_N -> "8002" Comparing "4307" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4308" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759385 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762346 ATOM PAIRS WERE FOUND FOR ATOM LIST 41743 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30025 from a total of 762346 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4308 -71.06901 -3.35461 0.81107 INTE EXTERN> -22.94875 -48.12026 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.069" Parameter: A <- "-71.069" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.9487" Parameter: B <- "-22.9487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1203" Parameter: C <- "-48.1203" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4308 TOTAL ENERGY = -71.069 RDTITL> * VAN DER WAALS = -22.9487 ELECTROSTATIC = -48.1203 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4308" Parameter: CONF_N -> "8002" Comparing "4308" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4309" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762346 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761565 ATOM PAIRS WERE FOUND FOR ATOM LIST 41811 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29642 from a total of 761565 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4309 -69.77026 -1.29875 0.79692 INTE EXTERN> -23.21897 -46.55130 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7703" Parameter: A <- "-69.7703" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.219" Parameter: B <- "-23.219" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5513" Parameter: C <- "-46.5513" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4309 TOTAL ENERGY = -69.7703 RDTITL> * VAN DER WAALS = -23.219 ELECTROSTATIC = -46.5513 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4309" Parameter: CONF_N -> "8002" Comparing "4309" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4310" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761565 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766710 ATOM PAIRS WERE FOUND FOR ATOM LIST 42137 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29871 from a total of 766710 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4310 -68.96231 -0.80795 0.71299 INTE EXTERN> -28.90211 -40.06021 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9623" Parameter: A <- "-68.9623" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9021" Parameter: B <- "-28.9021" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0602" Parameter: C <- "-40.0602" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4310 TOTAL ENERGY = -68.9623 RDTITL> * VAN DER WAALS = -28.9021 ELECTROSTATIC = -40.0602 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4310" Parameter: CONF_N -> "8002" Comparing "4310" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4311" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766710 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763297 ATOM PAIRS WERE FOUND FOR ATOM LIST 42004 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29296 from a total of 763297 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4311 -71.71413 2.75182 0.61592 INTE EXTERN> -29.99263 -41.72150 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7141" Parameter: A <- "-71.7141" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9926" Parameter: B <- "-29.9926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7215" Parameter: C <- "-41.7215" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4311 TOTAL ENERGY = -71.7141 RDTITL> * VAN DER WAALS = -29.9926 ELECTROSTATIC = -41.7215 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4311" Parameter: CONF_N -> "8002" Comparing "4311" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4312" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763297 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759263 ATOM PAIRS WERE FOUND FOR ATOM LIST 41738 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28852 from a total of 759263 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4312 -70.79690 -0.91724 0.62432 INTE EXTERN> -29.29895 -41.49795 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7969" Parameter: A <- "-70.7969" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2989" Parameter: B <- "-29.2989" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4979" Parameter: C <- "-41.4979" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4312 TOTAL ENERGY = -70.7969 RDTITL> * VAN DER WAALS = -29.2989 ELECTROSTATIC = -41.4979 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4312" Parameter: CONF_N -> "8002" Comparing "4312" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4313" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759263 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759333 ATOM PAIRS WERE FOUND FOR ATOM LIST 41650 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29219 from a total of 759333 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4313 -70.17042 -0.62647 0.64440 INTE EXTERN> -26.75220 -43.41823 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1704" Parameter: A <- "-70.1704" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7522" Parameter: B <- "-26.7522" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4182" Parameter: C <- "-43.4182" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4313 TOTAL ENERGY = -70.1704 RDTITL> * VAN DER WAALS = -26.7522 ELECTROSTATIC = -43.4182 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4313" Parameter: CONF_N -> "8002" Comparing "4313" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4314" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759333 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760669 ATOM PAIRS WERE FOUND FOR ATOM LIST 41745 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29166 from a total of 760669 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4314 -72.64240 2.47198 0.60080 INTE EXTERN> -27.71081 -44.93159 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6424" Parameter: A <- "-72.6424" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7108" Parameter: B <- "-27.7108" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9316" Parameter: C <- "-44.9316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4314 TOTAL ENERGY = -72.6424 RDTITL> * VAN DER WAALS = -27.7108 ELECTROSTATIC = -44.9316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4314" Parameter: CONF_N -> "8002" Comparing "4314" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4315" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760669 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761218 ATOM PAIRS WERE FOUND FOR ATOM LIST 41514 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29837 from a total of 761218 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4315 -79.50809 6.86569 0.62324 INTE EXTERN> -29.18104 -50.32705 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5081" Parameter: A <- "-79.5081" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.181" Parameter: B <- "-29.181" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3271" Parameter: C <- "-50.3271" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4315 TOTAL ENERGY = -79.5081 RDTITL> * VAN DER WAALS = -29.181 ELECTROSTATIC = -50.3271 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4315" Parameter: CONF_N -> "8002" Comparing "4315" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4316" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761218 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765299 ATOM PAIRS WERE FOUND FOR ATOM LIST 41989 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29755 from a total of 765299 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4316 -69.46132 -10.04677 0.63584 INTE EXTERN> -27.29726 -42.16405 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4613" Parameter: A <- "-69.4613" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2973" Parameter: B <- "-27.2973" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1641" Parameter: C <- "-42.1641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4316 TOTAL ENERGY = -69.4613 RDTITL> * VAN DER WAALS = -27.2973 ELECTROSTATIC = -42.1641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4316" Parameter: CONF_N -> "8002" Comparing "4316" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4317" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765299 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761903 ATOM PAIRS WERE FOUND FOR ATOM LIST 41681 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29487 from a total of 761903 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4317 -60.66085 -8.80047 0.69807 INTE EXTERN> -23.41937 -37.24147 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.6608" Parameter: A <- "-60.6608" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4194" Parameter: B <- "-23.4194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2415" Parameter: C <- "-37.2415" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4317 TOTAL ENERGY = -60.6608 RDTITL> * VAN DER WAALS = -23.4194 ELECTROSTATIC = -37.2415 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4317" Parameter: CONF_N -> "8002" Comparing "4317" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4318" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761903 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760678 ATOM PAIRS WERE FOUND FOR ATOM LIST 41681 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29539 from a total of 760678 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4318 -60.04040 -0.62044 0.60581 INTE EXTERN> -30.14231 -29.89810 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.0404" Parameter: A <- "-60.0404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1423" Parameter: B <- "-30.1423" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.8981" Parameter: C <- "-29.8981" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4318 TOTAL ENERGY = -60.0404 RDTITL> * VAN DER WAALS = -30.1423 ELECTROSTATIC = -29.8981 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4318" Parameter: CONF_N -> "8002" Comparing "4318" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4319" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760678 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765572 ATOM PAIRS WERE FOUND FOR ATOM LIST 41966 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29839 from a total of 765572 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4319 -71.20592 11.16551 0.73248 INTE EXTERN> -26.63318 -44.57273 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2059" Parameter: A <- "-71.2059" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6332" Parameter: B <- "-26.6332" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5727" Parameter: C <- "-44.5727" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4319 TOTAL ENERGY = -71.2059 RDTITL> * VAN DER WAALS = -26.6332 ELECTROSTATIC = -44.5727 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4319" Parameter: CONF_N -> "8002" Comparing "4319" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4320" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765572 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760523 ATOM PAIRS WERE FOUND FOR ATOM LIST 41664 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29342 from a total of 760523 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4320 -71.13012 -0.07580 0.66478 INTE EXTERN> -28.60247 -42.52764 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1301" Parameter: A <- "-71.1301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6025" Parameter: B <- "-28.6025" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5276" Parameter: C <- "-42.5276" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4320 TOTAL ENERGY = -71.1301 RDTITL> * VAN DER WAALS = -28.6025 ELECTROSTATIC = -42.5276 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4320" Parameter: CONF_N -> "8002" Comparing "4320" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4321" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760523 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755228 ATOM PAIRS WERE FOUND FOR ATOM LIST 41621 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29457 from a total of 755228 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4321 -66.70875 -4.42137 0.76748 INTE EXTERN> -22.86291 -43.84583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7087" Parameter: A <- "-66.7087" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.8629" Parameter: B <- "-22.8629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8458" Parameter: C <- "-43.8458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4321 TOTAL ENERGY = -66.7087 RDTITL> * VAN DER WAALS = -22.8629 ELECTROSTATIC = -43.8458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4321" Parameter: CONF_N -> "8002" Comparing "4321" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4322" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755228 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41842 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28962 from a total of 759110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4322 -63.94728 -2.76147 0.55427 INTE EXTERN> -29.68066 -34.26662 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.9473" Parameter: A <- "-63.9473" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6807" Parameter: B <- "-29.6807" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2666" Parameter: C <- "-34.2666" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4322 TOTAL ENERGY = -63.9473 RDTITL> * VAN DER WAALS = -29.6807 ELECTROSTATIC = -34.2666 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4322" Parameter: CONF_N -> "8002" Comparing "4322" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4323" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759861 ATOM PAIRS WERE FOUND FOR ATOM LIST 41730 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29152 from a total of 759861 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4323 -70.33934 6.39207 0.55862 INTE EXTERN> -30.37951 -39.95983 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3393" Parameter: A <- "-70.3393" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3795" Parameter: B <- "-30.3795" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9598" Parameter: C <- "-39.9598" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4323 TOTAL ENERGY = -70.3393 RDTITL> * VAN DER WAALS = -30.3795 ELECTROSTATIC = -39.9598 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4323" Parameter: CONF_N -> "8002" Comparing "4323" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4324" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759861 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757208 ATOM PAIRS WERE FOUND FOR ATOM LIST 41650 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29730 from a total of 757208 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4324 -66.44689 -3.89245 0.61587 INTE EXTERN> -27.94167 -38.50522 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4469" Parameter: A <- "-66.4469" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9417" Parameter: B <- "-27.9417" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5052" Parameter: C <- "-38.5052" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4324 TOTAL ENERGY = -66.4469 RDTITL> * VAN DER WAALS = -27.9417 ELECTROSTATIC = -38.5052 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4324" Parameter: CONF_N -> "8002" Comparing "4324" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4325" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757208 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755760 ATOM PAIRS WERE FOUND FOR ATOM LIST 41459 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29396 from a total of 755760 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4325 -67.72683 1.27994 0.72652 INTE EXTERN> -25.04577 -42.68106 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7268" Parameter: A <- "-67.7268" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0458" Parameter: B <- "-25.0458" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6811" Parameter: C <- "-42.6811" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4325 TOTAL ENERGY = -67.7268 RDTITL> * VAN DER WAALS = -25.0458 ELECTROSTATIC = -42.6811 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4325" Parameter: CONF_N -> "8002" Comparing "4325" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4326" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755760 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756651 ATOM PAIRS WERE FOUND FOR ATOM LIST 41532 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28794 from a total of 756651 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4326 -63.92422 -3.80262 0.64398 INTE EXTERN> -26.26510 -37.65912 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.9242" Parameter: A <- "-63.9242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2651" Parameter: B <- "-26.2651" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6591" Parameter: C <- "-37.6591" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4326 TOTAL ENERGY = -63.9242 RDTITL> * VAN DER WAALS = -26.2651 ELECTROSTATIC = -37.6591 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4326" Parameter: CONF_N -> "8002" Comparing "4326" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4327" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756651 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756398 ATOM PAIRS WERE FOUND FOR ATOM LIST 41438 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29202 from a total of 756398 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4327 -62.76272 -1.16149 0.65699 INTE EXTERN> -25.81048 -36.95224 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7627" Parameter: A <- "-62.7627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8105" Parameter: B <- "-25.8105" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9522" Parameter: C <- "-36.9522" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4327 TOTAL ENERGY = -62.7627 RDTITL> * VAN DER WAALS = -25.8105 ELECTROSTATIC = -36.9522 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4327" Parameter: CONF_N -> "8002" Comparing "4327" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4328" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756398 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749092 ATOM PAIRS WERE FOUND FOR ATOM LIST 41301 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28619 from a total of 749092 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4328 -66.34872 3.58600 0.54519 INTE EXTERN> -31.99223 -34.35649 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3487" Parameter: A <- "-66.3487" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9922" Parameter: B <- "-31.9922" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3565" Parameter: C <- "-34.3565" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4328 TOTAL ENERGY = -66.3487 RDTITL> * VAN DER WAALS = -31.9922 ELECTROSTATIC = -34.3565 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4328" Parameter: CONF_N -> "8002" Comparing "4328" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4329" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749092 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753262 ATOM PAIRS WERE FOUND FOR ATOM LIST 41495 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28809 from a total of 753262 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4329 -74.68473 8.33601 0.72504 INTE EXTERN> -24.60598 -50.07875 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6847" Parameter: A <- "-74.6847" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.606" Parameter: B <- "-24.606" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0788" Parameter: C <- "-50.0788" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4329 TOTAL ENERGY = -74.6847 RDTITL> * VAN DER WAALS = -24.606 ELECTROSTATIC = -50.0788 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4329" Parameter: CONF_N -> "8002" Comparing "4329" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4330" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753262 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755444 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29203 from a total of 755444 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4330 -70.13674 -4.54798 0.55452 INTE EXTERN> -31.04868 -39.08806 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1367" Parameter: A <- "-70.1367" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0487" Parameter: B <- "-31.0487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0881" Parameter: C <- "-39.0881" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4330 TOTAL ENERGY = -70.1367 RDTITL> * VAN DER WAALS = -31.0487 ELECTROSTATIC = -39.0881 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4330" Parameter: CONF_N -> "8002" Comparing "4330" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4331" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755444 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758245 ATOM PAIRS WERE FOUND FOR ATOM LIST 41619 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29621 from a total of 758245 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4331 -71.97075 1.83400 0.63226 INTE EXTERN> -29.56299 -42.40775 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9707" Parameter: A <- "-71.9707" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.563" Parameter: B <- "-29.563" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4078" Parameter: C <- "-42.4078" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4331 TOTAL ENERGY = -71.9707 RDTITL> * VAN DER WAALS = -29.563 ELECTROSTATIC = -42.4078 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4331" Parameter: CONF_N -> "8002" Comparing "4331" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4332" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758245 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757217 ATOM PAIRS WERE FOUND FOR ATOM LIST 41798 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29222 from a total of 757217 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4332 -69.79848 -2.17227 0.60057 INTE EXTERN> -31.93975 -37.85873 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7985" Parameter: A <- "-69.7985" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9397" Parameter: B <- "-31.9397" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8587" Parameter: C <- "-37.8587" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4332 TOTAL ENERGY = -69.7985 RDTITL> * VAN DER WAALS = -31.9397 ELECTROSTATIC = -37.8587 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4332" Parameter: CONF_N -> "8002" Comparing "4332" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4333" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757217 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755661 ATOM PAIRS WERE FOUND FOR ATOM LIST 41619 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29265 from a total of 755661 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4333 -62.14528 -7.65320 0.60689 INTE EXTERN> -26.86157 -35.28371 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.1453" Parameter: A <- "-62.1453" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8616" Parameter: B <- "-26.8616" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2837" Parameter: C <- "-35.2837" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4333 TOTAL ENERGY = -62.1453 RDTITL> * VAN DER WAALS = -26.8616 ELECTROSTATIC = -35.2837 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4333" Parameter: CONF_N -> "8002" Comparing "4333" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4334" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755661 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763162 ATOM PAIRS WERE FOUND FOR ATOM LIST 41861 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29297 from a total of 763162 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4334 -72.22418 10.07889 0.67420 INTE EXTERN> -27.37574 -44.84843 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2242" Parameter: A <- "-72.2242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3757" Parameter: B <- "-27.3757" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8484" Parameter: C <- "-44.8484" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4334 TOTAL ENERGY = -72.2242 RDTITL> * VAN DER WAALS = -27.3757 ELECTROSTATIC = -44.8484 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4334" Parameter: CONF_N -> "8002" Comparing "4334" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4335" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763162 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758282 ATOM PAIRS WERE FOUND FOR ATOM LIST 41608 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29562 from a total of 758282 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4335 -73.31950 1.09532 0.56840 INTE EXTERN> -32.26315 -41.05635 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3195" Parameter: A <- "-73.3195" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2631" Parameter: B <- "-32.2631" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0564" Parameter: C <- "-41.0564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4335 TOTAL ENERGY = -73.3195 RDTITL> * VAN DER WAALS = -32.2631 ELECTROSTATIC = -41.0564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4335" Parameter: CONF_N -> "8002" Comparing "4335" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4336" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758282 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754319 ATOM PAIRS WERE FOUND FOR ATOM LIST 41452 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29468 from a total of 754319 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4336 -73.43510 0.11560 0.71939 INTE EXTERN> -25.20863 -48.22646 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4351" Parameter: A <- "-73.4351" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2086" Parameter: B <- "-25.2086" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2265" Parameter: C <- "-48.2265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4336 TOTAL ENERGY = -73.4351 RDTITL> * VAN DER WAALS = -25.2086 ELECTROSTATIC = -48.2265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4336" Parameter: CONF_N -> "8002" Comparing "4336" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4337" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754319 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755637 ATOM PAIRS WERE FOUND FOR ATOM LIST 41659 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29498 from a total of 755637 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4337 -69.50466 -3.93044 0.73428 INTE EXTERN> -24.24222 -45.26244 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5047" Parameter: A <- "-69.5047" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2422" Parameter: B <- "-24.2422" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2624" Parameter: C <- "-45.2624" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4337 TOTAL ENERGY = -69.5047 RDTITL> * VAN DER WAALS = -24.2422 ELECTROSTATIC = -45.2624 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4337" Parameter: CONF_N -> "8002" Comparing "4337" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4338" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755637 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752152 ATOM PAIRS WERE FOUND FOR ATOM LIST 41413 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29275 from a total of 752152 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4338 -68.32850 -1.17616 0.66660 INTE EXTERN> -25.47077 -42.85774 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3285" Parameter: A <- "-68.3285" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4708" Parameter: B <- "-25.4708" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8577" Parameter: C <- "-42.8577" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4338 TOTAL ENERGY = -68.3285 RDTITL> * VAN DER WAALS = -25.4708 ELECTROSTATIC = -42.8577 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4338" Parameter: CONF_N -> "8002" Comparing "4338" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4339" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752152 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761365 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29990 from a total of 761365 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4339 -69.36058 1.03208 0.65537 INTE EXTERN> -25.43073 -43.92985 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3606" Parameter: A <- "-69.3606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4307" Parameter: B <- "-25.4307" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9299" Parameter: C <- "-43.9299" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4339 TOTAL ENERGY = -69.3606 RDTITL> * VAN DER WAALS = -25.4307 ELECTROSTATIC = -43.9299 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4339" Parameter: CONF_N -> "8002" Comparing "4339" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4340" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761365 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761571 ATOM PAIRS WERE FOUND FOR ATOM LIST 41561 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29648 from a total of 761571 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4340 -73.61372 4.25314 0.61046 INTE EXTERN> -29.79109 -43.82263 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6137" Parameter: A <- "-73.6137" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7911" Parameter: B <- "-29.7911" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8226" Parameter: C <- "-43.8226" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4340 TOTAL ENERGY = -73.6137 RDTITL> * VAN DER WAALS = -29.7911 ELECTROSTATIC = -43.8226 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4340" Parameter: CONF_N -> "8002" Comparing "4340" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4341" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761571 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754761 ATOM PAIRS WERE FOUND FOR ATOM LIST 41380 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29149 from a total of 754761 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4341 -60.94397 -12.66975 0.59961 INTE EXTERN> -26.15824 -34.78572 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.944" Parameter: A <- "-60.944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1582" Parameter: B <- "-26.1582" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7857" Parameter: C <- "-34.7857" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4341 TOTAL ENERGY = -60.944 RDTITL> * VAN DER WAALS = -26.1582 ELECTROSTATIC = -34.7857 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4341" Parameter: CONF_N -> "8002" Comparing "4341" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4342" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754761 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757429 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29045 from a total of 757429 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4342 -59.45917 -1.48479 0.64332 INTE EXTERN> -25.07003 -34.38914 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.4592" Parameter: A <- "-59.4592" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.07" Parameter: B <- "-25.07" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3891" Parameter: C <- "-34.3891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4342 TOTAL ENERGY = -59.4592 RDTITL> * VAN DER WAALS = -25.07 ELECTROSTATIC = -34.3891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4342" Parameter: CONF_N -> "8002" Comparing "4342" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4343" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757429 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754088 ATOM PAIRS WERE FOUND FOR ATOM LIST 41360 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29164 from a total of 754088 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4343 -74.52672 15.06755 0.62760 INTE EXTERN> -26.91949 -47.60723 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5267" Parameter: A <- "-74.5267" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9195" Parameter: B <- "-26.9195" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6072" Parameter: C <- "-47.6072" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4343 TOTAL ENERGY = -74.5267 RDTITL> * VAN DER WAALS = -26.9195 ELECTROSTATIC = -47.6072 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4343" Parameter: CONF_N -> "8002" Comparing "4343" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4344" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754088 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751240 ATOM PAIRS WERE FOUND FOR ATOM LIST 41174 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28718 from a total of 751240 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4344 -67.23746 -7.28926 0.59496 INTE EXTERN> -27.18743 -40.05003 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2375" Parameter: A <- "-67.2375" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1874" Parameter: B <- "-27.1874" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.05" Parameter: C <- "-40.05" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4344 TOTAL ENERGY = -67.2375 RDTITL> * VAN DER WAALS = -27.1874 ELECTROSTATIC = -40.05 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4344" Parameter: CONF_N -> "8002" Comparing "4344" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4345" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751240 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752063 ATOM PAIRS WERE FOUND FOR ATOM LIST 41399 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28095 from a total of 752063 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4345 -56.93100 -10.30646 0.60761 INTE EXTERN> -23.91852 -33.01248 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-56.931" Parameter: A <- "-56.931" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9185" Parameter: B <- "-23.9185" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.0125" Parameter: C <- "-33.0125" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4345 TOTAL ENERGY = -56.931 RDTITL> * VAN DER WAALS = -23.9185 ELECTROSTATIC = -33.0125 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4345" Parameter: CONF_N -> "8002" Comparing "4345" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4346" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752063 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757257 ATOM PAIRS WERE FOUND FOR ATOM LIST 41654 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28980 from a total of 757257 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4346 -56.94003 0.00903 0.65598 INTE EXTERN> -24.24202 -32.69801 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-56.94" Parameter: A <- "-56.94" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.242" Parameter: B <- "-24.242" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.698" Parameter: C <- "-32.698" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4346 TOTAL ENERGY = -56.94 RDTITL> * VAN DER WAALS = -24.242 ELECTROSTATIC = -32.698 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4346" Parameter: CONF_N -> "8002" Comparing "4346" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4347" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757257 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755781 ATOM PAIRS WERE FOUND FOR ATOM LIST 41428 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28787 from a total of 755781 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4347 -68.77097 11.83094 0.52919 INTE EXTERN> -26.82793 -41.94304 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.771" Parameter: A <- "-68.771" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8279" Parameter: B <- "-26.8279" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.943" Parameter: C <- "-41.943" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4347 TOTAL ENERGY = -68.771 RDTITL> * VAN DER WAALS = -26.8279 ELECTROSTATIC = -41.943 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4347" Parameter: CONF_N -> "8002" Comparing "4347" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4348" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755781 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758534 ATOM PAIRS WERE FOUND FOR ATOM LIST 41545 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28562 from a total of 758534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4348 -66.14670 -2.62427 0.45909 INTE EXTERN> -31.02561 -35.12110 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1467" Parameter: A <- "-66.1467" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0256" Parameter: B <- "-31.0256" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1211" Parameter: C <- "-35.1211" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4348 TOTAL ENERGY = -66.1467 RDTITL> * VAN DER WAALS = -31.0256 ELECTROSTATIC = -35.1211 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4348" Parameter: CONF_N -> "8002" Comparing "4348" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4349" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41797 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28475 from a total of 760794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4349 -62.14411 -4.00259 0.51939 INTE EXTERN> -27.77614 -34.36797 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.1441" Parameter: A <- "-62.1441" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7761" Parameter: B <- "-27.7761" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.368" Parameter: C <- "-34.368" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4349 TOTAL ENERGY = -62.1441 RDTITL> * VAN DER WAALS = -27.7761 ELECTROSTATIC = -34.368 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4349" Parameter: CONF_N -> "8002" Comparing "4349" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4350" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758302 ATOM PAIRS WERE FOUND FOR ATOM LIST 41540 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28908 from a total of 758302 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4350 -66.81274 4.66863 0.65044 INTE EXTERN> -26.21072 -40.60202 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8127" Parameter: A <- "-66.8127" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2107" Parameter: B <- "-26.2107" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.602" Parameter: C <- "-40.602" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4350 TOTAL ENERGY = -66.8127 RDTITL> * VAN DER WAALS = -26.2107 ELECTROSTATIC = -40.602 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4350" Parameter: CONF_N -> "8002" Comparing "4350" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4351" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758302 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756420 ATOM PAIRS WERE FOUND FOR ATOM LIST 41648 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28279 from a total of 756420 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4351 -66.82608 0.01334 0.54298 INTE EXTERN> -31.94142 -34.88465 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8261" Parameter: A <- "-66.8261" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9414" Parameter: B <- "-31.9414" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8847" Parameter: C <- "-34.8847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4351 TOTAL ENERGY = -66.8261 RDTITL> * VAN DER WAALS = -31.9414 ELECTROSTATIC = -34.8847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4351" Parameter: CONF_N -> "8002" Comparing "4351" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4352" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756420 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760113 ATOM PAIRS WERE FOUND FOR ATOM LIST 41606 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28953 from a total of 760113 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4352 -66.58025 -0.24583 0.63714 INTE EXTERN> -27.11851 -39.46174 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5802" Parameter: A <- "-66.5802" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1185" Parameter: B <- "-27.1185" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4617" Parameter: C <- "-39.4617" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4352 TOTAL ENERGY = -66.5802 RDTITL> * VAN DER WAALS = -27.1185 ELECTROSTATIC = -39.4617 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4352" Parameter: CONF_N -> "8002" Comparing "4352" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4353" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760113 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41935 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29145 from a total of 764110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4353 -68.75097 2.17073 0.72099 INTE EXTERN> -25.25030 -43.50067 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.751" Parameter: A <- "-68.751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2503" Parameter: B <- "-25.2503" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5007" Parameter: C <- "-43.5007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4353 TOTAL ENERGY = -68.751 RDTITL> * VAN DER WAALS = -25.2503 ELECTROSTATIC = -43.5007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4353" Parameter: CONF_N -> "8002" Comparing "4353" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4354" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763333 ATOM PAIRS WERE FOUND FOR ATOM LIST 41976 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28610 from a total of 763333 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4354 -73.74274 4.99177 0.62837 INTE EXTERN> -26.92486 -46.81788 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7427" Parameter: A <- "-73.7427" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9249" Parameter: B <- "-26.9249" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8179" Parameter: C <- "-46.8179" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4354 TOTAL ENERGY = -73.7427 RDTITL> * VAN DER WAALS = -26.9249 ELECTROSTATIC = -46.8179 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4354" Parameter: CONF_N -> "8002" Comparing "4354" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4355" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763333 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759952 ATOM PAIRS WERE FOUND FOR ATOM LIST 41769 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28701 from a total of 759952 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4355 -60.87915 -12.86359 0.55088 INTE EXTERN> -27.74136 -33.13779 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.8792" Parameter: A <- "-60.8792" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7414" Parameter: B <- "-27.7414" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1378" Parameter: C <- "-33.1378" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4355 TOTAL ENERGY = -60.8792 RDTITL> * VAN DER WAALS = -27.7414 ELECTROSTATIC = -33.1378 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4355" Parameter: CONF_N -> "8002" Comparing "4355" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4356" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759952 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767272 ATOM PAIRS WERE FOUND FOR ATOM LIST 42003 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28870 from a total of 767272 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4356 -69.54145 8.66229 0.54667 INTE EXTERN> -30.82724 -38.71421 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5414" Parameter: A <- "-69.5414" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8272" Parameter: B <- "-30.8272" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7142" Parameter: C <- "-38.7142" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4356 TOTAL ENERGY = -69.5414 RDTITL> * VAN DER WAALS = -30.8272 ELECTROSTATIC = -38.7142 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4356" Parameter: CONF_N -> "8002" Comparing "4356" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4357" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767272 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758997 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28952 from a total of 758997 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4357 -76.22924 6.68779 0.57047 INTE EXTERN> -29.82725 -46.40198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2292" Parameter: A <- "-76.2292" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8273" Parameter: B <- "-29.8273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.402" Parameter: C <- "-46.402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4357 TOTAL ENERGY = -76.2292 RDTITL> * VAN DER WAALS = -29.8273 ELECTROSTATIC = -46.402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4357" Parameter: CONF_N -> "8002" Comparing "4357" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4358" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758997 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762394 ATOM PAIRS WERE FOUND FOR ATOM LIST 41671 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28701 from a total of 762394 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4358 -69.44304 -6.78619 0.69138 INTE EXTERN> -24.84342 -44.59962 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.443" Parameter: A <- "-69.443" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8434" Parameter: B <- "-24.8434" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5996" Parameter: C <- "-44.5996" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4358 TOTAL ENERGY = -69.443 RDTITL> * VAN DER WAALS = -24.8434 ELECTROSTATIC = -44.5996 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4358" Parameter: CONF_N -> "8002" Comparing "4358" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4359" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762394 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758039 ATOM PAIRS WERE FOUND FOR ATOM LIST 41758 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28339 from a total of 758039 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4359 -65.49225 -3.95079 0.52169 INTE EXTERN> -30.29608 -35.19617 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4923" Parameter: A <- "-65.4923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2961" Parameter: B <- "-30.2961" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1962" Parameter: C <- "-35.1962" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4359 TOTAL ENERGY = -65.4923 RDTITL> * VAN DER WAALS = -30.2961 ELECTROSTATIC = -35.1962 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4359" Parameter: CONF_N -> "8002" Comparing "4359" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4360" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758039 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763780 ATOM PAIRS WERE FOUND FOR ATOM LIST 41980 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28895 from a total of 763780 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4360 -71.98275 6.49049 0.65543 INTE EXTERN> -27.36718 -44.61556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9827" Parameter: A <- "-71.9827" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3672" Parameter: B <- "-27.3672" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6156" Parameter: C <- "-44.6156" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4360 TOTAL ENERGY = -71.9827 RDTITL> * VAN DER WAALS = -27.3672 ELECTROSTATIC = -44.6156 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4360" Parameter: CONF_N -> "8002" Comparing "4360" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4361" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763780 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765830 ATOM PAIRS WERE FOUND FOR ATOM LIST 42044 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28949 from a total of 765830 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4361 -66.04776 -5.93499 0.60619 INTE EXTERN> -26.89993 -39.14783 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0478" Parameter: A <- "-66.0478" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8999" Parameter: B <- "-26.8999" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1478" Parameter: C <- "-39.1478" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4361 TOTAL ENERGY = -66.0478 RDTITL> * VAN DER WAALS = -26.8999 ELECTROSTATIC = -39.1478 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4361" Parameter: CONF_N -> "8002" Comparing "4361" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4362" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765830 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768264 ATOM PAIRS WERE FOUND FOR ATOM LIST 42061 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29820 from a total of 768264 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4362 -65.50314 -0.54462 0.58551 INTE EXTERN> -30.07146 -35.43168 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5031" Parameter: A <- "-65.5031" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0715" Parameter: B <- "-30.0715" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4317" Parameter: C <- "-35.4317" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4362 TOTAL ENERGY = -65.5031 RDTITL> * VAN DER WAALS = -30.0715 ELECTROSTATIC = -35.4317 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4362" Parameter: CONF_N -> "8002" Comparing "4362" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4363" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768264 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764578 ATOM PAIRS WERE FOUND FOR ATOM LIST 41911 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29366 from a total of 764578 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4363 -56.48304 -9.02010 0.60434 INTE EXTERN> -25.63735 -30.84570 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-56.483" Parameter: A <- "-56.483" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6373" Parameter: B <- "-25.6373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.8457" Parameter: C <- "-30.8457" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4363 TOTAL ENERGY = -56.483 RDTITL> * VAN DER WAALS = -25.6373 ELECTROSTATIC = -30.8457 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4363" Parameter: CONF_N -> "8002" Comparing "4363" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4364" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764578 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758098 ATOM PAIRS WERE FOUND FOR ATOM LIST 41679 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29210 from a total of 758098 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4364 -62.75571 6.27267 0.53856 INTE EXTERN> -29.94175 -32.81396 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7557" Parameter: A <- "-62.7557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9417" Parameter: B <- "-29.9417" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.814" Parameter: C <- "-32.814" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4364 TOTAL ENERGY = -62.7557 RDTITL> * VAN DER WAALS = -29.9417 ELECTROSTATIC = -32.814 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4364" Parameter: CONF_N -> "8002" Comparing "4364" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4365" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758098 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761914 ATOM PAIRS WERE FOUND FOR ATOM LIST 41706 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28515 from a total of 761914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4365 -63.60258 0.84687 0.58604 INTE EXTERN> -27.52711 -36.07547 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6026" Parameter: A <- "-63.6026" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5271" Parameter: B <- "-27.5271" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0755" Parameter: C <- "-36.0755" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4365 TOTAL ENERGY = -63.6026 RDTITL> * VAN DER WAALS = -27.5271 ELECTROSTATIC = -36.0755 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4365" Parameter: CONF_N -> "8002" Comparing "4365" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4366" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755482 ATOM PAIRS WERE FOUND FOR ATOM LIST 41442 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28520 from a total of 755482 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4366 -70.35816 6.75558 0.50668 INTE EXTERN> -29.43074 -40.92741 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3582" Parameter: A <- "-70.3582" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4307" Parameter: B <- "-29.4307" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9274" Parameter: C <- "-40.9274" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4366 TOTAL ENERGY = -70.3582 RDTITL> * VAN DER WAALS = -29.4307 ELECTROSTATIC = -40.9274 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4366" Parameter: CONF_N -> "8002" Comparing "4366" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4367" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755482 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758292 ATOM PAIRS WERE FOUND FOR ATOM LIST 41798 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28826 from a total of 758292 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4367 -69.58931 -0.76884 0.51627 INTE EXTERN> -30.54727 -39.04204 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5893" Parameter: A <- "-69.5893" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5473" Parameter: B <- "-30.5473" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.042" Parameter: C <- "-39.042" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4367 TOTAL ENERGY = -69.5893 RDTITL> * VAN DER WAALS = -30.5473 ELECTROSTATIC = -39.042 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4367" Parameter: CONF_N -> "8002" Comparing "4367" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4368" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758292 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763508 ATOM PAIRS WERE FOUND FOR ATOM LIST 41791 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29308 from a total of 763508 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4368 -68.16665 -1.42266 0.51408 INTE EXTERN> -31.35408 -36.81257 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1666" Parameter: A <- "-68.1666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3541" Parameter: B <- "-31.3541" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8126" Parameter: C <- "-36.8126" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4368 TOTAL ENERGY = -68.1666 RDTITL> * VAN DER WAALS = -31.3541 ELECTROSTATIC = -36.8126 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4368" Parameter: CONF_N -> "8002" Comparing "4368" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4369" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763508 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758753 ATOM PAIRS WERE FOUND FOR ATOM LIST 41441 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28922 from a total of 758753 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4369 -56.25665 -11.91000 0.63780 INTE EXTERN> -24.42723 -31.82942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-56.2566" Parameter: A <- "-56.2566" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4272" Parameter: B <- "-24.4272" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.8294" Parameter: C <- "-31.8294" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4369 TOTAL ENERGY = -56.2566 RDTITL> * VAN DER WAALS = -24.4272 ELECTROSTATIC = -31.8294 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4369" Parameter: CONF_N -> "8002" Comparing "4369" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4370" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758753 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753448 ATOM PAIRS WERE FOUND FOR ATOM LIST 41478 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28723 from a total of 753448 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4370 -65.65109 9.39444 0.55554 INTE EXTERN> -27.94599 -37.70510 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6511" Parameter: A <- "-65.6511" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.946" Parameter: B <- "-27.946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7051" Parameter: C <- "-37.7051" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4370 TOTAL ENERGY = -65.6511 RDTITL> * VAN DER WAALS = -27.946 ELECTROSTATIC = -37.7051 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4370" Parameter: CONF_N -> "8002" Comparing "4370" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4371" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753448 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758811 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28703 from a total of 758811 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4371 -69.07191 3.42082 0.55040 INTE EXTERN> -29.39332 -39.67859 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0719" Parameter: A <- "-69.0719" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3933" Parameter: B <- "-29.3933" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6786" Parameter: C <- "-39.6786" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4371 TOTAL ENERGY = -69.0719 RDTITL> * VAN DER WAALS = -29.3933 ELECTROSTATIC = -39.6786 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4371" Parameter: CONF_N -> "8002" Comparing "4371" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4372" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758811 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760925 ATOM PAIRS WERE FOUND FOR ATOM LIST 41734 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29516 from a total of 760925 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4372 -66.38056 -2.69135 0.62104 INTE EXTERN> -26.94635 -39.43421 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3806" Parameter: A <- "-66.3806" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9464" Parameter: B <- "-26.9464" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4342" Parameter: C <- "-39.4342" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4372 TOTAL ENERGY = -66.3806 RDTITL> * VAN DER WAALS = -26.9464 ELECTROSTATIC = -39.4342 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4372" Parameter: CONF_N -> "8002" Comparing "4372" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4373" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760925 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760457 ATOM PAIRS WERE FOUND FOR ATOM LIST 41768 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29119 from a total of 760457 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4373 -72.60169 6.22113 0.64767 INTE EXTERN> -28.02878 -44.57291 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6017" Parameter: A <- "-72.6017" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0288" Parameter: B <- "-28.0288" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5729" Parameter: C <- "-44.5729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4373 TOTAL ENERGY = -72.6017 RDTITL> * VAN DER WAALS = -28.0288 ELECTROSTATIC = -44.5729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4373" Parameter: CONF_N -> "8002" Comparing "4373" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4374" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760457 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760945 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29334 from a total of 760945 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4374 -69.79795 -2.80374 0.65120 INTE EXTERN> -28.26714 -41.53081 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.798" Parameter: A <- "-69.798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2671" Parameter: B <- "-28.2671" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5308" Parameter: C <- "-41.5308" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4374 TOTAL ENERGY = -69.798 RDTITL> * VAN DER WAALS = -28.2671 ELECTROSTATIC = -41.5308 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4374" Parameter: CONF_N -> "8002" Comparing "4374" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4375" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760945 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765316 ATOM PAIRS WERE FOUND FOR ATOM LIST 41954 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29907 from a total of 765316 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4375 -74.89961 5.10166 0.60059 INTE EXTERN> -28.06241 -46.83720 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8996" Parameter: A <- "-74.8996" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0624" Parameter: B <- "-28.0624" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8372" Parameter: C <- "-46.8372" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4375 TOTAL ENERGY = -74.8996 RDTITL> * VAN DER WAALS = -28.0624 ELECTROSTATIC = -46.8372 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4375" Parameter: CONF_N -> "8002" Comparing "4375" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4376" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765316 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760464 ATOM PAIRS WERE FOUND FOR ATOM LIST 41849 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29690 from a total of 760464 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4376 -68.88654 -6.01307 0.61272 INTE EXTERN> -30.12357 -38.76297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8865" Parameter: A <- "-68.8865" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1236" Parameter: B <- "-30.1236" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.763" Parameter: C <- "-38.763" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4376 TOTAL ENERGY = -68.8865 RDTITL> * VAN DER WAALS = -30.1236 ELECTROSTATIC = -38.763 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4376" Parameter: CONF_N -> "8002" Comparing "4376" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4377" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760464 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756581 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29168 from a total of 756581 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4377 -71.14125 2.25471 0.73105 INTE EXTERN> -23.37173 -47.76952 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1412" Parameter: A <- "-71.1412" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.3717" Parameter: B <- "-23.3717" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7695" Parameter: C <- "-47.7695" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4377 TOTAL ENERGY = -71.1412 RDTITL> * VAN DER WAALS = -23.3717 ELECTROSTATIC = -47.7695 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4377" Parameter: CONF_N -> "8002" Comparing "4377" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4378" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756581 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758736 ATOM PAIRS WERE FOUND FOR ATOM LIST 41683 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29455 from a total of 758736 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4378 -71.41168 0.27043 0.65138 INTE EXTERN> -26.65575 -44.75592 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4117" Parameter: A <- "-71.4117" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6558" Parameter: B <- "-26.6558" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7559" Parameter: C <- "-44.7559" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4378 TOTAL ENERGY = -71.4117 RDTITL> * VAN DER WAALS = -26.6558 ELECTROSTATIC = -44.7559 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4378" Parameter: CONF_N -> "8002" Comparing "4378" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4379" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758736 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41901 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29968 from a total of 761601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4379 -76.29868 4.88700 0.69194 INTE EXTERN> -27.73353 -48.56515 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2987" Parameter: A <- "-76.2987" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7335" Parameter: B <- "-27.7335" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5651" Parameter: C <- "-48.5651" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4379 TOTAL ENERGY = -76.2987 RDTITL> * VAN DER WAALS = -27.7335 ELECTROSTATIC = -48.5651 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4379" Parameter: CONF_N -> "8002" Comparing "4379" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4380" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758460 ATOM PAIRS WERE FOUND FOR ATOM LIST 41355 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29050 from a total of 758460 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4380 -66.05247 -10.24621 0.71118 INTE EXTERN> -24.05521 -41.99726 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0525" Parameter: A <- "-66.0525" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0552" Parameter: B <- "-24.0552" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9973" Parameter: C <- "-41.9973" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4380 TOTAL ENERGY = -66.0525 RDTITL> * VAN DER WAALS = -24.0552 ELECTROSTATIC = -41.9973 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4380" Parameter: CONF_N -> "8002" Comparing "4380" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4381" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758460 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759516 ATOM PAIRS WERE FOUND FOR ATOM LIST 41851 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29591 from a total of 759516 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4381 -67.72020 1.66773 0.60727 INTE EXTERN> -28.43257 -39.28763 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7202" Parameter: A <- "-67.7202" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4326" Parameter: B <- "-28.4326" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2876" Parameter: C <- "-39.2876" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4381 TOTAL ENERGY = -67.7202 RDTITL> * VAN DER WAALS = -28.4326 ELECTROSTATIC = -39.2876 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4381" Parameter: CONF_N -> "8002" Comparing "4381" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4382" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759516 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29786 from a total of 755422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4382 -74.62701 6.90681 0.62749 INTE EXTERN> -28.70467 -45.92234 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.627" Parameter: A <- "-74.627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7047" Parameter: B <- "-28.7047" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9223" Parameter: C <- "-45.9223" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4382 TOTAL ENERGY = -74.627 RDTITL> * VAN DER WAALS = -28.7047 ELECTROSTATIC = -45.9223 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4382" Parameter: CONF_N -> "8002" Comparing "4382" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4383" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765362 ATOM PAIRS WERE FOUND FOR ATOM LIST 42085 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30320 from a total of 765362 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4383 -75.70376 1.07675 0.66440 INTE EXTERN> -30.12578 -45.57798 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7038" Parameter: A <- "-75.7038" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1258" Parameter: B <- "-30.1258" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.578" Parameter: C <- "-45.578" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4383 TOTAL ENERGY = -75.7038 RDTITL> * VAN DER WAALS = -30.1258 ELECTROSTATIC = -45.578 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4383" Parameter: CONF_N -> "8002" Comparing "4383" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4384" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765362 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760673 ATOM PAIRS WERE FOUND FOR ATOM LIST 41644 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29147 from a total of 760673 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4384 -72.29711 -3.40664 0.70174 INTE EXTERN> -26.22907 -46.06804 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2971" Parameter: A <- "-72.2971" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2291" Parameter: B <- "-26.2291" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.068" Parameter: C <- "-46.068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4384 TOTAL ENERGY = -72.2971 RDTITL> * VAN DER WAALS = -26.2291 ELECTROSTATIC = -46.068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4384" Parameter: CONF_N -> "8002" Comparing "4384" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4385" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760673 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41581 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29011 from a total of 754586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4385 -70.70430 -1.59281 0.59209 INTE EXTERN> -31.07380 -39.63050 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7043" Parameter: A <- "-70.7043" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0738" Parameter: B <- "-31.0738" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6305" Parameter: C <- "-39.6305" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4385 TOTAL ENERGY = -70.7043 RDTITL> * VAN DER WAALS = -31.0738 ELECTROSTATIC = -39.6305 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4385" Parameter: CONF_N -> "8002" Comparing "4385" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4386" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755207 ATOM PAIRS WERE FOUND FOR ATOM LIST 41614 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29126 from a total of 755207 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4386 -70.89229 0.18799 0.59201 INTE EXTERN> -31.34027 -39.55203 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8923" Parameter: A <- "-70.8923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3403" Parameter: B <- "-31.3403" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.552" Parameter: C <- "-39.552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4386 TOTAL ENERGY = -70.8923 RDTITL> * VAN DER WAALS = -31.3403 ELECTROSTATIC = -39.552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4386" Parameter: CONF_N -> "8002" Comparing "4386" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4387" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755207 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759367 ATOM PAIRS WERE FOUND FOR ATOM LIST 41731 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28614 from a total of 759367 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4387 -79.75873 8.86643 0.62448 INTE EXTERN> -28.71408 -51.04465 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7587" Parameter: A <- "-79.7587" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7141" Parameter: B <- "-28.7141" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0447" Parameter: C <- "-51.0447" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4387 TOTAL ENERGY = -79.7587 RDTITL> * VAN DER WAALS = -28.7141 ELECTROSTATIC = -51.0447 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4387" Parameter: CONF_N -> "8002" Comparing "4387" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4388" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759367 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753394 ATOM PAIRS WERE FOUND FOR ATOM LIST 41558 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28929 from a total of 753394 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4388 -71.49171 -8.26702 0.63035 INTE EXTERN> -27.68636 -43.80535 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4917" Parameter: A <- "-71.4917" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6864" Parameter: B <- "-27.6864" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8053" Parameter: C <- "-43.8053" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4388 TOTAL ENERGY = -71.4917 RDTITL> * VAN DER WAALS = -27.6864 ELECTROSTATIC = -43.8053 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4388" Parameter: CONF_N -> "8002" Comparing "4388" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4389" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753394 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756592 ATOM PAIRS WERE FOUND FOR ATOM LIST 41663 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29310 from a total of 756592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4389 -68.28680 -3.20491 0.71676 INTE EXTERN> -20.59910 -47.68770 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2868" Parameter: A <- "-68.2868" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.5991" Parameter: B <- "-20.5991" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6877" Parameter: C <- "-47.6877" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4389 TOTAL ENERGY = -68.2868 RDTITL> * VAN DER WAALS = -20.5991 ELECTROSTATIC = -47.6877 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4389" Parameter: CONF_N -> "8002" Comparing "4389" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4390" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759800 ATOM PAIRS WERE FOUND FOR ATOM LIST 41784 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29196 from a total of 759800 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4390 -78.04167 9.75487 0.67763 INTE EXTERN> -27.99627 -50.04539 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0417" Parameter: A <- "-78.0417" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9963" Parameter: B <- "-27.9963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0454" Parameter: C <- "-50.0454" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4390 TOTAL ENERGY = -78.0417 RDTITL> * VAN DER WAALS = -27.9963 ELECTROSTATIC = -50.0454 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4390" Parameter: CONF_N -> "8002" Comparing "4390" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4391" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759800 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758215 ATOM PAIRS WERE FOUND FOR ATOM LIST 41692 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29735 from a total of 758215 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4391 -69.14231 -8.89936 0.56278 INTE EXTERN> -27.63370 -41.50861 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1423" Parameter: A <- "-69.1423" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6337" Parameter: B <- "-27.6337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5086" Parameter: C <- "-41.5086" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4391 TOTAL ENERGY = -69.1423 RDTITL> * VAN DER WAALS = -27.6337 ELECTROSTATIC = -41.5086 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4391" Parameter: CONF_N -> "8002" Comparing "4391" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4392" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758215 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755502 ATOM PAIRS WERE FOUND FOR ATOM LIST 41372 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29809 from a total of 755502 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4392 -78.46385 9.32154 0.64282 INTE EXTERN> -29.75334 -48.71051 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4638" Parameter: A <- "-78.4638" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7533" Parameter: B <- "-29.7533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7105" Parameter: C <- "-48.7105" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4392 TOTAL ENERGY = -78.4638 RDTITL> * VAN DER WAALS = -29.7533 ELECTROSTATIC = -48.7105 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4392" Parameter: CONF_N -> "8002" Comparing "4392" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4393" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755502 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758663 ATOM PAIRS WERE FOUND FOR ATOM LIST 41554 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30160 from a total of 758663 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4393 -81.04737 2.58352 0.70085 INTE EXTERN> -30.66656 -50.38081 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.0474" Parameter: A <- "-81.0474" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6666" Parameter: B <- "-30.6666" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3808" Parameter: C <- "-50.3808" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4393 TOTAL ENERGY = -81.0474 RDTITL> * VAN DER WAALS = -30.6666 ELECTROSTATIC = -50.3808 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4393" Parameter: CONF_N -> "8002" Comparing "4393" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4394" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758663 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751398 ATOM PAIRS WERE FOUND FOR ATOM LIST 41208 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29473 from a total of 751398 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4394 -76.16383 -4.88354 0.67808 INTE EXTERN> -28.29861 -47.86522 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1638" Parameter: A <- "-76.1638" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2986" Parameter: B <- "-28.2986" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8652" Parameter: C <- "-47.8652" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4394 TOTAL ENERGY = -76.1638 RDTITL> * VAN DER WAALS = -28.2986 ELECTROSTATIC = -47.8652 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4394" Parameter: CONF_N -> "8002" Comparing "4394" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4395" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751398 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755192 ATOM PAIRS WERE FOUND FOR ATOM LIST 41383 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29804 from a total of 755192 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4395 -74.52535 -1.63847 0.61339 INTE EXTERN> -29.59868 -44.92667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5254" Parameter: A <- "-74.5254" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5987" Parameter: B <- "-29.5987" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9267" Parameter: C <- "-44.9267" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4395 TOTAL ENERGY = -74.5254 RDTITL> * VAN DER WAALS = -29.5987 ELECTROSTATIC = -44.9267 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4395" Parameter: CONF_N -> "8002" Comparing "4395" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4396" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755192 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756326 ATOM PAIRS WERE FOUND FOR ATOM LIST 41576 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29797 from a total of 756326 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4396 -75.82939 1.30404 0.72474 INTE EXTERN> -27.60399 -48.22540 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8294" Parameter: A <- "-75.8294" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.604" Parameter: B <- "-27.604" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2254" Parameter: C <- "-48.2254" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4396 TOTAL ENERGY = -75.8294 RDTITL> * VAN DER WAALS = -27.604 ELECTROSTATIC = -48.2254 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4396" Parameter: CONF_N -> "8002" Comparing "4396" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4397" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756326 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753716 ATOM PAIRS WERE FOUND FOR ATOM LIST 41341 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29727 from a total of 753716 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4397 -66.55979 -9.26960 0.75091 INTE EXTERN> -23.44899 -43.11080 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5598" Parameter: A <- "-66.5598" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.449" Parameter: B <- "-23.449" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1108" Parameter: C <- "-43.1108" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4397 TOTAL ENERGY = -66.5598 RDTITL> * VAN DER WAALS = -23.449 ELECTROSTATIC = -43.1108 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4397" Parameter: CONF_N -> "8002" Comparing "4397" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4398" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753716 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759631 ATOM PAIRS WERE FOUND FOR ATOM LIST 41589 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29313 from a total of 759631 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4398 -70.66226 4.10247 0.75006 INTE EXTERN> -25.31180 -45.35046 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6623" Parameter: A <- "-70.6623" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3118" Parameter: B <- "-25.3118" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3505" Parameter: C <- "-45.3505" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4398 TOTAL ENERGY = -70.6623 RDTITL> * VAN DER WAALS = -25.3118 ELECTROSTATIC = -45.3505 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4398" Parameter: CONF_N -> "8002" Comparing "4398" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4399" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759631 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754877 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29208 from a total of 754877 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4399 -68.41276 -2.24950 0.73597 INTE EXTERN> -25.14426 -43.26850 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4128" Parameter: A <- "-68.4128" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1443" Parameter: B <- "-25.1443" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2685" Parameter: C <- "-43.2685" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4399 TOTAL ENERGY = -68.4128 RDTITL> * VAN DER WAALS = -25.1443 ELECTROSTATIC = -43.2685 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4399" Parameter: CONF_N -> "8002" Comparing "4399" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4400" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754877 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750141 ATOM PAIRS WERE FOUND FOR ATOM LIST 41400 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28759 from a total of 750141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4400 -71.07399 2.66123 0.56910 INTE EXTERN> -30.75456 -40.31942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.074" Parameter: A <- "-71.074" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7546" Parameter: B <- "-30.7546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3194" Parameter: C <- "-40.3194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4400 TOTAL ENERGY = -71.074 RDTITL> * VAN DER WAALS = -30.7546 ELECTROSTATIC = -40.3194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4400" Parameter: CONF_N -> "8002" Comparing "4400" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4401" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756512 ATOM PAIRS WERE FOUND FOR ATOM LIST 41495 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29176 from a total of 756512 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4401 -72.53113 1.45714 0.68936 INTE EXTERN> -27.18249 -45.34864 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5311" Parameter: A <- "-72.5311" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1825" Parameter: B <- "-27.1825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3486" Parameter: C <- "-45.3486" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4401 TOTAL ENERGY = -72.5311 RDTITL> * VAN DER WAALS = -27.1825 ELECTROSTATIC = -45.3486 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4401" Parameter: CONF_N -> "8002" Comparing "4401" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4402" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756512 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760690 ATOM PAIRS WERE FOUND FOR ATOM LIST 41768 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29383 from a total of 760690 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4402 -72.55986 0.02873 0.82317 INTE EXTERN> -20.65586 -51.90400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5599" Parameter: A <- "-72.5599" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.6559" Parameter: B <- "-20.6559" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.904" Parameter: C <- "-51.904" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4402 TOTAL ENERGY = -72.5599 RDTITL> * VAN DER WAALS = -20.6559 ELECTROSTATIC = -51.904 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4402" Parameter: CONF_N -> "8002" Comparing "4402" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4403" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760690 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757991 ATOM PAIRS WERE FOUND FOR ATOM LIST 41449 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29212 from a total of 757991 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4403 -76.58613 4.02627 0.69273 INTE EXTERN> -27.45790 -49.12823 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5861" Parameter: A <- "-76.5861" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4579" Parameter: B <- "-27.4579" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1282" Parameter: C <- "-49.1282" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4403 TOTAL ENERGY = -76.5861 RDTITL> * VAN DER WAALS = -27.4579 ELECTROSTATIC = -49.1282 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4403" Parameter: CONF_N -> "8002" Comparing "4403" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4404" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757991 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754178 ATOM PAIRS WERE FOUND FOR ATOM LIST 41362 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29173 from a total of 754178 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4404 -81.69585 5.10971 0.76771 INTE EXTERN> -26.14385 -55.55200 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6958" Parameter: A <- "-81.6958" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1438" Parameter: B <- "-26.1438" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.552" Parameter: C <- "-55.552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4404 TOTAL ENERGY = -81.6958 RDTITL> * VAN DER WAALS = -26.1438 ELECTROSTATIC = -55.552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4404" Parameter: CONF_N -> "8002" Comparing "4404" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4405" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754178 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757592 ATOM PAIRS WERE FOUND FOR ATOM LIST 41564 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29480 from a total of 757592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4405 -68.95448 -12.74137 0.63415 INTE EXTERN> -28.41360 -40.54087 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9545" Parameter: A <- "-68.9545" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4136" Parameter: B <- "-28.4136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5409" Parameter: C <- "-40.5409" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4405 TOTAL ENERGY = -68.9545 RDTITL> * VAN DER WAALS = -28.4136 ELECTROSTATIC = -40.5409 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4405" Parameter: CONF_N -> "8002" Comparing "4405" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4406" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755538 ATOM PAIRS WERE FOUND FOR ATOM LIST 41436 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29349 from a total of 755538 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4406 -82.49960 13.54512 0.78145 INTE EXTERN> -25.95898 -56.54062 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.4996" Parameter: A <- "-82.4996" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.959" Parameter: B <- "-25.959" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.5406" Parameter: C <- "-56.5406" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4406 TOTAL ENERGY = -82.4996 RDTITL> * VAN DER WAALS = -25.959 ELECTROSTATIC = -56.5406 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4406" Parameter: CONF_N -> "8002" Comparing "4406" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4407" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755538 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758026 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29181 from a total of 758026 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4407 -73.58734 -8.91226 0.68681 INTE EXTERN> -28.61766 -44.96968 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5873" Parameter: A <- "-73.5873" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6177" Parameter: B <- "-28.6177" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9697" Parameter: C <- "-44.9697" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4407 TOTAL ENERGY = -73.5873 RDTITL> * VAN DER WAALS = -28.6177 ELECTROSTATIC = -44.9697 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4407" Parameter: CONF_N -> "8002" Comparing "4407" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4408" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758026 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754972 ATOM PAIRS WERE FOUND FOR ATOM LIST 41524 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29092 from a total of 754972 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4408 -73.17846 -0.40888 0.73585 INTE EXTERN> -24.66169 -48.51678 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1785" Parameter: A <- "-73.1785" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6617" Parameter: B <- "-24.6617" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5168" Parameter: C <- "-48.5168" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4408 TOTAL ENERGY = -73.1785 RDTITL> * VAN DER WAALS = -24.6617 ELECTROSTATIC = -48.5168 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4408" Parameter: CONF_N -> "8002" Comparing "4408" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4409" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754972 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758458 ATOM PAIRS WERE FOUND FOR ATOM LIST 41644 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29176 from a total of 758458 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4409 -68.45353 -4.72493 0.71409 INTE EXTERN> -23.41692 -45.03661 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4535" Parameter: A <- "-68.4535" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4169" Parameter: B <- "-23.4169" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0366" Parameter: C <- "-45.0366" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4409 TOTAL ENERGY = -68.4535 RDTITL> * VAN DER WAALS = -23.4169 ELECTROSTATIC = -45.0366 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4409" Parameter: CONF_N -> "8002" Comparing "4409" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4410" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758458 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759830 ATOM PAIRS WERE FOUND FOR ATOM LIST 41688 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29672 from a total of 759830 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4410 -79.69442 11.24089 0.62653 INTE EXTERN> -30.20100 -49.49342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6944" Parameter: A <- "-79.6944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.201" Parameter: B <- "-30.201" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4934" Parameter: C <- "-49.4934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4410 TOTAL ENERGY = -79.6944 RDTITL> * VAN DER WAALS = -30.201 ELECTROSTATIC = -49.4934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4410" Parameter: CONF_N -> "8002" Comparing "4410" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4411" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759830 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759333 ATOM PAIRS WERE FOUND FOR ATOM LIST 41716 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29201 from a total of 759333 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4411 -77.55655 -2.13788 0.75370 INTE EXTERN> -25.97296 -51.58358 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5565" Parameter: A <- "-77.5565" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.973" Parameter: B <- "-25.973" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5836" Parameter: C <- "-51.5836" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4411 TOTAL ENERGY = -77.5565 RDTITL> * VAN DER WAALS = -25.973 ELECTROSTATIC = -51.5836 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4411" Parameter: CONF_N -> "8002" Comparing "4411" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4412" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759333 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762223 ATOM PAIRS WERE FOUND FOR ATOM LIST 41748 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29345 from a total of 762223 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4412 -78.46288 0.90634 0.64679 INTE EXTERN> -29.76726 -48.69562 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4629" Parameter: A <- "-78.4629" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7673" Parameter: B <- "-29.7673" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6956" Parameter: C <- "-48.6956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4412 TOTAL ENERGY = -78.4629 RDTITL> * VAN DER WAALS = -29.7673 ELECTROSTATIC = -48.6956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4412" Parameter: CONF_N -> "8002" Comparing "4412" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4413" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762223 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760347 ATOM PAIRS WERE FOUND FOR ATOM LIST 41743 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29247 from a total of 760347 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4413 -75.24013 -3.22275 0.73683 INTE EXTERN> -25.17347 -50.06666 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2401" Parameter: A <- "-75.2401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1735" Parameter: B <- "-25.1735" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0667" Parameter: C <- "-50.0667" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4413 TOTAL ENERGY = -75.2401 RDTITL> * VAN DER WAALS = -25.1735 ELECTROSTATIC = -50.0667 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4413" Parameter: CONF_N -> "8002" Comparing "4413" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4414" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760347 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749468 ATOM PAIRS WERE FOUND FOR ATOM LIST 41158 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28314 from a total of 749468 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4414 -75.04062 -0.19951 0.56745 INTE EXTERN> -30.59185 -44.44877 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0406" Parameter: A <- "-75.0406" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5919" Parameter: B <- "-30.5919" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4488" Parameter: C <- "-44.4488" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4414 TOTAL ENERGY = -75.0406 RDTITL> * VAN DER WAALS = -30.5919 ELECTROSTATIC = -44.4488 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4414" Parameter: CONF_N -> "8002" Comparing "4414" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4415" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749468 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759175 ATOM PAIRS WERE FOUND FOR ATOM LIST 41418 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29410 from a total of 759175 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4415 -70.41091 -4.62971 0.55888 INTE EXTERN> -32.39603 -38.01488 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4109" Parameter: A <- "-70.4109" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.396" Parameter: B <- "-32.396" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0149" Parameter: C <- "-38.0149" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4415 TOTAL ENERGY = -70.4109 RDTITL> * VAN DER WAALS = -32.396 ELECTROSTATIC = -38.0149 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4415" Parameter: CONF_N -> "8002" Comparing "4415" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4416" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759175 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753955 ATOM PAIRS WERE FOUND FOR ATOM LIST 41290 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28482 from a total of 753955 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4416 -70.11919 -0.29172 0.65203 INTE EXTERN> -26.39554 -43.72364 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1192" Parameter: A <- "-70.1192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3955" Parameter: B <- "-26.3955" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7236" Parameter: C <- "-43.7236" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4416 TOTAL ENERGY = -70.1192 RDTITL> * VAN DER WAALS = -26.3955 ELECTROSTATIC = -43.7236 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4416" Parameter: CONF_N -> "8002" Comparing "4416" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4417" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753955 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757382 ATOM PAIRS WERE FOUND FOR ATOM LIST 41558 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29182 from a total of 757382 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4417 -74.86601 4.74683 0.75710 INTE EXTERN> -24.50663 -50.35938 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.866" Parameter: A <- "-74.866" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5066" Parameter: B <- "-24.5066" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3594" Parameter: C <- "-50.3594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4417 TOTAL ENERGY = -74.866 RDTITL> * VAN DER WAALS = -24.5066 ELECTROSTATIC = -50.3594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4417" Parameter: CONF_N -> "8002" Comparing "4417" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4418" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757382 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755467 ATOM PAIRS WERE FOUND FOR ATOM LIST 41269 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28519 from a total of 755467 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4418 -68.16206 -6.70395 0.60185 INTE EXTERN> -26.16470 -41.99736 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1621" Parameter: A <- "-68.1621" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1647" Parameter: B <- "-26.1647" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9974" Parameter: C <- "-41.9974" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4418 TOTAL ENERGY = -68.1621 RDTITL> * VAN DER WAALS = -26.1647 ELECTROSTATIC = -41.9974 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4418" Parameter: CONF_N -> "8002" Comparing "4418" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4419" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755467 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753665 ATOM PAIRS WERE FOUND FOR ATOM LIST 41367 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28359 from a total of 753665 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4419 -73.38807 5.22600 0.62748 INTE EXTERN> -27.10665 -46.28142 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3881" Parameter: A <- "-73.3881" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1066" Parameter: B <- "-27.1066" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2814" Parameter: C <- "-46.2814" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4419 TOTAL ENERGY = -73.3881 RDTITL> * VAN DER WAALS = -27.1066 ELECTROSTATIC = -46.2814 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4419" Parameter: CONF_N -> "8002" Comparing "4419" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4420" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753665 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756338 ATOM PAIRS WERE FOUND FOR ATOM LIST 41454 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29291 from a total of 756338 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4420 -70.82004 -2.56803 0.64305 INTE EXTERN> -30.44741 -40.37263 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.82" Parameter: A <- "-70.82" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4474" Parameter: B <- "-30.4474" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3726" Parameter: C <- "-40.3726" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4420 TOTAL ENERGY = -70.82 RDTITL> * VAN DER WAALS = -30.4474 ELECTROSTATIC = -40.3726 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4420" Parameter: CONF_N -> "8002" Comparing "4420" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4421" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756338 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749731 ATOM PAIRS WERE FOUND FOR ATOM LIST 41136 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28331 from a total of 749731 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4421 -74.47370 3.65366 0.70929 INTE EXTERN> -26.25362 -48.22008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4737" Parameter: A <- "-74.4737" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2536" Parameter: B <- "-26.2536" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2201" Parameter: C <- "-48.2201" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4421 TOTAL ENERGY = -74.4737 RDTITL> * VAN DER WAALS = -26.2536 ELECTROSTATIC = -48.2201 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4421" Parameter: CONF_N -> "8002" Comparing "4421" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4422" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749731 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753643 ATOM PAIRS WERE FOUND FOR ATOM LIST 41363 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29104 from a total of 753643 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4422 -72.71814 -1.75556 0.53510 INTE EXTERN> -31.26597 -41.45217 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7181" Parameter: A <- "-72.7181" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.266" Parameter: B <- "-31.266" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4522" Parameter: C <- "-41.4522" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4422 TOTAL ENERGY = -72.7181 RDTITL> * VAN DER WAALS = -31.266 ELECTROSTATIC = -41.4522 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4422" Parameter: CONF_N -> "8002" Comparing "4422" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4423" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753643 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759640 ATOM PAIRS WERE FOUND FOR ATOM LIST 41627 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29305 from a total of 759640 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4423 -68.24635 -4.47179 0.53339 INTE EXTERN> -33.09680 -35.14955 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2464" Parameter: A <- "-68.2464" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0968" Parameter: B <- "-33.0968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1496" Parameter: C <- "-35.1496" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4423 TOTAL ENERGY = -68.2464 RDTITL> * VAN DER WAALS = -33.0968 ELECTROSTATIC = -35.1496 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4423" Parameter: CONF_N -> "8002" Comparing "4423" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4424" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759640 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752530 ATOM PAIRS WERE FOUND FOR ATOM LIST 41090 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28831 from a total of 752530 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4424 -66.88726 -1.35909 0.70654 INTE EXTERN> -23.66636 -43.22090 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8873" Parameter: A <- "-66.8873" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6664" Parameter: B <- "-23.6664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2209" Parameter: C <- "-43.2209" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4424 TOTAL ENERGY = -66.8873 RDTITL> * VAN DER WAALS = -23.6664 ELECTROSTATIC = -43.2209 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4424" Parameter: CONF_N -> "8002" Comparing "4424" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4425" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752530 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749297 ATOM PAIRS WERE FOUND FOR ATOM LIST 41095 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28841 from a total of 749297 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4425 -64.93454 -1.95273 0.50594 INTE EXTERN> -32.01248 -32.92206 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9345" Parameter: A <- "-64.9345" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0125" Parameter: B <- "-32.0125" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.9221" Parameter: C <- "-32.9221" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4425 TOTAL ENERGY = -64.9345 RDTITL> * VAN DER WAALS = -32.0125 ELECTROSTATIC = -32.9221 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4425" Parameter: CONF_N -> "8002" Comparing "4425" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4426" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749297 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755128 ATOM PAIRS WERE FOUND FOR ATOM LIST 41333 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28797 from a total of 755128 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4426 -73.81179 8.87726 0.67213 INTE EXTERN> -27.06414 -46.74765 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8118" Parameter: A <- "-73.8118" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0641" Parameter: B <- "-27.0641" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7477" Parameter: C <- "-46.7477" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4426 TOTAL ENERGY = -73.8118 RDTITL> * VAN DER WAALS = -27.0641 ELECTROSTATIC = -46.7477 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4426" Parameter: CONF_N -> "8002" Comparing "4426" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4427" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755128 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759552 ATOM PAIRS WERE FOUND FOR ATOM LIST 41564 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29026 from a total of 759552 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4427 -74.34550 0.53371 0.67282 INTE EXTERN> -27.38061 -46.96489 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3455" Parameter: A <- "-74.3455" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3806" Parameter: B <- "-27.3806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9649" Parameter: C <- "-46.9649" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4427 TOTAL ENERGY = -74.3455 RDTITL> * VAN DER WAALS = -27.3806 ELECTROSTATIC = -46.9649 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4427" Parameter: CONF_N -> "8002" Comparing "4427" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4428" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759552 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756251 ATOM PAIRS WERE FOUND FOR ATOM LIST 41337 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29155 from a total of 756251 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4428 -70.27147 -4.07403 0.56065 INTE EXTERN> -29.98554 -40.28593 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2715" Parameter: A <- "-70.2715" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9855" Parameter: B <- "-29.9855" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2859" Parameter: C <- "-40.2859" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4428 TOTAL ENERGY = -70.2715 RDTITL> * VAN DER WAALS = -29.9855 ELECTROSTATIC = -40.2859 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4428" Parameter: CONF_N -> "8002" Comparing "4428" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4429" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756251 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752018 ATOM PAIRS WERE FOUND FOR ATOM LIST 41089 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28625 from a total of 752018 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4429 -70.08930 -0.18218 0.57411 INTE EXTERN> -29.63552 -40.45377 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0893" Parameter: A <- "-70.0893" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6355" Parameter: B <- "-29.6355" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4538" Parameter: C <- "-40.4538" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4429 TOTAL ENERGY = -70.0893 RDTITL> * VAN DER WAALS = -29.6355 ELECTROSTATIC = -40.4538 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4429" Parameter: CONF_N -> "8002" Comparing "4429" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4430" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752018 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751248 ATOM PAIRS WERE FOUND FOR ATOM LIST 41215 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29014 from a total of 751248 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4430 -72.63329 2.54400 0.72013 INTE EXTERN> -25.74310 -46.89019 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6333" Parameter: A <- "-72.6333" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7431" Parameter: B <- "-25.7431" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8902" Parameter: C <- "-46.8902" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4430 TOTAL ENERGY = -72.6333 RDTITL> * VAN DER WAALS = -25.7431 ELECTROSTATIC = -46.8902 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4430" Parameter: CONF_N -> "8002" Comparing "4430" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4431" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751248 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754224 ATOM PAIRS WERE FOUND FOR ATOM LIST 41447 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29366 from a total of 754224 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4431 -72.02011 -0.61319 0.63567 INTE EXTERN> -26.90880 -45.11130 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0201" Parameter: A <- "-72.0201" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9088" Parameter: B <- "-26.9088" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1113" Parameter: C <- "-45.1113" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4431 TOTAL ENERGY = -72.0201 RDTITL> * VAN DER WAALS = -26.9088 ELECTROSTATIC = -45.1113 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4431" Parameter: CONF_N -> "8002" Comparing "4431" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4432" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754224 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749566 ATOM PAIRS WERE FOUND FOR ATOM LIST 41252 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28501 from a total of 749566 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4432 -72.16390 0.14380 0.66324 INTE EXTERN> -25.74197 -46.42194 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1639" Parameter: A <- "-72.1639" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.742" Parameter: B <- "-25.742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4219" Parameter: C <- "-46.4219" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4432 TOTAL ENERGY = -72.1639 RDTITL> * VAN DER WAALS = -25.742 ELECTROSTATIC = -46.4219 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4432" Parameter: CONF_N -> "8002" Comparing "4432" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4433" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749566 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754092 ATOM PAIRS WERE FOUND FOR ATOM LIST 41206 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29078 from a total of 754092 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4433 -74.34095 2.17704 0.59906 INTE EXTERN> -31.40892 -42.93203 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3409" Parameter: A <- "-74.3409" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4089" Parameter: B <- "-31.4089" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.932" Parameter: C <- "-42.932" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4433 TOTAL ENERGY = -74.3409 RDTITL> * VAN DER WAALS = -31.4089 ELECTROSTATIC = -42.932 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4433" Parameter: CONF_N -> "8002" Comparing "4433" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4434" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754092 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749527 ATOM PAIRS WERE FOUND FOR ATOM LIST 41122 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28946 from a total of 749527 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4434 -65.99593 -8.34501 0.60094 INTE EXTERN> -28.11817 -37.87776 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9959" Parameter: A <- "-65.9959" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1182" Parameter: B <- "-28.1182" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8778" Parameter: C <- "-37.8778" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4434 TOTAL ENERGY = -65.9959 RDTITL> * VAN DER WAALS = -28.1182 ELECTROSTATIC = -37.8778 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4434" Parameter: CONF_N -> "8002" Comparing "4434" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4435" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749527 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752020 ATOM PAIRS WERE FOUND FOR ATOM LIST 41375 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29309 from a total of 752020 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4435 -73.54411 7.54817 0.59063 INTE EXTERN> -30.73681 -42.80729 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5441" Parameter: A <- "-73.5441" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7368" Parameter: B <- "-30.7368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8073" Parameter: C <- "-42.8073" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4435 TOTAL ENERGY = -73.5441 RDTITL> * VAN DER WAALS = -30.7368 ELECTROSTATIC = -42.8073 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4435" Parameter: CONF_N -> "8002" Comparing "4435" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4436" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752020 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751738 ATOM PAIRS WERE FOUND FOR ATOM LIST 41284 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29155 from a total of 751738 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4436 -74.86552 1.32141 0.67126 INTE EXTERN> -26.69247 -48.17305 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8655" Parameter: A <- "-74.8655" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6925" Parameter: B <- "-26.6925" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.173" Parameter: C <- "-48.173" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4436 TOTAL ENERGY = -74.8655 RDTITL> * VAN DER WAALS = -26.6925 ELECTROSTATIC = -48.173 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4436" Parameter: CONF_N -> "8002" Comparing "4436" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4437" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751738 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757490 ATOM PAIRS WERE FOUND FOR ATOM LIST 41500 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29646 from a total of 757490 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4437 -79.05125 4.18574 0.73752 INTE EXTERN> -25.37954 -53.67171 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0513" Parameter: A <- "-79.0513" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3795" Parameter: B <- "-25.3795" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6717" Parameter: C <- "-53.6717" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4437 TOTAL ENERGY = -79.0513 RDTITL> * VAN DER WAALS = -25.3795 ELECTROSTATIC = -53.6717 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4437" Parameter: CONF_N -> "8002" Comparing "4437" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4438" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757490 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762386 ATOM PAIRS WERE FOUND FOR ATOM LIST 41826 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29955 from a total of 762386 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4438 -72.57637 -6.47488 0.65354 INTE EXTERN> -29.39441 -43.18196 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5764" Parameter: A <- "-72.5764" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3944" Parameter: B <- "-29.3944" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.182" Parameter: C <- "-43.182" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4438 TOTAL ENERGY = -72.5764 RDTITL> * VAN DER WAALS = -29.3944 ELECTROSTATIC = -43.182 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4438" Parameter: CONF_N -> "8002" Comparing "4438" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4439" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762386 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754311 ATOM PAIRS WERE FOUND FOR ATOM LIST 41259 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29775 from a total of 754311 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4439 -74.26900 1.69262 0.57346 INTE EXTERN> -33.28401 -40.98498 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.269" Parameter: A <- "-74.269" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.284" Parameter: B <- "-33.284" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.985" Parameter: C <- "-40.985" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4439 TOTAL ENERGY = -74.269 RDTITL> * VAN DER WAALS = -33.284 ELECTROSTATIC = -40.985 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4439" Parameter: CONF_N -> "8002" Comparing "4439" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4440" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754311 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746875 ATOM PAIRS WERE FOUND FOR ATOM LIST 41025 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29162 from a total of 746875 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4440 -73.43969 -0.82930 0.54908 INTE EXTERN> -32.00739 -41.43231 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4397" Parameter: A <- "-73.4397" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0074" Parameter: B <- "-32.0074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4323" Parameter: C <- "-41.4323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4440 TOTAL ENERGY = -73.4397 RDTITL> * VAN DER WAALS = -32.0074 ELECTROSTATIC = -41.4323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4440" Parameter: CONF_N -> "8002" Comparing "4440" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4441" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746875 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757907 ATOM PAIRS WERE FOUND FOR ATOM LIST 41494 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30260 from a total of 757907 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4441 -78.90546 5.46577 0.69574 INTE EXTERN> -29.52154 -49.38392 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9055" Parameter: A <- "-78.9055" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5215" Parameter: B <- "-29.5215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3839" Parameter: C <- "-49.3839" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4441 TOTAL ENERGY = -78.9055 RDTITL> * VAN DER WAALS = -29.5215 ELECTROSTATIC = -49.3839 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4441" Parameter: CONF_N -> "8002" Comparing "4441" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4442" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757907 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752744 ATOM PAIRS WERE FOUND FOR ATOM LIST 41441 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30241 from a total of 752744 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4442 -74.61437 -4.29109 0.63644 INTE EXTERN> -30.92737 -43.68700 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6144" Parameter: A <- "-74.6144" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9274" Parameter: B <- "-30.9274" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.687" Parameter: C <- "-43.687" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4442 TOTAL ENERGY = -74.6144 RDTITL> * VAN DER WAALS = -30.9274 ELECTROSTATIC = -43.687 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4442" Parameter: CONF_N -> "8002" Comparing "4442" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4443" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752744 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752467 ATOM PAIRS WERE FOUND FOR ATOM LIST 41281 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30053 from a total of 752467 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4443 -75.54434 0.92997 0.64530 INTE EXTERN> -28.48684 -47.05750 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5443" Parameter: A <- "-75.5443" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4868" Parameter: B <- "-28.4868" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0575" Parameter: C <- "-47.0575" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4443 TOTAL ENERGY = -75.5443 RDTITL> * VAN DER WAALS = -28.4868 ELECTROSTATIC = -47.0575 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4443" Parameter: CONF_N -> "8002" Comparing "4443" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4444" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752467 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755364 ATOM PAIRS WERE FOUND FOR ATOM LIST 41238 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30148 from a total of 755364 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4444 -76.88375 1.33941 0.63660 INTE EXTERN> -28.51970 -48.36406 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8838" Parameter: A <- "-76.8838" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5197" Parameter: B <- "-28.5197" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3641" Parameter: C <- "-48.3641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4444 TOTAL ENERGY = -76.8838 RDTITL> * VAN DER WAALS = -28.5197 ELECTROSTATIC = -48.3641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4444" Parameter: CONF_N -> "8002" Comparing "4444" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4445" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755364 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752915 ATOM PAIRS WERE FOUND FOR ATOM LIST 41318 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29529 from a total of 752915 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4445 -73.01521 -3.86854 0.50881 INTE EXTERN> -33.40097 -39.61424 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0152" Parameter: A <- "-73.0152" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.401" Parameter: B <- "-33.401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6142" Parameter: C <- "-39.6142" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4445 TOTAL ENERGY = -73.0152 RDTITL> * VAN DER WAALS = -33.401 ELECTROSTATIC = -39.6142 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4445" Parameter: CONF_N -> "8002" Comparing "4445" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4446" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752915 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754486 ATOM PAIRS WERE FOUND FOR ATOM LIST 41317 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30008 from a total of 754486 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4446 -75.13034 2.11513 0.58715 INTE EXTERN> -32.69501 -42.43533 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1303" Parameter: A <- "-75.1303" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.695" Parameter: B <- "-32.695" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4353" Parameter: C <- "-42.4353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4446 TOTAL ENERGY = -75.1303 RDTITL> * VAN DER WAALS = -32.695 ELECTROSTATIC = -42.4353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4446" Parameter: CONF_N -> "8002" Comparing "4446" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4447" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754486 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757655 ATOM PAIRS WERE FOUND FOR ATOM LIST 41567 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30002 from a total of 757655 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4447 -71.94817 -3.18217 0.76843 INTE EXTERN> -26.42289 -45.52528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9482" Parameter: A <- "-71.9482" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4229" Parameter: B <- "-26.4229" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5253" Parameter: C <- "-45.5253" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4447 TOTAL ENERGY = -71.9482 RDTITL> * VAN DER WAALS = -26.4229 ELECTROSTATIC = -45.5253 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4447" Parameter: CONF_N -> "8002" Comparing "4447" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4448" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757655 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755582 ATOM PAIRS WERE FOUND FOR ATOM LIST 41548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30300 from a total of 755582 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4448 -75.99119 4.04301 0.70816 INTE EXTERN> -28.97631 -47.01488 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9912" Parameter: A <- "-75.9912" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9763" Parameter: B <- "-28.9763" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0149" Parameter: C <- "-47.0149" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4448 TOTAL ENERGY = -75.9912 RDTITL> * VAN DER WAALS = -28.9763 ELECTROSTATIC = -47.0149 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4448" Parameter: CONF_N -> "8002" Comparing "4448" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4449" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755582 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756271 ATOM PAIRS WERE FOUND FOR ATOM LIST 41484 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29904 from a total of 756271 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4449 -75.45796 -0.53322 0.54604 INTE EXTERN> -35.34586 -40.11210 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.458" Parameter: A <- "-75.458" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.3459" Parameter: B <- "-35.3459" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1121" Parameter: C <- "-40.1121" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4449 TOTAL ENERGY = -75.458 RDTITL> * VAN DER WAALS = -35.3459 ELECTROSTATIC = -40.1121 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4449" Parameter: CONF_N -> "8002" Comparing "4449" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4450" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756271 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757401 ATOM PAIRS WERE FOUND FOR ATOM LIST 41678 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30093 from a total of 757401 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4450 -74.71960 -0.73836 0.63749 INTE EXTERN> -31.34864 -43.37096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7196" Parameter: A <- "-74.7196" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3486" Parameter: B <- "-31.3486" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.371" Parameter: C <- "-43.371" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4450 TOTAL ENERGY = -74.7196 RDTITL> * VAN DER WAALS = -31.3486 ELECTROSTATIC = -43.371 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4450" Parameter: CONF_N -> "8002" Comparing "4450" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4451" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757401 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766020 ATOM PAIRS WERE FOUND FOR ATOM LIST 42011 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30559 from a total of 766020 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4451 -76.21987 1.50027 0.70593 INTE EXTERN> -26.96696 -49.25291 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2199" Parameter: A <- "-76.2199" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.967" Parameter: B <- "-26.967" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2529" Parameter: C <- "-49.2529" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4451 TOTAL ENERGY = -76.2199 RDTITL> * VAN DER WAALS = -26.967 ELECTROSTATIC = -49.2529 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4451" Parameter: CONF_N -> "8002" Comparing "4451" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4452" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766020 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761016 ATOM PAIRS WERE FOUND FOR ATOM LIST 41836 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29883 from a total of 761016 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4452 -75.36457 -0.85531 0.68693 INTE EXTERN> -30.38602 -44.97854 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3646" Parameter: A <- "-75.3646" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.386" Parameter: B <- "-30.386" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9785" Parameter: C <- "-44.9785" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4452 TOTAL ENERGY = -75.3646 RDTITL> * VAN DER WAALS = -30.386 ELECTROSTATIC = -44.9785 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4452" Parameter: CONF_N -> "8002" Comparing "4452" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4453" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761016 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756025 ATOM PAIRS WERE FOUND FOR ATOM LIST 41457 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29822 from a total of 756025 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4453 -77.13766 1.77310 0.66865 INTE EXTERN> -29.04984 -48.08782 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1377" Parameter: A <- "-77.1377" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0498" Parameter: B <- "-29.0498" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0878" Parameter: C <- "-48.0878" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4453 TOTAL ENERGY = -77.1377 RDTITL> * VAN DER WAALS = -29.0498 ELECTROSTATIC = -48.0878 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4453" Parameter: CONF_N -> "8002" Comparing "4453" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4454" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756025 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758068 ATOM PAIRS WERE FOUND FOR ATOM LIST 41684 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29331 from a total of 758068 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4454 -71.23938 -5.89828 0.56107 INTE EXTERN> -31.35336 -39.88602 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2394" Parameter: A <- "-71.2394" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3534" Parameter: B <- "-31.3534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.886" Parameter: C <- "-39.886" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4454 TOTAL ENERGY = -71.2394 RDTITL> * VAN DER WAALS = -31.3534 ELECTROSTATIC = -39.886 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4454" Parameter: CONF_N -> "8002" Comparing "4454" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4455" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758068 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760682 ATOM PAIRS WERE FOUND FOR ATOM LIST 41885 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29876 from a total of 760682 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4455 -75.62390 4.38451 0.66122 INTE EXTERN> -28.34533 -47.27856 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6239" Parameter: A <- "-75.6239" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3453" Parameter: B <- "-28.3453" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2786" Parameter: C <- "-47.2786" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4455 TOTAL ENERGY = -75.6239 RDTITL> * VAN DER WAALS = -28.3453 ELECTROSTATIC = -47.2786 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4455" Parameter: CONF_N -> "8002" Comparing "4455" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4456" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760682 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41867 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29632 from a total of 759586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4456 -80.74027 5.11637 0.63988 INTE EXTERN> -29.97734 -50.76293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7403" Parameter: A <- "-80.7403" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9773" Parameter: B <- "-29.9773" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7629" Parameter: C <- "-50.7629" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4456 TOTAL ENERGY = -80.7403 RDTITL> * VAN DER WAALS = -29.9773 ELECTROSTATIC = -50.7629 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4456" Parameter: CONF_N -> "8002" Comparing "4456" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4457" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759191 ATOM PAIRS WERE FOUND FOR ATOM LIST 41694 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29508 from a total of 759191 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4457 -79.03993 -1.70034 0.61617 INTE EXTERN> -33.65288 -45.38705 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0399" Parameter: A <- "-79.0399" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6529" Parameter: B <- "-33.6529" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.387" Parameter: C <- "-45.387" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4457 TOTAL ENERGY = -79.0399 RDTITL> * VAN DER WAALS = -33.6529 ELECTROSTATIC = -45.387 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4457" Parameter: CONF_N -> "8002" Comparing "4457" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4458" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759191 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755508 ATOM PAIRS WERE FOUND FOR ATOM LIST 41388 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29905 from a total of 755508 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4458 -80.92190 1.88197 0.77187 INTE EXTERN> -26.23903 -54.68287 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9219" Parameter: A <- "-80.9219" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.239" Parameter: B <- "-26.239" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.6829" Parameter: C <- "-54.6829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4458 TOTAL ENERGY = -80.9219 RDTITL> * VAN DER WAALS = -26.239 ELECTROSTATIC = -54.6829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4458" Parameter: CONF_N -> "8002" Comparing "4458" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4459" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755508 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757510 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29874 from a total of 757510 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4459 -75.94596 -4.97594 0.68566 INTE EXTERN> -27.78655 -48.15941 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.946" Parameter: A <- "-75.946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7866" Parameter: B <- "-27.7866" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1594" Parameter: C <- "-48.1594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4459 TOTAL ENERGY = -75.946 RDTITL> * VAN DER WAALS = -27.7866 ELECTROSTATIC = -48.1594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4459" Parameter: CONF_N -> "8002" Comparing "4459" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4460" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757510 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758007 ATOM PAIRS WERE FOUND FOR ATOM LIST 41669 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29359 from a total of 758007 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4460 -76.31520 0.36923 0.53377 INTE EXTERN> -31.38490 -44.93030 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3152" Parameter: A <- "-76.3152" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3849" Parameter: B <- "-31.3849" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9303" Parameter: C <- "-44.9303" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4460 TOTAL ENERGY = -76.3152 RDTITL> * VAN DER WAALS = -31.3849 ELECTROSTATIC = -44.9303 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4460" Parameter: CONF_N -> "8002" Comparing "4460" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4461" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758007 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758701 ATOM PAIRS WERE FOUND FOR ATOM LIST 41826 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30007 from a total of 758701 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4461 -81.69749 5.38230 0.72229 INTE EXTERN> -29.70743 -51.99007 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6975" Parameter: A <- "-81.6975" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7074" Parameter: B <- "-29.7074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.9901" Parameter: C <- "-51.9901" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4461 TOTAL ENERGY = -81.6975 RDTITL> * VAN DER WAALS = -29.7074 ELECTROSTATIC = -51.9901 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4461" Parameter: CONF_N -> "8002" Comparing "4461" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4462" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758701 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762722 ATOM PAIRS WERE FOUND FOR ATOM LIST 41804 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29794 from a total of 762722 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4462 -76.31390 -5.38360 0.67035 INTE EXTERN> -26.83363 -49.48027 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3139" Parameter: A <- "-76.3139" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8336" Parameter: B <- "-26.8336" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4803" Parameter: C <- "-49.4803" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4462 TOTAL ENERGY = -76.3139 RDTITL> * VAN DER WAALS = -26.8336 ELECTROSTATIC = -49.4803 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4462" Parameter: CONF_N -> "8002" Comparing "4462" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4463" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762722 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760954 ATOM PAIRS WERE FOUND FOR ATOM LIST 41760 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29602 from a total of 760954 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4463 -73.27582 -3.03808 0.65045 INTE EXTERN> -27.89346 -45.38236 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2758" Parameter: A <- "-73.2758" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8935" Parameter: B <- "-27.8935" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3824" Parameter: C <- "-45.3824" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4463 TOTAL ENERGY = -73.2758 RDTITL> * VAN DER WAALS = -27.8935 ELECTROSTATIC = -45.3824 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4463" Parameter: CONF_N -> "8002" Comparing "4463" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4464" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760954 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757700 ATOM PAIRS WERE FOUND FOR ATOM LIST 41500 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29648 from a total of 757700 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4464 -74.10980 0.83398 0.64485 INTE EXTERN> -29.07440 -45.03540 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1098" Parameter: A <- "-74.1098" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0744" Parameter: B <- "-29.0744" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0354" Parameter: C <- "-45.0354" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4464 TOTAL ENERGY = -74.1098 RDTITL> * VAN DER WAALS = -29.0744 ELECTROSTATIC = -45.0354 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4464" Parameter: CONF_N -> "8002" Comparing "4464" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4465" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757700 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760478 ATOM PAIRS WERE FOUND FOR ATOM LIST 41802 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29576 from a total of 760478 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4465 -75.65620 1.54640 0.72298 INTE EXTERN> -27.49044 -48.16576 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6562" Parameter: A <- "-75.6562" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4904" Parameter: B <- "-27.4904" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1658" Parameter: C <- "-48.1658" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4465 TOTAL ENERGY = -75.6562 RDTITL> * VAN DER WAALS = -27.4904 ELECTROSTATIC = -48.1658 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4465" Parameter: CONF_N -> "8002" Comparing "4465" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4466" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760478 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757542 ATOM PAIRS WERE FOUND FOR ATOM LIST 41655 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28855 from a total of 757542 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4466 -67.05435 -8.60185 0.62755 INTE EXTERN> -27.43095 -39.62339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0543" Parameter: A <- "-67.0543" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.431" Parameter: B <- "-27.431" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6234" Parameter: C <- "-39.6234" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4466 TOTAL ENERGY = -67.0543 RDTITL> * VAN DER WAALS = -27.431 ELECTROSTATIC = -39.6234 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4466" Parameter: CONF_N -> "8002" Comparing "4466" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4467" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757542 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755493 ATOM PAIRS WERE FOUND FOR ATOM LIST 41531 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29567 from a total of 755493 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4467 -72.87239 5.81804 0.61563 INTE EXTERN> -29.48096 -43.39143 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8724" Parameter: A <- "-72.8724" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.481" Parameter: B <- "-29.481" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3914" Parameter: C <- "-43.3914" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4467 TOTAL ENERGY = -72.8724 RDTITL> * VAN DER WAALS = -29.481 ELECTROSTATIC = -43.3914 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4467" Parameter: CONF_N -> "8002" Comparing "4467" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4468" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755493 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755652 ATOM PAIRS WERE FOUND FOR ATOM LIST 41444 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28960 from a total of 755652 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4468 -79.73300 6.86061 0.64523 INTE EXTERN> -31.10744 -48.62556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.733" Parameter: A <- "-79.733" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1074" Parameter: B <- "-31.1074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6256" Parameter: C <- "-48.6256" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4468 TOTAL ENERGY = -79.733 RDTITL> * VAN DER WAALS = -31.1074 ELECTROSTATIC = -48.6256 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4468" Parameter: CONF_N -> "8002" Comparing "4468" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4469" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755652 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753850 ATOM PAIRS WERE FOUND FOR ATOM LIST 41406 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29373 from a total of 753850 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4469 -77.63183 -2.10117 0.72633 INTE EXTERN> -28.18935 -49.44248 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6318" Parameter: A <- "-77.6318" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1894" Parameter: B <- "-28.1894" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4425" Parameter: C <- "-49.4425" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4469 TOTAL ENERGY = -77.6318 RDTITL> * VAN DER WAALS = -28.1894 ELECTROSTATIC = -49.4425 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4469" Parameter: CONF_N -> "8002" Comparing "4469" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4470" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753850 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41704 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28684 from a total of 759118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4470 -78.85914 1.22731 0.73582 INTE EXTERN> -27.75093 -51.10821 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8591" Parameter: A <- "-78.8591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7509" Parameter: B <- "-27.7509" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1082" Parameter: C <- "-51.1082" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4470 TOTAL ENERGY = -78.8591 RDTITL> * VAN DER WAALS = -27.7509 ELECTROSTATIC = -51.1082 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4470" Parameter: CONF_N -> "8002" Comparing "4470" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4471" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758395 ATOM PAIRS WERE FOUND FOR ATOM LIST 41656 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29029 from a total of 758395 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4471 -77.58068 -1.27846 0.63214 INTE EXTERN> -32.84908 -44.73161 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5807" Parameter: A <- "-77.5807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8491" Parameter: B <- "-32.8491" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7316" Parameter: C <- "-44.7316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4471 TOTAL ENERGY = -77.5807 RDTITL> * VAN DER WAALS = -32.8491 ELECTROSTATIC = -44.7316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4471" Parameter: CONF_N -> "8002" Comparing "4471" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4472" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758395 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751688 ATOM PAIRS WERE FOUND FOR ATOM LIST 41328 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28781 from a total of 751688 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4472 -80.95144 3.37076 0.62793 INTE EXTERN> -31.08441 -49.86703 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9514" Parameter: A <- "-80.9514" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0844" Parameter: B <- "-31.0844" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.867" Parameter: C <- "-49.867" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4472 TOTAL ENERGY = -80.9514 RDTITL> * VAN DER WAALS = -31.0844 ELECTROSTATIC = -49.867 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4472" Parameter: CONF_N -> "8002" Comparing "4472" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4473" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751688 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752111 ATOM PAIRS WERE FOUND FOR ATOM LIST 41436 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29146 from a total of 752111 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4473 -81.84034 0.88889 0.79048 INTE EXTERN> -24.57687 -57.26347 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8403" Parameter: A <- "-81.8403" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5769" Parameter: B <- "-24.5769" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.2635" Parameter: C <- "-57.2635" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4473 TOTAL ENERGY = -81.8403 RDTITL> * VAN DER WAALS = -24.5769 ELECTROSTATIC = -57.2635 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4473" Parameter: CONF_N -> "8002" Comparing "4473" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4474" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752111 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760776 ATOM PAIRS WERE FOUND FOR ATOM LIST 41674 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29874 from a total of 760776 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4474 -76.53111 -5.30922 0.70757 INTE EXTERN> -25.47318 -51.05793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5311" Parameter: A <- "-76.5311" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4732" Parameter: B <- "-25.4732" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0579" Parameter: C <- "-51.0579" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4474 TOTAL ENERGY = -76.5311 RDTITL> * VAN DER WAALS = -25.4732 ELECTROSTATIC = -51.0579 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4474" Parameter: CONF_N -> "8002" Comparing "4474" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4475" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760776 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756662 ATOM PAIRS WERE FOUND FOR ATOM LIST 41471 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29635 from a total of 756662 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4475 -68.96406 -7.56705 0.53482 INTE EXTERN> -32.84028 -36.12379 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9641" Parameter: A <- "-68.9641" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8403" Parameter: B <- "-32.8403" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1238" Parameter: C <- "-36.1238" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4475 TOTAL ENERGY = -68.9641 RDTITL> * VAN DER WAALS = -32.8403 ELECTROSTATIC = -36.1238 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4475" Parameter: CONF_N -> "8002" Comparing "4475" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4476" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756662 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752443 ATOM PAIRS WERE FOUND FOR ATOM LIST 41133 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29301 from a total of 752443 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4476 -73.38589 4.42182 0.62402 INTE EXTERN> -28.45026 -44.93563 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3859" Parameter: A <- "-73.3859" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4503" Parameter: B <- "-28.4503" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9356" Parameter: C <- "-44.9356" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4476 TOTAL ENERGY = -73.3859 RDTITL> * VAN DER WAALS = -28.4503 ELECTROSTATIC = -44.9356 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4476" Parameter: CONF_N -> "8002" Comparing "4476" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4477" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752443 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754776 ATOM PAIRS WERE FOUND FOR ATOM LIST 41411 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29388 from a total of 754776 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4477 -73.50153 0.11564 0.77717 INTE EXTERN> -24.62579 -48.87574 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5015" Parameter: A <- "-73.5015" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6258" Parameter: B <- "-24.6258" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8757" Parameter: C <- "-48.8757" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4477 TOTAL ENERGY = -73.5015 RDTITL> * VAN DER WAALS = -24.6258 ELECTROSTATIC = -48.8757 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4477" Parameter: CONF_N -> "8002" Comparing "4477" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4478" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754776 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752768 ATOM PAIRS WERE FOUND FOR ATOM LIST 41518 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29644 from a total of 752768 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4478 -72.07806 -1.42347 0.52556 INTE EXTERN> -33.01177 -39.06629 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0781" Parameter: A <- "-72.0781" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0118" Parameter: B <- "-33.0118" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0663" Parameter: C <- "-39.0663" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4478 TOTAL ENERGY = -72.0781 RDTITL> * VAN DER WAALS = -33.0118 ELECTROSTATIC = -39.0663 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4478" Parameter: CONF_N -> "8002" Comparing "4478" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4479" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752768 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756540 ATOM PAIRS WERE FOUND FOR ATOM LIST 41682 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29505 from a total of 756540 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4479 -77.41006 5.33201 0.72888 INTE EXTERN> -26.97547 -50.43459 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4101" Parameter: A <- "-77.4101" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9755" Parameter: B <- "-26.9755" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4346" Parameter: C <- "-50.4346" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4479 TOTAL ENERGY = -77.4101 RDTITL> * VAN DER WAALS = -26.9755 ELECTROSTATIC = -50.4346 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4479" Parameter: CONF_N -> "8002" Comparing "4479" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4480" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756540 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761104 ATOM PAIRS WERE FOUND FOR ATOM LIST 41496 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30208 from a total of 761104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4480 -73.95567 -3.45440 0.73101 INTE EXTERN> -27.11854 -46.83712 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9557" Parameter: A <- "-73.9557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1185" Parameter: B <- "-27.1185" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8371" Parameter: C <- "-46.8371" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4480 TOTAL ENERGY = -73.9557 RDTITL> * VAN DER WAALS = -27.1185 ELECTROSTATIC = -46.8371 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4480" Parameter: CONF_N -> "8002" Comparing "4480" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4481" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760555 ATOM PAIRS WERE FOUND FOR ATOM LIST 41693 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30112 from a total of 760555 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4481 -75.21557 1.25990 0.80090 INTE EXTERN> -22.70915 -52.50642 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2156" Parameter: A <- "-75.2156" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.7091" Parameter: B <- "-22.7091" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5064" Parameter: C <- "-52.5064" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4481 TOTAL ENERGY = -75.2156 RDTITL> * VAN DER WAALS = -22.7091 ELECTROSTATIC = -52.5064 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4481" Parameter: CONF_N -> "8002" Comparing "4481" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4482" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760555 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757461 ATOM PAIRS WERE FOUND FOR ATOM LIST 41679 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30428 from a total of 757461 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4482 -75.83522 0.61965 0.61864 INTE EXTERN> -32.31642 -43.51880 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8352" Parameter: A <- "-75.8352" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3164" Parameter: B <- "-32.3164" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5188" Parameter: C <- "-43.5188" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4482 TOTAL ENERGY = -75.8352 RDTITL> * VAN DER WAALS = -32.3164 ELECTROSTATIC = -43.5188 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4482" Parameter: CONF_N -> "8002" Comparing "4482" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4483" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757461 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749178 ATOM PAIRS WERE FOUND FOR ATOM LIST 41151 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29399 from a total of 749178 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4483 -75.13897 -0.69626 0.61406 INTE EXTERN> -29.95155 -45.18741 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.139" Parameter: A <- "-75.139" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9516" Parameter: B <- "-29.9516" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1874" Parameter: C <- "-45.1874" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4483 TOTAL ENERGY = -75.139 RDTITL> * VAN DER WAALS = -29.9516 ELECTROSTATIC = -45.1874 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4483" Parameter: CONF_N -> "8002" Comparing "4483" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4484" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749178 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759986 ATOM PAIRS WERE FOUND FOR ATOM LIST 41472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29536 from a total of 759986 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4484 -75.78334 0.64438 0.61521 INTE EXTERN> -31.96492 -43.81842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7833" Parameter: A <- "-75.7833" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9649" Parameter: B <- "-31.9649" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8184" Parameter: C <- "-43.8184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4484 TOTAL ENERGY = -75.7833 RDTITL> * VAN DER WAALS = -31.9649 ELECTROSTATIC = -43.8184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4484" Parameter: CONF_N -> "8002" Comparing "4484" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4485" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759986 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757679 ATOM PAIRS WERE FOUND FOR ATOM LIST 41466 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29411 from a total of 757679 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4485 -81.24692 5.46358 0.70865 INTE EXTERN> -27.06651 -54.18041 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.2469" Parameter: A <- "-81.2469" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0665" Parameter: B <- "-27.0665" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.1804" Parameter: C <- "-54.1804" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4485 TOTAL ENERGY = -81.2469 RDTITL> * VAN DER WAALS = -27.0665 ELECTROSTATIC = -54.1804 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4485" Parameter: CONF_N -> "8002" Comparing "4485" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4486" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757679 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759061 ATOM PAIRS WERE FOUND FOR ATOM LIST 41671 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29327 from a total of 759061 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4486 -75.38571 -5.86120 0.68623 INTE EXTERN> -27.09460 -48.29111 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3857" Parameter: A <- "-75.3857" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0946" Parameter: B <- "-27.0946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2911" Parameter: C <- "-48.2911" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4486 TOTAL ENERGY = -75.3857 RDTITL> * VAN DER WAALS = -27.0946 ELECTROSTATIC = -48.2911 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4486" Parameter: CONF_N -> "8002" Comparing "4486" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4487" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759061 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758034 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29634 from a total of 758034 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4487 -75.05354 -0.33217 0.57841 INTE EXTERN> -30.85876 -44.19478 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0535" Parameter: A <- "-75.0535" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8588" Parameter: B <- "-30.8588" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1948" Parameter: C <- "-44.1948" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4487 TOTAL ENERGY = -75.0535 RDTITL> * VAN DER WAALS = -30.8588 ELECTROSTATIC = -44.1948 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4487" Parameter: CONF_N -> "8002" Comparing "4487" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4488" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758034 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758605 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30074 from a total of 758605 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4488 -85.20954 10.15600 0.69731 INTE EXTERN> -31.43498 -53.77456 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.2095" Parameter: A <- "-85.2095" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.435" Parameter: B <- "-31.435" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.7746" Parameter: C <- "-53.7746" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4488 TOTAL ENERGY = -85.2095 RDTITL> * VAN DER WAALS = -31.435 ELECTROSTATIC = -53.7746 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4488" Parameter: CONF_N -> "8002" Comparing "4488" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4489" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758605 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761800 ATOM PAIRS WERE FOUND FOR ATOM LIST 41816 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30065 from a total of 761800 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4489 -68.43384 -16.77570 0.61102 INTE EXTERN> -32.34939 -36.08445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4338" Parameter: A <- "-68.4338" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3494" Parameter: B <- "-32.3494" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0844" Parameter: C <- "-36.0844" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4489 TOTAL ENERGY = -68.4338 RDTITL> * VAN DER WAALS = -32.3494 ELECTROSTATIC = -36.0844 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4489" Parameter: CONF_N -> "8002" Comparing "4489" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4490" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761800 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752064 ATOM PAIRS WERE FOUND FOR ATOM LIST 41398 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29864 from a total of 752064 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4490 -74.64116 6.20733 0.66741 INTE EXTERN> -28.84866 -45.79250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6412" Parameter: A <- "-74.6412" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8487" Parameter: B <- "-28.8487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7925" Parameter: C <- "-45.7925" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4490 TOTAL ENERGY = -74.6412 RDTITL> * VAN DER WAALS = -28.8487 ELECTROSTATIC = -45.7925 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4490" Parameter: CONF_N -> "8002" Comparing "4490" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4491" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752064 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751825 ATOM PAIRS WERE FOUND FOR ATOM LIST 41483 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30662 from a total of 751825 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4491 -72.99657 -1.64459 0.63550 INTE EXTERN> -32.94736 -40.04922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9966" Parameter: A <- "-72.9966" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9474" Parameter: B <- "-32.9474" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0492" Parameter: C <- "-40.0492" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4491 TOTAL ENERGY = -72.9966 RDTITL> * VAN DER WAALS = -32.9474 ELECTROSTATIC = -40.0492 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4491" Parameter: CONF_N -> "8002" Comparing "4491" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4492" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751825 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759261 ATOM PAIRS WERE FOUND FOR ATOM LIST 41657 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30227 from a total of 759261 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4492 -79.11506 6.11848 0.65573 INTE EXTERN> -28.05110 -51.06396 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1151" Parameter: A <- "-79.1151" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0511" Parameter: B <- "-28.0511" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.064" Parameter: C <- "-51.064" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4492 TOTAL ENERGY = -79.1151 RDTITL> * VAN DER WAALS = -28.0511 ELECTROSTATIC = -51.064 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4492" Parameter: CONF_N -> "8002" Comparing "4492" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4493" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759261 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756273 ATOM PAIRS WERE FOUND FOR ATOM LIST 41404 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30406 from a total of 756273 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4493 -85.86775 6.75269 0.69764 INTE EXTERN> -30.62403 -55.24371 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.8677" Parameter: A <- "-85.8677" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.624" Parameter: B <- "-30.624" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.2437" Parameter: C <- "-55.2437" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4493 TOTAL ENERGY = -85.8677 RDTITL> * VAN DER WAALS = -30.624 ELECTROSTATIC = -55.2437 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4493" Parameter: CONF_N -> "8002" Comparing "4493" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4494" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756273 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758856 ATOM PAIRS WERE FOUND FOR ATOM LIST 41729 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29840 from a total of 758856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4494 -79.62777 -6.23998 0.72182 INTE EXTERN> -30.05188 -49.57589 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6278" Parameter: A <- "-79.6278" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0519" Parameter: B <- "-30.0519" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5759" Parameter: C <- "-49.5759" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4494 TOTAL ENERGY = -79.6278 RDTITL> * VAN DER WAALS = -30.0519 ELECTROSTATIC = -49.5759 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4494" Parameter: CONF_N -> "8002" Comparing "4494" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4495" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754724 ATOM PAIRS WERE FOUND FOR ATOM LIST 41277 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30059 from a total of 754724 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4495 -76.97761 -2.65015 0.69494 INTE EXTERN> -27.93978 -49.03784 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9776" Parameter: A <- "-76.9776" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9398" Parameter: B <- "-27.9398" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0378" Parameter: C <- "-49.0378" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4495 TOTAL ENERGY = -76.9776 RDTITL> * VAN DER WAALS = -27.9398 ELECTROSTATIC = -49.0378 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4495" Parameter: CONF_N -> "8002" Comparing "4495" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4496" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754724 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750471 ATOM PAIRS WERE FOUND FOR ATOM LIST 41196 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29783 from a total of 750471 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4496 -72.38952 -4.58809 0.67777 INTE EXTERN> -29.58648 -42.80304 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3895" Parameter: A <- "-72.3895" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5865" Parameter: B <- "-29.5865" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.803" Parameter: C <- "-42.803" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4496 TOTAL ENERGY = -72.3895 RDTITL> * VAN DER WAALS = -29.5865 ELECTROSTATIC = -42.803 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4496" Parameter: CONF_N -> "8002" Comparing "4496" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4497" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750471 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751374 ATOM PAIRS WERE FOUND FOR ATOM LIST 41200 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30001 from a total of 751374 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4497 -81.88033 9.49081 0.68789 INTE EXTERN> -30.44853 -51.43181 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8803" Parameter: A <- "-81.8803" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4485" Parameter: B <- "-30.4485" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4318" Parameter: C <- "-51.4318" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4497 TOTAL ENERGY = -81.8803 RDTITL> * VAN DER WAALS = -30.4485 ELECTROSTATIC = -51.4318 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4497" Parameter: CONF_N -> "8002" Comparing "4497" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4498" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751374 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759515 ATOM PAIRS WERE FOUND FOR ATOM LIST 41573 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30198 from a total of 759515 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4498 -76.96634 -4.91399 0.65476 INTE EXTERN> -30.24457 -46.72177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9663" Parameter: A <- "-76.9663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2446" Parameter: B <- "-30.2446" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7218" Parameter: C <- "-46.7218" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4498 TOTAL ENERGY = -76.9663 RDTITL> * VAN DER WAALS = -30.2446 ELECTROSTATIC = -46.7218 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4498" Parameter: CONF_N -> "8002" Comparing "4498" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4499" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759515 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762346 ATOM PAIRS WERE FOUND FOR ATOM LIST 41923 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29900 from a total of 762346 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4499 -81.91314 4.94679 0.60877 INTE EXTERN> -32.13296 -49.78017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9131" Parameter: A <- "-81.9131" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.133" Parameter: B <- "-32.133" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7802" Parameter: C <- "-49.7802" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4499 TOTAL ENERGY = -81.9131 RDTITL> * VAN DER WAALS = -32.133 ELECTROSTATIC = -49.7802 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4499" Parameter: CONF_N -> "8002" Comparing "4499" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4500" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762346 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757974 ATOM PAIRS WERE FOUND FOR ATOM LIST 41548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29813 from a total of 757974 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4500 -67.91537 -13.99777 0.75737 INTE EXTERN> -24.83414 -43.08123 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9154" Parameter: A <- "-67.9154" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8341" Parameter: B <- "-24.8341" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0812" Parameter: C <- "-43.0812" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4500 TOTAL ENERGY = -67.9154 RDTITL> * VAN DER WAALS = -24.8341 ELECTROSTATIC = -43.0812 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4500" Parameter: CONF_N -> "8002" Comparing "4500" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4501" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757974 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761133 ATOM PAIRS WERE FOUND FOR ATOM LIST 41709 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30213 from a total of 761133 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4501 -83.56063 15.64526 0.66052 INTE EXTERN> -29.13742 -54.42320 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.5606" Parameter: A <- "-83.5606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1374" Parameter: B <- "-29.1374" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.4232" Parameter: C <- "-54.4232" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4501 TOTAL ENERGY = -83.5606 RDTITL> * VAN DER WAALS = -29.1374 ELECTROSTATIC = -54.4232 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4501" Parameter: CONF_N -> "8002" Comparing "4501" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4502" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761133 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761449 ATOM PAIRS WERE FOUND FOR ATOM LIST 41851 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30345 from a total of 761449 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4502 -77.00752 -6.55311 0.69801 INTE EXTERN> -27.74410 -49.26343 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0075" Parameter: A <- "-77.0075" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7441" Parameter: B <- "-27.7441" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2634" Parameter: C <- "-49.2634" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4502 TOTAL ENERGY = -77.0075 RDTITL> * VAN DER WAALS = -27.7441 ELECTROSTATIC = -49.2634 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4502" Parameter: CONF_N -> "8002" Comparing "4502" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4503" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761449 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754150 ATOM PAIRS WERE FOUND FOR ATOM LIST 41391 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30046 from a total of 754150 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4503 -71.21100 -5.79653 0.60943 INTE EXTERN> -29.88292 -41.32808 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.211" Parameter: A <- "-71.211" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8829" Parameter: B <- "-29.8829" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3281" Parameter: C <- "-41.3281" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4503 TOTAL ENERGY = -71.211 RDTITL> * VAN DER WAALS = -29.8829 ELECTROSTATIC = -41.3281 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4503" Parameter: CONF_N -> "8002" Comparing "4503" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4504" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754150 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763273 ATOM PAIRS WERE FOUND FOR ATOM LIST 41904 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29808 from a total of 763273 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4504 -73.55786 2.34686 0.59470 INTE EXTERN> -33.14871 -40.40914 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5579" Parameter: A <- "-73.5579" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1487" Parameter: B <- "-33.1487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4091" Parameter: C <- "-40.4091" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4504 TOTAL ENERGY = -73.5579 RDTITL> * VAN DER WAALS = -33.1487 ELECTROSTATIC = -40.4091 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4504" Parameter: CONF_N -> "8002" Comparing "4504" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4505" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763273 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757786 ATOM PAIRS WERE FOUND FOR ATOM LIST 41555 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30599 from a total of 757786 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4505 -80.29656 6.73870 0.72120 INTE EXTERN> -27.08361 -53.21295 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2966" Parameter: A <- "-80.2966" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0836" Parameter: B <- "-27.0836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.213" Parameter: C <- "-53.213" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4505 TOTAL ENERGY = -80.2966 RDTITL> * VAN DER WAALS = -27.0836 ELECTROSTATIC = -53.213 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4505" Parameter: CONF_N -> "8002" Comparing "4505" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4506" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757786 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754216 ATOM PAIRS WERE FOUND FOR ATOM LIST 41484 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29701 from a total of 754216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4506 -78.08177 -2.21479 0.63674 INTE EXTERN> -29.95034 -48.13143 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0818" Parameter: A <- "-78.0818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9503" Parameter: B <- "-29.9503" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1314" Parameter: C <- "-48.1314" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4506 TOTAL ENERGY = -78.0818 RDTITL> * VAN DER WAALS = -29.9503 ELECTROSTATIC = -48.1314 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4506" Parameter: CONF_N -> "8002" Comparing "4506" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4507" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762359 ATOM PAIRS WERE FOUND FOR ATOM LIST 41919 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30651 from a total of 762359 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4507 -84.19360 6.11183 0.69931 INTE EXTERN> -27.79273 -56.40087 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.1936" Parameter: A <- "-84.1936" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7927" Parameter: B <- "-27.7927" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.4009" Parameter: C <- "-56.4009" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4507 TOTAL ENERGY = -84.1936 RDTITL> * VAN DER WAALS = -27.7927 ELECTROSTATIC = -56.4009 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4507" Parameter: CONF_N -> "8002" Comparing "4507" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4508" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762359 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759543 ATOM PAIRS WERE FOUND FOR ATOM LIST 41650 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30653 from a total of 759543 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4508 -79.51702 -4.67658 0.65465 INTE EXTERN> -31.08768 -48.42935 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.517" Parameter: A <- "-79.517" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0877" Parameter: B <- "-31.0877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4293" Parameter: C <- "-48.4293" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4508 TOTAL ENERGY = -79.517 RDTITL> * VAN DER WAALS = -31.0877 ELECTROSTATIC = -48.4293 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4508" Parameter: CONF_N -> "8002" Comparing "4508" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4509" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759543 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764241 ATOM PAIRS WERE FOUND FOR ATOM LIST 41857 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30912 from a total of 764241 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4509 -75.92325 -3.59377 0.82674 INTE EXTERN> -23.48498 -52.43827 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9233" Parameter: A <- "-75.9233" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.485" Parameter: B <- "-23.485" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.4383" Parameter: C <- "-52.4383" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4509 TOTAL ENERGY = -75.9233 RDTITL> * VAN DER WAALS = -23.485 ELECTROSTATIC = -52.4383 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4509" Parameter: CONF_N -> "8002" Comparing "4509" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4510" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764241 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758914 ATOM PAIRS WERE FOUND FOR ATOM LIST 41630 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29858 from a total of 758914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4510 -77.12962 1.20637 0.64507 INTE EXTERN> -31.20995 -45.91967 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1296" Parameter: A <- "-77.1296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.21" Parameter: B <- "-31.21" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9197" Parameter: C <- "-45.9197" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4510 TOTAL ENERGY = -77.1296 RDTITL> * VAN DER WAALS = -31.21 ELECTROSTATIC = -45.9197 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4510" Parameter: CONF_N -> "8002" Comparing "4510" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4511" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754481 ATOM PAIRS WERE FOUND FOR ATOM LIST 41492 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30040 from a total of 754481 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4511 -75.24901 -1.88061 0.65078 INTE EXTERN> -30.66016 -44.58885 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.249" Parameter: A <- "-75.249" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6602" Parameter: B <- "-30.6602" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5888" Parameter: C <- "-44.5888" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4511 TOTAL ENERGY = -75.249 RDTITL> * VAN DER WAALS = -30.6602 ELECTROSTATIC = -44.5888 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4511" Parameter: CONF_N -> "8002" Comparing "4511" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4512" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754481 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755763 ATOM PAIRS WERE FOUND FOR ATOM LIST 41467 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30375 from a total of 755763 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4512 -80.56566 5.31666 0.65881 INTE EXTERN> -31.97619 -48.58947 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5657" Parameter: A <- "-80.5657" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9762" Parameter: B <- "-31.9762" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5895" Parameter: C <- "-48.5895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4512 TOTAL ENERGY = -80.5657 RDTITL> * VAN DER WAALS = -31.9762 ELECTROSTATIC = -48.5895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4512" Parameter: CONF_N -> "8002" Comparing "4512" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4513" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755763 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748189 ATOM PAIRS WERE FOUND FOR ATOM LIST 41108 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29842 from a total of 748189 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4513 -77.80911 -2.75656 0.70534 INTE EXTERN> -29.20183 -48.60727 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8091" Parameter: A <- "-77.8091" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2018" Parameter: B <- "-29.2018" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6073" Parameter: C <- "-48.6073" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4513 TOTAL ENERGY = -77.8091 RDTITL> * VAN DER WAALS = -29.2018 ELECTROSTATIC = -48.6073 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4513" Parameter: CONF_N -> "8002" Comparing "4513" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4514" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748189 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751955 ATOM PAIRS WERE FOUND FOR ATOM LIST 41360 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29768 from a total of 751955 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4514 -72.60397 -5.20514 0.73268 INTE EXTERN> -26.20259 -46.40138 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.604" Parameter: A <- "-72.604" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2026" Parameter: B <- "-26.2026" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4014" Parameter: C <- "-46.4014" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4514 TOTAL ENERGY = -72.604 RDTITL> * VAN DER WAALS = -26.2026 ELECTROSTATIC = -46.4014 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4514" Parameter: CONF_N -> "8002" Comparing "4514" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4515" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751955 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757071 ATOM PAIRS WERE FOUND FOR ATOM LIST 41502 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29617 from a total of 757071 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4515 -81.18344 8.57948 0.68274 INTE EXTERN> -29.64782 -51.53562 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1834" Parameter: A <- "-81.1834" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6478" Parameter: B <- "-29.6478" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5356" Parameter: C <- "-51.5356" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4515 TOTAL ENERGY = -81.1834 RDTITL> * VAN DER WAALS = -29.6478 ELECTROSTATIC = -51.5356 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4515" Parameter: CONF_N -> "8002" Comparing "4515" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4516" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757071 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762301 ATOM PAIRS WERE FOUND FOR ATOM LIST 41676 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29800 from a total of 762301 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4516 -79.14572 -2.03772 0.79780 INTE EXTERN> -24.33472 -54.81100 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1457" Parameter: A <- "-79.1457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3347" Parameter: B <- "-24.3347" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.811" Parameter: C <- "-54.811" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4516 TOTAL ENERGY = -79.1457 RDTITL> * VAN DER WAALS = -24.3347 ELECTROSTATIC = -54.811 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4516" Parameter: CONF_N -> "8002" Comparing "4516" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4517" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762301 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754303 ATOM PAIRS WERE FOUND FOR ATOM LIST 41477 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29282 from a total of 754303 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4517 -78.53800 -0.60772 0.72905 INTE EXTERN> -26.82146 -51.71654 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.538" Parameter: A <- "-78.538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8215" Parameter: B <- "-26.8215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7165" Parameter: C <- "-51.7165" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4517 TOTAL ENERGY = -78.538 RDTITL> * VAN DER WAALS = -26.8215 ELECTROSTATIC = -51.7165 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4517" Parameter: CONF_N -> "8002" Comparing "4517" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4518" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754303 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750511 ATOM PAIRS WERE FOUND FOR ATOM LIST 40959 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28569 from a total of 750511 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4518 -78.67760 0.13959 0.68452 INTE EXTERN> -27.96059 -50.71700 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6776" Parameter: A <- "-78.6776" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9606" Parameter: B <- "-27.9606" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.717" Parameter: C <- "-50.717" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4518 TOTAL ENERGY = -78.6776 RDTITL> * VAN DER WAALS = -27.9606 ELECTROSTATIC = -50.717 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4518" Parameter: CONF_N -> "8002" Comparing "4518" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4519" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750511 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759108 ATOM PAIRS WERE FOUND FOR ATOM LIST 41550 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29441 from a total of 759108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4519 -73.90986 -4.76773 0.63863 INTE EXTERN> -30.89007 -43.01979 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9099" Parameter: A <- "-73.9099" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8901" Parameter: B <- "-30.8901" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0198" Parameter: C <- "-43.0198" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4519 TOTAL ENERGY = -73.9099 RDTITL> * VAN DER WAALS = -30.8901 ELECTROSTATIC = -43.0198 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4519" Parameter: CONF_N -> "8002" Comparing "4519" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4520" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756276 ATOM PAIRS WERE FOUND FOR ATOM LIST 41509 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29226 from a total of 756276 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4520 -82.97893 9.06906 0.71701 INTE EXTERN> -29.51536 -53.46356 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9789" Parameter: A <- "-82.9789" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5154" Parameter: B <- "-29.5154" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4636" Parameter: C <- "-53.4636" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4520 TOTAL ENERGY = -82.9789 RDTITL> * VAN DER WAALS = -29.5154 ELECTROSTATIC = -53.4636 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4520" Parameter: CONF_N -> "8002" Comparing "4520" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4521" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756276 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757712 ATOM PAIRS WERE FOUND FOR ATOM LIST 41564 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29037 from a total of 757712 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4521 -70.79655 -12.18237 0.74652 INTE EXTERN> -24.91080 -45.88575 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7966" Parameter: A <- "-70.7966" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9108" Parameter: B <- "-24.9108" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8858" Parameter: C <- "-45.8858" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4521 TOTAL ENERGY = -70.7966 RDTITL> * VAN DER WAALS = -24.9108 ELECTROSTATIC = -45.8858 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4521" Parameter: CONF_N -> "8002" Comparing "4521" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4522" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757712 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752151 ATOM PAIRS WERE FOUND FOR ATOM LIST 41459 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28791 from a total of 752151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4522 -70.98067 0.18412 0.55873 INTE EXTERN> -29.43602 -41.54465 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9807" Parameter: A <- "-70.9807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.436" Parameter: B <- "-29.436" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5447" Parameter: C <- "-41.5447" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4522 TOTAL ENERGY = -70.9807 RDTITL> * VAN DER WAALS = -29.436 ELECTROSTATIC = -41.5447 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4522" Parameter: CONF_N -> "8002" Comparing "4522" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4523" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749495 ATOM PAIRS WERE FOUND FOR ATOM LIST 41114 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29219 from a total of 749495 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4523 -70.02376 -0.95692 0.59338 INTE EXTERN> -28.79612 -41.22764 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0238" Parameter: A <- "-70.0238" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7961" Parameter: B <- "-28.7961" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2276" Parameter: C <- "-41.2276" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4523 TOTAL ENERGY = -70.0238 RDTITL> * VAN DER WAALS = -28.7961 ELECTROSTATIC = -41.2276 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4523" Parameter: CONF_N -> "8002" Comparing "4523" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4524" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749495 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751330 ATOM PAIRS WERE FOUND FOR ATOM LIST 41287 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29577 from a total of 751330 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4524 -77.55906 7.53531 0.64326 INTE EXTERN> -30.75061 -46.80846 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5591" Parameter: A <- "-77.5591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7506" Parameter: B <- "-30.7506" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8085" Parameter: C <- "-46.8085" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4524 TOTAL ENERGY = -77.5591 RDTITL> * VAN DER WAALS = -30.7506 ELECTROSTATIC = -46.8085 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4524" Parameter: CONF_N -> "8002" Comparing "4524" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4525" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751330 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752191 ATOM PAIRS WERE FOUND FOR ATOM LIST 41391 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29337 from a total of 752191 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4525 -77.30016 -0.25890 0.70632 INTE EXTERN> -28.33818 -48.96198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3002" Parameter: A <- "-77.3002" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3382" Parameter: B <- "-28.3382" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.962" Parameter: C <- "-48.962" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4525 TOTAL ENERGY = -77.3002 RDTITL> * VAN DER WAALS = -28.3382 ELECTROSTATIC = -48.962 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4525" Parameter: CONF_N -> "8002" Comparing "4525" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4526" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752191 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755535 ATOM PAIRS WERE FOUND FOR ATOM LIST 41520 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29672 from a total of 755535 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4526 -72.63862 -4.66154 0.60879 INTE EXTERN> -30.91956 -41.71906 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6386" Parameter: A <- "-72.6386" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9196" Parameter: B <- "-30.9196" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7191" Parameter: C <- "-41.7191" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4526 TOTAL ENERGY = -72.6386 RDTITL> * VAN DER WAALS = -30.9196 ELECTROSTATIC = -41.7191 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4526" Parameter: CONF_N -> "8002" Comparing "4526" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4527" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755535 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750356 ATOM PAIRS WERE FOUND FOR ATOM LIST 41158 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29558 from a total of 750356 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4527 -66.44928 -6.18934 0.59712 INTE EXTERN> -30.37002 -36.07926 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4493" Parameter: A <- "-66.4493" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.37" Parameter: B <- "-30.37" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0793" Parameter: C <- "-36.0793" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4527 TOTAL ENERGY = -66.4493 RDTITL> * VAN DER WAALS = -30.37 ELECTROSTATIC = -36.0793 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4527" Parameter: CONF_N -> "8002" Comparing "4527" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4528" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750356 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758330 ATOM PAIRS WERE FOUND FOR ATOM LIST 41438 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29736 from a total of 758330 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4528 -74.20210 7.75281 0.66149 INTE EXTERN> -29.48284 -44.71925 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2021" Parameter: A <- "-74.2021" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4828" Parameter: B <- "-29.4828" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7193" Parameter: C <- "-44.7193" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4528 TOTAL ENERGY = -74.2021 RDTITL> * VAN DER WAALS = -29.4828 ELECTROSTATIC = -44.7193 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4528" Parameter: CONF_N -> "8002" Comparing "4528" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4529" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758330 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758689 ATOM PAIRS WERE FOUND FOR ATOM LIST 41501 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29805 from a total of 758689 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4529 -73.36843 -0.83367 0.63898 INTE EXTERN> -27.87090 -45.49753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3684" Parameter: A <- "-73.3684" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8709" Parameter: B <- "-27.8709" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4975" Parameter: C <- "-45.4975" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4529 TOTAL ENERGY = -73.3684 RDTITL> * VAN DER WAALS = -27.8709 ELECTROSTATIC = -45.4975 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4529" Parameter: CONF_N -> "8002" Comparing "4529" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4530" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758689 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759680 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30308 from a total of 759680 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4530 -74.54141 1.17298 0.58670 INTE EXTERN> -31.51450 -43.02690 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5414" Parameter: A <- "-74.5414" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5145" Parameter: B <- "-31.5145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0269" Parameter: C <- "-43.0269" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4530 TOTAL ENERGY = -74.5414 RDTITL> * VAN DER WAALS = -31.5145 ELECTROSTATIC = -43.0269 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4530" Parameter: CONF_N -> "8002" Comparing "4530" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4531" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759680 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757111 ATOM PAIRS WERE FOUND FOR ATOM LIST 41536 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30031 from a total of 757111 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4531 -78.11761 3.57620 0.75126 INTE EXTERN> -29.83531 -48.28230 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1176" Parameter: A <- "-78.1176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8353" Parameter: B <- "-29.8353" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2823" Parameter: C <- "-48.2823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4531 TOTAL ENERGY = -78.1176 RDTITL> * VAN DER WAALS = -29.8353 ELECTROSTATIC = -48.2823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4531" Parameter: CONF_N -> "8002" Comparing "4531" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4532" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757111 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751892 ATOM PAIRS WERE FOUND FOR ATOM LIST 41334 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29479 from a total of 751892 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4532 -74.39462 -3.72298 0.61549 INTE EXTERN> -30.27083 -44.12380 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3946" Parameter: A <- "-74.3946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2708" Parameter: B <- "-30.2708" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1238" Parameter: C <- "-44.1238" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4532 TOTAL ENERGY = -74.3946 RDTITL> * VAN DER WAALS = -30.2708 ELECTROSTATIC = -44.1238 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4532" Parameter: CONF_N -> "8002" Comparing "4532" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4533" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751892 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41822 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30409 from a total of 759958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4533 -81.13921 6.74458 0.65696 INTE EXTERN> -29.72842 -51.41079 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1392" Parameter: A <- "-81.1392" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7284" Parameter: B <- "-29.7284" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4108" Parameter: C <- "-51.4108" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4533 TOTAL ENERGY = -81.1392 RDTITL> * VAN DER WAALS = -29.7284 ELECTROSTATIC = -51.4108 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4533" Parameter: CONF_N -> "8002" Comparing "4533" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4534" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760137 ATOM PAIRS WERE FOUND FOR ATOM LIST 41694 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30202 from a total of 760137 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4534 -77.84917 -3.29004 0.67947 INTE EXTERN> -27.66344 -50.18573 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8492" Parameter: A <- "-77.8492" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6634" Parameter: B <- "-27.6634" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1857" Parameter: C <- "-50.1857" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4534 TOTAL ENERGY = -77.8492 RDTITL> * VAN DER WAALS = -27.6634 ELECTROSTATIC = -50.1857 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4534" Parameter: CONF_N -> "8002" Comparing "4534" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4535" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760137 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757892 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30222 from a total of 757892 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4535 -73.55135 -4.29782 0.58825 INTE EXTERN> -29.82074 -43.73061 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5514" Parameter: A <- "-73.5514" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8207" Parameter: B <- "-29.8207" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7306" Parameter: C <- "-43.7306" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4535 TOTAL ENERGY = -73.5514 RDTITL> * VAN DER WAALS = -29.8207 ELECTROSTATIC = -43.7306 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4535" Parameter: CONF_N -> "8002" Comparing "4535" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4536" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757892 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759783 ATOM PAIRS WERE FOUND FOR ATOM LIST 41615 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30190 from a total of 759783 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4536 -71.19353 -2.35782 0.70096 INTE EXTERN> -24.97593 -46.21761 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1935" Parameter: A <- "-71.1935" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9759" Parameter: B <- "-24.9759" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2176" Parameter: C <- "-46.2176" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4536 TOTAL ENERGY = -71.1935 RDTITL> * VAN DER WAALS = -24.9759 ELECTROSTATIC = -46.2176 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4536" Parameter: CONF_N -> "8002" Comparing "4536" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4537" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759783 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762492 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30723 from a total of 762492 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4537 -63.76658 -7.42695 0.64749 INTE EXTERN> -22.93678 -40.82981 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7666" Parameter: A <- "-63.7666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.9368" Parameter: B <- "-22.9368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8298" Parameter: C <- "-40.8298" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4537 TOTAL ENERGY = -63.7666 RDTITL> * VAN DER WAALS = -22.9368 ELECTROSTATIC = -40.8298 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4537" Parameter: CONF_N -> "8002" Comparing "4537" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4538" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762492 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759802 ATOM PAIRS WERE FOUND FOR ATOM LIST 41936 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30355 from a total of 759802 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4538 -73.33427 9.56768 0.52426 INTE EXTERN> -32.63100 -40.70327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3343" Parameter: A <- "-73.3343" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.631" Parameter: B <- "-32.631" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7033" Parameter: C <- "-40.7033" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4538 TOTAL ENERGY = -73.3343 RDTITL> * VAN DER WAALS = -32.631 ELECTROSTATIC = -40.7033 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4538" Parameter: CONF_N -> "8002" Comparing "4538" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4539" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759802 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758125 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30009 from a total of 758125 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4539 -69.74878 -3.58549 0.57985 INTE EXTERN> -31.42946 -38.31932 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7488" Parameter: A <- "-69.7488" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4295" Parameter: B <- "-31.4295" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3193" Parameter: C <- "-38.3193" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4539 TOTAL ENERGY = -69.7488 RDTITL> * VAN DER WAALS = -31.4295 ELECTROSTATIC = -38.3193 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4539" Parameter: CONF_N -> "8002" Comparing "4539" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4540" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758125 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757992 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30072 from a total of 757992 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4540 -73.02925 3.28047 0.59851 INTE EXTERN> -31.09454 -41.93471 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0293" Parameter: A <- "-73.0293" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0945" Parameter: B <- "-31.0945" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9347" Parameter: C <- "-41.9347" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4540 TOTAL ENERGY = -73.0293 RDTITL> * VAN DER WAALS = -31.0945 ELECTROSTATIC = -41.9347 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4540" Parameter: CONF_N -> "8002" Comparing "4540" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4541" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757992 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757781 ATOM PAIRS WERE FOUND FOR ATOM LIST 41566 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30361 from a total of 757781 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4541 -70.70263 -2.32662 0.59369 INTE EXTERN> -31.85595 -38.84668 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7026" Parameter: A <- "-70.7026" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.856" Parameter: B <- "-31.856" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8467" Parameter: C <- "-38.8467" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4541 TOTAL ENERGY = -70.7026 RDTITL> * VAN DER WAALS = -31.856 ELECTROSTATIC = -38.8467 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4541" Parameter: CONF_N -> "8002" Comparing "4541" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4542" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757781 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753911 ATOM PAIRS WERE FOUND FOR ATOM LIST 41468 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29794 from a total of 753911 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4542 -77.40320 6.70056 0.60422 INTE EXTERN> -32.22633 -45.17687 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4032" Parameter: A <- "-77.4032" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2263" Parameter: B <- "-32.2263" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1769" Parameter: C <- "-45.1769" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4542 TOTAL ENERGY = -77.4032 RDTITL> * VAN DER WAALS = -32.2263 ELECTROSTATIC = -45.1769 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4542" Parameter: CONF_N -> "8002" Comparing "4542" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4543" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753911 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755409 ATOM PAIRS WERE FOUND FOR ATOM LIST 41505 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30597 from a total of 755409 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4543 -68.40315 -9.00005 0.74126 INTE EXTERN> -25.93200 -42.47115 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4031" Parameter: A <- "-68.4031" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.932" Parameter: B <- "-25.932" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4712" Parameter: C <- "-42.4712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4543 TOTAL ENERGY = -68.4031 RDTITL> * VAN DER WAALS = -25.932 ELECTROSTATIC = -42.4712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4543" Parameter: CONF_N -> "8002" Comparing "4543" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4544" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755409 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750482 ATOM PAIRS WERE FOUND FOR ATOM LIST 41224 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29948 from a total of 750482 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4544 -71.89013 3.48698 0.60908 INTE EXTERN> -30.25378 -41.63635 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8901" Parameter: A <- "-71.8901" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2538" Parameter: B <- "-30.2538" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6364" Parameter: C <- "-41.6364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4544 TOTAL ENERGY = -71.8901 RDTITL> * VAN DER WAALS = -30.2538 ELECTROSTATIC = -41.6364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4544" Parameter: CONF_N -> "8002" Comparing "4544" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4545" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750482 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754585 ATOM PAIRS WERE FOUND FOR ATOM LIST 41481 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30261 from a total of 754585 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4545 -70.56136 -1.32877 0.66016 INTE EXTERN> -30.85085 -39.71051 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5614" Parameter: A <- "-70.5614" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8508" Parameter: B <- "-30.8508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7105" Parameter: C <- "-39.7105" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4545 TOTAL ENERGY = -70.5614 RDTITL> * VAN DER WAALS = -30.8508 ELECTROSTATIC = -39.7105 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4545" Parameter: CONF_N -> "8002" Comparing "4545" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4546" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754585 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756067 ATOM PAIRS WERE FOUND FOR ATOM LIST 41430 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29679 from a total of 756067 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4546 -73.05193 2.49057 0.61964 INTE EXTERN> -29.82889 -43.22304 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0519" Parameter: A <- "-73.0519" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8289" Parameter: B <- "-29.8289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.223" Parameter: C <- "-43.223" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4546 TOTAL ENERGY = -73.0519 RDTITL> * VAN DER WAALS = -29.8289 ELECTROSTATIC = -43.223 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4546" Parameter: CONF_N -> "8002" Comparing "4546" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4547" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756067 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759381 ATOM PAIRS WERE FOUND FOR ATOM LIST 41695 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29590 from a total of 759381 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4547 -76.62612 3.57419 0.62750 INTE EXTERN> -31.91024 -44.71588 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6261" Parameter: A <- "-76.6261" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9102" Parameter: B <- "-31.9102" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7159" Parameter: C <- "-44.7159" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4547 TOTAL ENERGY = -76.6261 RDTITL> * VAN DER WAALS = -31.9102 ELECTROSTATIC = -44.7159 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4547" Parameter: CONF_N -> "8002" Comparing "4547" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4548" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759381 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755507 ATOM PAIRS WERE FOUND FOR ATOM LIST 41365 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 755507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4548 -70.71379 -5.91233 0.69574 INTE EXTERN> -25.98431 -44.72948 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7138" Parameter: A <- "-70.7138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9843" Parameter: B <- "-25.9843" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7295" Parameter: C <- "-44.7295" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4548 TOTAL ENERGY = -70.7138 RDTITL> * VAN DER WAALS = -25.9843 ELECTROSTATIC = -44.7295 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4548" Parameter: CONF_N -> "8002" Comparing "4548" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4549" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756822 ATOM PAIRS WERE FOUND FOR ATOM LIST 41462 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30138 from a total of 756822 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4549 -78.76161 8.04782 0.69878 INTE EXTERN> -26.68099 -52.08062 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7616" Parameter: A <- "-78.7616" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.681" Parameter: B <- "-26.681" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0806" Parameter: C <- "-52.0806" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4549 TOTAL ENERGY = -78.7616 RDTITL> * VAN DER WAALS = -26.681 ELECTROSTATIC = -52.0806 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4549" Parameter: CONF_N -> "8002" Comparing "4549" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4550" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756822 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755175 ATOM PAIRS WERE FOUND FOR ATOM LIST 41452 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30171 from a total of 755175 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4550 -82.57249 3.81088 0.69381 INTE EXTERN> -29.09312 -53.47937 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5725" Parameter: A <- "-82.5725" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0931" Parameter: B <- "-29.0931" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4794" Parameter: C <- "-53.4794" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4550 TOTAL ENERGY = -82.5725 RDTITL> * VAN DER WAALS = -29.0931 ELECTROSTATIC = -53.4794 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4550" Parameter: CONF_N -> "8002" Comparing "4550" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4551" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755175 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759765 ATOM PAIRS WERE FOUND FOR ATOM LIST 41561 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30281 from a total of 759765 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4551 -78.07608 -4.49641 0.65317 INTE EXTERN> -29.07419 -49.00189 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0761" Parameter: A <- "-78.0761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0742" Parameter: B <- "-29.0742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0019" Parameter: C <- "-49.0019" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4551 TOTAL ENERGY = -78.0761 RDTITL> * VAN DER WAALS = -29.0742 ELECTROSTATIC = -49.0019 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4551" Parameter: CONF_N -> "8002" Comparing "4551" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4552" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759765 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758453 ATOM PAIRS WERE FOUND FOR ATOM LIST 41444 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29846 from a total of 758453 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4552 -72.53772 -5.53836 0.60056 INTE EXTERN> -29.75768 -42.78004 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5377" Parameter: A <- "-72.5377" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7577" Parameter: B <- "-29.7577" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.78" Parameter: C <- "-42.78" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4552 TOTAL ENERGY = -72.5377 RDTITL> * VAN DER WAALS = -29.7577 ELECTROSTATIC = -42.78 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4552" Parameter: CONF_N -> "8002" Comparing "4552" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4553" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758453 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756666 ATOM PAIRS WERE FOUND FOR ATOM LIST 41337 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29470 from a total of 756666 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4553 -69.01395 -3.52377 0.53985 INTE EXTERN> -29.40482 -39.60913 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0139" Parameter: A <- "-69.0139" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4048" Parameter: B <- "-29.4048" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6091" Parameter: C <- "-39.6091" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4553 TOTAL ENERGY = -69.0139 RDTITL> * VAN DER WAALS = -29.4048 ELECTROSTATIC = -39.6091 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4553" Parameter: CONF_N -> "8002" Comparing "4553" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4554" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756666 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764883 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29911 from a total of 764883 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4554 -68.34039 -0.67356 0.66145 INTE EXTERN> -26.96992 -41.37047 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3404" Parameter: A <- "-68.3404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9699" Parameter: B <- "-26.9699" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3705" Parameter: C <- "-41.3705" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4554 TOTAL ENERGY = -68.3404 RDTITL> * VAN DER WAALS = -26.9699 ELECTROSTATIC = -41.3705 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4554" Parameter: CONF_N -> "8002" Comparing "4554" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4555" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764883 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760273 ATOM PAIRS WERE FOUND FOR ATOM LIST 41434 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30195 from a total of 760273 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4555 -73.28592 4.94553 0.68916 INTE EXTERN> -25.39184 -47.89408 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2859" Parameter: A <- "-73.2859" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3918" Parameter: B <- "-25.3918" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8941" Parameter: C <- "-47.8941" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4555 TOTAL ENERGY = -73.2859 RDTITL> * VAN DER WAALS = -25.3918 ELECTROSTATIC = -47.8941 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4555" Parameter: CONF_N -> "8002" Comparing "4555" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4556" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760273 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762786 ATOM PAIRS WERE FOUND FOR ATOM LIST 41793 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30163 from a total of 762786 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4556 -74.27793 0.99202 0.62366 INTE EXTERN> -30.70388 -43.57405 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2779" Parameter: A <- "-74.2779" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7039" Parameter: B <- "-30.7039" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5741" Parameter: C <- "-43.5741" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4556 TOTAL ENERGY = -74.2779 RDTITL> * VAN DER WAALS = -30.7039 ELECTROSTATIC = -43.5741 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4556" Parameter: CONF_N -> "8002" Comparing "4556" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4557" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762786 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758783 ATOM PAIRS WERE FOUND FOR ATOM LIST 41618 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30056 from a total of 758783 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4557 -71.42975 -2.84819 0.58946 INTE EXTERN> -29.97541 -41.45434 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4297" Parameter: A <- "-71.4297" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9754" Parameter: B <- "-29.9754" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4543" Parameter: C <- "-41.4543" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4557 TOTAL ENERGY = -71.4297 RDTITL> * VAN DER WAALS = -29.9754 ELECTROSTATIC = -41.4543 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4557" Parameter: CONF_N -> "8002" Comparing "4557" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4558" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758783 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760555 ATOM PAIRS WERE FOUND FOR ATOM LIST 41745 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30090 from a total of 760555 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4558 -68.97621 -2.45354 0.64330 INTE EXTERN> -27.11648 -41.85973 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9762" Parameter: A <- "-68.9762" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1165" Parameter: B <- "-27.1165" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8597" Parameter: C <- "-41.8597" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4558 TOTAL ENERGY = -68.9762 RDTITL> * VAN DER WAALS = -27.1165 ELECTROSTATIC = -41.8597 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4558" Parameter: CONF_N -> "8002" Comparing "4558" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4559" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760555 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757644 ATOM PAIRS WERE FOUND FOR ATOM LIST 41418 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29719 from a total of 757644 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4559 -70.16058 1.18437 0.53365 INTE EXTERN> -31.72492 -38.43566 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1606" Parameter: A <- "-70.1606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7249" Parameter: B <- "-31.7249" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4357" Parameter: C <- "-38.4357" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4559 TOTAL ENERGY = -70.1606 RDTITL> * VAN DER WAALS = -31.7249 ELECTROSTATIC = -38.4357 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4559" Parameter: CONF_N -> "8002" Comparing "4559" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4560" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757644 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757826 ATOM PAIRS WERE FOUND FOR ATOM LIST 41641 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29437 from a total of 757826 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4560 -71.19328 1.03270 0.58729 INTE EXTERN> -30.35077 -40.84251 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1933" Parameter: A <- "-71.1933" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3508" Parameter: B <- "-30.3508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8425" Parameter: C <- "-40.8425" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4560 TOTAL ENERGY = -71.1933 RDTITL> * VAN DER WAALS = -30.3508 ELECTROSTATIC = -40.8425 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4560" Parameter: CONF_N -> "8002" Comparing "4560" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4561" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757826 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762945 ATOM PAIRS WERE FOUND FOR ATOM LIST 41842 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30221 from a total of 762945 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4561 -79.19354 8.00026 0.60855 INTE EXTERN> -28.84419 -50.34935 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1935" Parameter: A <- "-79.1935" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8442" Parameter: B <- "-28.8442" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3493" Parameter: C <- "-50.3493" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4561 TOTAL ENERGY = -79.1935 RDTITL> * VAN DER WAALS = -28.8442 ELECTROSTATIC = -50.3493 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4561" Parameter: CONF_N -> "8002" Comparing "4561" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4562" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762945 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766226 ATOM PAIRS WERE FOUND FOR ATOM LIST 42132 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30180 from a total of 766226 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4562 -73.15180 -6.04174 0.59589 INTE EXTERN> -33.40831 -39.74350 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1518" Parameter: A <- "-73.1518" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4083" Parameter: B <- "-33.4083" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7435" Parameter: C <- "-39.7435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4562 TOTAL ENERGY = -73.1518 RDTITL> * VAN DER WAALS = -33.4083 ELECTROSTATIC = -39.7435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4562" Parameter: CONF_N -> "8002" Comparing "4562" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4563" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766226 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752017 ATOM PAIRS WERE FOUND FOR ATOM LIST 41416 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29873 from a total of 752017 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4563 -71.66527 -1.48653 0.58385 INTE EXTERN> -31.71142 -39.95385 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6653" Parameter: A <- "-71.6653" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7114" Parameter: B <- "-31.7114" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9539" Parameter: C <- "-39.9539" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4563 TOTAL ENERGY = -71.6653 RDTITL> * VAN DER WAALS = -31.7114 ELECTROSTATIC = -39.9539 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4563" Parameter: CONF_N -> "8002" Comparing "4563" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4564" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752017 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757221 ATOM PAIRS WERE FOUND FOR ATOM LIST 41310 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29438 from a total of 757221 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4564 -73.51727 1.85200 0.64378 INTE EXTERN> -28.51410 -45.00317 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5173" Parameter: A <- "-73.5173" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5141" Parameter: B <- "-28.5141" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0032" Parameter: C <- "-45.0032" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4564 TOTAL ENERGY = -73.5173 RDTITL> * VAN DER WAALS = -28.5141 ELECTROSTATIC = -45.0032 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4564" Parameter: CONF_N -> "8002" Comparing "4564" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4565" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757221 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756543 ATOM PAIRS WERE FOUND FOR ATOM LIST 41394 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29638 from a total of 756543 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4565 -76.69005 3.17278 0.62436 INTE EXTERN> -31.62009 -45.06996 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.69" Parameter: A <- "-76.69" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6201" Parameter: B <- "-31.6201" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.07" Parameter: C <- "-45.07" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4565 TOTAL ENERGY = -76.69 RDTITL> * VAN DER WAALS = -31.6201 ELECTROSTATIC = -45.07 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4565" Parameter: CONF_N -> "8002" Comparing "4565" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4566" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756543 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756749 ATOM PAIRS WERE FOUND FOR ATOM LIST 41439 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29111 from a total of 756749 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4566 -75.09540 -1.59465 0.66566 INTE EXTERN> -31.08616 -44.00924 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0954" Parameter: A <- "-75.0954" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0862" Parameter: B <- "-31.0862" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0092" Parameter: C <- "-44.0092" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4566 TOTAL ENERGY = -75.0954 RDTITL> * VAN DER WAALS = -31.0862 ELECTROSTATIC = -44.0092 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4566" Parameter: CONF_N -> "8002" Comparing "4566" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4567" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756749 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761113 ATOM PAIRS WERE FOUND FOR ATOM LIST 42007 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29869 from a total of 761113 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4567 -77.37817 2.28277 0.73759 INTE EXTERN> -25.86070 -51.51747 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3782" Parameter: A <- "-77.3782" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8607" Parameter: B <- "-25.8607" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5175" Parameter: C <- "-51.5175" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4567 TOTAL ENERGY = -77.3782 RDTITL> * VAN DER WAALS = -25.8607 ELECTROSTATIC = -51.5175 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4567" Parameter: CONF_N -> "8002" Comparing "4567" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4568" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761113 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761336 ATOM PAIRS WERE FOUND FOR ATOM LIST 41537 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29328 from a total of 761336 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4568 -80.28121 2.90304 0.62907 INTE EXTERN> -30.72675 -49.55445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2812" Parameter: A <- "-80.2812" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7268" Parameter: B <- "-30.7268" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5545" Parameter: C <- "-49.5545" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4568 TOTAL ENERGY = -80.2812 RDTITL> * VAN DER WAALS = -30.7268 ELECTROSTATIC = -49.5545 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4568" Parameter: CONF_N -> "8002" Comparing "4568" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4569" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761336 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756925 ATOM PAIRS WERE FOUND FOR ATOM LIST 41482 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29457 from a total of 756925 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4569 -74.56015 -5.72105 0.66357 INTE EXTERN> -28.84377 -45.71638 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5602" Parameter: A <- "-74.5602" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8438" Parameter: B <- "-28.8438" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7164" Parameter: C <- "-45.7164" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4569 TOTAL ENERGY = -74.5602 RDTITL> * VAN DER WAALS = -28.8438 ELECTROSTATIC = -45.7164 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4569" Parameter: CONF_N -> "8002" Comparing "4569" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4570" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756925 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758729 ATOM PAIRS WERE FOUND FOR ATOM LIST 41787 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29898 from a total of 758729 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4570 -77.94764 3.38749 0.70303 INTE EXTERN> -29.86044 -48.08721 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9476" Parameter: A <- "-77.9476" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8604" Parameter: B <- "-29.8604" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0872" Parameter: C <- "-48.0872" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4570 TOTAL ENERGY = -77.9476 RDTITL> * VAN DER WAALS = -29.8604 ELECTROSTATIC = -48.0872 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4570" Parameter: CONF_N -> "8002" Comparing "4570" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4571" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758729 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757663 ATOM PAIRS WERE FOUND FOR ATOM LIST 41528 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29631 from a total of 757663 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4571 -77.46190 -0.48575 0.65191 INTE EXTERN> -28.87992 -48.58198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4619" Parameter: A <- "-77.4619" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8799" Parameter: B <- "-28.8799" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.582" Parameter: C <- "-48.582" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4571 TOTAL ENERGY = -77.4619 RDTITL> * VAN DER WAALS = -28.8799 ELECTROSTATIC = -48.582 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4571" Parameter: CONF_N -> "8002" Comparing "4571" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4572" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757663 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758812 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29258 from a total of 758812 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4572 -71.28310 -6.17879 0.59749 INTE EXTERN> -29.71791 -41.56519 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2831" Parameter: A <- "-71.2831" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7179" Parameter: B <- "-29.7179" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5652" Parameter: C <- "-41.5652" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4572 TOTAL ENERGY = -71.2831 RDTITL> * VAN DER WAALS = -29.7179 ELECTROSTATIC = -41.5652 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4572" Parameter: CONF_N -> "8002" Comparing "4572" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4573" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758812 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759674 ATOM PAIRS WERE FOUND FOR ATOM LIST 41513 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29939 from a total of 759674 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4573 -71.72597 0.44286 0.68658 INTE EXTERN> -26.37233 -45.35363 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.726" Parameter: A <- "-71.726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3723" Parameter: B <- "-26.3723" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3536" Parameter: C <- "-45.3536" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4573 TOTAL ENERGY = -71.726 RDTITL> * VAN DER WAALS = -26.3723 ELECTROSTATIC = -45.3536 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4573" Parameter: CONF_N -> "8002" Comparing "4573" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4574" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759674 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755507 ATOM PAIRS WERE FOUND FOR ATOM LIST 41364 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29527 from a total of 755507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4574 -67.15248 -4.57349 0.62366 INTE EXTERN> -27.86010 -39.29237 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1525" Parameter: A <- "-67.1525" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8601" Parameter: B <- "-27.8601" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2924" Parameter: C <- "-39.2924" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4574 TOTAL ENERGY = -67.1525 RDTITL> * VAN DER WAALS = -27.8601 ELECTROSTATIC = -39.2924 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4574" Parameter: CONF_N -> "8002" Comparing "4574" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4575" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752357 ATOM PAIRS WERE FOUND FOR ATOM LIST 41278 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28752 from a total of 752357 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4575 -70.39172 3.23924 0.79308 INTE EXTERN> -21.03364 -49.35808 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3917" Parameter: A <- "-70.3917" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.0336" Parameter: B <- "-21.0336" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3581" Parameter: C <- "-49.3581" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4575 TOTAL ENERGY = -70.3917 RDTITL> * VAN DER WAALS = -21.0336 ELECTROSTATIC = -49.3581 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4575" Parameter: CONF_N -> "8002" Comparing "4575" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4576" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752357 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759822 ATOM PAIRS WERE FOUND FOR ATOM LIST 41528 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29149 from a total of 759822 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4576 -71.87202 1.48031 0.64347 INTE EXTERN> -31.57033 -40.30170 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.872" Parameter: A <- "-71.872" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5703" Parameter: B <- "-31.5703" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3017" Parameter: C <- "-40.3017" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4576 TOTAL ENERGY = -71.872 RDTITL> * VAN DER WAALS = -31.5703 ELECTROSTATIC = -40.3017 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4576" Parameter: CONF_N -> "8002" Comparing "4576" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4577" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759822 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758083 ATOM PAIRS WERE FOUND FOR ATOM LIST 41782 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29489 from a total of 758083 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4577 -73.20004 1.32802 0.69448 INTE EXTERN> -26.33164 -46.86841 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2" Parameter: A <- "-73.2" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3316" Parameter: B <- "-26.3316" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8684" Parameter: C <- "-46.8684" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4577 TOTAL ENERGY = -73.2 RDTITL> * VAN DER WAALS = -26.3316 ELECTROSTATIC = -46.8684 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4577" Parameter: CONF_N -> "8002" Comparing "4577" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4578" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758083 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753287 ATOM PAIRS WERE FOUND FOR ATOM LIST 41619 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29541 from a total of 753287 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4578 -68.50912 -4.69092 0.72374 INTE EXTERN> -27.90884 -40.60028 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5091" Parameter: A <- "-68.5091" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9088" Parameter: B <- "-27.9088" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6003" Parameter: C <- "-40.6003" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4578 TOTAL ENERGY = -68.5091 RDTITL> * VAN DER WAALS = -27.9088 ELECTROSTATIC = -40.6003 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4578" Parameter: CONF_N -> "8002" Comparing "4578" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4579" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753287 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753803 ATOM PAIRS WERE FOUND FOR ATOM LIST 41535 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29002 from a total of 753803 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4579 -78.68605 10.17693 0.63685 INTE EXTERN> -29.21187 -49.47418 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.686" Parameter: A <- "-78.686" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2119" Parameter: B <- "-29.2119" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4742" Parameter: C <- "-49.4742" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4579 TOTAL ENERGY = -78.686 RDTITL> * VAN DER WAALS = -29.2119 ELECTROSTATIC = -49.4742 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4579" Parameter: CONF_N -> "8002" Comparing "4579" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4580" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753803 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763967 ATOM PAIRS WERE FOUND FOR ATOM LIST 41895 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29786 from a total of 763967 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4580 -74.99487 -3.69117 0.55175 INTE EXTERN> -33.52502 -41.46986 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9949" Parameter: A <- "-74.9949" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.525" Parameter: B <- "-33.525" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4699" Parameter: C <- "-41.4699" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4580 TOTAL ENERGY = -74.9949 RDTITL> * VAN DER WAALS = -33.525 ELECTROSTATIC = -41.4699 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4580" Parameter: CONF_N -> "8002" Comparing "4580" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4581" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763967 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759773 ATOM PAIRS WERE FOUND FOR ATOM LIST 41702 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29879 from a total of 759773 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4581 -80.41092 5.41604 0.62555 INTE EXTERN> -32.06871 -48.34221 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4109" Parameter: A <- "-80.4109" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0687" Parameter: B <- "-32.0687" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3422" Parameter: C <- "-48.3422" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4581 TOTAL ENERGY = -80.4109 RDTITL> * VAN DER WAALS = -32.0687 ELECTROSTATIC = -48.3422 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4581" Parameter: CONF_N -> "8002" Comparing "4581" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4582" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759773 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760273 ATOM PAIRS WERE FOUND FOR ATOM LIST 41492 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29399 from a total of 760273 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4582 -72.42515 -7.98577 0.71445 INTE EXTERN> -28.26343 -44.16172 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4251" Parameter: A <- "-72.4251" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2634" Parameter: B <- "-28.2634" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1617" Parameter: C <- "-44.1617" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4582 TOTAL ENERGY = -72.4251 RDTITL> * VAN DER WAALS = -28.2634 ELECTROSTATIC = -44.1617 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4582" Parameter: CONF_N -> "8002" Comparing "4582" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4583" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760273 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761120 ATOM PAIRS WERE FOUND FOR ATOM LIST 41799 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29368 from a total of 761120 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4583 -76.46944 4.04429 0.64408 INTE EXTERN> -30.58826 -45.88118 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4694" Parameter: A <- "-76.4694" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5883" Parameter: B <- "-30.5883" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8812" Parameter: C <- "-45.8812" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4583 TOTAL ENERGY = -76.4694 RDTITL> * VAN DER WAALS = -30.5883 ELECTROSTATIC = -45.8812 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4583" Parameter: CONF_N -> "8002" Comparing "4583" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4584" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761120 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754038 ATOM PAIRS WERE FOUND FOR ATOM LIST 41465 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29727 from a total of 754038 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4584 -84.47079 8.00135 0.76916 INTE EXTERN> -27.39615 -57.07464 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.4708" Parameter: A <- "-84.4708" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3962" Parameter: B <- "-27.3962" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.0746" Parameter: C <- "-57.0746" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4584 TOTAL ENERGY = -84.4708 RDTITL> * VAN DER WAALS = -27.3962 ELECTROSTATIC = -57.0746 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4584" Parameter: CONF_N -> "8002" Comparing "4584" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4585" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754038 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758343 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29994 from a total of 758343 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4585 -83.41503 -1.05576 0.66801 INTE EXTERN> -30.21982 -53.19521 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.415" Parameter: A <- "-83.415" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2198" Parameter: B <- "-30.2198" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.1952" Parameter: C <- "-53.1952" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4585 TOTAL ENERGY = -83.415 RDTITL> * VAN DER WAALS = -30.2198 ELECTROSTATIC = -53.1952 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4585" Parameter: CONF_N -> "8002" Comparing "4585" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4586" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758343 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756855 ATOM PAIRS WERE FOUND FOR ATOM LIST 41339 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29949 from a total of 756855 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4586 -88.57584 5.16081 0.70865 INTE EXTERN> -29.58421 -58.99164 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.5758" Parameter: A <- "-88.5758" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5842" Parameter: B <- "-29.5842" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.9916" Parameter: C <- "-58.9916" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4586 TOTAL ENERGY = -88.5758 RDTITL> * VAN DER WAALS = -29.5842 ELECTROSTATIC = -58.9916 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4586" Parameter: CONF_N -> "8002" Comparing "4586" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4587" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756855 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757643 ATOM PAIRS WERE FOUND FOR ATOM LIST 41545 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29899 from a total of 757643 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4587 -74.37077 -14.20507 0.72580 INTE EXTERN> -23.37749 -50.99328 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3708" Parameter: A <- "-74.3708" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.3775" Parameter: B <- "-23.3775" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9933" Parameter: C <- "-50.9933" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4587 TOTAL ENERGY = -74.3708 RDTITL> * VAN DER WAALS = -23.3775 ELECTROSTATIC = -50.9933 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4587" Parameter: CONF_N -> "8002" Comparing "4587" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4588" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757643 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755468 ATOM PAIRS WERE FOUND FOR ATOM LIST 41412 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29776 from a total of 755468 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4588 -81.65013 7.27936 0.72208 INTE EXTERN> -27.58955 -54.06058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6501" Parameter: A <- "-81.6501" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5895" Parameter: B <- "-27.5895" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0606" Parameter: C <- "-54.0606" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4588 TOTAL ENERGY = -81.6501 RDTITL> * VAN DER WAALS = -27.5895 ELECTROSTATIC = -54.0606 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4588" Parameter: CONF_N -> "8002" Comparing "4588" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4589" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755468 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759591 ATOM PAIRS WERE FOUND FOR ATOM LIST 41652 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29474 from a total of 759591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4589 -79.55289 -2.09724 0.69363 INTE EXTERN> -29.37298 -50.17991 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5529" Parameter: A <- "-79.5529" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.373" Parameter: B <- "-29.373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1799" Parameter: C <- "-50.1799" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4589 TOTAL ENERGY = -79.5529 RDTITL> * VAN DER WAALS = -29.373 ELECTROSTATIC = -50.1799 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4589" Parameter: CONF_N -> "8002" Comparing "4589" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4590" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761375 ATOM PAIRS WERE FOUND FOR ATOM LIST 41845 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30078 from a total of 761375 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4590 -81.29780 1.74491 0.68712 INTE EXTERN> -27.42643 -53.87138 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.2978" Parameter: A <- "-81.2978" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4264" Parameter: B <- "-27.4264" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8714" Parameter: C <- "-53.8714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4590 TOTAL ENERGY = -81.2978 RDTITL> * VAN DER WAALS = -27.4264 ELECTROSTATIC = -53.8714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4590" Parameter: CONF_N -> "8002" Comparing "4590" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4591" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761375 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757683 ATOM PAIRS WERE FOUND FOR ATOM LIST 41625 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29528 from a total of 757683 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4591 -82.12199 0.82419 0.75631 INTE EXTERN> -24.93867 -57.18332 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.122" Parameter: A <- "-82.122" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9387" Parameter: B <- "-24.9387" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.1833" Parameter: C <- "-57.1833" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4591 TOTAL ENERGY = -82.122 RDTITL> * VAN DER WAALS = -24.9387 ELECTROSTATIC = -57.1833 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4591" Parameter: CONF_N -> "8002" Comparing "4591" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4592" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757683 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755496 ATOM PAIRS WERE FOUND FOR ATOM LIST 41480 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29318 from a total of 755496 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4592 -81.57465 -0.54734 0.78338 INTE EXTERN> -27.08985 -54.48480 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5746" Parameter: A <- "-81.5746" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0899" Parameter: B <- "-27.0899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.4848" Parameter: C <- "-54.4848" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4592 TOTAL ENERGY = -81.5746 RDTITL> * VAN DER WAALS = -27.0899 ELECTROSTATIC = -54.4848 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4592" Parameter: CONF_N -> "8002" Comparing "4592" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4593" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755496 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758767 ATOM PAIRS WERE FOUND FOR ATOM LIST 41511 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29194 from a total of 758767 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4593 -75.86674 -5.70791 0.69502 INTE EXTERN> -26.98468 -48.88206 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8667" Parameter: A <- "-75.8667" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9847" Parameter: B <- "-26.9847" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8821" Parameter: C <- "-48.8821" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4593 TOTAL ENERGY = -75.8667 RDTITL> * VAN DER WAALS = -26.9847 ELECTROSTATIC = -48.8821 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4593" Parameter: CONF_N -> "8002" Comparing "4593" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4594" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758767 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755269 ATOM PAIRS WERE FOUND FOR ATOM LIST 41449 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28850 from a total of 755269 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4594 -79.44171 3.57497 0.69559 INTE EXTERN> -25.76552 -53.67619 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4417" Parameter: A <- "-79.4417" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7655" Parameter: B <- "-25.7655" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6762" Parameter: C <- "-53.6762" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4594 TOTAL ENERGY = -79.4417 RDTITL> * VAN DER WAALS = -25.7655 ELECTROSTATIC = -53.6762 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4594" Parameter: CONF_N -> "8002" Comparing "4594" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4595" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755269 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752067 ATOM PAIRS WERE FOUND FOR ATOM LIST 41283 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29280 from a total of 752067 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4595 -80.14687 0.70516 0.80688 INTE EXTERN> -23.54408 -56.60278 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1469" Parameter: A <- "-80.1469" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.5441" Parameter: B <- "-23.5441" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.6028" Parameter: C <- "-56.6028" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4595 TOTAL ENERGY = -80.1469 RDTITL> * VAN DER WAALS = -23.5441 ELECTROSTATIC = -56.6028 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4595" Parameter: CONF_N -> "8002" Comparing "4595" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4596" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752067 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754995 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29431 from a total of 754995 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4596 -82.12039 1.97352 0.69472 INTE EXTERN> -27.55223 -54.56816 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.1204" Parameter: A <- "-82.1204" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5522" Parameter: B <- "-27.5522" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.5682" Parameter: C <- "-54.5682" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4596 TOTAL ENERGY = -82.1204 RDTITL> * VAN DER WAALS = -27.5522 ELECTROSTATIC = -54.5682 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4596" Parameter: CONF_N -> "8002" Comparing "4596" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4597" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754995 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752833 ATOM PAIRS WERE FOUND FOR ATOM LIST 41270 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29164 from a total of 752833 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4597 -78.67889 -3.44149 0.70020 INTE EXTERN> -26.17861 -52.50028 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6789" Parameter: A <- "-78.6789" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1786" Parameter: B <- "-26.1786" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5003" Parameter: C <- "-52.5003" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4597 TOTAL ENERGY = -78.6789 RDTITL> * VAN DER WAALS = -26.1786 ELECTROSTATIC = -52.5003 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4597" Parameter: CONF_N -> "8002" Comparing "4597" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4598" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752833 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758654 ATOM PAIRS WERE FOUND FOR ATOM LIST 41671 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29556 from a total of 758654 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4598 -80.60530 1.92641 0.68834 INTE EXTERN> -27.01039 -53.59491 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6053" Parameter: A <- "-80.6053" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0104" Parameter: B <- "-27.0104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.5949" Parameter: C <- "-53.5949" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4598 TOTAL ENERGY = -80.6053 RDTITL> * VAN DER WAALS = -27.0104 ELECTROSTATIC = -53.5949 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4598" Parameter: CONF_N -> "8002" Comparing "4598" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4599" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758654 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760594 ATOM PAIRS WERE FOUND FOR ATOM LIST 41732 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28986 from a total of 760594 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4599 -81.46250 0.85721 0.72617 INTE EXTERN> -27.56708 -53.89542 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4625" Parameter: A <- "-81.4625" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5671" Parameter: B <- "-27.5671" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8954" Parameter: C <- "-53.8954" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4599 TOTAL ENERGY = -81.4625 RDTITL> * VAN DER WAALS = -27.5671 ELECTROSTATIC = -53.8954 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4599" Parameter: CONF_N -> "8002" Comparing "4599" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4600" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760594 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756926 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28732 from a total of 756926 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4600 -62.55788 -18.90462 0.48244 INTE EXTERN> -31.87609 -30.68179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5579" Parameter: A <- "-62.5579" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8761" Parameter: B <- "-31.8761" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.6818" Parameter: C <- "-30.6818" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4600 TOTAL ENERGY = -62.5579 RDTITL> * VAN DER WAALS = -31.8761 ELECTROSTATIC = -30.6818 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4600" Parameter: CONF_N -> "8002" Comparing "4600" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4601" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756926 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757095 ATOM PAIRS WERE FOUND FOR ATOM LIST 41289 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29453 from a total of 757095 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4601 -74.29594 11.73806 0.59243 INTE EXTERN> -29.80426 -44.49168 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2959" Parameter: A <- "-74.2959" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8043" Parameter: B <- "-29.8043" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4917" Parameter: C <- "-44.4917" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4601 TOTAL ENERGY = -74.2959 RDTITL> * VAN DER WAALS = -29.8043 ELECTROSTATIC = -44.4917 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4601" Parameter: CONF_N -> "8002" Comparing "4601" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4602" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757095 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765421 ATOM PAIRS WERE FOUND FOR ATOM LIST 41814 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29903 from a total of 765421 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4602 -67.87605 -6.41990 0.63435 INTE EXTERN> -25.95208 -41.92397 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.876" Parameter: A <- "-67.876" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9521" Parameter: B <- "-25.9521" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.924" Parameter: C <- "-41.924" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4602 TOTAL ENERGY = -67.876 RDTITL> * VAN DER WAALS = -25.9521 ELECTROSTATIC = -41.924 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4602" Parameter: CONF_N -> "8002" Comparing "4602" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4603" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765421 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753186 ATOM PAIRS WERE FOUND FOR ATOM LIST 41270 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28867 from a total of 753186 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4603 -67.41771 -0.45833 0.74252 INTE EXTERN> -21.50513 -45.91258 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4177" Parameter: A <- "-67.4177" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.5051" Parameter: B <- "-21.5051" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9126" Parameter: C <- "-45.9126" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4603 TOTAL ENERGY = -67.4177 RDTITL> * VAN DER WAALS = -21.5051 ELECTROSTATIC = -45.9126 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4603" Parameter: CONF_N -> "8002" Comparing "4603" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4604" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753186 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756757 ATOM PAIRS WERE FOUND FOR ATOM LIST 41469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29227 from a total of 756757 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4604 -77.07608 9.65837 0.75949 INTE EXTERN> -27.61083 -49.46525 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0761" Parameter: A <- "-77.0761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6108" Parameter: B <- "-27.6108" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4652" Parameter: C <- "-49.4652" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4604 TOTAL ENERGY = -77.0761 RDTITL> * VAN DER WAALS = -27.6108 ELECTROSTATIC = -49.4652 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4604" Parameter: CONF_N -> "8002" Comparing "4604" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4605" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756757 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755067 ATOM PAIRS WERE FOUND FOR ATOM LIST 41483 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28489 from a total of 755067 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4605 -65.20936 -11.86673 0.76512 INTE EXTERN> -26.14106 -39.06829 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2094" Parameter: A <- "-65.2094" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1411" Parameter: B <- "-26.1411" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0683" Parameter: C <- "-39.0683" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4605 TOTAL ENERGY = -65.2094 RDTITL> * VAN DER WAALS = -26.1411 ELECTROSTATIC = -39.0683 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4605" Parameter: CONF_N -> "8002" Comparing "4605" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4606" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755067 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762076 ATOM PAIRS WERE FOUND FOR ATOM LIST 41665 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28978 from a total of 762076 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4606 -72.66392 7.45457 0.90297 INTE EXTERN> -19.85750 -52.80643 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6639" Parameter: A <- "-72.6639" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-19.8575" Parameter: B <- "-19.8575" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8064" Parameter: C <- "-52.8064" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4606 TOTAL ENERGY = -72.6639 RDTITL> * VAN DER WAALS = -19.8575 ELECTROSTATIC = -52.8064 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4606" Parameter: CONF_N -> "8002" Comparing "4606" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4607" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762076 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765791 ATOM PAIRS WERE FOUND FOR ATOM LIST 42042 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29173 from a total of 765791 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4607 -72.71002 0.04609 0.65078 INTE EXTERN> -28.09889 -44.61113 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.71" Parameter: A <- "-72.71" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0989" Parameter: B <- "-28.0989" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6111" Parameter: C <- "-44.6111" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4607 TOTAL ENERGY = -72.71 RDTITL> * VAN DER WAALS = -28.0989 ELECTROSTATIC = -44.6111 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4607" Parameter: CONF_N -> "8002" Comparing "4607" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4608" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765791 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758216 ATOM PAIRS WERE FOUND FOR ATOM LIST 41240 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29453 from a total of 758216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4608 -68.37984 -4.33018 0.58496 INTE EXTERN> -27.09509 -41.28475 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3798" Parameter: A <- "-68.3798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0951" Parameter: B <- "-27.0951" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2847" Parameter: C <- "-41.2847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4608 TOTAL ENERGY = -68.3798 RDTITL> * VAN DER WAALS = -27.0951 ELECTROSTATIC = -41.2847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4608" Parameter: CONF_N -> "8002" Comparing "4608" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4609" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757285 ATOM PAIRS WERE FOUND FOR ATOM LIST 41558 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28241 from a total of 757285 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4609 -70.37907 1.99923 0.70531 INTE EXTERN> -22.73903 -47.64005 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3791" Parameter: A <- "-70.3791" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.739" Parameter: B <- "-22.739" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.64" Parameter: C <- "-47.64" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4609 TOTAL ENERGY = -70.3791 RDTITL> * VAN DER WAALS = -22.739 ELECTROSTATIC = -47.64 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4609" Parameter: CONF_N -> "8002" Comparing "4609" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4610" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757285 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757740 ATOM PAIRS WERE FOUND FOR ATOM LIST 41754 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28574 from a total of 757740 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4610 -70.96975 0.59068 0.54280 INTE EXTERN> -29.29343 -41.67631 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9697" Parameter: A <- "-70.9697" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2934" Parameter: B <- "-29.2934" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6763" Parameter: C <- "-41.6763" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4610 TOTAL ENERGY = -70.9697 RDTITL> * VAN DER WAALS = -29.2934 ELECTROSTATIC = -41.6763 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4610" Parameter: CONF_N -> "8002" Comparing "4610" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4611" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757740 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756170 ATOM PAIRS WERE FOUND FOR ATOM LIST 41447 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28764 from a total of 756170 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4611 -63.35893 -7.61082 0.53100 INTE EXTERN> -27.93453 -35.42439 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3589" Parameter: A <- "-63.3589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9345" Parameter: B <- "-27.9345" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4244" Parameter: C <- "-35.4244" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4611 TOTAL ENERGY = -63.3589 RDTITL> * VAN DER WAALS = -27.9345 ELECTROSTATIC = -35.4244 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4611" Parameter: CONF_N -> "8002" Comparing "4611" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4612" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756170 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761698 ATOM PAIRS WERE FOUND FOR ATOM LIST 41778 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28955 from a total of 761698 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4612 -67.45401 4.09509 0.64662 INTE EXTERN> -26.58299 -40.87102 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.454" Parameter: A <- "-67.454" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.583" Parameter: B <- "-26.583" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.871" Parameter: C <- "-40.871" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4612 TOTAL ENERGY = -67.454 RDTITL> * VAN DER WAALS = -26.583 ELECTROSTATIC = -40.871 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4612" Parameter: CONF_N -> "8002" Comparing "4612" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4613" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761698 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756790 ATOM PAIRS WERE FOUND FOR ATOM LIST 41490 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29341 from a total of 756790 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4613 -79.96160 12.50759 0.69838 INTE EXTERN> -25.33843 -54.62317 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9616" Parameter: A <- "-79.9616" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3384" Parameter: B <- "-25.3384" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.6232" Parameter: C <- "-54.6232" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4613 TOTAL ENERGY = -79.9616 RDTITL> * VAN DER WAALS = -25.3384 ELECTROSTATIC = -54.6232 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4613" Parameter: CONF_N -> "8002" Comparing "4613" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4614" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756790 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756053 ATOM PAIRS WERE FOUND FOR ATOM LIST 41390 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29076 from a total of 756053 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4614 -76.55621 -3.40539 0.65676 INTE EXTERN> -23.87312 -52.68309 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5562" Parameter: A <- "-76.5562" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8731" Parameter: B <- "-23.8731" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6831" Parameter: C <- "-52.6831" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4614 TOTAL ENERGY = -76.5562 RDTITL> * VAN DER WAALS = -23.8731 ELECTROSTATIC = -52.6831 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4614" Parameter: CONF_N -> "8002" Comparing "4614" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4615" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756053 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754926 ATOM PAIRS WERE FOUND FOR ATOM LIST 41283 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29113 from a total of 754926 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4615 -71.80558 -4.75062 0.62073 INTE EXTERN> -27.13086 -44.67473 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8056" Parameter: A <- "-71.8056" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1309" Parameter: B <- "-27.1309" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6747" Parameter: C <- "-44.6747" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4615 TOTAL ENERGY = -71.8056 RDTITL> * VAN DER WAALS = -27.1309 ELECTROSTATIC = -44.6747 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4615" Parameter: CONF_N -> "8002" Comparing "4615" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4616" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754926 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751684 ATOM PAIRS WERE FOUND FOR ATOM LIST 41191 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29476 from a total of 751684 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4616 -70.85220 -0.95338 0.61814 INTE EXTERN> -28.56990 -42.28231 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8522" Parameter: A <- "-70.8522" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5699" Parameter: B <- "-28.5699" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2823" Parameter: C <- "-42.2823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4616 TOTAL ENERGY = -70.8522 RDTITL> * VAN DER WAALS = -28.5699 ELECTROSTATIC = -42.2823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4616" Parameter: CONF_N -> "8002" Comparing "4616" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4617" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751684 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751637 ATOM PAIRS WERE FOUND FOR ATOM LIST 41132 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28397 from a total of 751637 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4617 -67.31788 -3.53432 0.63973 INTE EXTERN> -25.89130 -41.42658 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3179" Parameter: A <- "-67.3179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8913" Parameter: B <- "-25.8913" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4266" Parameter: C <- "-41.4266" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4617 TOTAL ENERGY = -67.3179 RDTITL> * VAN DER WAALS = -25.8913 ELECTROSTATIC = -41.4266 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4617" Parameter: CONF_N -> "8002" Comparing "4617" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4618" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751637 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757646 ATOM PAIRS WERE FOUND FOR ATOM LIST 41533 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29129 from a total of 757646 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4618 -70.40981 3.09194 0.56974 INTE EXTERN> -29.02824 -41.38158 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4098" Parameter: A <- "-70.4098" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0282" Parameter: B <- "-29.0282" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3816" Parameter: C <- "-41.3816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4618 TOTAL ENERGY = -70.4098 RDTITL> * VAN DER WAALS = -29.0282 ELECTROSTATIC = -41.3816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4618" Parameter: CONF_N -> "8002" Comparing "4618" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4619" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757646 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756003 ATOM PAIRS WERE FOUND FOR ATOM LIST 41421 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28285 from a total of 756003 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4619 -70.19512 -0.21469 0.51185 INTE EXTERN> -29.05260 -41.14252 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1951" Parameter: A <- "-70.1951" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0526" Parameter: B <- "-29.0526" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1425" Parameter: C <- "-41.1425" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4619 TOTAL ENERGY = -70.1951 RDTITL> * VAN DER WAALS = -29.0526 ELECTROSTATIC = -41.1425 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4619" Parameter: CONF_N -> "8002" Comparing "4619" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4620" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756003 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760670 ATOM PAIRS WERE FOUND FOR ATOM LIST 41528 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29069 from a total of 760670 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4620 -71.53424 1.33911 0.58060 INTE EXTERN> -28.12765 -43.40659 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5342" Parameter: A <- "-71.5342" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1276" Parameter: B <- "-28.1276" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4066" Parameter: C <- "-43.4066" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4620 TOTAL ENERGY = -71.5342 RDTITL> * VAN DER WAALS = -28.1276 ELECTROSTATIC = -43.4066 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4620" Parameter: CONF_N -> "8002" Comparing "4620" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4621" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760670 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759792 ATOM PAIRS WERE FOUND FOR ATOM LIST 41770 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29126 from a total of 759792 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4621 -78.25153 6.71730 0.64875 INTE EXTERN> -27.74391 -50.50762 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2515" Parameter: A <- "-78.2515" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7439" Parameter: B <- "-27.7439" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5076" Parameter: C <- "-50.5076" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4621 TOTAL ENERGY = -78.2515 RDTITL> * VAN DER WAALS = -27.7439 ELECTROSTATIC = -50.5076 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4621" Parameter: CONF_N -> "8002" Comparing "4621" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4622" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759792 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759620 ATOM PAIRS WERE FOUND FOR ATOM LIST 41577 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29550 from a total of 759620 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4622 -74.64914 -3.60239 0.61677 INTE EXTERN> -27.36072 -47.28842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6491" Parameter: A <- "-74.6491" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3607" Parameter: B <- "-27.3607" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2884" Parameter: C <- "-47.2884" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4622 TOTAL ENERGY = -74.6491 RDTITL> * VAN DER WAALS = -27.3607 ELECTROSTATIC = -47.2884 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4622" Parameter: CONF_N -> "8002" Comparing "4622" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4623" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759620 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761951 ATOM PAIRS WERE FOUND FOR ATOM LIST 41791 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28668 from a total of 761951 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4623 -76.09428 1.44514 0.60992 INTE EXTERN> -30.96054 -45.13374 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0943" Parameter: A <- "-76.0943" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9605" Parameter: B <- "-30.9605" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1337" Parameter: C <- "-45.1337" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4623 TOTAL ENERGY = -76.0943 RDTITL> * VAN DER WAALS = -30.9605 ELECTROSTATIC = -45.1337 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4623" Parameter: CONF_N -> "8002" Comparing "4623" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4624" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761951 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754901 ATOM PAIRS WERE FOUND FOR ATOM LIST 41179 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28751 from a total of 754901 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4624 -72.99460 -3.09968 0.68962 INTE EXTERN> -26.40773 -46.58687 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9946" Parameter: A <- "-72.9946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4077" Parameter: B <- "-26.4077" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5869" Parameter: C <- "-46.5869" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4624 TOTAL ENERGY = -72.9946 RDTITL> * VAN DER WAALS = -26.4077 ELECTROSTATIC = -46.5869 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4624" Parameter: CONF_N -> "8002" Comparing "4624" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4625" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754901 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756126 ATOM PAIRS WERE FOUND FOR ATOM LIST 41539 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28633 from a total of 756126 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4625 -73.12458 0.12998 0.61519 INTE EXTERN> -26.81450 -46.31008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1246" Parameter: A <- "-73.1246" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8145" Parameter: B <- "-26.8145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3101" Parameter: C <- "-46.3101" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4625 TOTAL ENERGY = -73.1246 RDTITL> * VAN DER WAALS = -26.8145 ELECTROSTATIC = -46.3101 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4625" Parameter: CONF_N -> "8002" Comparing "4625" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4626" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756126 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748860 ATOM PAIRS WERE FOUND FOR ATOM LIST 41321 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28931 from a total of 748860 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4626 -79.99785 6.87327 0.63144 INTE EXTERN> -29.26515 -50.73270 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9978" Parameter: A <- "-79.9978" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2652" Parameter: B <- "-29.2652" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7327" Parameter: C <- "-50.7327" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4626 TOTAL ENERGY = -79.9978 RDTITL> * VAN DER WAALS = -29.2652 ELECTROSTATIC = -50.7327 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4626" Parameter: CONF_N -> "8002" Comparing "4626" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4627" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748860 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756914 ATOM PAIRS WERE FOUND FOR ATOM LIST 41298 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29054 from a total of 756914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4627 -79.48652 -0.51132 0.63936 INTE EXTERN> -30.80816 -48.67836 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4865" Parameter: A <- "-79.4865" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8082" Parameter: B <- "-30.8082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6784" Parameter: C <- "-48.6784" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4627 TOTAL ENERGY = -79.4865 RDTITL> * VAN DER WAALS = -30.8082 ELECTROSTATIC = -48.6784 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4627" Parameter: CONF_N -> "8002" Comparing "4627" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4628" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756349 ATOM PAIRS WERE FOUND FOR ATOM LIST 41257 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29093 from a total of 756349 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4628 -73.35507 -6.13146 0.69998 INTE EXTERN> -26.36274 -46.99233 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3551" Parameter: A <- "-73.3551" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3627" Parameter: B <- "-26.3627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9923" Parameter: C <- "-46.9923" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4628 TOTAL ENERGY = -73.3551 RDTITL> * VAN DER WAALS = -26.3627 ELECTROSTATIC = -46.9923 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4628" Parameter: CONF_N -> "8002" Comparing "4628" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4629" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756349 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759921 ATOM PAIRS WERE FOUND FOR ATOM LIST 41418 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29215 from a total of 759921 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4629 -69.32340 -4.03167 0.70566 INTE EXTERN> -24.56895 -44.75445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3234" Parameter: A <- "-69.3234" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5689" Parameter: B <- "-24.5689" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7545" Parameter: C <- "-44.7545" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4629 TOTAL ENERGY = -69.3234 RDTITL> * VAN DER WAALS = -24.5689 ELECTROSTATIC = -44.7545 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4629" Parameter: CONF_N -> "8002" Comparing "4629" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4630" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759921 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757921 ATOM PAIRS WERE FOUND FOR ATOM LIST 41578 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28993 from a total of 757921 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4630 -68.45572 -0.86768 0.63738 INTE EXTERN> -27.09560 -41.36012 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4557" Parameter: A <- "-68.4557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0956" Parameter: B <- "-27.0956" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3601" Parameter: C <- "-41.3601" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4630 TOTAL ENERGY = -68.4557 RDTITL> * VAN DER WAALS = -27.0956 ELECTROSTATIC = -41.3601 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4630" Parameter: CONF_N -> "8002" Comparing "4630" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4631" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757921 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757023 ATOM PAIRS WERE FOUND FOR ATOM LIST 41519 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29705 from a total of 757023 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4631 -78.09814 9.64241 0.71903 INTE EXTERN> -27.22889 -50.86925 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0981" Parameter: A <- "-78.0981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2289" Parameter: B <- "-27.2289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8692" Parameter: C <- "-50.8692" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4631 TOTAL ENERGY = -78.0981 RDTITL> * VAN DER WAALS = -27.2289 ELECTROSTATIC = -50.8692 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4631" Parameter: CONF_N -> "8002" Comparing "4631" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4632" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757023 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757814 ATOM PAIRS WERE FOUND FOR ATOM LIST 41411 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29238 from a total of 757814 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4632 -72.99508 -5.10306 0.65464 INTE EXTERN> -26.44579 -46.54929 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9951" Parameter: A <- "-72.9951" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4458" Parameter: B <- "-26.4458" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5493" Parameter: C <- "-46.5493" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4632 TOTAL ENERGY = -72.9951 RDTITL> * VAN DER WAALS = -26.4458 ELECTROSTATIC = -46.5493 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4632" Parameter: CONF_N -> "8002" Comparing "4632" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4633" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757814 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752657 ATOM PAIRS WERE FOUND FOR ATOM LIST 41427 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29116 from a total of 752657 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4633 -75.17201 2.17693 0.77080 INTE EXTERN> -24.74689 -50.42512 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.172" Parameter: A <- "-75.172" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7469" Parameter: B <- "-24.7469" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4251" Parameter: C <- "-50.4251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4633 TOTAL ENERGY = -75.172 RDTITL> * VAN DER WAALS = -24.7469 ELECTROSTATIC = -50.4251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4633" Parameter: CONF_N -> "8002" Comparing "4633" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4634" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752657 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758369 ATOM PAIRS WERE FOUND FOR ATOM LIST 41751 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29571 from a total of 758369 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4634 -74.45559 -0.71642 0.62987 INTE EXTERN> -31.52884 -42.92676 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4556" Parameter: A <- "-74.4556" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5288" Parameter: B <- "-31.5288" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9268" Parameter: C <- "-42.9268" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4634 TOTAL ENERGY = -74.4556 RDTITL> * VAN DER WAALS = -31.5288 ELECTROSTATIC = -42.9268 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4634" Parameter: CONF_N -> "8002" Comparing "4634" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4635" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758369 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41280 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29974 from a total of 754422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4635 -78.06444 3.60885 0.64538 INTE EXTERN> -30.25828 -47.80616 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0644" Parameter: A <- "-78.0644" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2583" Parameter: B <- "-30.2583" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8062" Parameter: C <- "-47.8062" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4635 TOTAL ENERGY = -78.0644 RDTITL> * VAN DER WAALS = -30.2583 ELECTROSTATIC = -47.8062 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4635" Parameter: CONF_N -> "8002" Comparing "4635" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4636" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749632 ATOM PAIRS WERE FOUND FOR ATOM LIST 41033 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29153 from a total of 749632 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4636 -79.16110 1.09666 0.73797 INTE EXTERN> -27.30143 -51.85967 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1611" Parameter: A <- "-79.1611" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3014" Parameter: B <- "-27.3014" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8597" Parameter: C <- "-51.8597" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4636 TOTAL ENERGY = -79.1611 RDTITL> * VAN DER WAALS = -27.3014 ELECTROSTATIC = -51.8597 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4636" Parameter: CONF_N -> "8002" Comparing "4636" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4637" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749632 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750641 ATOM PAIRS WERE FOUND FOR ATOM LIST 41235 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29345 from a total of 750641 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4637 -70.22274 -8.93837 0.71753 INTE EXTERN> -23.35247 -46.87027 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2227" Parameter: A <- "-70.2227" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.3525" Parameter: B <- "-23.3525" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8703" Parameter: C <- "-46.8703" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4637 TOTAL ENERGY = -70.2227 RDTITL> * VAN DER WAALS = -23.3525 ELECTROSTATIC = -46.8703 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4637" Parameter: CONF_N -> "8002" Comparing "4637" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4638" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750641 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759346 ATOM PAIRS WERE FOUND FOR ATOM LIST 41554 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30144 from a total of 759346 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4638 -74.14953 3.92680 0.61134 INTE EXTERN> -31.29941 -42.85012 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1495" Parameter: A <- "-74.1495" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2994" Parameter: B <- "-31.2994" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8501" Parameter: C <- "-42.8501" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4638 TOTAL ENERGY = -74.1495 RDTITL> * VAN DER WAALS = -31.2994 ELECTROSTATIC = -42.8501 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4638" Parameter: CONF_N -> "8002" Comparing "4638" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4639" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759346 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750446 ATOM PAIRS WERE FOUND FOR ATOM LIST 41282 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28775 from a total of 750446 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4639 -65.74000 -8.40953 0.73979 INTE EXTERN> -21.96025 -43.77975 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.74" Parameter: A <- "-65.74" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.9602" Parameter: B <- "-21.9602" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7798" Parameter: C <- "-43.7798" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4639 TOTAL ENERGY = -65.74 RDTITL> * VAN DER WAALS = -21.9602 ELECTROSTATIC = -43.7798 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4639" Parameter: CONF_N -> "8002" Comparing "4639" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4640" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750446 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759729 ATOM PAIRS WERE FOUND FOR ATOM LIST 41752 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29560 from a total of 759729 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4640 -72.02245 6.28245 0.75037 INTE EXTERN> -24.28126 -47.74119 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0224" Parameter: A <- "-72.0224" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2813" Parameter: B <- "-24.2813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7412" Parameter: C <- "-47.7412" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4640 TOTAL ENERGY = -72.0224 RDTITL> * VAN DER WAALS = -24.2813 ELECTROSTATIC = -47.7412 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4640" Parameter: CONF_N -> "8002" Comparing "4640" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4641" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759729 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753631 ATOM PAIRS WERE FOUND FOR ATOM LIST 41267 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29403 from a total of 753631 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4641 -76.02649 4.00404 0.70098 INTE EXTERN> -25.95368 -50.07281 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0265" Parameter: A <- "-76.0265" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9537" Parameter: B <- "-25.9537" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0728" Parameter: C <- "-50.0728" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4641 TOTAL ENERGY = -76.0265 RDTITL> * VAN DER WAALS = -25.9537 ELECTROSTATIC = -50.0728 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4641" Parameter: CONF_N -> "8002" Comparing "4641" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4642" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753631 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761774 ATOM PAIRS WERE FOUND FOR ATOM LIST 42008 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29904 from a total of 761774 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4642 -76.59904 0.57255 0.73442 INTE EXTERN> -27.68544 -48.91360 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.599" Parameter: A <- "-76.599" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6854" Parameter: B <- "-27.6854" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9136" Parameter: C <- "-48.9136" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4642 TOTAL ENERGY = -76.599 RDTITL> * VAN DER WAALS = -27.6854 ELECTROSTATIC = -48.9136 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4642" Parameter: CONF_N -> "8002" Comparing "4642" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4643" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761774 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757505 ATOM PAIRS WERE FOUND FOR ATOM LIST 41424 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29932 from a total of 757505 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4643 -76.09615 -0.50289 0.61287 INTE EXTERN> -32.99902 -43.09713 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0962" Parameter: A <- "-76.0962" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.999" Parameter: B <- "-32.999" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0971" Parameter: C <- "-43.0971" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4643 TOTAL ENERGY = -76.0962 RDTITL> * VAN DER WAALS = -32.999 ELECTROSTATIC = -43.0971 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4643" Parameter: CONF_N -> "8002" Comparing "4643" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4644" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757505 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758223 ATOM PAIRS WERE FOUND FOR ATOM LIST 41602 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29707 from a total of 758223 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4644 -74.96184 -1.13431 0.64356 INTE EXTERN> -31.05439 -43.90745 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9618" Parameter: A <- "-74.9618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0544" Parameter: B <- "-31.0544" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9075" Parameter: C <- "-43.9075" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4644 TOTAL ENERGY = -74.9618 RDTITL> * VAN DER WAALS = -31.0544 ELECTROSTATIC = -43.9075 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4644" Parameter: CONF_N -> "8002" Comparing "4644" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4645" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758223 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757604 ATOM PAIRS WERE FOUND FOR ATOM LIST 41586 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29319 from a total of 757604 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4645 -73.89278 -1.06906 0.67472 INTE EXTERN> -28.19794 -45.69484 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8928" Parameter: A <- "-73.8928" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1979" Parameter: B <- "-28.1979" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6948" Parameter: C <- "-45.6948" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4645 TOTAL ENERGY = -73.8928 RDTITL> * VAN DER WAALS = -28.1979 ELECTROSTATIC = -45.6948 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4645" Parameter: CONF_N -> "8002" Comparing "4645" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4646" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757604 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755443 ATOM PAIRS WERE FOUND FOR ATOM LIST 41518 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30099 from a total of 755443 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4646 -67.63186 -6.26092 0.71438 INTE EXTERN> -22.50570 -45.12616 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6319" Parameter: A <- "-67.6319" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.5057" Parameter: B <- "-22.5057" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1262" Parameter: C <- "-45.1262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4646 TOTAL ENERGY = -67.6319 RDTITL> * VAN DER WAALS = -22.5057 ELECTROSTATIC = -45.1262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4646" Parameter: CONF_N -> "8002" Comparing "4646" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4647" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755443 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41798 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29966 from a total of 760601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4647 -75.07391 7.44205 0.66712 INTE EXTERN> -29.86519 -45.20872 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0739" Parameter: A <- "-75.0739" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8652" Parameter: B <- "-29.8652" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2087" Parameter: C <- "-45.2087" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4647 TOTAL ENERGY = -75.0739 RDTITL> * VAN DER WAALS = -29.8652 ELECTROSTATIC = -45.2087 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4647" Parameter: CONF_N -> "8002" Comparing "4647" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4648" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755759 ATOM PAIRS WERE FOUND FOR ATOM LIST 41503 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28988 from a total of 755759 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4648 -74.88889 -0.18502 0.70157 INTE EXTERN> -28.81824 -46.07065 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8889" Parameter: A <- "-74.8889" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8182" Parameter: B <- "-28.8182" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0706" Parameter: C <- "-46.0706" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4648 TOTAL ENERGY = -74.8889 RDTITL> * VAN DER WAALS = -28.8182 ELECTROSTATIC = -46.0706 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4648" Parameter: CONF_N -> "8002" Comparing "4648" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4649" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755759 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754412 ATOM PAIRS WERE FOUND FOR ATOM LIST 41570 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29018 from a total of 754412 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4649 -74.69948 -0.18941 0.65859 INTE EXTERN> -29.38863 -45.31085 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6995" Parameter: A <- "-74.6995" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3886" Parameter: B <- "-29.3886" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3109" Parameter: C <- "-45.3109" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4649 TOTAL ENERGY = -74.6995 RDTITL> * VAN DER WAALS = -29.3886 ELECTROSTATIC = -45.3109 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4649" Parameter: CONF_N -> "8002" Comparing "4649" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4650" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754412 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758815 ATOM PAIRS WERE FOUND FOR ATOM LIST 41670 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29682 from a total of 758815 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4650 -73.09650 -1.60298 0.66971 INTE EXTERN> -30.10618 -42.99032 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0965" Parameter: A <- "-73.0965" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1062" Parameter: B <- "-30.1062" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9903" Parameter: C <- "-42.9903" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4650 TOTAL ENERGY = -73.0965 RDTITL> * VAN DER WAALS = -30.1062 ELECTROSTATIC = -42.9903 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4650" Parameter: CONF_N -> "8002" Comparing "4650" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4651" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758815 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756701 ATOM PAIRS WERE FOUND FOR ATOM LIST 41682 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29627 from a total of 756701 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4651 -78.98102 5.88453 0.71067 INTE EXTERN> -28.30735 -50.67367 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.981" Parameter: A <- "-78.981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3074" Parameter: B <- "-28.3074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6737" Parameter: C <- "-50.6737" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4651 TOTAL ENERGY = -78.981 RDTITL> * VAN DER WAALS = -28.3074 ELECTROSTATIC = -50.6737 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4651" Parameter: CONF_N -> "8002" Comparing "4651" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4652" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756701 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762312 ATOM PAIRS WERE FOUND FOR ATOM LIST 41884 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29939 from a total of 762312 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4652 -68.14472 -10.83631 0.71247 INTE EXTERN> -28.10264 -40.04207 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1447" Parameter: A <- "-68.1447" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1026" Parameter: B <- "-28.1026" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0421" Parameter: C <- "-40.0421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4652 TOTAL ENERGY = -68.1447 RDTITL> * VAN DER WAALS = -28.1026 ELECTROSTATIC = -40.0421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4652" Parameter: CONF_N -> "8002" Comparing "4652" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4653" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762312 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765893 ATOM PAIRS WERE FOUND FOR ATOM LIST 41767 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29640 from a total of 765893 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4653 -71.88067 3.73595 0.64092 INTE EXTERN> -31.92449 -39.95618 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8807" Parameter: A <- "-71.8807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9245" Parameter: B <- "-31.9245" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9562" Parameter: C <- "-39.9562" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4653 TOTAL ENERGY = -71.8807 RDTITL> * VAN DER WAALS = -31.9245 ELECTROSTATIC = -39.9562 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4653" Parameter: CONF_N -> "8002" Comparing "4653" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4654" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765893 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761902 ATOM PAIRS WERE FOUND FOR ATOM LIST 41801 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29492 from a total of 761902 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4654 -76.92302 5.04235 0.63301 INTE EXTERN> -32.50973 -44.41329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.923" Parameter: A <- "-76.923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5097" Parameter: B <- "-32.5097" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4133" Parameter: C <- "-44.4133" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4654 TOTAL ENERGY = -76.923 RDTITL> * VAN DER WAALS = -32.5097 ELECTROSTATIC = -44.4133 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4654" Parameter: CONF_N -> "8002" Comparing "4654" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4655" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761902 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762582 ATOM PAIRS WERE FOUND FOR ATOM LIST 41897 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29790 from a total of 762582 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4655 -76.50397 -0.41905 0.73337 INTE EXTERN> -28.61502 -47.88895 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.504" Parameter: A <- "-76.504" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.615" Parameter: B <- "-28.615" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.889" Parameter: C <- "-47.889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4655 TOTAL ENERGY = -76.504 RDTITL> * VAN DER WAALS = -28.615 ELECTROSTATIC = -47.889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4655" Parameter: CONF_N -> "8002" Comparing "4655" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4656" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762582 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764384 ATOM PAIRS WERE FOUND FOR ATOM LIST 42019 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30496 from a total of 764384 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4656 -73.15698 -3.34699 0.70061 INTE EXTERN> -28.24868 -44.90830 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.157" Parameter: A <- "-73.157" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2487" Parameter: B <- "-28.2487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9083" Parameter: C <- "-44.9083" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4656 TOTAL ENERGY = -73.157 RDTITL> * VAN DER WAALS = -28.2487 ELECTROSTATIC = -44.9083 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4656" Parameter: CONF_N -> "8002" Comparing "4656" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4657" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764384 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766531 ATOM PAIRS WERE FOUND FOR ATOM LIST 41888 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30173 from a total of 766531 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4657 -76.11840 2.96141 0.69320 INTE EXTERN> -29.27400 -46.84439 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1184" Parameter: A <- "-76.1184" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.274" Parameter: B <- "-29.274" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8444" Parameter: C <- "-46.8444" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4657 TOTAL ENERGY = -76.1184 RDTITL> * VAN DER WAALS = -29.274 ELECTROSTATIC = -46.8444 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4657" Parameter: CONF_N -> "8002" Comparing "4657" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4658" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766531 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762173 ATOM PAIRS WERE FOUND FOR ATOM LIST 41830 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30388 from a total of 762173 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4658 -78.83158 2.71319 0.76156 INTE EXTERN> -28.32876 -50.50282 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8316" Parameter: A <- "-78.8316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3288" Parameter: B <- "-28.3288" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5028" Parameter: C <- "-50.5028" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4658 TOTAL ENERGY = -78.8316 RDTITL> * VAN DER WAALS = -28.3288 ELECTROSTATIC = -50.5028 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4658" Parameter: CONF_N -> "8002" Comparing "4658" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4659" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762173 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762846 ATOM PAIRS WERE FOUND FOR ATOM LIST 41933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30380 from a total of 762846 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4659 -73.90249 -4.92910 0.68107 INTE EXTERN> -30.16376 -43.73873 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9025" Parameter: A <- "-73.9025" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1638" Parameter: B <- "-30.1638" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7387" Parameter: C <- "-43.7387" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4659 TOTAL ENERGY = -73.9025 RDTITL> * VAN DER WAALS = -30.1638 ELECTROSTATIC = -43.7387 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4659" Parameter: CONF_N -> "8002" Comparing "4659" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4660" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762846 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771055 ATOM PAIRS WERE FOUND FOR ATOM LIST 42265 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 31001 from a total of 771055 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4660 -80.90252 7.00004 0.66569 INTE EXTERN> -31.40574 -49.49678 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9025" Parameter: A <- "-80.9025" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4057" Parameter: B <- "-31.4057" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4968" Parameter: C <- "-49.4968" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4660 TOTAL ENERGY = -80.9025 RDTITL> * VAN DER WAALS = -31.4057 ELECTROSTATIC = -49.4968 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4660" Parameter: CONF_N -> "8002" Comparing "4660" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4661" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771055 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764272 ATOM PAIRS WERE FOUND FOR ATOM LIST 42139 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30592 from a total of 764272 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4661 -75.92590 -4.97663 0.59010 INTE EXTERN> -32.63031 -43.29558 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9259" Parameter: A <- "-75.9259" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6303" Parameter: B <- "-32.6303" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2956" Parameter: C <- "-43.2956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4661 TOTAL ENERGY = -75.9259 RDTITL> * VAN DER WAALS = -32.6303 ELECTROSTATIC = -43.2956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4661" Parameter: CONF_N -> "8002" Comparing "4661" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4662" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764272 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759077 ATOM PAIRS WERE FOUND FOR ATOM LIST 41823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29869 from a total of 759077 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4662 -76.52428 0.59839 0.83586 INTE EXTERN> -22.67680 -53.84748 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5243" Parameter: A <- "-76.5243" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.6768" Parameter: B <- "-22.6768" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8475" Parameter: C <- "-53.8475" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4662 TOTAL ENERGY = -76.5243 RDTITL> * VAN DER WAALS = -22.6768 ELECTROSTATIC = -53.8475 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4662" Parameter: CONF_N -> "8002" Comparing "4662" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4663" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759077 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763650 ATOM PAIRS WERE FOUND FOR ATOM LIST 41749 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29807 from a total of 763650 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4663 -66.74422 -9.78007 0.70206 INTE EXTERN> -27.93378 -38.81043 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7442" Parameter: A <- "-66.7442" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9338" Parameter: B <- "-27.9338" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8104" Parameter: C <- "-38.8104" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4663 TOTAL ENERGY = -66.7442 RDTITL> * VAN DER WAALS = -27.9338 ELECTROSTATIC = -38.8104 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4663" Parameter: CONF_N -> "8002" Comparing "4663" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4664" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763650 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760117 ATOM PAIRS WERE FOUND FOR ATOM LIST 41624 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29564 from a total of 760117 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4664 -69.91534 3.17112 0.69051 INTE EXTERN> -30.37956 -39.53577 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9153" Parameter: A <- "-69.9153" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3796" Parameter: B <- "-30.3796" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5358" Parameter: C <- "-39.5358" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4664 TOTAL ENERGY = -69.9153 RDTITL> * VAN DER WAALS = -30.3796 ELECTROSTATIC = -39.5358 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4664" Parameter: CONF_N -> "8002" Comparing "4664" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4665" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760117 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759080 ATOM PAIRS WERE FOUND FOR ATOM LIST 41567 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29328 from a total of 759080 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4665 -70.48674 0.57140 0.71747 INTE EXTERN> -28.09997 -42.38677 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4867" Parameter: A <- "-70.4867" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1" Parameter: B <- "-28.1" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3868" Parameter: C <- "-42.3868" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4665 TOTAL ENERGY = -70.4867 RDTITL> * VAN DER WAALS = -28.1 ELECTROSTATIC = -42.3868 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4665" Parameter: CONF_N -> "8002" Comparing "4665" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4666" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759080 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761489 ATOM PAIRS WERE FOUND FOR ATOM LIST 41701 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29686 from a total of 761489 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4666 -73.49733 3.01059 0.71061 INTE EXTERN> -27.93687 -45.56046 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4973" Parameter: A <- "-73.4973" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9369" Parameter: B <- "-27.9369" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5605" Parameter: C <- "-45.5605" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4666 TOTAL ENERGY = -73.4973 RDTITL> * VAN DER WAALS = -27.9369 ELECTROSTATIC = -45.5605 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4666" Parameter: CONF_N -> "8002" Comparing "4666" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4667" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761489 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765440 ATOM PAIRS WERE FOUND FOR ATOM LIST 41939 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29408 from a total of 765440 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4667 -70.67919 -2.81814 0.71763 INTE EXTERN> -28.47411 -42.20508 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6792" Parameter: A <- "-70.6792" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4741" Parameter: B <- "-28.4741" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2051" Parameter: C <- "-42.2051" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4667 TOTAL ENERGY = -70.6792 RDTITL> * VAN DER WAALS = -28.4741 ELECTROSTATIC = -42.2051 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4667" Parameter: CONF_N -> "8002" Comparing "4667" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4668" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765440 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759515 ATOM PAIRS WERE FOUND FOR ATOM LIST 41629 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29058 from a total of 759515 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4668 -78.35499 7.67580 0.68380 INTE EXTERN> -29.59680 -48.75819 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.355" Parameter: A <- "-78.355" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5968" Parameter: B <- "-29.5968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7582" Parameter: C <- "-48.7582" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4668 TOTAL ENERGY = -78.355 RDTITL> * VAN DER WAALS = -29.5968 ELECTROSTATIC = -48.7582 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4668" Parameter: CONF_N -> "8002" Comparing "4668" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4669" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759515 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758956 ATOM PAIRS WERE FOUND FOR ATOM LIST 41463 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28805 from a total of 758956 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4669 -76.10530 -2.24968 0.67579 INTE EXTERN> -30.79495 -45.31035 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1053" Parameter: A <- "-76.1053" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.795" Parameter: B <- "-30.795" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3104" Parameter: C <- "-45.3104" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4669 TOTAL ENERGY = -76.1053 RDTITL> * VAN DER WAALS = -30.795 ELECTROSTATIC = -45.3104 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4669" Parameter: CONF_N -> "8002" Comparing "4669" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4670" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758956 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753055 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29392 from a total of 753055 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4670 -75.26738 -0.83792 0.76098 INTE EXTERN> -25.12810 -50.13928 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2674" Parameter: A <- "-75.2674" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1281" Parameter: B <- "-25.1281" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1393" Parameter: C <- "-50.1393" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4670 TOTAL ENERGY = -75.2674 RDTITL> * VAN DER WAALS = -25.1281 ELECTROSTATIC = -50.1393 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4670" Parameter: CONF_N -> "8002" Comparing "4670" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4671" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753055 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766044 ATOM PAIRS WERE FOUND FOR ATOM LIST 42093 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29470 from a total of 766044 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4671 -78.35674 3.08936 0.68901 INTE EXTERN> -29.58815 -48.76858 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3567" Parameter: A <- "-78.3567" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5882" Parameter: B <- "-29.5882" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7686" Parameter: C <- "-48.7686" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4671 TOTAL ENERGY = -78.3567 RDTITL> * VAN DER WAALS = -29.5882 ELECTROSTATIC = -48.7686 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4671" Parameter: CONF_N -> "8002" Comparing "4671" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4672" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766044 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763584 ATOM PAIRS WERE FOUND FOR ATOM LIST 41897 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29256 from a total of 763584 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4672 -72.04422 -6.31251 0.65907 INTE EXTERN> -28.11286 -43.93136 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0442" Parameter: A <- "-72.0442" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1129" Parameter: B <- "-28.1129" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9314" Parameter: C <- "-43.9314" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4672 TOTAL ENERGY = -72.0442 RDTITL> * VAN DER WAALS = -28.1129 ELECTROSTATIC = -43.9314 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4672" Parameter: CONF_N -> "8002" Comparing "4672" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4673" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763584 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761370 ATOM PAIRS WERE FOUND FOR ATOM LIST 41677 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29078 from a total of 761370 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4673 -74.38407 2.33984 0.68299 INTE EXTERN> -31.91891 -42.46516 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3841" Parameter: A <- "-74.3841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9189" Parameter: B <- "-31.9189" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4652" Parameter: C <- "-42.4652" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4673 TOTAL ENERGY = -74.3841 RDTITL> * VAN DER WAALS = -31.9189 ELECTROSTATIC = -42.4652 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4673" Parameter: CONF_N -> "8002" Comparing "4673" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4674" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761370 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756020 ATOM PAIRS WERE FOUND FOR ATOM LIST 41624 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29708 from a total of 756020 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4674 -69.90822 -4.47585 0.63889 INTE EXTERN> -27.88173 -42.02649 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9082" Parameter: A <- "-69.9082" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8817" Parameter: B <- "-27.8817" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0265" Parameter: C <- "-42.0265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4674 TOTAL ENERGY = -69.9082 RDTITL> * VAN DER WAALS = -27.8817 ELECTROSTATIC = -42.0265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4674" Parameter: CONF_N -> "8002" Comparing "4674" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4675" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756020 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759069 ATOM PAIRS WERE FOUND FOR ATOM LIST 41681 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29526 from a total of 759069 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4675 -73.67972 3.77150 0.66376 INTE EXTERN> -29.55246 -44.12727 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6797" Parameter: A <- "-73.6797" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5525" Parameter: B <- "-29.5525" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1273" Parameter: C <- "-44.1273" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4675 TOTAL ENERGY = -73.6797 RDTITL> * VAN DER WAALS = -29.5525 ELECTROSTATIC = -44.1273 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4675" Parameter: CONF_N -> "8002" Comparing "4675" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4676" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759069 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760974 ATOM PAIRS WERE FOUND FOR ATOM LIST 41611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28900 from a total of 760974 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4676 -67.91393 -5.76579 0.75201 INTE EXTERN> -26.27085 -41.64308 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9139" Parameter: A <- "-67.9139" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2709" Parameter: B <- "-26.2709" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6431" Parameter: C <- "-41.6431" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4676 TOTAL ENERGY = -67.9139 RDTITL> * VAN DER WAALS = -26.2709 ELECTROSTATIC = -41.6431 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4676" Parameter: CONF_N -> "8002" Comparing "4676" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4677" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760974 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757415 ATOM PAIRS WERE FOUND FOR ATOM LIST 41501 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29362 from a total of 757415 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4677 -71.81608 3.90215 0.64755 INTE EXTERN> -26.69358 -45.12250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8161" Parameter: A <- "-71.8161" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6936" Parameter: B <- "-26.6936" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1225" Parameter: C <- "-45.1225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4677 TOTAL ENERGY = -71.8161 RDTITL> * VAN DER WAALS = -26.6936 ELECTROSTATIC = -45.1225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4677" Parameter: CONF_N -> "8002" Comparing "4677" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4678" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757415 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754705 ATOM PAIRS WERE FOUND FOR ATOM LIST 41339 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29474 from a total of 754705 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4678 -69.49851 -2.31757 0.61668 INTE EXTERN> -28.34806 -41.15045 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4985" Parameter: A <- "-69.4985" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3481" Parameter: B <- "-28.3481" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1504" Parameter: C <- "-41.1504" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4678 TOTAL ENERGY = -69.4985 RDTITL> * VAN DER WAALS = -28.3481 ELECTROSTATIC = -41.1504 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4678" Parameter: CONF_N -> "8002" Comparing "4678" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4679" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754705 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759298 ATOM PAIRS WERE FOUND FOR ATOM LIST 41635 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29306 from a total of 759298 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4679 -72.54054 3.04203 0.65815 INTE EXTERN> -27.79078 -44.74976 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5405" Parameter: A <- "-72.5405" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7908" Parameter: B <- "-27.7908" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7498" Parameter: C <- "-44.7498" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4679 TOTAL ENERGY = -72.5405 RDTITL> * VAN DER WAALS = -27.7908 ELECTROSTATIC = -44.7498 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4679" Parameter: CONF_N -> "8002" Comparing "4679" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4680" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759298 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764906 ATOM PAIRS WERE FOUND FOR ATOM LIST 41876 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28717 from a total of 764906 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4680 -75.92061 3.38006 0.74107 INTE EXTERN> -28.11886 -47.80175 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9206" Parameter: A <- "-75.9206" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1189" Parameter: B <- "-28.1189" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8017" Parameter: C <- "-47.8017" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4680 TOTAL ENERGY = -75.9206 RDTITL> * VAN DER WAALS = -28.1189 ELECTROSTATIC = -47.8017 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4680" Parameter: CONF_N -> "8002" Comparing "4680" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4681" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764906 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763837 ATOM PAIRS WERE FOUND FOR ATOM LIST 41687 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29533 from a total of 763837 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4681 -72.90588 -3.01472 0.72924 INTE EXTERN> -23.95689 -48.94899 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9059" Parameter: A <- "-72.9059" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9569" Parameter: B <- "-23.9569" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.949" Parameter: C <- "-48.949" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4681 TOTAL ENERGY = -72.9059 RDTITL> * VAN DER WAALS = -23.9569 ELECTROSTATIC = -48.949 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4681" Parameter: CONF_N -> "8002" Comparing "4681" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4682" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763837 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762590 ATOM PAIRS WERE FOUND FOR ATOM LIST 41851 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29616 from a total of 762590 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4682 -69.06489 -3.84099 0.87359 INTE EXTERN> -23.20438 -45.86051 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0649" Parameter: A <- "-69.0649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.2044" Parameter: B <- "-23.2044" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8605" Parameter: C <- "-45.8605" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4682 TOTAL ENERGY = -69.0649 RDTITL> * VAN DER WAALS = -23.2044 ELECTROSTATIC = -45.8605 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4682" Parameter: CONF_N -> "8002" Comparing "4682" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4683" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762590 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762347 ATOM PAIRS WERE FOUND FOR ATOM LIST 41696 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29355 from a total of 762347 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4683 -71.02554 1.96065 0.73807 INTE EXTERN> -27.67022 -43.35532 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0255" Parameter: A <- "-71.0255" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6702" Parameter: B <- "-27.6702" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3553" Parameter: C <- "-43.3553" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4683 TOTAL ENERGY = -71.0255 RDTITL> * VAN DER WAALS = -27.6702 ELECTROSTATIC = -43.3553 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4683" Parameter: CONF_N -> "8002" Comparing "4683" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4684" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762347 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765004 ATOM PAIRS WERE FOUND FOR ATOM LIST 42005 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29654 from a total of 765004 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4684 -70.53121 -0.49433 0.74071 INTE EXTERN> -28.42352 -42.10769 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5312" Parameter: A <- "-70.5312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4235" Parameter: B <- "-28.4235" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1077" Parameter: C <- "-42.1077" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4684 TOTAL ENERGY = -70.5312 RDTITL> * VAN DER WAALS = -28.4235 ELECTROSTATIC = -42.1077 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4684" Parameter: CONF_N -> "8002" Comparing "4684" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4685" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765004 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766005 ATOM PAIRS WERE FOUND FOR ATOM LIST 41913 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29532 from a total of 766005 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4685 -73.54913 3.01792 0.61772 INTE EXTERN> -30.70992 -42.83921 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5491" Parameter: A <- "-73.5491" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7099" Parameter: B <- "-30.7099" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8392" Parameter: C <- "-42.8392" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4685 TOTAL ENERGY = -73.5491 RDTITL> * VAN DER WAALS = -30.7099 ELECTROSTATIC = -42.8392 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4685" Parameter: CONF_N -> "8002" Comparing "4685" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4686" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766005 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765768 ATOM PAIRS WERE FOUND FOR ATOM LIST 41830 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29325 from a total of 765768 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4686 -76.92793 3.37880 0.68159 INTE EXTERN> -29.41019 -47.51774 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9279" Parameter: A <- "-76.9279" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4102" Parameter: B <- "-29.4102" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5177" Parameter: C <- "-47.5177" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4686 TOTAL ENERGY = -76.9279 RDTITL> * VAN DER WAALS = -29.4102 ELECTROSTATIC = -47.5177 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4686" Parameter: CONF_N -> "8002" Comparing "4686" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4687" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765768 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761214 ATOM PAIRS WERE FOUND FOR ATOM LIST 41715 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29495 from a total of 761214 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4687 -73.64801 -3.27992 0.64801 INTE EXTERN> -28.98203 -44.66598 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.648" Parameter: A <- "-73.648" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.982" Parameter: B <- "-28.982" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.666" Parameter: C <- "-44.666" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4687 TOTAL ENERGY = -73.648 RDTITL> * VAN DER WAALS = -28.982 ELECTROSTATIC = -44.666 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4687" Parameter: CONF_N -> "8002" Comparing "4687" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4688" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761214 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760017 ATOM PAIRS WERE FOUND FOR ATOM LIST 41710 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29291 from a total of 760017 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4688 -72.08035 -1.56765 0.78513 INTE EXTERN> -26.19970 -45.88066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0804" Parameter: A <- "-72.0804" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1997" Parameter: B <- "-26.1997" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8807" Parameter: C <- "-45.8807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4688 TOTAL ENERGY = -72.0804 RDTITL> * VAN DER WAALS = -26.1997 ELECTROSTATIC = -45.8807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4688" Parameter: CONF_N -> "8002" Comparing "4688" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4689" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760017 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760886 ATOM PAIRS WERE FOUND FOR ATOM LIST 41600 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29194 from a total of 760886 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4689 -70.29638 -1.78397 0.69418 INTE EXTERN> -26.85882 -43.43756 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2964" Parameter: A <- "-70.2964" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8588" Parameter: B <- "-26.8588" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4376" Parameter: C <- "-43.4376" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4689 TOTAL ENERGY = -70.2964 RDTITL> * VAN DER WAALS = -26.8588 ELECTROSTATIC = -43.4376 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4689" Parameter: CONF_N -> "8002" Comparing "4689" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4690" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760886 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757529 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30178 from a total of 757529 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4690 -74.69035 4.39397 0.72038 INTE EXTERN> -25.92190 -48.76845 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6904" Parameter: A <- "-74.6904" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9219" Parameter: B <- "-25.9219" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7685" Parameter: C <- "-48.7685" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4690 TOTAL ENERGY = -74.6904 RDTITL> * VAN DER WAALS = -25.9219 ELECTROSTATIC = -48.7685 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4690" Parameter: CONF_N -> "8002" Comparing "4690" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4691" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757529 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759261 ATOM PAIRS WERE FOUND FOR ATOM LIST 41363 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30238 from a total of 759261 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4691 -71.02491 -3.66544 0.62622 INTE EXTERN> -30.28282 -40.74209 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0249" Parameter: A <- "-71.0249" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2828" Parameter: B <- "-30.2828" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7421" Parameter: C <- "-40.7421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4691 TOTAL ENERGY = -71.0249 RDTITL> * VAN DER WAALS = -30.2828 ELECTROSTATIC = -40.7421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4691" Parameter: CONF_N -> "8002" Comparing "4691" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4692" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759261 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757088 ATOM PAIRS WERE FOUND FOR ATOM LIST 41404 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29549 from a total of 757088 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4692 -74.55682 3.53191 0.72088 INTE EXTERN> -27.22146 -47.33536 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5568" Parameter: A <- "-74.5568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2215" Parameter: B <- "-27.2215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3354" Parameter: C <- "-47.3354" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4692 TOTAL ENERGY = -74.5568 RDTITL> * VAN DER WAALS = -27.2215 ELECTROSTATIC = -47.3354 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4692" Parameter: CONF_N -> "8002" Comparing "4692" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4693" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757088 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760206 ATOM PAIRS WERE FOUND FOR ATOM LIST 41724 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29753 from a total of 760206 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4693 -73.44616 -1.11065 0.63072 INTE EXTERN> -29.55053 -43.89563 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4462" Parameter: A <- "-73.4462" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5505" Parameter: B <- "-29.5505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8956" Parameter: C <- "-43.8956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4693 TOTAL ENERGY = -73.4462 RDTITL> * VAN DER WAALS = -29.5505 ELECTROSTATIC = -43.8956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4693" Parameter: CONF_N -> "8002" Comparing "4693" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4694" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760206 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757890 ATOM PAIRS WERE FOUND FOR ATOM LIST 41406 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29033 from a total of 757890 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4694 -81.34316 7.89699 0.77615 INTE EXTERN> -26.59695 -54.74620 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.3432" Parameter: A <- "-81.3432" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.597" Parameter: B <- "-26.597" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.7462" Parameter: C <- "-54.7462" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4694 TOTAL ENERGY = -81.3432 RDTITL> * VAN DER WAALS = -26.597 ELECTROSTATIC = -54.7462 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4694" Parameter: CONF_N -> "8002" Comparing "4694" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4695" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757890 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764299 ATOM PAIRS WERE FOUND FOR ATOM LIST 41785 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30069 from a total of 764299 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4695 -78.07723 -3.26592 0.67893 INTE EXTERN> -27.31297 -50.76427 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0772" Parameter: A <- "-78.0772" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.313" Parameter: B <- "-27.313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7643" Parameter: C <- "-50.7643" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4695 TOTAL ENERGY = -78.0772 RDTITL> * VAN DER WAALS = -27.313 ELECTROSTATIC = -50.7643 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4695" Parameter: CONF_N -> "8002" Comparing "4695" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4696" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764299 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762535 ATOM PAIRS WERE FOUND FOR ATOM LIST 41883 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29268 from a total of 762535 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4696 -73.04879 -5.02845 0.59356 INTE EXTERN> -32.41741 -40.63138 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0488" Parameter: A <- "-73.0488" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4174" Parameter: B <- "-32.4174" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6314" Parameter: C <- "-40.6314" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4696 TOTAL ENERGY = -73.0488 RDTITL> * VAN DER WAALS = -32.4174 ELECTROSTATIC = -40.6314 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4696" Parameter: CONF_N -> "8002" Comparing "4696" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4697" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762535 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764000 ATOM PAIRS WERE FOUND FOR ATOM LIST 41759 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29979 from a total of 764000 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4697 -77.06302 4.01423 0.77290 INTE EXTERN> -24.07069 -52.99233 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.063" Parameter: A <- "-77.063" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0707" Parameter: B <- "-24.0707" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9923" Parameter: C <- "-52.9923" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4697 TOTAL ENERGY = -77.063 RDTITL> * VAN DER WAALS = -24.0707 ELECTROSTATIC = -52.9923 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4697" Parameter: CONF_N -> "8002" Comparing "4697" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4698" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764000 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758424 ATOM PAIRS WERE FOUND FOR ATOM LIST 41540 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29942 from a total of 758424 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4698 -74.06970 -2.99332 0.66215 INTE EXTERN> -31.66290 -42.40681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0697" Parameter: A <- "-74.0697" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6629" Parameter: B <- "-31.6629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4068" Parameter: C <- "-42.4068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4698 TOTAL ENERGY = -74.0697 RDTITL> * VAN DER WAALS = -31.6629 ELECTROSTATIC = -42.4068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4698" Parameter: CONF_N -> "8002" Comparing "4698" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4699" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758424 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762644 ATOM PAIRS WERE FOUND FOR ATOM LIST 41762 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29522 from a total of 762644 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4699 -73.24564 -0.82406 0.81220 INTE EXTERN> -23.96742 -49.27822 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2456" Parameter: A <- "-73.2456" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9674" Parameter: B <- "-23.9674" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2782" Parameter: C <- "-49.2782" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4699 TOTAL ENERGY = -73.2456 RDTITL> * VAN DER WAALS = -23.9674 ELECTROSTATIC = -49.2782 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4699" Parameter: CONF_N -> "8002" Comparing "4699" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4700" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762644 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764498 ATOM PAIRS WERE FOUND FOR ATOM LIST 41931 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29089 from a total of 764498 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4700 -76.13205 2.88641 0.69939 INTE EXTERN> -27.00987 -49.12219 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1321" Parameter: A <- "-76.1321" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0099" Parameter: B <- "-27.0099" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1222" Parameter: C <- "-49.1222" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4700 TOTAL ENERGY = -76.1321 RDTITL> * VAN DER WAALS = -27.0099 ELECTROSTATIC = -49.1222 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4700" Parameter: CONF_N -> "8002" Comparing "4700" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4701" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764498 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758566 ATOM PAIRS WERE FOUND FOR ATOM LIST 41631 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29244 from a total of 758566 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4701 -73.78082 -2.35123 0.67966 INTE EXTERN> -28.75790 -45.02293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7808" Parameter: A <- "-73.7808" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7579" Parameter: B <- "-28.7579" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0229" Parameter: C <- "-45.0229" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4701 TOTAL ENERGY = -73.7808 RDTITL> * VAN DER WAALS = -28.7579 ELECTROSTATIC = -45.0229 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4701" Parameter: CONF_N -> "8002" Comparing "4701" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4702" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758566 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760209 ATOM PAIRS WERE FOUND FOR ATOM LIST 41685 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30424 from a total of 760209 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4702 -80.28371 6.50289 0.75484 INTE EXTERN> -25.81457 -54.46913 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2837" Parameter: A <- "-80.2837" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8146" Parameter: B <- "-25.8146" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.4691" Parameter: C <- "-54.4691" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4702 TOTAL ENERGY = -80.2837 RDTITL> * VAN DER WAALS = -25.8146 ELECTROSTATIC = -54.4691 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4702" Parameter: CONF_N -> "8002" Comparing "4702" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4703" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760209 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757512 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29939 from a total of 757512 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4703 -73.86938 -6.41433 0.73756 INTE EXTERN> -22.08199 -51.78738 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8694" Parameter: A <- "-73.8694" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.082" Parameter: B <- "-22.082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7874" Parameter: C <- "-51.7874" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4703 TOTAL ENERGY = -73.8694 RDTITL> * VAN DER WAALS = -22.082 ELECTROSTATIC = -51.7874 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4703" Parameter: CONF_N -> "8002" Comparing "4703" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4704" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757512 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762669 ATOM PAIRS WERE FOUND FOR ATOM LIST 41724 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29901 from a total of 762669 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4704 -75.31933 1.44996 0.63370 INTE EXTERN> -31.22798 -44.09135 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3193" Parameter: A <- "-75.3193" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.228" Parameter: B <- "-31.228" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0914" Parameter: C <- "-44.0914" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4704 TOTAL ENERGY = -75.3193 RDTITL> * VAN DER WAALS = -31.228 ELECTROSTATIC = -44.0914 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4704" Parameter: CONF_N -> "8002" Comparing "4704" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4705" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762669 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758809 ATOM PAIRS WERE FOUND FOR ATOM LIST 41610 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29101 from a total of 758809 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4705 -75.93980 0.62046 0.67046 INTE EXTERN> -30.49969 -45.44010 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9398" Parameter: A <- "-75.9398" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4997" Parameter: B <- "-30.4997" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4401" Parameter: C <- "-45.4401" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4705 TOTAL ENERGY = -75.9398 RDTITL> * VAN DER WAALS = -30.4997 ELECTROSTATIC = -45.4401 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4705" Parameter: CONF_N -> "8002" Comparing "4705" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4706" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758809 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753907 ATOM PAIRS WERE FOUND FOR ATOM LIST 41388 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29475 from a total of 753907 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4706 -73.28189 -2.65791 0.75167 INTE EXTERN> -23.66292 -49.61897 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2819" Parameter: A <- "-73.2819" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6629" Parameter: B <- "-23.6629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.619" Parameter: C <- "-49.619" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4706 TOTAL ENERGY = -73.2819 RDTITL> * VAN DER WAALS = -23.6629 ELECTROSTATIC = -49.619 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4706" Parameter: CONF_N -> "8002" Comparing "4706" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4707" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753907 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751582 ATOM PAIRS WERE FOUND FOR ATOM LIST 41248 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28972 from a total of 751582 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4707 -70.08384 -3.19805 0.59814 INTE EXTERN> -30.60107 -39.48276 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0838" Parameter: A <- "-70.0838" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6011" Parameter: B <- "-30.6011" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4828" Parameter: C <- "-39.4828" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4707 TOTAL ENERGY = -70.0838 RDTITL> * VAN DER WAALS = -30.6011 ELECTROSTATIC = -39.4828 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4707" Parameter: CONF_N -> "8002" Comparing "4707" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4708" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751582 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749420 ATOM PAIRS WERE FOUND FOR ATOM LIST 41296 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28917 from a total of 749420 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4708 -70.14937 0.06553 0.60893 INTE EXTERN> -30.14789 -40.00148 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1494" Parameter: A <- "-70.1494" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1479" Parameter: B <- "-30.1479" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0015" Parameter: C <- "-40.0015" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4708 TOTAL ENERGY = -70.1494 RDTITL> * VAN DER WAALS = -30.1479 ELECTROSTATIC = -40.0015 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4708" Parameter: CONF_N -> "8002" Comparing "4708" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4709" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749420 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753122 ATOM PAIRS WERE FOUND FOR ATOM LIST 41436 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29060 from a total of 753122 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4709 -70.01539 -0.13398 0.54587 INTE EXTERN> -29.39267 -40.62272 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0154" Parameter: A <- "-70.0154" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3927" Parameter: B <- "-29.3927" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6227" Parameter: C <- "-40.6227" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4709 TOTAL ENERGY = -70.0154 RDTITL> * VAN DER WAALS = -29.3927 ELECTROSTATIC = -40.6227 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4709" Parameter: CONF_N -> "8002" Comparing "4709" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4710" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753122 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755775 ATOM PAIRS WERE FOUND FOR ATOM LIST 41406 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29033 from a total of 755775 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4710 -66.90797 -3.10742 0.74666 INTE EXTERN> -26.84861 -40.05935 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.908" Parameter: A <- "-66.908" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8486" Parameter: B <- "-26.8486" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0594" Parameter: C <- "-40.0594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4710 TOTAL ENERGY = -66.908 RDTITL> * VAN DER WAALS = -26.8486 ELECTROSTATIC = -40.0594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4710" Parameter: CONF_N -> "8002" Comparing "4710" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4711" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755775 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752809 ATOM PAIRS WERE FOUND FOR ATOM LIST 41187 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29380 from a total of 752809 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4711 -66.72652 -0.18144 0.68685 INTE EXTERN> -27.86538 -38.86114 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7265" Parameter: A <- "-66.7265" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8654" Parameter: B <- "-27.8654" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8611" Parameter: C <- "-38.8611" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4711 TOTAL ENERGY = -66.7265 RDTITL> * VAN DER WAALS = -27.8654 ELECTROSTATIC = -38.8611 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4711" Parameter: CONF_N -> "8002" Comparing "4711" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4712" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752809 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755952 ATOM PAIRS WERE FOUND FOR ATOM LIST 41329 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29503 from a total of 755952 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4712 -74.77964 8.05311 0.68609 INTE EXTERN> -30.04496 -44.73468 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7796" Parameter: A <- "-74.7796" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.045" Parameter: B <- "-30.045" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7347" Parameter: C <- "-44.7347" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4712 TOTAL ENERGY = -74.7796 RDTITL> * VAN DER WAALS = -30.045 ELECTROSTATIC = -44.7347 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4712" Parameter: CONF_N -> "8002" Comparing "4712" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4713" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755952 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751792 ATOM PAIRS WERE FOUND FOR ATOM LIST 41246 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29406 from a total of 751792 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4713 -65.37230 -9.40734 0.65662 INTE EXTERN> -26.11289 -39.25942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3723" Parameter: A <- "-65.3723" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1129" Parameter: B <- "-26.1129" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2594" Parameter: C <- "-39.2594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4713 TOTAL ENERGY = -65.3723 RDTITL> * VAN DER WAALS = -26.1129 ELECTROSTATIC = -39.2594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4713" Parameter: CONF_N -> "8002" Comparing "4713" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4714" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751792 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753249 ATOM PAIRS WERE FOUND FOR ATOM LIST 41177 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28469 from a total of 753249 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4714 -65.10166 -0.27065 0.57358 INTE EXTERN> -29.83716 -35.26449 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1017" Parameter: A <- "-65.1017" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8372" Parameter: B <- "-29.8372" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2645" Parameter: C <- "-35.2645" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4714 TOTAL ENERGY = -65.1017 RDTITL> * VAN DER WAALS = -29.8372 ELECTROSTATIC = -35.2645 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4714" Parameter: CONF_N -> "8002" Comparing "4714" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4715" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753249 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752689 ATOM PAIRS WERE FOUND FOR ATOM LIST 41268 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28413 from a total of 752689 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4715 -63.84748 -1.25417 0.59442 INTE EXTERN> -28.35915 -35.48833 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.8475" Parameter: A <- "-63.8475" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3592" Parameter: B <- "-28.3592" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4883" Parameter: C <- "-35.4883" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4715 TOTAL ENERGY = -63.8475 RDTITL> * VAN DER WAALS = -28.3592 ELECTROSTATIC = -35.4883 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4715" Parameter: CONF_N -> "8002" Comparing "4715" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4716" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752689 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755067 ATOM PAIRS WERE FOUND FOR ATOM LIST 41089 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28497 from a total of 755067 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4716 -67.69171 3.84423 0.74498 INTE EXTERN> -23.02793 -44.66378 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6917" Parameter: A <- "-67.6917" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.0279" Parameter: B <- "-23.0279" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6638" Parameter: C <- "-44.6638" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4716 TOTAL ENERGY = -67.6917 RDTITL> * VAN DER WAALS = -23.0279 ELECTROSTATIC = -44.6638 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4716" Parameter: CONF_N -> "8002" Comparing "4716" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4717" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755067 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757817 ATOM PAIRS WERE FOUND FOR ATOM LIST 41452 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29086 from a total of 757817 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4717 -72.39098 4.69927 0.60875 INTE EXTERN> -29.11066 -43.28032 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.391" Parameter: A <- "-72.391" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1107" Parameter: B <- "-29.1107" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2803" Parameter: C <- "-43.2803" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4717 TOTAL ENERGY = -72.391 RDTITL> * VAN DER WAALS = -29.1107 ELECTROSTATIC = -43.2803 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4717" Parameter: CONF_N -> "8002" Comparing "4717" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4718" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757817 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750975 ATOM PAIRS WERE FOUND FOR ATOM LIST 41135 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28992 from a total of 750975 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4718 -70.48294 -1.90804 0.74288 INTE EXTERN> -25.25114 -45.23181 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4829" Parameter: A <- "-70.4829" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2511" Parameter: B <- "-25.2511" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2318" Parameter: C <- "-45.2318" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4718 TOTAL ENERGY = -70.4829 RDTITL> * VAN DER WAALS = -25.2511 ELECTROSTATIC = -45.2318 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4718" Parameter: CONF_N -> "8002" Comparing "4718" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4719" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750975 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751530 ATOM PAIRS WERE FOUND FOR ATOM LIST 41063 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29273 from a total of 751530 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4719 -73.47831 2.99537 0.73163 INTE EXTERN> -24.11003 -49.36829 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4783" Parameter: A <- "-73.4783" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.11" Parameter: B <- "-24.11" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3683" Parameter: C <- "-49.3683" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4719 TOTAL ENERGY = -73.4783 RDTITL> * VAN DER WAALS = -24.11 ELECTROSTATIC = -49.3683 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4719" Parameter: CONF_N -> "8002" Comparing "4719" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4720" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751530 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753112 ATOM PAIRS WERE FOUND FOR ATOM LIST 41325 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29542 from a total of 753112 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4720 -69.17497 -4.30334 0.70322 INTE EXTERN> -29.44466 -39.73031 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.175" Parameter: A <- "-69.175" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4447" Parameter: B <- "-29.4447" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7303" Parameter: C <- "-39.7303" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4720 TOTAL ENERGY = -69.175 RDTITL> * VAN DER WAALS = -29.4447 ELECTROSTATIC = -39.7303 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4720" Parameter: CONF_N -> "8002" Comparing "4720" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4721" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753112 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761565 ATOM PAIRS WERE FOUND FOR ATOM LIST 41653 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29948 from a total of 761565 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4721 -76.14289 6.96792 0.75727 INTE EXTERN> -26.48542 -49.65747 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1429" Parameter: A <- "-76.1429" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4854" Parameter: B <- "-26.4854" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6575" Parameter: C <- "-49.6575" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4721 TOTAL ENERGY = -76.1429 RDTITL> * VAN DER WAALS = -26.4854 ELECTROSTATIC = -49.6575 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4721" Parameter: CONF_N -> "8002" Comparing "4721" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4722" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761565 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757751 ATOM PAIRS WERE FOUND FOR ATOM LIST 41420 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30032 from a total of 757751 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4722 -64.21627 -11.92662 0.71300 INTE EXTERN> -23.37540 -40.84087 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2163" Parameter: A <- "-64.2163" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.3754" Parameter: B <- "-23.3754" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8409" Parameter: C <- "-40.8409" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4722 TOTAL ENERGY = -64.2163 RDTITL> * VAN DER WAALS = -23.3754 ELECTROSTATIC = -40.8409 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4722" Parameter: CONF_N -> "8002" Comparing "4722" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4723" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757751 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751428 ATOM PAIRS WERE FOUND FOR ATOM LIST 41329 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29083 from a total of 751428 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4723 -70.95492 6.73865 0.76513 INTE EXTERN> -23.23281 -47.72211 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9549" Parameter: A <- "-70.9549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.2328" Parameter: B <- "-23.2328" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7221" Parameter: C <- "-47.7221" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4723 TOTAL ENERGY = -70.9549 RDTITL> * VAN DER WAALS = -23.2328 ELECTROSTATIC = -47.7221 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4723" Parameter: CONF_N -> "8002" Comparing "4723" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4724" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751428 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745829 ATOM PAIRS WERE FOUND FOR ATOM LIST 40957 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28998 from a total of 745829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4724 -71.65490 0.69998 0.64173 INTE EXTERN> -28.12804 -43.52685 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6549" Parameter: A <- "-71.6549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.128" Parameter: B <- "-28.128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5269" Parameter: C <- "-43.5269" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4724 TOTAL ENERGY = -71.6549 RDTITL> * VAN DER WAALS = -28.128 ELECTROSTATIC = -43.5269 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4724" Parameter: CONF_N -> "8002" Comparing "4724" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4725" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751272 ATOM PAIRS WERE FOUND FOR ATOM LIST 41150 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29681 from a total of 751272 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4725 -70.83320 -0.82170 0.69714 INTE EXTERN> -27.23639 -43.59680 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8332" Parameter: A <- "-70.8332" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2364" Parameter: B <- "-27.2364" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5968" Parameter: C <- "-43.5968" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4725 TOTAL ENERGY = -70.8332 RDTITL> * VAN DER WAALS = -27.2364 ELECTROSTATIC = -43.5968 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4725" Parameter: CONF_N -> "8002" Comparing "4725" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4726" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751272 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758514 ATOM PAIRS WERE FOUND FOR ATOM LIST 41627 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30238 from a total of 758514 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4726 -70.07187 -0.76133 0.68021 INTE EXTERN> -29.35516 -40.71672 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0719" Parameter: A <- "-70.0719" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3552" Parameter: B <- "-29.3552" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7167" Parameter: C <- "-40.7167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4726 TOTAL ENERGY = -70.0719 RDTITL> * VAN DER WAALS = -29.3552 ELECTROSTATIC = -40.7167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4726" Parameter: CONF_N -> "8002" Comparing "4726" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4727" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758514 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753966 ATOM PAIRS WERE FOUND FOR ATOM LIST 41408 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29737 from a total of 753966 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4727 -74.82377 4.75189 0.70275 INTE EXTERN> -28.17614 -46.64762 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8238" Parameter: A <- "-74.8238" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1761" Parameter: B <- "-28.1761" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6476" Parameter: C <- "-46.6476" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4727 TOTAL ENERGY = -74.8238 RDTITL> * VAN DER WAALS = -28.1761 ELECTROSTATIC = -46.6476 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4727" Parameter: CONF_N -> "8002" Comparing "4727" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4728" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753966 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756217 ATOM PAIRS WERE FOUND FOR ATOM LIST 41478 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29205 from a total of 756217 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4728 -73.61116 -1.21261 0.63899 INTE EXTERN> -30.53669 -43.07447 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6112" Parameter: A <- "-73.6112" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5367" Parameter: B <- "-30.5367" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0745" Parameter: C <- "-43.0745" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4728 TOTAL ENERGY = -73.6112 RDTITL> * VAN DER WAALS = -30.5367 ELECTROSTATIC = -43.0745 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4728" Parameter: CONF_N -> "8002" Comparing "4728" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4729" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756217 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755721 ATOM PAIRS WERE FOUND FOR ATOM LIST 41387 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29528 from a total of 755721 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4729 -78.81891 5.20775 0.63905 INTE EXTERN> -31.96992 -46.84899 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8189" Parameter: A <- "-78.8189" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9699" Parameter: B <- "-31.9699" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.849" Parameter: C <- "-46.849" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4729 TOTAL ENERGY = -78.8189 RDTITL> * VAN DER WAALS = -31.9699 ELECTROSTATIC = -46.849 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4729" Parameter: CONF_N -> "8002" Comparing "4729" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4730" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755721 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761075 ATOM PAIRS WERE FOUND FOR ATOM LIST 41934 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29297 from a total of 761075 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4730 -71.58234 -7.23657 0.59130 INTE EXTERN> -30.78889 -40.79346 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5823" Parameter: A <- "-71.5823" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7889" Parameter: B <- "-30.7889" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7935" Parameter: C <- "-40.7935" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4730 TOTAL ENERGY = -71.5823 RDTITL> * VAN DER WAALS = -30.7889 ELECTROSTATIC = -40.7935 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4730" Parameter: CONF_N -> "8002" Comparing "4730" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4731" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761075 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760419 ATOM PAIRS WERE FOUND FOR ATOM LIST 41540 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29499 from a total of 760419 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4731 -69.28549 -2.29685 0.78908 INTE EXTERN> -20.15377 -49.13172 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2855" Parameter: A <- "-69.2855" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.1538" Parameter: B <- "-20.1538" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1317" Parameter: C <- "-49.1317" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4731 TOTAL ENERGY = -69.2855 RDTITL> * VAN DER WAALS = -20.1538 ELECTROSTATIC = -49.1317 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4731" Parameter: CONF_N -> "8002" Comparing "4731" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4732" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760419 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754482 ATOM PAIRS WERE FOUND FOR ATOM LIST 41288 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29254 from a total of 754482 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4732 -77.90629 8.62079 0.60068 INTE EXTERN> -30.60411 -47.30218 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9063" Parameter: A <- "-77.9063" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6041" Parameter: B <- "-30.6041" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3022" Parameter: C <- "-47.3022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4732 TOTAL ENERGY = -77.9063 RDTITL> * VAN DER WAALS = -30.6041 ELECTROSTATIC = -47.3022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4732" Parameter: CONF_N -> "8002" Comparing "4732" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4733" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754482 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755904 ATOM PAIRS WERE FOUND FOR ATOM LIST 41261 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29063 from a total of 755904 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4733 -68.20392 -9.70237 0.66290 INTE EXTERN> -26.80471 -41.39921 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2039" Parameter: A <- "-68.2039" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8047" Parameter: B <- "-26.8047" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3992" Parameter: C <- "-41.3992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4733 TOTAL ENERGY = -68.2039 RDTITL> * VAN DER WAALS = -26.8047 ELECTROSTATIC = -41.3992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4733" Parameter: CONF_N -> "8002" Comparing "4733" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4734" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755904 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753658 ATOM PAIRS WERE FOUND FOR ATOM LIST 41165 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28817 from a total of 753658 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4734 -73.54965 5.34573 0.67920 INTE EXTERN> -27.83935 -45.71031 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5497" Parameter: A <- "-73.5497" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8393" Parameter: B <- "-27.8393" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7103" Parameter: C <- "-45.7103" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4734 TOTAL ENERGY = -73.5497 RDTITL> * VAN DER WAALS = -27.8393 ELECTROSTATIC = -45.7103 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4734" Parameter: CONF_N -> "8002" Comparing "4734" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4735" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753658 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753832 ATOM PAIRS WERE FOUND FOR ATOM LIST 41338 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29256 from a total of 753832 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4735 -75.01843 1.46877 0.77022 INTE EXTERN> -23.97360 -51.04482 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0184" Parameter: A <- "-75.0184" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9736" Parameter: B <- "-23.9736" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0448" Parameter: C <- "-51.0448" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4735 TOTAL ENERGY = -75.0184 RDTITL> * VAN DER WAALS = -23.9736 ELECTROSTATIC = -51.0448 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4735" Parameter: CONF_N -> "8002" Comparing "4735" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4736" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753832 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753687 ATOM PAIRS WERE FOUND FOR ATOM LIST 41234 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28734 from a total of 753687 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4736 -72.71916 -2.29926 0.62726 INTE EXTERN> -28.41620 -44.30296 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7192" Parameter: A <- "-72.7192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4162" Parameter: B <- "-28.4162" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.303" Parameter: C <- "-44.303" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4736 TOTAL ENERGY = -72.7192 RDTITL> * VAN DER WAALS = -28.4162 ELECTROSTATIC = -44.303 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4736" Parameter: CONF_N -> "8002" Comparing "4736" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4737" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753687 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757738 ATOM PAIRS WERE FOUND FOR ATOM LIST 41406 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29455 from a total of 757738 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4737 -67.46679 -5.25237 0.55608 INTE EXTERN> -27.49249 -39.97430 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4668" Parameter: A <- "-67.4668" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4925" Parameter: B <- "-27.4925" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9743" Parameter: C <- "-39.9743" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4737 TOTAL ENERGY = -67.4668 RDTITL> * VAN DER WAALS = -27.4925 ELECTROSTATIC = -39.9743 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4737" Parameter: CONF_N -> "8002" Comparing "4737" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4738" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757738 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760916 ATOM PAIRS WERE FOUND FOR ATOM LIST 41534 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29877 from a total of 760916 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4738 -75.83920 8.37241 0.62380 INTE EXTERN> -31.04330 -44.79590 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8392" Parameter: A <- "-75.8392" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0433" Parameter: B <- "-31.0433" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7959" Parameter: C <- "-44.7959" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4738 TOTAL ENERGY = -75.8392 RDTITL> * VAN DER WAALS = -31.0433 ELECTROSTATIC = -44.7959 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4738" Parameter: CONF_N -> "8002" Comparing "4738" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4739" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760916 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760226 ATOM PAIRS WERE FOUND FOR ATOM LIST 41550 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29589 from a total of 760226 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4739 -71.61673 -4.22246 0.71290 INTE EXTERN> -27.67043 -43.94630 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6167" Parameter: A <- "-71.6167" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6704" Parameter: B <- "-27.6704" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9463" Parameter: C <- "-43.9463" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4739 TOTAL ENERGY = -71.6167 RDTITL> * VAN DER WAALS = -27.6704 ELECTROSTATIC = -43.9463 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4739" Parameter: CONF_N -> "8002" Comparing "4739" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4740" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760226 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765288 ATOM PAIRS WERE FOUND FOR ATOM LIST 41840 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29774 from a total of 765288 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4740 -72.23825 0.62152 0.69892 INTE EXTERN> -23.92785 -48.31040 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2383" Parameter: A <- "-72.2383" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9279" Parameter: B <- "-23.9279" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3104" Parameter: C <- "-48.3104" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4740 TOTAL ENERGY = -72.2383 RDTITL> * VAN DER WAALS = -23.9279 ELECTROSTATIC = -48.3104 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4740" Parameter: CONF_N -> "8002" Comparing "4740" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4741" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765288 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763365 ATOM PAIRS WERE FOUND FOR ATOM LIST 41690 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29667 from a total of 763365 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4741 -80.60263 8.36438 0.68583 INTE EXTERN> -28.81562 -51.78701 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6026" Parameter: A <- "-80.6026" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8156" Parameter: B <- "-28.8156" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.787" Parameter: C <- "-51.787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4741 TOTAL ENERGY = -80.6026 RDTITL> * VAN DER WAALS = -28.8156 ELECTROSTATIC = -51.787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4741" Parameter: CONF_N -> "8002" Comparing "4741" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4742" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763365 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758068 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29477 from a total of 758068 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4742 -74.13922 -6.46341 0.66529 INTE EXTERN> -26.67754 -47.46168 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1392" Parameter: A <- "-74.1392" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6775" Parameter: B <- "-26.6775" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4617" Parameter: C <- "-47.4617" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4742 TOTAL ENERGY = -74.1392 RDTITL> * VAN DER WAALS = -26.6775 ELECTROSTATIC = -47.4617 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4742" Parameter: CONF_N -> "8002" Comparing "4742" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4743" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758068 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756470 ATOM PAIRS WERE FOUND FOR ATOM LIST 41469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29508 from a total of 756470 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4743 -73.16422 -0.97500 0.64962 INTE EXTERN> -26.16248 -47.00174 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1642" Parameter: A <- "-73.1642" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1625" Parameter: B <- "-26.1625" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0017" Parameter: C <- "-47.0017" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4743 TOTAL ENERGY = -73.1642 RDTITL> * VAN DER WAALS = -26.1625 ELECTROSTATIC = -47.0017 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4743" Parameter: CONF_N -> "8002" Comparing "4743" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4744" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756470 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762147 ATOM PAIRS WERE FOUND FOR ATOM LIST 41607 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29566 from a total of 762147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4744 -70.49898 -2.66524 0.64139 INTE EXTERN> -27.90306 -42.59591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.499" Parameter: A <- "-70.499" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9031" Parameter: B <- "-27.9031" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5959" Parameter: C <- "-42.5959" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4744 TOTAL ENERGY = -70.499 RDTITL> * VAN DER WAALS = -27.9031 ELECTROSTATIC = -42.5959 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4744" Parameter: CONF_N -> "8002" Comparing "4744" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4745" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759839 ATOM PAIRS WERE FOUND FOR ATOM LIST 41621 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28654 from a total of 759839 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4745 -79.78919 9.29022 0.60752 INTE EXTERN> -30.26549 -49.52370 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7892" Parameter: A <- "-79.7892" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2655" Parameter: B <- "-30.2655" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5237" Parameter: C <- "-49.5237" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4745 TOTAL ENERGY = -79.7892 RDTITL> * VAN DER WAALS = -30.2655 ELECTROSTATIC = -49.5237 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4745" Parameter: CONF_N -> "8002" Comparing "4745" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4746" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759839 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757717 ATOM PAIRS WERE FOUND FOR ATOM LIST 41348 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28951 from a total of 757717 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4746 -65.18308 -14.60612 0.72487 INTE EXTERN> -25.98921 -39.19387 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1831" Parameter: A <- "-65.1831" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9892" Parameter: B <- "-25.9892" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1939" Parameter: C <- "-39.1939" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4746 TOTAL ENERGY = -65.1831 RDTITL> * VAN DER WAALS = -25.9892 ELECTROSTATIC = -39.1939 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4746" Parameter: CONF_N -> "8002" Comparing "4746" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4747" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757717 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757296 ATOM PAIRS WERE FOUND FOR ATOM LIST 41415 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29356 from a total of 757296 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4747 -72.74523 7.56215 0.64807 INTE EXTERN> -26.77702 -45.96821 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7452" Parameter: A <- "-72.7452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.777" Parameter: B <- "-26.777" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9682" Parameter: C <- "-45.9682" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4747 TOTAL ENERGY = -72.7452 RDTITL> * VAN DER WAALS = -26.777 ELECTROSTATIC = -45.9682 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4747" Parameter: CONF_N -> "8002" Comparing "4747" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4748" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757296 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759837 ATOM PAIRS WERE FOUND FOR ATOM LIST 41381 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28846 from a total of 759837 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4748 -73.20953 0.46430 0.63120 INTE EXTERN> -28.02735 -45.18218 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2095" Parameter: A <- "-73.2095" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0274" Parameter: B <- "-28.0274" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1822" Parameter: C <- "-45.1822" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4748 TOTAL ENERGY = -73.2095 RDTITL> * VAN DER WAALS = -28.0274 ELECTROSTATIC = -45.1822 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4748" Parameter: CONF_N -> "8002" Comparing "4748" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4749" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759837 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756207 ATOM PAIRS WERE FOUND FOR ATOM LIST 41396 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29515 from a total of 756207 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4749 -67.91930 -5.29023 0.60900 INTE EXTERN> -28.42495 -39.49436 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9193" Parameter: A <- "-67.9193" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4249" Parameter: B <- "-28.4249" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4944" Parameter: C <- "-39.4944" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4749 TOTAL ENERGY = -67.9193 RDTITL> * VAN DER WAALS = -28.4249 ELECTROSTATIC = -39.4944 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4749" Parameter: CONF_N -> "8002" Comparing "4749" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4750" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756207 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756024 ATOM PAIRS WERE FOUND FOR ATOM LIST 41379 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29871 from a total of 756024 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4750 -72.78119 4.86189 0.61450 INTE EXTERN> -28.46025 -44.32094 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7812" Parameter: A <- "-72.7812" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4602" Parameter: B <- "-28.4602" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3209" Parameter: C <- "-44.3209" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4750 TOTAL ENERGY = -72.7812 RDTITL> * VAN DER WAALS = -28.4602 ELECTROSTATIC = -44.3209 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4750" Parameter: CONF_N -> "8002" Comparing "4750" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4751" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756024 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757129 ATOM PAIRS WERE FOUND FOR ATOM LIST 41488 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29257 from a total of 757129 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4751 -68.25607 -4.52512 0.64186 INTE EXTERN> -25.48113 -42.77495 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2561" Parameter: A <- "-68.2561" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4811" Parameter: B <- "-25.4811" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7749" Parameter: C <- "-42.7749" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4751 TOTAL ENERGY = -68.2561 RDTITL> * VAN DER WAALS = -25.4811 ELECTROSTATIC = -42.7749 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4751" Parameter: CONF_N -> "8002" Comparing "4751" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4752" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757129 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753146 ATOM PAIRS WERE FOUND FOR ATOM LIST 41296 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29208 from a total of 753146 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4752 -65.57339 -2.68269 0.50235 INTE EXTERN> -31.48042 -34.09297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5734" Parameter: A <- "-65.5734" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4804" Parameter: B <- "-31.4804" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.093" Parameter: C <- "-34.093" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4752 TOTAL ENERGY = -65.5734 RDTITL> * VAN DER WAALS = -31.4804 ELECTROSTATIC = -34.093 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4752" Parameter: CONF_N -> "8002" Comparing "4752" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4753" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753146 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753458 ATOM PAIRS WERE FOUND FOR ATOM LIST 41225 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29314 from a total of 753458 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4753 -73.19846 7.62507 0.64179 INTE EXTERN> -29.03901 -44.15945 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1985" Parameter: A <- "-73.1985" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.039" Parameter: B <- "-29.039" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1594" Parameter: C <- "-44.1594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4753 TOTAL ENERGY = -73.1985 RDTITL> * VAN DER WAALS = -29.039 ELECTROSTATIC = -44.1594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4753" Parameter: CONF_N -> "8002" Comparing "4753" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4754" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753458 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756303 ATOM PAIRS WERE FOUND FOR ATOM LIST 41321 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29545 from a total of 756303 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4754 -63.36152 -9.83694 0.56270 INTE EXTERN> -30.14115 -33.22037 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3615" Parameter: A <- "-63.3615" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1411" Parameter: B <- "-30.1411" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2204" Parameter: C <- "-33.2204" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4754 TOTAL ENERGY = -63.3615 RDTITL> * VAN DER WAALS = -30.1411 ELECTROSTATIC = -33.2204 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4754" Parameter: CONF_N -> "8002" Comparing "4754" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4755" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756303 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755793 ATOM PAIRS WERE FOUND FOR ATOM LIST 41225 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29227 from a total of 755793 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4755 -69.02432 5.66281 0.57999 INTE EXTERN> -28.95694 -40.06738 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0243" Parameter: A <- "-69.0243" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9569" Parameter: B <- "-28.9569" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0674" Parameter: C <- "-40.0674" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4755 TOTAL ENERGY = -69.0243 RDTITL> * VAN DER WAALS = -28.9569 ELECTROSTATIC = -40.0674 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4755" Parameter: CONF_N -> "8002" Comparing "4755" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4756" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755793 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753944 ATOM PAIRS WERE FOUND FOR ATOM LIST 41081 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29192 from a total of 753944 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4756 -61.75525 -7.26907 0.61665 INTE EXTERN> -28.02799 -33.72725 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.7552" Parameter: A <- "-61.7552" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.028" Parameter: B <- "-28.028" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7273" Parameter: C <- "-33.7273" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4756 TOTAL ENERGY = -61.7552 RDTITL> * VAN DER WAALS = -28.028 ELECTROSTATIC = -33.7273 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4756" Parameter: CONF_N -> "8002" Comparing "4756" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4757" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753944 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755106 ATOM PAIRS WERE FOUND FOR ATOM LIST 41364 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29790 from a total of 755106 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4757 -70.02091 8.26566 0.63125 INTE EXTERN> -31.45768 -38.56323 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0209" Parameter: A <- "-70.0209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4577" Parameter: B <- "-31.4577" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5632" Parameter: C <- "-38.5632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4757 TOTAL ENERGY = -70.0209 RDTITL> * VAN DER WAALS = -31.4577 ELECTROSTATIC = -38.5632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4757" Parameter: CONF_N -> "8002" Comparing "4757" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4758" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755106 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761290 ATOM PAIRS WERE FOUND FOR ATOM LIST 41503 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29852 from a total of 761290 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4758 -75.22301 5.20210 0.69009 INTE EXTERN> -28.78325 -46.43975 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.223" Parameter: A <- "-75.223" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7833" Parameter: B <- "-28.7833" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4398" Parameter: C <- "-46.4398" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4758 TOTAL ENERGY = -75.223 RDTITL> * VAN DER WAALS = -28.7833 ELECTROSTATIC = -46.4398 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4758" Parameter: CONF_N -> "8002" Comparing "4758" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4759" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761290 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761286 ATOM PAIRS WERE FOUND FOR ATOM LIST 41701 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29391 from a total of 761286 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4759 -70.25784 -4.96517 0.59342 INTE EXTERN> -32.10132 -38.15652 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2578" Parameter: A <- "-70.2578" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1013" Parameter: B <- "-32.1013" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1565" Parameter: C <- "-38.1565" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4759 TOTAL ENERGY = -70.2578 RDTITL> * VAN DER WAALS = -32.1013 ELECTROSTATIC = -38.1565 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4759" Parameter: CONF_N -> "8002" Comparing "4759" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4760" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761286 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758415 ATOM PAIRS WERE FOUND FOR ATOM LIST 41698 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28944 from a total of 758415 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4760 -75.03938 4.78154 0.61167 INTE EXTERN> -30.51447 -44.52491 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0394" Parameter: A <- "-75.0394" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5145" Parameter: B <- "-30.5145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5249" Parameter: C <- "-44.5249" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4760 TOTAL ENERGY = -75.0394 RDTITL> * VAN DER WAALS = -30.5145 ELECTROSTATIC = -44.5249 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4760" Parameter: CONF_N -> "8002" Comparing "4760" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4761" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758415 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764938 ATOM PAIRS WERE FOUND FOR ATOM LIST 41811 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29541 from a total of 764938 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4761 -68.56475 -6.47463 0.67587 INTE EXTERN> -28.07733 -40.48742 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5648" Parameter: A <- "-68.5648" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0773" Parameter: B <- "-28.0773" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4874" Parameter: C <- "-40.4874" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4761 TOTAL ENERGY = -68.5648 RDTITL> * VAN DER WAALS = -28.0773 ELECTROSTATIC = -40.4874 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4761" Parameter: CONF_N -> "8002" Comparing "4761" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4762" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764938 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760864 ATOM PAIRS WERE FOUND FOR ATOM LIST 41649 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29133 from a total of 760864 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4762 -69.67579 1.11104 0.61118 INTE EXTERN> -29.44372 -40.23207 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6758" Parameter: A <- "-69.6758" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4437" Parameter: B <- "-29.4437" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2321" Parameter: C <- "-40.2321" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4762 TOTAL ENERGY = -69.6758 RDTITL> * VAN DER WAALS = -29.4437 ELECTROSTATIC = -40.2321 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4762" Parameter: CONF_N -> "8002" Comparing "4762" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4763" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760864 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764897 ATOM PAIRS WERE FOUND FOR ATOM LIST 41757 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29262 from a total of 764897 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4763 -70.12564 0.44985 0.62379 INTE EXTERN> -30.40179 -39.72385 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1256" Parameter: A <- "-70.1256" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4018" Parameter: B <- "-30.4018" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7239" Parameter: C <- "-39.7239" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4763 TOTAL ENERGY = -70.1256 RDTITL> * VAN DER WAALS = -30.4018 ELECTROSTATIC = -39.7239 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4763" Parameter: CONF_N -> "8002" Comparing "4763" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4764" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764897 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763208 ATOM PAIRS WERE FOUND FOR ATOM LIST 41862 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29713 from a total of 763208 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4764 -73.27381 3.14817 0.89960 INTE EXTERN> -21.51832 -51.75549 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2738" Parameter: A <- "-73.2738" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.5183" Parameter: B <- "-21.5183" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7555" Parameter: C <- "-51.7555" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4764 TOTAL ENERGY = -73.2738 RDTITL> * VAN DER WAALS = -21.5183 ELECTROSTATIC = -51.7555 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4764" Parameter: CONF_N -> "8002" Comparing "4764" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4765" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763208 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764445 ATOM PAIRS WERE FOUND FOR ATOM LIST 41885 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29117 from a total of 764445 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4765 -73.02005 -0.25376 0.85877 INTE EXTERN> -22.51859 -50.50146 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.02" Parameter: A <- "-73.02" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.5186" Parameter: B <- "-22.5186" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5015" Parameter: C <- "-50.5015" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4765 TOTAL ENERGY = -73.02 RDTITL> * VAN DER WAALS = -22.5186 ELECTROSTATIC = -50.5015 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4765" Parameter: CONF_N -> "8002" Comparing "4765" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4766" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764445 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764192 ATOM PAIRS WERE FOUND FOR ATOM LIST 41886 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29846 from a total of 764192 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4766 -73.36130 0.34126 0.69810 INTE EXTERN> -28.01506 -45.34624 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3613" Parameter: A <- "-73.3613" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0151" Parameter: B <- "-28.0151" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3462" Parameter: C <- "-45.3462" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4766 TOTAL ENERGY = -73.3613 RDTITL> * VAN DER WAALS = -28.0151 ELECTROSTATIC = -45.3462 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4766" Parameter: CONF_N -> "8002" Comparing "4766" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4767" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764192 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767482 ATOM PAIRS WERE FOUND FOR ATOM LIST 41946 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29461 from a total of 767482 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4767 -79.65222 6.29092 0.70853 INTE EXTERN> -29.30134 -50.35089 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6522" Parameter: A <- "-79.6522" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3013" Parameter: B <- "-29.3013" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3509" Parameter: C <- "-50.3509" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4767 TOTAL ENERGY = -79.6522 RDTITL> * VAN DER WAALS = -29.3013 ELECTROSTATIC = -50.3509 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4767" Parameter: CONF_N -> "8002" Comparing "4767" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4768" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767482 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767443 ATOM PAIRS WERE FOUND FOR ATOM LIST 42189 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29798 from a total of 767443 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4768 -71.92161 -7.73061 0.65596 INTE EXTERN> -30.10302 -41.81859 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9216" Parameter: A <- "-71.9216" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.103" Parameter: B <- "-30.103" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8186" Parameter: C <- "-41.8186" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4768 TOTAL ENERGY = -71.9216 RDTITL> * VAN DER WAALS = -30.103 ELECTROSTATIC = -41.8186 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4768" Parameter: CONF_N -> "8002" Comparing "4768" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4769" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767443 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764843 ATOM PAIRS WERE FOUND FOR ATOM LIST 42024 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28817 from a total of 764843 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4769 -71.83474 -0.08687 0.70941 INTE EXTERN> -28.72779 -43.10695 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8347" Parameter: A <- "-71.8347" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7278" Parameter: B <- "-28.7278" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1069" Parameter: C <- "-43.1069" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4769 TOTAL ENERGY = -71.8347 RDTITL> * VAN DER WAALS = -28.7278 ELECTROSTATIC = -43.1069 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4769" Parameter: CONF_N -> "8002" Comparing "4769" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4770" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764843 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760902 ATOM PAIRS WERE FOUND FOR ATOM LIST 41574 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29159 from a total of 760902 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4770 -70.41577 -1.41896 0.81582 INTE EXTERN> -20.97661 -49.43916 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4158" Parameter: A <- "-70.4158" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.9766" Parameter: B <- "-20.9766" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4392" Parameter: C <- "-49.4392" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4770 TOTAL ENERGY = -70.4158 RDTITL> * VAN DER WAALS = -20.9766 ELECTROSTATIC = -49.4392 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4770" Parameter: CONF_N -> "8002" Comparing "4770" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4771" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760902 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768210 ATOM PAIRS WERE FOUND FOR ATOM LIST 42104 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30320 from a total of 768210 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4771 -72.96250 2.54673 0.63445 INTE EXTERN> -32.15088 -40.81162 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9625" Parameter: A <- "-72.9625" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1509" Parameter: B <- "-32.1509" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8116" Parameter: C <- "-40.8116" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4771 TOTAL ENERGY = -72.9625 RDTITL> * VAN DER WAALS = -32.1509 ELECTROSTATIC = -40.8116 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4771" Parameter: CONF_N -> "8002" Comparing "4771" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4772" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768210 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768260 ATOM PAIRS WERE FOUND FOR ATOM LIST 42246 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30184 from a total of 768260 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4772 -76.27352 3.31102 0.68677 INTE EXTERN> -29.50243 -46.77110 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2735" Parameter: A <- "-76.2735" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5024" Parameter: B <- "-29.5024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7711" Parameter: C <- "-46.7711" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4772 TOTAL ENERGY = -76.2735 RDTITL> * VAN DER WAALS = -29.5024 ELECTROSTATIC = -46.7711 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4772" Parameter: CONF_N -> "8002" Comparing "4772" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4773" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768260 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758982 ATOM PAIRS WERE FOUND FOR ATOM LIST 41681 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29658 from a total of 758982 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4773 -74.48701 -1.78651 0.70122 INTE EXTERN> -29.62147 -44.86554 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.487" Parameter: A <- "-74.487" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6215" Parameter: B <- "-29.6215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8655" Parameter: C <- "-44.8655" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4773 TOTAL ENERGY = -74.487 RDTITL> * VAN DER WAALS = -29.6215 ELECTROSTATIC = -44.8655 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4773" Parameter: CONF_N -> "8002" Comparing "4773" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4774" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758982 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761875 ATOM PAIRS WERE FOUND FOR ATOM LIST 41725 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30223 from a total of 761875 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4774 -72.19033 -2.29668 0.66720 INTE EXTERN> -29.42699 -42.76334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1903" Parameter: A <- "-72.1903" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.427" Parameter: B <- "-29.427" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7633" Parameter: C <- "-42.7633" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4774 TOTAL ENERGY = -72.1903 RDTITL> * VAN DER WAALS = -29.427 ELECTROSTATIC = -42.7633 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4774" Parameter: CONF_N -> "8002" Comparing "4774" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4775" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761875 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763876 ATOM PAIRS WERE FOUND FOR ATOM LIST 42007 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29204 from a total of 763876 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4775 -77.57125 5.38093 0.62819 INTE EXTERN> -32.53083 -45.04042 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5713" Parameter: A <- "-77.5713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5308" Parameter: B <- "-32.5308" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0404" Parameter: C <- "-45.0404" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4775 TOTAL ENERGY = -77.5713 RDTITL> * VAN DER WAALS = -32.5308 ELECTROSTATIC = -45.0404 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4775" Parameter: CONF_N -> "8002" Comparing "4775" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4776" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763876 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764058 ATOM PAIRS WERE FOUND FOR ATOM LIST 41791 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29451 from a total of 764058 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4776 -73.73456 -3.83670 0.71988 INTE EXTERN> -27.95686 -45.77770 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7346" Parameter: A <- "-73.7346" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9569" Parameter: B <- "-27.9569" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7777" Parameter: C <- "-45.7777" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4776 TOTAL ENERGY = -73.7346 RDTITL> * VAN DER WAALS = -27.9569 ELECTROSTATIC = -45.7777 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4776" Parameter: CONF_N -> "8002" Comparing "4776" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4777" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764058 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760430 ATOM PAIRS WERE FOUND FOR ATOM LIST 41680 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29587 from a total of 760430 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4777 -70.95937 -2.77519 0.73185 INTE EXTERN> -25.95735 -45.00202 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9594" Parameter: A <- "-70.9594" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9573" Parameter: B <- "-25.9573" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.002" Parameter: C <- "-45.002" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4777 TOTAL ENERGY = -70.9594 RDTITL> * VAN DER WAALS = -25.9573 ELECTROSTATIC = -45.002 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4777" Parameter: CONF_N -> "8002" Comparing "4777" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4778" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760430 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762933 ATOM PAIRS WERE FOUND FOR ATOM LIST 41782 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30231 from a total of 762933 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4778 -75.97853 5.01916 0.66537 INTE EXTERN> -28.08199 -47.89654 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9785" Parameter: A <- "-75.9785" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.082" Parameter: B <- "-28.082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8965" Parameter: C <- "-47.8965" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4778 TOTAL ENERGY = -75.9785 RDTITL> * VAN DER WAALS = -28.082 ELECTROSTATIC = -47.8965 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4778" Parameter: CONF_N -> "8002" Comparing "4778" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4779" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762933 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761797 ATOM PAIRS WERE FOUND FOR ATOM LIST 41747 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29831 from a total of 761797 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4779 -76.83946 0.86093 0.62587 INTE EXTERN> -31.26006 -45.57940 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8395" Parameter: A <- "-76.8395" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2601" Parameter: B <- "-31.2601" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5794" Parameter: C <- "-45.5794" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4779 TOTAL ENERGY = -76.8395 RDTITL> * VAN DER WAALS = -31.2601 ELECTROSTATIC = -45.5794 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4779" Parameter: CONF_N -> "8002" Comparing "4779" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4780" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761797 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768439 ATOM PAIRS WERE FOUND FOR ATOM LIST 42298 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30128 from a total of 768439 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4780 -75.97041 -0.86905 0.76295 INTE EXTERN> -27.87766 -48.09274 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9704" Parameter: A <- "-75.9704" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8777" Parameter: B <- "-27.8777" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0927" Parameter: C <- "-48.0927" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4780 TOTAL ENERGY = -75.9704 RDTITL> * VAN DER WAALS = -27.8777 ELECTROSTATIC = -48.0927 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4780" Parameter: CONF_N -> "8002" Comparing "4780" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4781" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768439 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767946 ATOM PAIRS WERE FOUND FOR ATOM LIST 42016 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30107 from a total of 767946 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4781 -77.87778 1.90737 0.64845 INTE EXTERN> -31.86993 -46.00785 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8778" Parameter: A <- "-77.8778" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8699" Parameter: B <- "-31.8699" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0079" Parameter: C <- "-46.0079" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4781 TOTAL ENERGY = -77.8778 RDTITL> * VAN DER WAALS = -31.8699 ELECTROSTATIC = -46.0079 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4781" Parameter: CONF_N -> "8002" Comparing "4781" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4782" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767946 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41970 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30016 from a total of 763958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4782 -69.37337 -8.50441 0.69967 INTE EXTERN> -24.72386 -44.64951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3734" Parameter: A <- "-69.3734" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7239" Parameter: B <- "-24.7239" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6495" Parameter: C <- "-44.6495" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4782 TOTAL ENERGY = -69.3734 RDTITL> * VAN DER WAALS = -24.7239 ELECTROSTATIC = -44.6495 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4782" Parameter: CONF_N -> "8002" Comparing "4782" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4783" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760122 ATOM PAIRS WERE FOUND FOR ATOM LIST 41767 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30031 from a total of 760122 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4783 -76.07241 6.69904 0.80754 INTE EXTERN> -23.79293 -52.27949 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0724" Parameter: A <- "-76.0724" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7929" Parameter: B <- "-23.7929" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2795" Parameter: C <- "-52.2795" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4783 TOTAL ENERGY = -76.0724 RDTITL> * VAN DER WAALS = -23.7929 ELECTROSTATIC = -52.2795 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4783" Parameter: CONF_N -> "8002" Comparing "4783" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4784" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760122 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760998 ATOM PAIRS WERE FOUND FOR ATOM LIST 41995 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29740 from a total of 760998 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4784 -83.27049 7.19808 0.72791 INTE EXTERN> -27.81577 -55.45472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.2705" Parameter: A <- "-83.2705" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8158" Parameter: B <- "-27.8158" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.4547" Parameter: C <- "-55.4547" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4784 TOTAL ENERGY = -83.2705 RDTITL> * VAN DER WAALS = -27.8158 ELECTROSTATIC = -55.4547 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4784" Parameter: CONF_N -> "8002" Comparing "4784" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4785" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760998 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764211 ATOM PAIRS WERE FOUND FOR ATOM LIST 41773 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30530 from a total of 764211 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4785 -83.90597 0.63547 0.74035 INTE EXTERN> -26.12095 -57.78502 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.906" Parameter: A <- "-83.906" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1209" Parameter: B <- "-26.1209" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.785" Parameter: C <- "-57.785" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4785 TOTAL ENERGY = -83.906 RDTITL> * VAN DER WAALS = -26.1209 ELECTROSTATIC = -57.785 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4785" Parameter: CONF_N -> "8002" Comparing "4785" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4786" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764211 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763383 ATOM PAIRS WERE FOUND FOR ATOM LIST 41773 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30309 from a total of 763383 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4786 -73.61372 -10.29225 0.74799 INTE EXTERN> -28.25033 -45.36339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6137" Parameter: A <- "-73.6137" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2503" Parameter: B <- "-28.2503" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3634" Parameter: C <- "-45.3634" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4786 TOTAL ENERGY = -73.6137 RDTITL> * VAN DER WAALS = -28.2503 ELECTROSTATIC = -45.3634 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4786" Parameter: CONF_N -> "8002" Comparing "4786" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4787" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763383 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762060 ATOM PAIRS WERE FOUND FOR ATOM LIST 41873 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30261 from a total of 762060 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4787 -73.77047 0.15675 0.73335 INTE EXTERN> -26.99811 -46.77236 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7705" Parameter: A <- "-73.7705" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9981" Parameter: B <- "-26.9981" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7724" Parameter: C <- "-46.7724" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4787 TOTAL ENERGY = -73.7705 RDTITL> * VAN DER WAALS = -26.9981 ELECTROSTATIC = -46.7724 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4787" Parameter: CONF_N -> "8002" Comparing "4787" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4788" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762060 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765097 ATOM PAIRS WERE FOUND FOR ATOM LIST 41955 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30198 from a total of 765097 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4788 -77.99863 4.22816 0.68587 INTE EXTERN> -27.99881 -49.99982 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9986" Parameter: A <- "-77.9986" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9988" Parameter: B <- "-27.9988" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9998" Parameter: C <- "-49.9998" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4788 TOTAL ENERGY = -77.9986 RDTITL> * VAN DER WAALS = -27.9988 ELECTROSTATIC = -49.9998 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4788" Parameter: CONF_N -> "8002" Comparing "4788" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4789" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765097 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760850 ATOM PAIRS WERE FOUND FOR ATOM LIST 41783 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30099 from a total of 760850 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4789 -77.66262 -0.33601 0.80575 INTE EXTERN> -23.65212 -54.01050 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6626" Parameter: A <- "-77.6626" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6521" Parameter: B <- "-23.6521" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0105" Parameter: C <- "-54.0105" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4789 TOTAL ENERGY = -77.6626 RDTITL> * VAN DER WAALS = -23.6521 ELECTROSTATIC = -54.0105 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4789" Parameter: CONF_N -> "8002" Comparing "4789" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4790" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760850 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765789 ATOM PAIRS WERE FOUND FOR ATOM LIST 42055 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30537 from a total of 765789 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4790 -80.77643 3.11381 0.69193 INTE EXTERN> -30.12020 -50.65623 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7764" Parameter: A <- "-80.7764" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1202" Parameter: B <- "-30.1202" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6562" Parameter: C <- "-50.6562" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4790 TOTAL ENERGY = -80.7764 RDTITL> * VAN DER WAALS = -30.1202 ELECTROSTATIC = -50.6562 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4790" Parameter: CONF_N -> "8002" Comparing "4790" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4791" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765789 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764522 ATOM PAIRS WERE FOUND FOR ATOM LIST 42020 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30360 from a total of 764522 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4791 -73.28980 -7.48663 0.75061 INTE EXTERN> -27.99013 -45.29966 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2898" Parameter: A <- "-73.2898" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9901" Parameter: B <- "-27.9901" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2997" Parameter: C <- "-45.2997" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4791 TOTAL ENERGY = -73.2898 RDTITL> * VAN DER WAALS = -27.9901 ELECTROSTATIC = -45.2997 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4791" Parameter: CONF_N -> "8002" Comparing "4791" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4792" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764522 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763168 ATOM PAIRS WERE FOUND FOR ATOM LIST 41639 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30093 from a total of 763168 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4792 -73.11511 -0.17469 0.62714 INTE EXTERN> -31.64667 -41.46844 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1151" Parameter: A <- "-73.1151" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6467" Parameter: B <- "-31.6467" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4684" Parameter: C <- "-41.4684" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4792 TOTAL ENERGY = -73.1151 RDTITL> * VAN DER WAALS = -31.6467 ELECTROSTATIC = -41.4684 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4792" Parameter: CONF_N -> "8002" Comparing "4792" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4793" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763168 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760725 ATOM PAIRS WERE FOUND FOR ATOM LIST 41518 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30222 from a total of 760725 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4793 -77.23356 4.11845 0.68120 INTE EXTERN> -28.39608 -48.83748 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2336" Parameter: A <- "-77.2336" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3961" Parameter: B <- "-28.3961" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8375" Parameter: C <- "-48.8375" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4793 TOTAL ENERGY = -77.2336 RDTITL> * VAN DER WAALS = -28.3961 ELECTROSTATIC = -48.8375 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4793" Parameter: CONF_N -> "8002" Comparing "4793" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4794" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760725 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762082 ATOM PAIRS WERE FOUND FOR ATOM LIST 41852 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29832 from a total of 762082 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4794 -74.34614 -2.88742 0.71908 INTE EXTERN> -29.45121 -44.89493 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3461" Parameter: A <- "-74.3461" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4512" Parameter: B <- "-29.4512" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8949" Parameter: C <- "-44.8949" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4794 TOTAL ENERGY = -74.3461 RDTITL> * VAN DER WAALS = -29.4512 ELECTROSTATIC = -44.8949 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4794" Parameter: CONF_N -> "8002" Comparing "4794" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4795" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762082 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758915 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29954 from a total of 758915 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4795 -82.53465 8.18851 0.69325 INTE EXTERN> -27.91268 -54.62197 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5347" Parameter: A <- "-82.5347" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9127" Parameter: B <- "-27.9127" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.622" Parameter: C <- "-54.622" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4795 TOTAL ENERGY = -82.5347 RDTITL> * VAN DER WAALS = -27.9127 ELECTROSTATIC = -54.622 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4795" Parameter: CONF_N -> "8002" Comparing "4795" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4796" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758915 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761744 ATOM PAIRS WERE FOUND FOR ATOM LIST 41821 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30215 from a total of 761744 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4796 -77.88184 -4.65281 0.76146 INTE EXTERN> -24.00582 -53.87603 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8818" Parameter: A <- "-77.8818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0058" Parameter: B <- "-24.0058" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.876" Parameter: C <- "-53.876" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4796 TOTAL ENERGY = -77.8818 RDTITL> * VAN DER WAALS = -24.0058 ELECTROSTATIC = -53.876 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4796" Parameter: CONF_N -> "8002" Comparing "4796" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4797" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761744 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763449 ATOM PAIRS WERE FOUND FOR ATOM LIST 41910 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29457 from a total of 763449 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4797 -71.41907 -6.46278 0.69088 INTE EXTERN> -26.06947 -45.34960 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4191" Parameter: A <- "-71.4191" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0695" Parameter: B <- "-26.0695" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3496" Parameter: C <- "-45.3496" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4797 TOTAL ENERGY = -71.4191 RDTITL> * VAN DER WAALS = -26.0695 ELECTROSTATIC = -45.3496 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4797" Parameter: CONF_N -> "8002" Comparing "4797" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4798" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763449 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757170 ATOM PAIRS WERE FOUND FOR ATOM LIST 41431 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29837 from a total of 757170 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4798 -71.05392 -0.36515 0.66382 INTE EXTERN> -30.27596 -40.77796 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0539" Parameter: A <- "-71.0539" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.276" Parameter: B <- "-30.276" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.778" Parameter: C <- "-40.778" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4798 TOTAL ENERGY = -71.0539 RDTITL> * VAN DER WAALS = -30.276 ELECTROSTATIC = -40.778 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4798" Parameter: CONF_N -> "8002" Comparing "4798" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4799" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757170 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762567 ATOM PAIRS WERE FOUND FOR ATOM LIST 41790 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30431 from a total of 762567 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4799 -84.37919 13.32527 0.79399 INTE EXTERN> -26.58973 -57.78946 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.3792" Parameter: A <- "-84.3792" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5897" Parameter: B <- "-26.5897" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.7895" Parameter: C <- "-57.7895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4799 TOTAL ENERGY = -84.3792 RDTITL> * VAN DER WAALS = -26.5897 ELECTROSTATIC = -57.7895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4799" Parameter: CONF_N -> "8002" Comparing "4799" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4800" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762567 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759503 ATOM PAIRS WERE FOUND FOR ATOM LIST 41665 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30049 from a total of 759503 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4800 -72.92787 -11.45132 0.54930 INTE EXTERN> -33.93309 -38.99478 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9279" Parameter: A <- "-72.9279" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9331" Parameter: B <- "-33.9331" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9948" Parameter: C <- "-38.9948" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4800 TOTAL ENERGY = -72.9279 RDTITL> * VAN DER WAALS = -33.9331 ELECTROSTATIC = -38.9948 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4800" Parameter: CONF_N -> "8002" Comparing "4800" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4801" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759503 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759320 ATOM PAIRS WERE FOUND FOR ATOM LIST 41517 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30072 from a total of 759320 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4801 -73.72397 0.79609 0.74762 INTE EXTERN> -26.38564 -47.33833 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.724" Parameter: A <- "-73.724" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3856" Parameter: B <- "-26.3856" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3383" Parameter: C <- "-47.3383" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4801 TOTAL ENERGY = -73.724 RDTITL> * VAN DER WAALS = -26.3856 ELECTROSTATIC = -47.3383 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4801" Parameter: CONF_N -> "8002" Comparing "4801" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4802" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759320 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766219 ATOM PAIRS WERE FOUND FOR ATOM LIST 42070 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30430 from a total of 766219 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4802 -77.05533 3.33137 0.69340 INTE EXTERN> -30.85728 -46.19805 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0553" Parameter: A <- "-77.0553" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8573" Parameter: B <- "-30.8573" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1981" Parameter: C <- "-46.1981" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4802 TOTAL ENERGY = -77.0553 RDTITL> * VAN DER WAALS = -30.8573 ELECTROSTATIC = -46.1981 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4802" Parameter: CONF_N -> "8002" Comparing "4802" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4803" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766219 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770373 ATOM PAIRS WERE FOUND FOR ATOM LIST 41971 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30512 from a total of 770373 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4803 -77.09026 0.03493 0.62165 INTE EXTERN> -35.33503 -41.75523 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0903" Parameter: A <- "-77.0903" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.335" Parameter: B <- "-35.335" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7552" Parameter: C <- "-41.7552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4803 TOTAL ENERGY = -77.0903 RDTITL> * VAN DER WAALS = -35.335 ELECTROSTATIC = -41.7552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4803" Parameter: CONF_N -> "8002" Comparing "4803" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4804" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770373 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762866 ATOM PAIRS WERE FOUND FOR ATOM LIST 42014 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29852 from a total of 762866 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4804 -70.37302 -6.71724 0.79501 INTE EXTERN> -23.68924 -46.68378 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.373" Parameter: A <- "-70.373" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6892" Parameter: B <- "-23.6892" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6838" Parameter: C <- "-46.6838" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4804 TOTAL ENERGY = -70.373 RDTITL> * VAN DER WAALS = -23.6892 ELECTROSTATIC = -46.6838 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4804" Parameter: CONF_N -> "8002" Comparing "4804" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4805" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762866 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769775 ATOM PAIRS WERE FOUND FOR ATOM LIST 42054 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30775 from a total of 769775 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4805 -75.43013 5.05710 0.75313 INTE EXTERN> -28.00306 -47.42706 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4301" Parameter: A <- "-75.4301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0031" Parameter: B <- "-28.0031" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4271" Parameter: C <- "-47.4271" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4805 TOTAL ENERGY = -75.4301 RDTITL> * VAN DER WAALS = -28.0031 ELECTROSTATIC = -47.4271 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4805" Parameter: CONF_N -> "8002" Comparing "4805" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4806" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769775 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759827 ATOM PAIRS WERE FOUND FOR ATOM LIST 41675 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29712 from a total of 759827 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4806 -76.91288 1.48276 0.63197 INTE EXTERN> -30.10742 -46.80546 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9129" Parameter: A <- "-76.9129" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1074" Parameter: B <- "-30.1074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8055" Parameter: C <- "-46.8055" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4806 TOTAL ENERGY = -76.9129 RDTITL> * VAN DER WAALS = -30.1074 ELECTROSTATIC = -46.8055 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4806" Parameter: CONF_N -> "8002" Comparing "4806" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4807" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759827 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759594 ATOM PAIRS WERE FOUND FOR ATOM LIST 41718 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29498 from a total of 759594 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4807 -74.61613 -2.29675 0.66983 INTE EXTERN> -29.45671 -45.15943 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6161" Parameter: A <- "-74.6161" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4567" Parameter: B <- "-29.4567" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1594" Parameter: C <- "-45.1594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4807 TOTAL ENERGY = -74.6161 RDTITL> * VAN DER WAALS = -29.4567 ELECTROSTATIC = -45.1594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4807" Parameter: CONF_N -> "8002" Comparing "4807" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4808" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759594 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768020 ATOM PAIRS WERE FOUND FOR ATOM LIST 42032 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30144 from a total of 768020 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4808 -74.23217 -0.38396 0.66016 INTE EXTERN> -31.56686 -42.66531 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2322" Parameter: A <- "-74.2322" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5669" Parameter: B <- "-31.5669" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6653" Parameter: C <- "-42.6653" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4808 TOTAL ENERGY = -74.2322 RDTITL> * VAN DER WAALS = -31.5669 ELECTROSTATIC = -42.6653 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4808" Parameter: CONF_N -> "8002" Comparing "4808" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4809" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768020 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763171 ATOM PAIRS WERE FOUND FOR ATOM LIST 41730 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30424 from a total of 763171 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4809 -77.13146 2.89929 0.63323 INTE EXTERN> -31.47580 -45.65565 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1315" Parameter: A <- "-77.1315" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4758" Parameter: B <- "-31.4758" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6557" Parameter: C <- "-45.6557" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4809 TOTAL ENERGY = -77.1315 RDTITL> * VAN DER WAALS = -31.4758 ELECTROSTATIC = -45.6557 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4809" Parameter: CONF_N -> "8002" Comparing "4809" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4810" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763171 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759811 ATOM PAIRS WERE FOUND FOR ATOM LIST 41510 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29937 from a total of 759811 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4810 -73.78479 -3.34667 0.65518 INTE EXTERN> -31.43374 -42.35105 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7848" Parameter: A <- "-73.7848" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4337" Parameter: B <- "-31.4337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.351" Parameter: C <- "-42.351" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4810 TOTAL ENERGY = -73.7848 RDTITL> * VAN DER WAALS = -31.4337 ELECTROSTATIC = -42.351 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4810" Parameter: CONF_N -> "8002" Comparing "4810" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4811" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759811 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759849 ATOM PAIRS WERE FOUND FOR ATOM LIST 41536 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30111 from a total of 759849 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4811 -77.78233 3.99755 0.69157 INTE EXTERN> -28.58544 -49.19689 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7823" Parameter: A <- "-77.7823" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5854" Parameter: B <- "-28.5854" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1969" Parameter: C <- "-49.1969" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4811 TOTAL ENERGY = -77.7823 RDTITL> * VAN DER WAALS = -28.5854 ELECTROSTATIC = -49.1969 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4811" Parameter: CONF_N -> "8002" Comparing "4811" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4812" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759849 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757096 ATOM PAIRS WERE FOUND FOR ATOM LIST 41404 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29321 from a total of 757096 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4812 -74.88374 -2.89859 0.69872 INTE EXTERN> -26.89147 -47.99227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8837" Parameter: A <- "-74.8837" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8915" Parameter: B <- "-26.8915" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9923" Parameter: C <- "-47.9923" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4812 TOTAL ENERGY = -74.8837 RDTITL> * VAN DER WAALS = -26.8915 ELECTROSTATIC = -47.9923 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4812" Parameter: CONF_N -> "8002" Comparing "4812" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4813" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757096 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755647 ATOM PAIRS WERE FOUND FOR ATOM LIST 41555 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29294 from a total of 755647 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4813 -73.49809 -1.38565 0.67989 INTE EXTERN> -28.61082 -44.88727 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4981" Parameter: A <- "-73.4981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6108" Parameter: B <- "-28.6108" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8873" Parameter: C <- "-44.8873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4813 TOTAL ENERGY = -73.4981 RDTITL> * VAN DER WAALS = -28.6108 ELECTROSTATIC = -44.8873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4813" Parameter: CONF_N -> "8002" Comparing "4813" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4814" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755647 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758845 ATOM PAIRS WERE FOUND FOR ATOM LIST 41624 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29835 from a total of 758845 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4814 -69.81998 -3.67811 0.65020 INTE EXTERN> -29.81317 -40.00681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.82" Parameter: A <- "-69.82" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8132" Parameter: B <- "-29.8132" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0068" Parameter: C <- "-40.0068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4814 TOTAL ENERGY = -69.82 RDTITL> * VAN DER WAALS = -29.8132 ELECTROSTATIC = -40.0068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4814" Parameter: CONF_N -> "8002" Comparing "4814" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4815" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758845 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763348 ATOM PAIRS WERE FOUND FOR ATOM LIST 41754 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29596 from a total of 763348 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4815 -79.04507 9.22509 0.79175 INTE EXTERN> -26.94527 -52.09980 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0451" Parameter: A <- "-79.0451" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9453" Parameter: B <- "-26.9453" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0998" Parameter: C <- "-52.0998" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4815 TOTAL ENERGY = -79.0451 RDTITL> * VAN DER WAALS = -26.9453 ELECTROSTATIC = -52.0998 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4815" Parameter: CONF_N -> "8002" Comparing "4815" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4816" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763348 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765916 ATOM PAIRS WERE FOUND FOR ATOM LIST 41978 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30303 from a total of 765916 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4816 -79.79007 0.74500 0.69111 INTE EXTERN> -33.92615 -45.86391 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7901" Parameter: A <- "-79.7901" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9262" Parameter: B <- "-33.9262" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8639" Parameter: C <- "-45.8639" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4816 TOTAL ENERGY = -79.7901 RDTITL> * VAN DER WAALS = -33.9262 ELECTROSTATIC = -45.8639 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4816" Parameter: CONF_N -> "8002" Comparing "4816" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4817" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765916 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763976 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 763976 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4817 -77.47204 -2.31802 0.67502 INTE EXTERN> -31.61879 -45.85325 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.472" Parameter: A <- "-77.472" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6188" Parameter: B <- "-31.6188" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8532" Parameter: C <- "-45.8532" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4817 TOTAL ENERGY = -77.472 RDTITL> * VAN DER WAALS = -31.6188 ELECTROSTATIC = -45.8532 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4817" Parameter: CONF_N -> "8002" Comparing "4817" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4818" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763976 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763762 ATOM PAIRS WERE FOUND FOR ATOM LIST 41926 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30960 from a total of 763762 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4818 -75.59682 -1.87522 0.71820 INTE EXTERN> -29.82629 -45.77053 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5968" Parameter: A <- "-75.5968" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8263" Parameter: B <- "-29.8263" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7705" Parameter: C <- "-45.7705" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4818 TOTAL ENERGY = -75.5968 RDTITL> * VAN DER WAALS = -29.8263 ELECTROSTATIC = -45.7705 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4818" Parameter: CONF_N -> "8002" Comparing "4818" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4819" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763762 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758373 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30359 from a total of 758373 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4819 -73.46161 -2.13521 0.69308 INTE EXTERN> -29.94842 -43.51318 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4616" Parameter: A <- "-73.4616" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9484" Parameter: B <- "-29.9484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5132" Parameter: C <- "-43.5132" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4819 TOTAL ENERGY = -73.4616 RDTITL> * VAN DER WAALS = -29.9484 ELECTROSTATIC = -43.5132 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4819" Parameter: CONF_N -> "8002" Comparing "4819" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4820" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758373 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757305 ATOM PAIRS WERE FOUND FOR ATOM LIST 41520 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29917 from a total of 757305 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4820 -73.77496 0.31336 0.74178 INTE EXTERN> -26.12326 -47.65171 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.775" Parameter: A <- "-73.775" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1233" Parameter: B <- "-26.1233" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6517" Parameter: C <- "-47.6517" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4820 TOTAL ENERGY = -73.775 RDTITL> * VAN DER WAALS = -26.1233 ELECTROSTATIC = -47.6517 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4820" Parameter: CONF_N -> "8002" Comparing "4820" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4821" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757305 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763213 ATOM PAIRS WERE FOUND FOR ATOM LIST 41892 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30241 from a total of 763213 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4821 -74.20058 0.42562 0.79689 INTE EXTERN> -24.79618 -49.40441 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2006" Parameter: A <- "-74.2006" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7962" Parameter: B <- "-24.7962" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4044" Parameter: C <- "-49.4044" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4821 TOTAL ENERGY = -74.2006 RDTITL> * VAN DER WAALS = -24.7962 ELECTROSTATIC = -49.4044 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4821" Parameter: CONF_N -> "8002" Comparing "4821" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4822" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763213 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761589 ATOM PAIRS WERE FOUND FOR ATOM LIST 41557 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29841 from a total of 761589 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4822 -77.17599 2.97540 0.71994 INTE EXTERN> -30.06140 -47.11459 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.176" Parameter: A <- "-77.176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0614" Parameter: B <- "-30.0614" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1146" Parameter: C <- "-47.1146" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4822 TOTAL ENERGY = -77.176 RDTITL> * VAN DER WAALS = -30.0614 ELECTROSTATIC = -47.1146 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4822" Parameter: CONF_N -> "8002" Comparing "4822" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4823" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761589 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761602 ATOM PAIRS WERE FOUND FOR ATOM LIST 41871 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30025 from a total of 761602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4823 -69.92211 -7.25388 0.57609 INTE EXTERN> -31.37832 -38.54378 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9221" Parameter: A <- "-69.9221" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3783" Parameter: B <- "-31.3783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5438" Parameter: C <- "-38.5438" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4823 TOTAL ENERGY = -69.9221 RDTITL> * VAN DER WAALS = -31.3783 ELECTROSTATIC = -38.5438 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4823" Parameter: CONF_N -> "8002" Comparing "4823" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4824" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760011 ATOM PAIRS WERE FOUND FOR ATOM LIST 41530 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30434 from a total of 760011 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4824 -74.90667 4.98457 0.67831 INTE EXTERN> -31.30105 -43.60562 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9067" Parameter: A <- "-74.9067" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3011" Parameter: B <- "-31.3011" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6056" Parameter: C <- "-43.6056" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4824 TOTAL ENERGY = -74.9067 RDTITL> * VAN DER WAALS = -31.3011 ELECTROSTATIC = -43.6056 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4824" Parameter: CONF_N -> "8002" Comparing "4824" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4825" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760011 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762674 ATOM PAIRS WERE FOUND FOR ATOM LIST 41835 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29986 from a total of 762674 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4825 -82.22540 7.31873 0.78595 INTE EXTERN> -26.03783 -56.18758 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.2254" Parameter: A <- "-82.2254" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0378" Parameter: B <- "-26.0378" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.1876" Parameter: C <- "-56.1876" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4825 TOTAL ENERGY = -82.2254 RDTITL> * VAN DER WAALS = -26.0378 ELECTROSTATIC = -56.1876 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4825" Parameter: CONF_N -> "8002" Comparing "4825" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4826" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762674 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760251 ATOM PAIRS WERE FOUND FOR ATOM LIST 41606 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30269 from a total of 760251 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4826 -74.68971 -7.53570 0.86065 INTE EXTERN> -24.59660 -50.09311 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6897" Parameter: A <- "-74.6897" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5966" Parameter: B <- "-24.5966" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0931" Parameter: C <- "-50.0931" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4826 TOTAL ENERGY = -74.6897 RDTITL> * VAN DER WAALS = -24.5966 ELECTROSTATIC = -50.0931 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4826" Parameter: CONF_N -> "8002" Comparing "4826" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4827" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760251 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754743 ATOM PAIRS WERE FOUND FOR ATOM LIST 41266 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29624 from a total of 754743 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4827 -76.55344 1.86373 0.73410 INTE EXTERN> -29.64839 -46.90504 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5534" Parameter: A <- "-76.5534" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6484" Parameter: B <- "-29.6484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.905" Parameter: C <- "-46.905" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4827 TOTAL ENERGY = -76.5534 RDTITL> * VAN DER WAALS = -29.6484 ELECTROSTATIC = -46.905 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4827" Parameter: CONF_N -> "8002" Comparing "4827" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4828" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754743 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759560 ATOM PAIRS WERE FOUND FOR ATOM LIST 41369 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29380 from a total of 759560 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4828 -70.00167 -6.55177 0.62409 INTE EXTERN> -29.48605 -40.51561 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0017" Parameter: A <- "-70.0017" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4861" Parameter: B <- "-29.4861" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5156" Parameter: C <- "-40.5156" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4828 TOTAL ENERGY = -70.0017 RDTITL> * VAN DER WAALS = -29.4861 ELECTROSTATIC = -40.5156 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4828" Parameter: CONF_N -> "8002" Comparing "4828" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4829" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759560 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759332 ATOM PAIRS WERE FOUND FOR ATOM LIST 41417 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29481 from a total of 759332 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4829 -75.30915 5.30748 0.62168 INTE EXTERN> -30.09263 -45.21652 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3091" Parameter: A <- "-75.3091" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0926" Parameter: B <- "-30.0926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2165" Parameter: C <- "-45.2165" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4829 TOTAL ENERGY = -75.3091 RDTITL> * VAN DER WAALS = -30.0926 ELECTROSTATIC = -45.2165 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4829" Parameter: CONF_N -> "8002" Comparing "4829" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4830" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759332 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762839 ATOM PAIRS WERE FOUND FOR ATOM LIST 41531 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29917 from a total of 762839 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4830 -76.61199 1.30285 0.78625 INTE EXTERN> -24.05076 -52.56124 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.612" Parameter: A <- "-76.612" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0508" Parameter: B <- "-24.0508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5612" Parameter: C <- "-52.5612" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4830 TOTAL ENERGY = -76.612 RDTITL> * VAN DER WAALS = -24.0508 ELECTROSTATIC = -52.5612 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4830" Parameter: CONF_N -> "8002" Comparing "4830" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4831" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762839 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761527 ATOM PAIRS WERE FOUND FOR ATOM LIST 41559 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29592 from a total of 761527 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4831 -78.20022 1.58823 0.64382 INTE EXTERN> -31.57542 -46.62480 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2002" Parameter: A <- "-78.2002" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5754" Parameter: B <- "-31.5754" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6248" Parameter: C <- "-46.6248" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4831 TOTAL ENERGY = -78.2002 RDTITL> * VAN DER WAALS = -31.5754 ELECTROSTATIC = -46.6248 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4831" Parameter: CONF_N -> "8002" Comparing "4831" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4832" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761527 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766432 ATOM PAIRS WERE FOUND FOR ATOM LIST 41885 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29507 from a total of 766432 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4832 -77.51643 -0.68379 0.69346 INTE EXTERN> -29.43548 -48.08095 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5164" Parameter: A <- "-77.5164" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4355" Parameter: B <- "-29.4355" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.081" Parameter: C <- "-48.081" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4832 TOTAL ENERGY = -77.5164 RDTITL> * VAN DER WAALS = -29.4355 ELECTROSTATIC = -48.081 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4832" Parameter: CONF_N -> "8002" Comparing "4832" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4833" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766432 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764138 ATOM PAIRS WERE FOUND FOR ATOM LIST 41910 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29350 from a total of 764138 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4833 -76.61949 -0.89694 0.75991 INTE EXTERN> -23.91805 -52.70143 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6195" Parameter: A <- "-76.6195" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9181" Parameter: B <- "-23.9181" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.7014" Parameter: C <- "-52.7014" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4833 TOTAL ENERGY = -76.6195 RDTITL> * VAN DER WAALS = -23.9181 ELECTROSTATIC = -52.7014 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4833" Parameter: CONF_N -> "8002" Comparing "4833" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4834" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764138 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764338 ATOM PAIRS WERE FOUND FOR ATOM LIST 41846 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29664 from a total of 764338 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4834 -80.07430 3.45482 0.63048 INTE EXTERN> -33.37744 -46.69687 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0743" Parameter: A <- "-80.0743" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3774" Parameter: B <- "-33.3774" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6969" Parameter: C <- "-46.6969" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4834 TOTAL ENERGY = -80.0743 RDTITL> * VAN DER WAALS = -33.3774 ELECTROSTATIC = -46.6969 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4834" Parameter: CONF_N -> "8002" Comparing "4834" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4835" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764338 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757237 ATOM PAIRS WERE FOUND FOR ATOM LIST 41451 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29728 from a total of 757237 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4835 -75.68769 -4.38662 0.82976 INTE EXTERN> -23.36833 -52.31936 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6877" Parameter: A <- "-75.6877" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.3683" Parameter: B <- "-23.3683" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3194" Parameter: C <- "-52.3194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4835 TOTAL ENERGY = -75.6877 RDTITL> * VAN DER WAALS = -23.3683 ELECTROSTATIC = -52.3194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4835" Parameter: CONF_N -> "8002" Comparing "4835" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4836" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757237 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755346 ATOM PAIRS WERE FOUND FOR ATOM LIST 41314 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29581 from a total of 755346 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4836 -75.95505 0.26736 0.68231 INTE EXTERN> -31.35604 -44.59900 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.955" Parameter: A <- "-75.955" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.356" Parameter: B <- "-31.356" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.599" Parameter: C <- "-44.599" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4836 TOTAL ENERGY = -75.955 RDTITL> * VAN DER WAALS = -31.356 ELECTROSTATIC = -44.599 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4836" Parameter: CONF_N -> "8002" Comparing "4836" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4837" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755346 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759201 ATOM PAIRS WERE FOUND FOR ATOM LIST 41564 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29946 from a total of 759201 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4837 -70.96515 -4.98990 0.83465 INTE EXTERN> -24.08950 -46.87565 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9651" Parameter: A <- "-70.9651" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0895" Parameter: B <- "-24.0895" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8756" Parameter: C <- "-46.8756" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4837 TOTAL ENERGY = -70.9651 RDTITL> * VAN DER WAALS = -24.0895 ELECTROSTATIC = -46.8756 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4837" Parameter: CONF_N -> "8002" Comparing "4837" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4838" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759201 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761388 ATOM PAIRS WERE FOUND FOR ATOM LIST 41588 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29491 from a total of 761388 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4838 -74.78180 3.81666 0.78410 INTE EXTERN> -25.75073 -49.03107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7818" Parameter: A <- "-74.7818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7507" Parameter: B <- "-25.7507" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0311" Parameter: C <- "-49.0311" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4838 TOTAL ENERGY = -74.7818 RDTITL> * VAN DER WAALS = -25.7507 ELECTROSTATIC = -49.0311 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4838" Parameter: CONF_N -> "8002" Comparing "4838" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4839" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761388 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764813 ATOM PAIRS WERE FOUND FOR ATOM LIST 41940 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29730 from a total of 764813 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4839 -71.31275 -3.46905 0.61297 INTE EXTERN> -32.08446 -39.22829 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3128" Parameter: A <- "-71.3128" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0845" Parameter: B <- "-32.0845" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2283" Parameter: C <- "-39.2283" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4839 TOTAL ENERGY = -71.3128 RDTITL> * VAN DER WAALS = -32.0845 ELECTROSTATIC = -39.2283 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4839" Parameter: CONF_N -> "8002" Comparing "4839" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4840" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764813 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769993 ATOM PAIRS WERE FOUND FOR ATOM LIST 42063 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30189 from a total of 769993 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4840 -71.90418 0.59142 0.80469 INTE EXTERN> -26.73846 -45.16572 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9042" Parameter: A <- "-71.9042" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7385" Parameter: B <- "-26.7385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1657" Parameter: C <- "-45.1657" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4840 TOTAL ENERGY = -71.9042 RDTITL> * VAN DER WAALS = -26.7385 ELECTROSTATIC = -45.1657 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4840" Parameter: CONF_N -> "8002" Comparing "4840" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4841" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769993 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763153 ATOM PAIRS WERE FOUND FOR ATOM LIST 41681 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28989 from a total of 763153 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4841 -77.47200 5.56782 0.70470 INTE EXTERN> -28.06249 -49.40950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.472" Parameter: A <- "-77.472" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0625" Parameter: B <- "-28.0625" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4095" Parameter: C <- "-49.4095" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4841 TOTAL ENERGY = -77.472 RDTITL> * VAN DER WAALS = -28.0625 ELECTROSTATIC = -49.4095 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4841" Parameter: CONF_N -> "8002" Comparing "4841" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4842" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763153 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41895 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29411 from a total of 766118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4842 -71.92148 -5.55052 0.65199 INTE EXTERN> -29.65516 -42.26633 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9215" Parameter: A <- "-71.9215" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6552" Parameter: B <- "-29.6552" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2663" Parameter: C <- "-42.2663" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4842 TOTAL ENERGY = -71.9215 RDTITL> * VAN DER WAALS = -29.6552 ELECTROSTATIC = -42.2663 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4842" Parameter: CONF_N -> "8002" Comparing "4842" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4843" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763402 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29396 from a total of 763402 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4843 -75.66460 3.74312 0.74735 INTE EXTERN> -28.58292 -47.08168 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6646" Parameter: A <- "-75.6646" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5829" Parameter: B <- "-28.5829" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0817" Parameter: C <- "-47.0817" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4843 TOTAL ENERGY = -75.6646 RDTITL> * VAN DER WAALS = -28.5829 ELECTROSTATIC = -47.0817 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4843" Parameter: CONF_N -> "8002" Comparing "4843" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4844" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763402 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768310 ATOM PAIRS WERE FOUND FOR ATOM LIST 41918 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30104 from a total of 768310 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4844 -74.93663 -0.72797 0.65822 INTE EXTERN> -29.03468 -45.90196 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9366" Parameter: A <- "-74.9366" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0347" Parameter: B <- "-29.0347" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.902" Parameter: C <- "-45.902" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4844 TOTAL ENERGY = -74.9366 RDTITL> * VAN DER WAALS = -29.0347 ELECTROSTATIC = -45.902 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4844" Parameter: CONF_N -> "8002" Comparing "4844" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4845" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768310 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765182 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29663 from a total of 765182 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4845 -75.64468 0.70804 0.58476 INTE EXTERN> -31.42149 -44.22319 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6447" Parameter: A <- "-75.6447" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4215" Parameter: B <- "-31.4215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2232" Parameter: C <- "-44.2232" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4845 TOTAL ENERGY = -75.6447 RDTITL> * VAN DER WAALS = -31.4215 ELECTROSTATIC = -44.2232 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4845" Parameter: CONF_N -> "8002" Comparing "4845" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4846" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765182 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761449 ATOM PAIRS WERE FOUND FOR ATOM LIST 41706 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29752 from a total of 761449 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4846 -79.31265 3.66798 0.67625 INTE EXTERN> -29.86899 -49.44367 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.3127" Parameter: A <- "-79.3127" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.869" Parameter: B <- "-29.869" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4437" Parameter: C <- "-49.4437" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4846 TOTAL ENERGY = -79.3127 RDTITL> * VAN DER WAALS = -29.869 ELECTROSTATIC = -49.4437 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4846" Parameter: CONF_N -> "8002" Comparing "4846" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4847" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761449 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763944 ATOM PAIRS WERE FOUND FOR ATOM LIST 41933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30089 from a total of 763944 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4847 -79.28907 -0.02359 0.69721 INTE EXTERN> -30.13577 -49.15329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2891" Parameter: A <- "-79.2891" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1358" Parameter: B <- "-30.1358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1533" Parameter: C <- "-49.1533" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4847 TOTAL ENERGY = -79.2891 RDTITL> * VAN DER WAALS = -30.1358 ELECTROSTATIC = -49.1533 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4847" Parameter: CONF_N -> "8002" Comparing "4847" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4848" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763944 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762821 ATOM PAIRS WERE FOUND FOR ATOM LIST 41580 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30360 from a total of 762821 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4848 -77.17391 -2.11516 0.71322 INTE EXTERN> -27.91420 -49.25971 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1739" Parameter: A <- "-77.1739" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9142" Parameter: B <- "-27.9142" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2597" Parameter: C <- "-49.2597" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4848 TOTAL ENERGY = -77.1739 RDTITL> * VAN DER WAALS = -27.9142 ELECTROSTATIC = -49.2597 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4848" Parameter: CONF_N -> "8002" Comparing "4848" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4849" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762821 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754431 ATOM PAIRS WERE FOUND FOR ATOM LIST 41272 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29449 from a total of 754431 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4849 -75.80469 -1.36922 0.74910 INTE EXTERN> -27.38238 -48.42231 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8047" Parameter: A <- "-75.8047" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3824" Parameter: B <- "-27.3824" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4223" Parameter: C <- "-48.4223" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4849 TOTAL ENERGY = -75.8047 RDTITL> * VAN DER WAALS = -27.3824 ELECTROSTATIC = -48.4223 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4849" Parameter: CONF_N -> "8002" Comparing "4849" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4850" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754431 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762059 ATOM PAIRS WERE FOUND FOR ATOM LIST 41523 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29488 from a total of 762059 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4850 -82.51731 6.71262 0.78740 INTE EXTERN> -25.72025 -56.79707 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5173" Parameter: A <- "-82.5173" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7202" Parameter: B <- "-25.7202" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.7971" Parameter: C <- "-56.7971" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4850 TOTAL ENERGY = -82.5173 RDTITL> * VAN DER WAALS = -25.7202 ELECTROSTATIC = -56.7971 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4850" Parameter: CONF_N -> "8002" Comparing "4850" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4851" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762059 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765232 ATOM PAIRS WERE FOUND FOR ATOM LIST 41865 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30236 from a total of 765232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4851 -74.78244 -7.73487 0.64611 INTE EXTERN> -31.13960 -43.64284 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7824" Parameter: A <- "-74.7824" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1396" Parameter: B <- "-31.1396" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6428" Parameter: C <- "-43.6428" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4851 TOTAL ENERGY = -74.7824 RDTITL> * VAN DER WAALS = -31.1396 ELECTROSTATIC = -43.6428 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4851" Parameter: CONF_N -> "8002" Comparing "4851" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4852" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762178 ATOM PAIRS WERE FOUND FOR ATOM LIST 41751 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30321 from a total of 762178 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4852 -80.37063 5.58819 0.68958 INTE EXTERN> -27.48703 -52.88360 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3706" Parameter: A <- "-80.3706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.487" Parameter: B <- "-27.487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8836" Parameter: C <- "-52.8836" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4852 TOTAL ENERGY = -80.3706 RDTITL> * VAN DER WAALS = -27.487 ELECTROSTATIC = -52.8836 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4852" Parameter: CONF_N -> "8002" Comparing "4852" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4853" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762178 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765599 ATOM PAIRS WERE FOUND FOR ATOM LIST 41984 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30621 from a total of 765599 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4853 -79.00377 -1.36687 0.59402 INTE EXTERN> -34.08617 -44.91760 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0038" Parameter: A <- "-79.0038" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0862" Parameter: B <- "-34.0862" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9176" Parameter: C <- "-44.9176" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4853 TOTAL ENERGY = -79.0038 RDTITL> * VAN DER WAALS = -34.0862 ELECTROSTATIC = -44.9176 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4853" Parameter: CONF_N -> "8002" Comparing "4853" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4854" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765599 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764187 ATOM PAIRS WERE FOUND FOR ATOM LIST 41987 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30017 from a total of 764187 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4854 -76.66631 -2.33746 0.83837 INTE EXTERN> -23.72106 -52.94525 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6663" Parameter: A <- "-76.6663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7211" Parameter: B <- "-23.7211" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9452" Parameter: C <- "-52.9452" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4854 TOTAL ENERGY = -76.6663 RDTITL> * VAN DER WAALS = -23.7211 ELECTROSTATIC = -52.9452 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4854" Parameter: CONF_N -> "8002" Comparing "4854" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4855" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764187 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760170 ATOM PAIRS WERE FOUND FOR ATOM LIST 41783 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29499 from a total of 760170 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4855 -77.90248 1.23617 0.76737 INTE EXTERN> -25.38316 -52.51932 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9025" Parameter: A <- "-77.9025" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3832" Parameter: B <- "-25.3832" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5193" Parameter: C <- "-52.5193" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4855 TOTAL ENERGY = -77.9025 RDTITL> * VAN DER WAALS = -25.3832 ELECTROSTATIC = -52.5193 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4855" Parameter: CONF_N -> "8002" Comparing "4855" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4856" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760170 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763706 ATOM PAIRS WERE FOUND FOR ATOM LIST 41859 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 763706 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4856 -74.32570 -3.57678 0.76584 INTE EXTERN> -26.43827 -47.88743 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3257" Parameter: A <- "-74.3257" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4383" Parameter: B <- "-26.4383" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8874" Parameter: C <- "-47.8874" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4856 TOTAL ENERGY = -74.3257 RDTITL> * VAN DER WAALS = -26.4383 ELECTROSTATIC = -47.8874 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4856" Parameter: CONF_N -> "8002" Comparing "4856" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4857" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763706 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767341 ATOM PAIRS WERE FOUND FOR ATOM LIST 42093 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30090 from a total of 767341 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4857 -69.70910 -4.61660 0.75120 INTE EXTERN> -25.65733 -44.05177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7091" Parameter: A <- "-69.7091" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6573" Parameter: B <- "-25.6573" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0518" Parameter: C <- "-44.0518" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4857 TOTAL ENERGY = -69.7091 RDTITL> * VAN DER WAALS = -25.6573 ELECTROSTATIC = -44.0518 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4857" Parameter: CONF_N -> "8002" Comparing "4857" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4858" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767341 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762248 ATOM PAIRS WERE FOUND FOR ATOM LIST 41690 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29790 from a total of 762248 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4858 -79.74441 10.03532 0.66932 INTE EXTERN> -30.77576 -48.96865 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7444" Parameter: A <- "-79.7444" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7758" Parameter: B <- "-30.7758" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9687" Parameter: C <- "-48.9687" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4858 TOTAL ENERGY = -79.7444 RDTITL> * VAN DER WAALS = -30.7758 ELECTROSTATIC = -48.9687 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4858" Parameter: CONF_N -> "8002" Comparing "4858" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4859" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762248 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768451 ATOM PAIRS WERE FOUND FOR ATOM LIST 42047 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29548 from a total of 768451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4859 -75.50101 -4.24341 0.70353 INTE EXTERN> -30.56459 -44.93641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.501" Parameter: A <- "-75.501" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5646" Parameter: B <- "-30.5646" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9364" Parameter: C <- "-44.9364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4859 TOTAL ENERGY = -75.501 RDTITL> * VAN DER WAALS = -30.5646 ELECTROSTATIC = -44.9364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4859" Parameter: CONF_N -> "8002" Comparing "4859" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4860" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769141 ATOM PAIRS WERE FOUND FOR ATOM LIST 41965 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30400 from a total of 769141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4860 -81.65248 6.15147 0.72552 INTE EXTERN> -29.51441 -52.13807 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6525" Parameter: A <- "-81.6525" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5144" Parameter: B <- "-29.5144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1381" Parameter: C <- "-52.1381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4860 TOTAL ENERGY = -81.6525 RDTITL> * VAN DER WAALS = -29.5144 ELECTROSTATIC = -52.1381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4860" Parameter: CONF_N -> "8002" Comparing "4860" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4861" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761225 ATOM PAIRS WERE FOUND FOR ATOM LIST 41772 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29766 from a total of 761225 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4861 -75.83471 -5.81777 0.72137 INTE EXTERN> -29.38704 -46.44767 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8347" Parameter: A <- "-75.8347" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.387" Parameter: B <- "-29.387" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4477" Parameter: C <- "-46.4477" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4861 TOTAL ENERGY = -75.8347 RDTITL> * VAN DER WAALS = -29.387 ELECTROSTATIC = -46.4477 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4861" Parameter: CONF_N -> "8002" Comparing "4861" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4862" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761225 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761866 ATOM PAIRS WERE FOUND FOR ATOM LIST 41621 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30474 from a total of 761866 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4862 -79.56803 3.73331 0.76831 INTE EXTERN> -25.94487 -53.62315 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.568" Parameter: A <- "-79.568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9449" Parameter: B <- "-25.9449" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6232" Parameter: C <- "-53.6232" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4862 TOTAL ENERGY = -79.568 RDTITL> * VAN DER WAALS = -25.9449 ELECTROSTATIC = -53.6232 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4862" Parameter: CONF_N -> "8002" Comparing "4862" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4863" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761866 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771466 ATOM PAIRS WERE FOUND FOR ATOM LIST 42085 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30261 from a total of 771466 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4863 -78.79683 -0.77119 0.85141 INTE EXTERN> -25.83056 -52.96627 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7968" Parameter: A <- "-78.7968" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8306" Parameter: B <- "-25.8306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9663" Parameter: C <- "-52.9663" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4863 TOTAL ENERGY = -78.7968 RDTITL> * VAN DER WAALS = -25.8306 ELECTROSTATIC = -52.9663 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4863" Parameter: CONF_N -> "8002" Comparing "4863" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4864" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771466 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764682 ATOM PAIRS WERE FOUND FOR ATOM LIST 41780 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29577 from a total of 764682 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4864 -79.04143 0.24460 0.69621 INTE EXTERN> -29.77989 -49.26154 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0414" Parameter: A <- "-79.0414" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7799" Parameter: B <- "-29.7799" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2615" Parameter: C <- "-49.2615" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4864 TOTAL ENERGY = -79.0414 RDTITL> * VAN DER WAALS = -29.7799 ELECTROSTATIC = -49.2615 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4864" Parameter: CONF_N -> "8002" Comparing "4864" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4865" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764682 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768755 ATOM PAIRS WERE FOUND FOR ATOM LIST 42025 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29794 from a total of 768755 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4865 -68.45894 -10.58249 0.63526 INTE EXTERN> -29.24649 -39.21245 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4589" Parameter: A <- "-68.4589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2465" Parameter: B <- "-29.2465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2125" Parameter: C <- "-39.2125" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4865 TOTAL ENERGY = -68.4589 RDTITL> * VAN DER WAALS = -29.2465 ELECTROSTATIC = -39.2125 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4865" Parameter: CONF_N -> "8002" Comparing "4865" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4866" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768755 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767318 ATOM PAIRS WERE FOUND FOR ATOM LIST 42023 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30057 from a total of 767318 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4866 -74.30986 5.85091 0.68277 INTE EXTERN> -29.33729 -44.97257 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3099" Parameter: A <- "-74.3099" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3373" Parameter: B <- "-29.3373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9726" Parameter: C <- "-44.9726" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4866 TOTAL ENERGY = -74.3099 RDTITL> * VAN DER WAALS = -29.3373 ELECTROSTATIC = -44.9726 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4866" Parameter: CONF_N -> "8002" Comparing "4866" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4867" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767318 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766301 ATOM PAIRS WERE FOUND FOR ATOM LIST 41982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29787 from a total of 766301 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4867 -73.59109 -0.71877 0.55983 INTE EXTERN> -33.92483 -39.66626 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5911" Parameter: A <- "-73.5911" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9248" Parameter: B <- "-33.9248" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6663" Parameter: C <- "-39.6663" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4867 TOTAL ENERGY = -73.5911 RDTITL> * VAN DER WAALS = -33.9248 ELECTROSTATIC = -39.6663 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4867" Parameter: CONF_N -> "8002" Comparing "4867" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4868" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766301 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768204 ATOM PAIRS WERE FOUND FOR ATOM LIST 42023 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30225 from a total of 768204 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4868 -83.09060 9.49951 0.67749 INTE EXTERN> -29.23236 -53.85824 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.0906" Parameter: A <- "-83.0906" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2324" Parameter: B <- "-29.2324" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8582" Parameter: C <- "-53.8582" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4868 TOTAL ENERGY = -83.0906 RDTITL> * VAN DER WAALS = -29.2324 ELECTROSTATIC = -53.8582 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4868" Parameter: CONF_N -> "8002" Comparing "4868" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4869" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768204 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766218 ATOM PAIRS WERE FOUND FOR ATOM LIST 41882 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30293 from a total of 766218 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4869 -88.15384 5.06324 0.73745 INTE EXTERN> -30.05806 -58.09579 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.1538" Parameter: A <- "-88.1538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0581" Parameter: B <- "-30.0581" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.0958" Parameter: C <- "-58.0958" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4869 TOTAL ENERGY = -88.1538 RDTITL> * VAN DER WAALS = -30.0581 ELECTROSTATIC = -58.0958 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4869" Parameter: CONF_N -> "8002" Comparing "4869" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4870" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766218 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763677 ATOM PAIRS WERE FOUND FOR ATOM LIST 41753 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29961 from a total of 763677 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4870 -70.38150 -17.77234 0.61971 INTE EXTERN> -30.61834 -39.76316 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3815" Parameter: A <- "-70.3815" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6183" Parameter: B <- "-30.6183" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7632" Parameter: C <- "-39.7632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4870 TOTAL ENERGY = -70.3815 RDTITL> * VAN DER WAALS = -30.6183 ELECTROSTATIC = -39.7632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4870" Parameter: CONF_N -> "8002" Comparing "4870" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4871" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763677 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764395 ATOM PAIRS WERE FOUND FOR ATOM LIST 41712 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30980 from a total of 764395 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4871 -85.99713 15.61563 0.67671 INTE EXTERN> -29.22531 -56.77182 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.9971" Parameter: A <- "-85.9971" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2253" Parameter: B <- "-29.2253" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.7718" Parameter: C <- "-56.7718" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4871 TOTAL ENERGY = -85.9971 RDTITL> * VAN DER WAALS = -29.2253 ELECTROSTATIC = -56.7718 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4871" Parameter: CONF_N -> "8002" Comparing "4871" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4872" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764395 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766015 ATOM PAIRS WERE FOUND FOR ATOM LIST 41853 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30243 from a total of 766015 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4872 -78.38858 -7.60855 0.77797 INTE EXTERN> -27.16209 -51.22648 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3886" Parameter: A <- "-78.3886" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1621" Parameter: B <- "-27.1621" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2265" Parameter: C <- "-51.2265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4872 TOTAL ENERGY = -78.3886 RDTITL> * VAN DER WAALS = -27.1621 ELECTROSTATIC = -51.2265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4872" Parameter: CONF_N -> "8002" Comparing "4872" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4873" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766015 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769110 ATOM PAIRS WERE FOUND FOR ATOM LIST 42172 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30154 from a total of 769110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4873 -80.17534 1.78676 0.73870 INTE EXTERN> -27.29720 -52.87814 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1753" Parameter: A <- "-80.1753" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2972" Parameter: B <- "-27.2972" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8781" Parameter: C <- "-52.8781" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4873 TOTAL ENERGY = -80.1753 RDTITL> * VAN DER WAALS = -27.2972 ELECTROSTATIC = -52.8781 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4873" Parameter: CONF_N -> "8002" Comparing "4873" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4874" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763286 ATOM PAIRS WERE FOUND FOR ATOM LIST 41789 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30086 from a total of 763286 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4874 -77.22833 -2.94700 0.68582 INTE EXTERN> -28.70279 -48.52554 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2283" Parameter: A <- "-77.2283" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7028" Parameter: B <- "-28.7028" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5255" Parameter: C <- "-48.5255" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4874 TOTAL ENERGY = -77.2283 RDTITL> * VAN DER WAALS = -28.7028 ELECTROSTATIC = -48.5255 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4874" Parameter: CONF_N -> "8002" Comparing "4874" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4875" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763286 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762565 ATOM PAIRS WERE FOUND FOR ATOM LIST 41647 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30044 from a total of 762565 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4875 -77.74876 0.52043 0.69587 INTE EXTERN> -28.74075 -49.00801 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7488" Parameter: A <- "-77.7488" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7408" Parameter: B <- "-28.7408" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.008" Parameter: C <- "-49.008" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4875 TOTAL ENERGY = -77.7488 RDTITL> * VAN DER WAALS = -28.7408 ELECTROSTATIC = -49.008 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4875" Parameter: CONF_N -> "8002" Comparing "4875" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4876" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762565 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768819 ATOM PAIRS WERE FOUND FOR ATOM LIST 42251 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29968 from a total of 768819 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4876 -86.11572 8.36696 0.77206 INTE EXTERN> -28.38819 -57.72753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.1157" Parameter: A <- "-86.1157" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3882" Parameter: B <- "-28.3882" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.7275" Parameter: C <- "-57.7275" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4876 TOTAL ENERGY = -86.1157 RDTITL> * VAN DER WAALS = -28.3882 ELECTROSTATIC = -57.7275 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4876" Parameter: CONF_N -> "8002" Comparing "4876" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4877" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768819 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766321 ATOM PAIRS WERE FOUND FOR ATOM LIST 42227 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30143 from a total of 766321 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4877 -76.26831 -9.84741 0.61175 INTE EXTERN> -30.60376 -45.66455 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2683" Parameter: A <- "-76.2683" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6038" Parameter: B <- "-30.6038" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6645" Parameter: C <- "-45.6645" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4877 TOTAL ENERGY = -76.2683 RDTITL> * VAN DER WAALS = -30.6038 ELECTROSTATIC = -45.6645 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4877" Parameter: CONF_N -> "8002" Comparing "4877" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4878" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766321 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760748 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29449 from a total of 760748 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4878 -79.04159 2.77329 0.70861 INTE EXTERN> -27.23826 -51.80333 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0416" Parameter: A <- "-79.0416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2383" Parameter: B <- "-27.2383" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8033" Parameter: C <- "-51.8033" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4878 TOTAL ENERGY = -79.0416 RDTITL> * VAN DER WAALS = -27.2383 ELECTROSTATIC = -51.8033 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4878" Parameter: CONF_N -> "8002" Comparing "4878" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4879" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760748 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768998 ATOM PAIRS WERE FOUND FOR ATOM LIST 42136 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30827 from a total of 768998 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4879 -84.94739 5.90580 0.73179 INTE EXTERN> -25.95009 -58.99730 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.9474" Parameter: A <- "-84.9474" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9501" Parameter: B <- "-25.9501" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.9973" Parameter: C <- "-58.9973" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4879 TOTAL ENERGY = -84.9474 RDTITL> * VAN DER WAALS = -25.9501 ELECTROSTATIC = -58.9973 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4879" Parameter: CONF_N -> "8002" Comparing "4879" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4880" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768998 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765196 ATOM PAIRS WERE FOUND FOR ATOM LIST 41950 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29979 from a total of 765196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4880 -73.43867 -11.50872 0.60256 INTE EXTERN> -30.25936 -43.17931 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4387" Parameter: A <- "-73.4387" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2594" Parameter: B <- "-30.2594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1793" Parameter: C <- "-43.1793" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4880 TOTAL ENERGY = -73.4387 RDTITL> * VAN DER WAALS = -30.2594 ELECTROSTATIC = -43.1793 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4880" Parameter: CONF_N -> "8002" Comparing "4880" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4881" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761728 ATOM PAIRS WERE FOUND FOR ATOM LIST 41900 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29846 from a total of 761728 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4881 -73.01430 -0.42437 0.65447 INTE EXTERN> -26.43015 -46.58415 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0143" Parameter: A <- "-73.0143" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4302" Parameter: B <- "-26.4302" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5841" Parameter: C <- "-46.5841" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4881 TOTAL ENERGY = -73.0143 RDTITL> * VAN DER WAALS = -26.4302 ELECTROSTATIC = -46.5841 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4881" Parameter: CONF_N -> "8002" Comparing "4881" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4882" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761728 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762077 ATOM PAIRS WERE FOUND FOR ATOM LIST 41718 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30822 from a total of 762077 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4882 -75.72410 2.70980 0.67401 INTE EXTERN> -28.29771 -47.42640 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7241" Parameter: A <- "-75.7241" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2977" Parameter: B <- "-28.2977" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4264" Parameter: C <- "-47.4264" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4882 TOTAL ENERGY = -75.7241 RDTITL> * VAN DER WAALS = -28.2977 ELECTROSTATIC = -47.4264 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4882" Parameter: CONF_N -> "8002" Comparing "4882" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4883" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762077 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765977 ATOM PAIRS WERE FOUND FOR ATOM LIST 42043 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30677 from a total of 765977 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4883 -80.60683 4.88272 0.71505 INTE EXTERN> -26.81672 -53.79010 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6068" Parameter: A <- "-80.6068" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8167" Parameter: B <- "-26.8167" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.7901" Parameter: C <- "-53.7901" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4883 TOTAL ENERGY = -80.6068 RDTITL> * VAN DER WAALS = -26.8167 ELECTROSTATIC = -53.7901 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4883" Parameter: CONF_N -> "8002" Comparing "4883" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4884" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765977 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759502 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30380 from a total of 759502 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4884 -77.91557 -2.69126 0.73019 INTE EXTERN> -26.20001 -51.71556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9156" Parameter: A <- "-77.9156" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2" Parameter: B <- "-26.2" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7156" Parameter: C <- "-51.7156" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4884 TOTAL ENERGY = -77.9156 RDTITL> * VAN DER WAALS = -26.2 ELECTROSTATIC = -51.7156 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4884" Parameter: CONF_N -> "8002" Comparing "4884" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4885" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759502 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767599 ATOM PAIRS WERE FOUND FOR ATOM LIST 42138 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30690 from a total of 767599 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4885 -75.76937 -2.14619 0.83968 INTE EXTERN> -23.44263 -52.32674 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7694" Parameter: A <- "-75.7694" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4426" Parameter: B <- "-23.4426" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3267" Parameter: C <- "-52.3267" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4885 TOTAL ENERGY = -75.7694 RDTITL> * VAN DER WAALS = -23.4426 ELECTROSTATIC = -52.3267 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4885" Parameter: CONF_N -> "8002" Comparing "4885" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4886" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767599 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763551 ATOM PAIRS WERE FOUND FOR ATOM LIST 41956 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29153 from a total of 763551 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4886 -81.06974 5.30037 0.86977 INTE EXTERN> -22.56308 -58.50666 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.0697" Parameter: A <- "-81.0697" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.5631" Parameter: B <- "-22.5631" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.5067" Parameter: C <- "-58.5067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4886 TOTAL ENERGY = -81.0697 RDTITL> * VAN DER WAALS = -22.5631 ELECTROSTATIC = -58.5067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4886" Parameter: CONF_N -> "8002" Comparing "4886" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4887" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763551 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768027 ATOM PAIRS WERE FOUND FOR ATOM LIST 42109 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29551 from a total of 768027 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4887 -75.60666 -5.46308 0.66322 INTE EXTERN> -28.81787 -46.78880 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6067" Parameter: A <- "-75.6067" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8179" Parameter: B <- "-28.8179" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7888" Parameter: C <- "-46.7888" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4887 TOTAL ENERGY = -75.6067 RDTITL> * VAN DER WAALS = -28.8179 ELECTROSTATIC = -46.7888 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4887" Parameter: CONF_N -> "8002" Comparing "4887" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4888" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768027 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765093 ATOM PAIRS WERE FOUND FOR ATOM LIST 41889 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29548 from a total of 765093 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4888 -78.50121 2.89455 0.68176 INTE EXTERN> -26.35051 -52.15070 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5012" Parameter: A <- "-78.5012" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3505" Parameter: B <- "-26.3505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1507" Parameter: C <- "-52.1507" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4888 TOTAL ENERGY = -78.5012 RDTITL> * VAN DER WAALS = -26.3505 ELECTROSTATIC = -52.1507 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4888" Parameter: CONF_N -> "8002" Comparing "4888" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4889" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765093 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764065 ATOM PAIRS WERE FOUND FOR ATOM LIST 41946 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30179 from a total of 764065 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4889 -79.70295 1.20174 0.80324 INTE EXTERN> -23.78792 -55.91504 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.703" Parameter: A <- "-79.703" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7879" Parameter: B <- "-23.7879" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.915" Parameter: C <- "-55.915" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4889 TOTAL ENERGY = -79.703 RDTITL> * VAN DER WAALS = -23.7879 ELECTROSTATIC = -55.915 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4889" Parameter: CONF_N -> "8002" Comparing "4889" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4890" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764065 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768816 ATOM PAIRS WERE FOUND FOR ATOM LIST 41964 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30309 from a total of 768816 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4890 -78.50937 -1.19359 0.87578 INTE EXTERN> -23.20849 -55.30087 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5094" Parameter: A <- "-78.5094" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.2085" Parameter: B <- "-23.2085" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.3009" Parameter: C <- "-55.3009" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4890 TOTAL ENERGY = -78.5094 RDTITL> * VAN DER WAALS = -23.2085 ELECTROSTATIC = -55.3009 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4890" Parameter: CONF_N -> "8002" Comparing "4890" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4891" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768816 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765595 ATOM PAIRS WERE FOUND FOR ATOM LIST 41867 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30312 from a total of 765595 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4891 -70.11370 -8.39567 0.65567 INTE EXTERN> -29.22119 -40.89251 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1137" Parameter: A <- "-70.1137" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2212" Parameter: B <- "-29.2212" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8925" Parameter: C <- "-40.8925" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4891 TOTAL ENERGY = -70.1137 RDTITL> * VAN DER WAALS = -29.2212 ELECTROSTATIC = -40.8925 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4891" Parameter: CONF_N -> "8002" Comparing "4891" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4892" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765595 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770190 ATOM PAIRS WERE FOUND FOR ATOM LIST 42336 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30124 from a total of 770190 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4892 -75.23376 5.12006 0.61541 INTE EXTERN> -30.52556 -44.70819 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2338" Parameter: A <- "-75.2338" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5256" Parameter: B <- "-30.5256" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7082" Parameter: C <- "-44.7082" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4892 TOTAL ENERGY = -75.2338 RDTITL> * VAN DER WAALS = -30.5256 ELECTROSTATIC = -44.7082 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4892" Parameter: CONF_N -> "8002" Comparing "4892" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4893" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770190 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764187 ATOM PAIRS WERE FOUND FOR ATOM LIST 41850 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30072 from a total of 764187 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4893 -80.12675 4.89300 0.75377 INTE EXTERN> -28.20811 -51.91864 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1268" Parameter: A <- "-80.1268" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2081" Parameter: B <- "-28.2081" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.9186" Parameter: C <- "-51.9186" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4893 TOTAL ENERGY = -80.1268 RDTITL> * VAN DER WAALS = -28.2081 ELECTROSTATIC = -51.9186 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4893" Parameter: CONF_N -> "8002" Comparing "4893" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4894" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764187 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763596 ATOM PAIRS WERE FOUND FOR ATOM LIST 42038 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29934 from a total of 763596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4894 -74.86558 -5.26118 0.80774 INTE EXTERN> -26.04621 -48.81936 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8656" Parameter: A <- "-74.8656" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0462" Parameter: B <- "-26.0462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8194" Parameter: C <- "-48.8194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4894 TOTAL ENERGY = -74.8656 RDTITL> * VAN DER WAALS = -26.0462 ELECTROSTATIC = -48.8194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4894" Parameter: CONF_N -> "8002" Comparing "4894" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4895" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764387 ATOM PAIRS WERE FOUND FOR ATOM LIST 41793 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29966 from a total of 764387 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4895 -74.30222 -0.56335 0.69533 INTE EXTERN> -29.92614 -44.37609 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3022" Parameter: A <- "-74.3022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9261" Parameter: B <- "-29.9261" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3761" Parameter: C <- "-44.3761" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4895 TOTAL ENERGY = -74.3022 RDTITL> * VAN DER WAALS = -29.9261 ELECTROSTATIC = -44.3761 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4895" Parameter: CONF_N -> "8002" Comparing "4895" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4896" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764387 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761418 ATOM PAIRS WERE FOUND FOR ATOM LIST 41724 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30401 from a total of 761418 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4896 -70.32439 -3.97783 0.70844 INTE EXTERN> -26.59422 -43.73017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3244" Parameter: A <- "-70.3244" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5942" Parameter: B <- "-26.5942" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7302" Parameter: C <- "-43.7302" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4896 TOTAL ENERGY = -70.3244 RDTITL> * VAN DER WAALS = -26.5942 ELECTROSTATIC = -43.7302 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4896" Parameter: CONF_N -> "8002" Comparing "4896" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4897" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761418 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764099 ATOM PAIRS WERE FOUND FOR ATOM LIST 41686 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30651 from a total of 764099 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4897 -70.40248 0.07809 0.73888 INTE EXTERN> -28.00007 -42.40241 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4025" Parameter: A <- "-70.4025" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0001" Parameter: B <- "-28.0001" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4024" Parameter: C <- "-42.4024" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4897 TOTAL ENERGY = -70.4025 RDTITL> * VAN DER WAALS = -28.0001 ELECTROSTATIC = -42.4024 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4897" Parameter: CONF_N -> "8002" Comparing "4897" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4898" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764099 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765404 ATOM PAIRS WERE FOUND FOR ATOM LIST 42110 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29889 from a total of 765404 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4898 -76.92923 6.52674 0.58991 INTE EXTERN> -32.62738 -44.30184 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9292" Parameter: A <- "-76.9292" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6274" Parameter: B <- "-32.6274" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3018" Parameter: C <- "-44.3018" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4898 TOTAL ENERGY = -76.9292 RDTITL> * VAN DER WAALS = -32.6274 ELECTROSTATIC = -44.3018 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4898" Parameter: CONF_N -> "8002" Comparing "4898" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4899" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765404 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763386 ATOM PAIRS WERE FOUND FOR ATOM LIST 41915 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29925 from a total of 763386 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4899 -75.34175 -1.58748 0.71683 INTE EXTERN> -27.47975 -47.86200 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3417" Parameter: A <- "-75.3417" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4797" Parameter: B <- "-27.4797" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.862" Parameter: C <- "-47.862" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4899 TOTAL ENERGY = -75.3417 RDTITL> * VAN DER WAALS = -27.4797 ELECTROSTATIC = -47.862 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4899" Parameter: CONF_N -> "8002" Comparing "4899" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4900" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763386 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765756 ATOM PAIRS WERE FOUND FOR ATOM LIST 41845 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30326 from a total of 765756 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4900 -75.39709 0.05534 0.73343 INTE EXTERN> -25.29860 -50.09849 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3971" Parameter: A <- "-75.3971" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2986" Parameter: B <- "-25.2986" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0985" Parameter: C <- "-50.0985" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4900 TOTAL ENERGY = -75.3971 RDTITL> * VAN DER WAALS = -25.2986 ELECTROSTATIC = -50.0985 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4900" Parameter: CONF_N -> "8002" Comparing "4900" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4901" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765756 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766528 ATOM PAIRS WERE FOUND FOR ATOM LIST 42016 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30054 from a total of 766528 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4901 -74.58029 -0.81680 0.83438 INTE EXTERN> -21.29867 -53.28162 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5803" Parameter: A <- "-74.5803" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.2987" Parameter: B <- "-21.2987" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.2816" Parameter: C <- "-53.2816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4901 TOTAL ENERGY = -74.5803 RDTITL> * VAN DER WAALS = -21.2987 ELECTROSTATIC = -53.2816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4901" Parameter: CONF_N -> "8002" Comparing "4901" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4902" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766528 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766134 ATOM PAIRS WERE FOUND FOR ATOM LIST 41880 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29978 from a total of 766134 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4902 -74.14918 -0.43110 0.60430 INTE EXTERN> -31.42548 -42.72370 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1492" Parameter: A <- "-74.1492" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4255" Parameter: B <- "-31.4255" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7237" Parameter: C <- "-42.7237" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4902 TOTAL ENERGY = -74.1492 RDTITL> * VAN DER WAALS = -31.4255 ELECTROSTATIC = -42.7237 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4902" Parameter: CONF_N -> "8002" Comparing "4902" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4903" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766134 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766251 ATOM PAIRS WERE FOUND FOR ATOM LIST 41920 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29981 from a total of 766251 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4903 -81.13888 6.98970 0.67583 INTE EXTERN> -28.28564 -52.85325 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1389" Parameter: A <- "-81.1389" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2856" Parameter: B <- "-28.2856" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8532" Parameter: C <- "-52.8532" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4903 TOTAL ENERGY = -81.1389 RDTITL> * VAN DER WAALS = -28.2856 ELECTROSTATIC = -52.8532 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4903" Parameter: CONF_N -> "8002" Comparing "4903" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4904" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766251 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765311 ATOM PAIRS WERE FOUND FOR ATOM LIST 41751 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30738 from a total of 765311 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4904 -84.46971 3.33082 0.67129 INTE EXTERN> -33.05943 -51.41028 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.4697" Parameter: A <- "-84.4697" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0594" Parameter: B <- "-33.0594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4103" Parameter: C <- "-51.4103" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4904 TOTAL ENERGY = -84.4697 RDTITL> * VAN DER WAALS = -33.0594 ELECTROSTATIC = -51.4103 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4904" Parameter: CONF_N -> "8002" Comparing "4904" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4905" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765311 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768113 ATOM PAIRS WERE FOUND FOR ATOM LIST 41910 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30408 from a total of 768113 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4905 -75.64071 -8.82900 0.69634 INTE EXTERN> -28.48135 -47.15936 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6407" Parameter: A <- "-75.6407" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4813" Parameter: B <- "-28.4813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1594" Parameter: C <- "-47.1594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4905 TOTAL ENERGY = -75.6407 RDTITL> * VAN DER WAALS = -28.4813 ELECTROSTATIC = -47.1594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4905" Parameter: CONF_N -> "8002" Comparing "4905" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4906" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768113 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763038 ATOM PAIRS WERE FOUND FOR ATOM LIST 41814 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29923 from a total of 763038 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4906 -76.99892 1.35821 0.66637 INTE EXTERN> -28.65868 -48.34024 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9989" Parameter: A <- "-76.9989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6587" Parameter: B <- "-28.6587" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3402" Parameter: C <- "-48.3402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4906 TOTAL ENERGY = -76.9989 RDTITL> * VAN DER WAALS = -28.6587 ELECTROSTATIC = -48.3402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4906" Parameter: CONF_N -> "8002" Comparing "4906" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4907" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763038 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759366 ATOM PAIRS WERE FOUND FOR ATOM LIST 41425 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29657 from a total of 759366 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4907 -79.28592 2.28700 0.67320 INTE EXTERN> -29.69171 -49.59421 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2859" Parameter: A <- "-79.2859" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6917" Parameter: B <- "-29.6917" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5942" Parameter: C <- "-49.5942" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4907 TOTAL ENERGY = -79.2859 RDTITL> * VAN DER WAALS = -29.6917 ELECTROSTATIC = -49.5942 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4907" Parameter: CONF_N -> "8002" Comparing "4907" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4908" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759366 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764134 ATOM PAIRS WERE FOUND FOR ATOM LIST 41710 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30229 from a total of 764134 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4908 -76.43303 -2.85290 0.74215 INTE EXTERN> -26.56020 -49.87282 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.433" Parameter: A <- "-76.433" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5602" Parameter: B <- "-26.5602" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8728" Parameter: C <- "-49.8728" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4908 TOTAL ENERGY = -76.433 RDTITL> * VAN DER WAALS = -26.5602 ELECTROSTATIC = -49.8728 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4908" Parameter: CONF_N -> "8002" Comparing "4908" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4909" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764134 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766945 ATOM PAIRS WERE FOUND FOR ATOM LIST 42017 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30219 from a total of 766945 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4909 -78.67478 2.24176 0.66316 INTE EXTERN> -29.66291 -49.01187 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6748" Parameter: A <- "-78.6748" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6629" Parameter: B <- "-29.6629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0119" Parameter: C <- "-49.0119" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4909 TOTAL ENERGY = -78.6748 RDTITL> * VAN DER WAALS = -29.6629 ELECTROSTATIC = -49.0119 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4909" Parameter: CONF_N -> "8002" Comparing "4909" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4910" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766945 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762611 ATOM PAIRS WERE FOUND FOR ATOM LIST 41578 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29898 from a total of 762611 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4910 -72.80498 -5.86980 0.66352 INTE EXTERN> -29.40409 -43.40089 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.805" Parameter: A <- "-72.805" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4041" Parameter: B <- "-29.4041" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4009" Parameter: C <- "-43.4009" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4910 TOTAL ENERGY = -72.805 RDTITL> * VAN DER WAALS = -29.4041 ELECTROSTATIC = -43.4009 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4910" Parameter: CONF_N -> "8002" Comparing "4910" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4911" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762611 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765859 ATOM PAIRS WERE FOUND FOR ATOM LIST 41991 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30085 from a total of 765859 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4911 -73.13130 0.32632 0.78654 INTE EXTERN> -25.55166 -47.57964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1313" Parameter: A <- "-73.1313" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5517" Parameter: B <- "-25.5517" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5796" Parameter: C <- "-47.5796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4911 TOTAL ENERGY = -73.1313 RDTITL> * VAN DER WAALS = -25.5517 ELECTROSTATIC = -47.5796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4911" Parameter: CONF_N -> "8002" Comparing "4911" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4912" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765859 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41582 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28979 from a total of 760586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4912 -72.92941 -0.20189 0.62735 INTE EXTERN> -29.75606 -43.17335 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9294" Parameter: A <- "-72.9294" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7561" Parameter: B <- "-29.7561" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1733" Parameter: C <- "-43.1733" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4912 TOTAL ENERGY = -72.9294 RDTITL> * VAN DER WAALS = -29.7561 ELECTROSTATIC = -43.1733 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4912" Parameter: CONF_N -> "8002" Comparing "4912" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4913" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763228 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29562 from a total of 763228 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4913 -73.30044 0.37103 0.57382 INTE EXTERN> -32.42346 -40.87697 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3004" Parameter: A <- "-73.3004" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4235" Parameter: B <- "-32.4235" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.877" Parameter: C <- "-40.877" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4913 TOTAL ENERGY = -73.3004 RDTITL> * VAN DER WAALS = -32.4235 ELECTROSTATIC = -40.877 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4913" Parameter: CONF_N -> "8002" Comparing "4913" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4914" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763228 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765341 ATOM PAIRS WERE FOUND FOR ATOM LIST 41923 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29568 from a total of 765341 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4914 -80.78821 7.48777 0.67778 INTE EXTERN> -28.72913 -52.05907 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7882" Parameter: A <- "-80.7882" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7291" Parameter: B <- "-28.7291" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0591" Parameter: C <- "-52.0591" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4914 TOTAL ENERGY = -80.7882 RDTITL> * VAN DER WAALS = -28.7291 ELECTROSTATIC = -52.0591 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4914" Parameter: CONF_N -> "8002" Comparing "4914" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4915" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765341 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762471 ATOM PAIRS WERE FOUND FOR ATOM LIST 41688 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29840 from a total of 762471 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4915 -78.94881 -1.83940 0.66354 INTE EXTERN> -32.08344 -46.86537 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9488" Parameter: A <- "-78.9488" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0834" Parameter: B <- "-32.0834" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8654" Parameter: C <- "-46.8654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4915 TOTAL ENERGY = -78.9488 RDTITL> * VAN DER WAALS = -32.0834 ELECTROSTATIC = -46.8654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4915" Parameter: CONF_N -> "8002" Comparing "4915" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4916" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762471 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765815 ATOM PAIRS WERE FOUND FOR ATOM LIST 41857 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30377 from a total of 765815 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4916 -76.22632 -2.72249 0.68165 INTE EXTERN> -28.41654 -47.80978 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2263" Parameter: A <- "-76.2263" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4165" Parameter: B <- "-28.4165" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8098" Parameter: C <- "-47.8098" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4916 TOTAL ENERGY = -76.2263 RDTITL> * VAN DER WAALS = -28.4165 ELECTROSTATIC = -47.8098 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4916" Parameter: CONF_N -> "8002" Comparing "4916" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4917" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765815 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769248 ATOM PAIRS WERE FOUND FOR ATOM LIST 42082 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30081 from a total of 769248 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4917 -79.94396 3.71764 0.62231 INTE EXTERN> -31.79157 -48.15239 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.944" Parameter: A <- "-79.944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7916" Parameter: B <- "-31.7916" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1524" Parameter: C <- "-48.1524" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4917 TOTAL ENERGY = -79.944 RDTITL> * VAN DER WAALS = -31.7916 ELECTROSTATIC = -48.1524 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4917" Parameter: CONF_N -> "8002" Comparing "4917" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4918" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769248 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762069 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30274 from a total of 762069 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4918 -72.79811 -7.14585 0.50581 INTE EXTERN> -36.46114 -36.33698 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7981" Parameter: A <- "-72.7981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.4611" Parameter: B <- "-36.4611" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.337" Parameter: C <- "-36.337" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4918 TOTAL ENERGY = -72.7981 RDTITL> * VAN DER WAALS = -36.4611 ELECTROSTATIC = -36.337 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4918" Parameter: CONF_N -> "8002" Comparing "4918" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4919" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762069 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765752 ATOM PAIRS WERE FOUND FOR ATOM LIST 41799 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30510 from a total of 765752 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4919 -77.65987 4.86176 0.72131 INTE EXTERN> -25.58649 -52.07338 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6599" Parameter: A <- "-77.6599" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5865" Parameter: B <- "-25.5865" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0734" Parameter: C <- "-52.0734" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4919 TOTAL ENERGY = -77.6599 RDTITL> * VAN DER WAALS = -25.5865 ELECTROSTATIC = -52.0734 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4919" Parameter: CONF_N -> "8002" Comparing "4919" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4920" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765752 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770667 ATOM PAIRS WERE FOUND FOR ATOM LIST 42133 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30656 from a total of 770667 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4920 -79.29389 1.63402 0.72917 INTE EXTERN> -29.37473 -49.91916 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2939" Parameter: A <- "-79.2939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3747" Parameter: B <- "-29.3747" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9192" Parameter: C <- "-49.9192" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4920 TOTAL ENERGY = -79.2939 RDTITL> * VAN DER WAALS = -29.3747 ELECTROSTATIC = -49.9192 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4920" Parameter: CONF_N -> "8002" Comparing "4920" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4921" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770667 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767971 ATOM PAIRS WERE FOUND FOR ATOM LIST 41909 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30537 from a total of 767971 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4921 -79.47020 0.17630 0.77486 INTE EXTERN> -25.47188 -53.99832 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4702" Parameter: A <- "-79.4702" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4719" Parameter: B <- "-25.4719" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.9983" Parameter: C <- "-53.9983" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4921 TOTAL ENERGY = -79.4702 RDTITL> * VAN DER WAALS = -25.4719 ELECTROSTATIC = -53.9983 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4921" Parameter: CONF_N -> "8002" Comparing "4921" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4922" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767971 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769277 ATOM PAIRS WERE FOUND FOR ATOM LIST 42053 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30721 from a total of 769277 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4922 -76.31731 -3.15288 0.58266 INTE EXTERN> -31.90985 -44.40747 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3173" Parameter: A <- "-76.3173" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9098" Parameter: B <- "-31.9098" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4075" Parameter: C <- "-44.4075" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4922 TOTAL ENERGY = -76.3173 RDTITL> * VAN DER WAALS = -31.9098 ELECTROSTATIC = -44.4075 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4922" Parameter: CONF_N -> "8002" Comparing "4922" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4923" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769277 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765091 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30464 from a total of 765091 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4923 -77.01938 0.70207 0.63506 INTE EXTERN> -32.06036 -44.95902 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0194" Parameter: A <- "-77.0194" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0604" Parameter: B <- "-32.0604" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.959" Parameter: C <- "-44.959" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4923 TOTAL ENERGY = -77.0194 RDTITL> * VAN DER WAALS = -32.0604 ELECTROSTATIC = -44.959 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4923" Parameter: CONF_N -> "8002" Comparing "4923" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4924" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765091 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766713 ATOM PAIRS WERE FOUND FOR ATOM LIST 42045 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30806 from a total of 766713 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4924 -77.46028 0.44090 0.61975 INTE EXTERN> -31.28733 -46.17295 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4603" Parameter: A <- "-77.4603" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2873" Parameter: B <- "-31.2873" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1729" Parameter: C <- "-46.1729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4924 TOTAL ENERGY = -77.4603 RDTITL> * VAN DER WAALS = -31.2873 ELECTROSTATIC = -46.1729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4924" Parameter: CONF_N -> "8002" Comparing "4924" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4925" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766713 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765272 ATOM PAIRS WERE FOUND FOR ATOM LIST 41803 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30205 from a total of 765272 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4925 -83.84571 6.38543 0.66908 INTE EXTERN> -30.77161 -53.07410 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.8457" Parameter: A <- "-83.8457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7716" Parameter: B <- "-30.7716" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0741" Parameter: C <- "-53.0741" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4925 TOTAL ENERGY = -83.8457 RDTITL> * VAN DER WAALS = -30.7716 ELECTROSTATIC = -53.0741 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4925" Parameter: CONF_N -> "8002" Comparing "4925" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4926" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765272 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766152 ATOM PAIRS WERE FOUND FOR ATOM LIST 41913 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30298 from a total of 766152 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4926 -78.45241 -5.39330 0.68475 INTE EXTERN> -29.94604 -48.50637 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4524" Parameter: A <- "-78.4524" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.946" Parameter: B <- "-29.946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5064" Parameter: C <- "-48.5064" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4926 TOTAL ENERGY = -78.4524 RDTITL> * VAN DER WAALS = -29.946 ELECTROSTATIC = -48.5064 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4926" Parameter: CONF_N -> "8002" Comparing "4926" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4927" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766152 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764792 ATOM PAIRS WERE FOUND FOR ATOM LIST 41771 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30009 from a total of 764792 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4927 -78.52959 0.07718 0.73378 INTE EXTERN> -24.44966 -54.07993 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5296" Parameter: A <- "-78.5296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4497" Parameter: B <- "-24.4497" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0799" Parameter: C <- "-54.0799" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4927 TOTAL ENERGY = -78.5296 RDTITL> * VAN DER WAALS = -24.4497 ELECTROSTATIC = -54.0799 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4927" Parameter: CONF_N -> "8002" Comparing "4927" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4928" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764792 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759704 ATOM PAIRS WERE FOUND FOR ATOM LIST 41554 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30020 from a total of 759704 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4928 -80.80778 2.27818 0.68487 INTE EXTERN> -30.22836 -50.57942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.8078" Parameter: A <- "-80.8078" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2284" Parameter: B <- "-30.2284" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5794" Parameter: C <- "-50.5794" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4928 TOTAL ENERGY = -80.8078 RDTITL> * VAN DER WAALS = -30.2284 ELECTROSTATIC = -50.5794 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4928" Parameter: CONF_N -> "8002" Comparing "4928" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4929" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759704 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767802 ATOM PAIRS WERE FOUND FOR ATOM LIST 41916 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30356 from a total of 767802 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4929 -84.39786 3.59008 0.71104 INTE EXTERN> -26.61250 -57.78536 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.3979" Parameter: A <- "-84.3979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6125" Parameter: B <- "-26.6125" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.7854" Parameter: C <- "-57.7854" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4929 TOTAL ENERGY = -84.3979 RDTITL> * VAN DER WAALS = -26.6125 ELECTROSTATIC = -57.7854 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4929" Parameter: CONF_N -> "8002" Comparing "4929" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4930" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767802 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766449 ATOM PAIRS WERE FOUND FOR ATOM LIST 41882 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30065 from a total of 766449 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4930 -76.49117 -7.90668 0.77500 INTE EXTERN> -23.62774 -52.86343 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4912" Parameter: A <- "-76.4912" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6277" Parameter: B <- "-23.6277" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8634" Parameter: C <- "-52.8634" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4930 TOTAL ENERGY = -76.4912 RDTITL> * VAN DER WAALS = -23.6277 ELECTROSTATIC = -52.8634 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4930" Parameter: CONF_N -> "8002" Comparing "4930" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4931" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766449 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757541 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29694 from a total of 757541 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4931 -79.21129 2.72011 0.68740 INTE EXTERN> -27.39457 -51.81671 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2113" Parameter: A <- "-79.2113" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3946" Parameter: B <- "-27.3946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8167" Parameter: C <- "-51.8167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4931 TOTAL ENERGY = -79.2113 RDTITL> * VAN DER WAALS = -27.3946 ELECTROSTATIC = -51.8167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4931" Parameter: CONF_N -> "8002" Comparing "4931" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4932" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757541 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757082 ATOM PAIRS WERE FOUND FOR ATOM LIST 41446 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30749 from a total of 757082 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4932 -82.95320 3.74192 0.68057 INTE EXTERN> -29.92093 -53.03227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9532" Parameter: A <- "-82.9532" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9209" Parameter: B <- "-29.9209" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0323" Parameter: C <- "-53.0323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4932 TOTAL ENERGY = -82.9532 RDTITL> * VAN DER WAALS = -29.9209 ELECTROSTATIC = -53.0323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4932" Parameter: CONF_N -> "8002" Comparing "4932" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4933" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757082 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759438 ATOM PAIRS WERE FOUND FOR ATOM LIST 41667 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30302 from a total of 759438 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4933 -81.80689 -1.14632 0.76193 INTE EXTERN> -27.58706 -54.21983 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8069" Parameter: A <- "-81.8069" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5871" Parameter: B <- "-27.5871" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2198" Parameter: C <- "-54.2198" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4933 TOTAL ENERGY = -81.8069 RDTITL> * VAN DER WAALS = -27.5871 ELECTROSTATIC = -54.2198 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4933" Parameter: CONF_N -> "8002" Comparing "4933" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4934" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759438 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759077 ATOM PAIRS WERE FOUND FOR ATOM LIST 41691 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30794 from a total of 759077 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4934 -81.71005 -0.09684 0.69439 INTE EXTERN> -29.42448 -52.28557 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.71" Parameter: A <- "-81.71" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4245" Parameter: B <- "-29.4245" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2856" Parameter: C <- "-52.2856" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4934 TOTAL ENERGY = -81.71 RDTITL> * VAN DER WAALS = -29.4245 ELECTROSTATIC = -52.2856 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4934" Parameter: CONF_N -> "8002" Comparing "4934" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4935" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759077 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770548 ATOM PAIRS WERE FOUND FOR ATOM LIST 42120 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30909 from a total of 770548 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4935 -77.17047 -4.53958 0.64775 INTE EXTERN> -31.84099 -45.32948 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1705" Parameter: A <- "-77.1705" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.841" Parameter: B <- "-31.841" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3295" Parameter: C <- "-45.3295" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4935 TOTAL ENERGY = -77.1705 RDTITL> * VAN DER WAALS = -31.841 ELECTROSTATIC = -45.3295 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4935" Parameter: CONF_N -> "8002" Comparing "4935" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4936" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770548 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765639 ATOM PAIRS WERE FOUND FOR ATOM LIST 41738 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30235 from a total of 765639 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4936 -79.30482 2.13435 0.68291 INTE EXTERN> -28.00393 -51.30089 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.3048" Parameter: A <- "-79.3048" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0039" Parameter: B <- "-28.0039" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3009" Parameter: C <- "-51.3009" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4936 TOTAL ENERGY = -79.3048 RDTITL> * VAN DER WAALS = -28.0039 ELECTROSTATIC = -51.3009 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4936" Parameter: CONF_N -> "8002" Comparing "4936" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4937" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765639 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764047 ATOM PAIRS WERE FOUND FOR ATOM LIST 41736 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30328 from a total of 764047 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4937 -74.98103 -4.32379 0.65399 INTE EXTERN> -28.14355 -46.83747 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.981" Parameter: A <- "-74.981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1436" Parameter: B <- "-28.1436" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8375" Parameter: C <- "-46.8375" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4937 TOTAL ENERGY = -74.981 RDTITL> * VAN DER WAALS = -28.1436 ELECTROSTATIC = -46.8375 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4937" Parameter: CONF_N -> "8002" Comparing "4937" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4938" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764047 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762366 ATOM PAIRS WERE FOUND FOR ATOM LIST 41756 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30583 from a total of 762366 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4938 -75.44953 0.46850 0.67531 INTE EXTERN> -28.38851 -47.06102 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4495" Parameter: A <- "-75.4495" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3885" Parameter: B <- "-28.3885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.061" Parameter: C <- "-47.061" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4938 TOTAL ENERGY = -75.4495 RDTITL> * VAN DER WAALS = -28.3885 ELECTROSTATIC = -47.061 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4938" Parameter: CONF_N -> "8002" Comparing "4938" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4939" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762366 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760852 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30449 from a total of 760852 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4939 -83.50994 8.06041 0.70041 INTE EXTERN> -30.53447 -52.97548 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.5099" Parameter: A <- "-83.5099" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5345" Parameter: B <- "-30.5345" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9755" Parameter: C <- "-52.9755" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4939 TOTAL ENERGY = -83.5099 RDTITL> * VAN DER WAALS = -30.5345 ELECTROSTATIC = -52.9755 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4939" Parameter: CONF_N -> "8002" Comparing "4939" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4940" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760852 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756324 ATOM PAIRS WERE FOUND FOR ATOM LIST 41393 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29821 from a total of 756324 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4940 -73.96549 -9.54446 0.68438 INTE EXTERN> -31.66249 -42.30300 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9655" Parameter: A <- "-73.9655" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6625" Parameter: B <- "-31.6625" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.303" Parameter: C <- "-42.303" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4940 TOTAL ENERGY = -73.9655 RDTITL> * VAN DER WAALS = -31.6625 ELECTROSTATIC = -42.303 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4940" Parameter: CONF_N -> "8002" Comparing "4940" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4941" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756324 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760097 ATOM PAIRS WERE FOUND FOR ATOM LIST 41752 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30700 from a total of 760097 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4941 -70.09111 -3.87438 0.65893 INTE EXTERN> -31.84187 -38.24924 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0911" Parameter: A <- "-70.0911" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8419" Parameter: B <- "-31.8419" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2492" Parameter: C <- "-38.2492" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4941 TOTAL ENERGY = -70.0911 RDTITL> * VAN DER WAALS = -31.8419 ELECTROSTATIC = -38.2492 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4941" Parameter: CONF_N -> "8002" Comparing "4941" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4942" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760097 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758699 ATOM PAIRS WERE FOUND FOR ATOM LIST 41730 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30247 from a total of 758699 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4942 -82.01590 11.92479 0.57289 INTE EXTERN> -34.78117 -47.23474 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.0159" Parameter: A <- "-82.0159" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.7812" Parameter: B <- "-34.7812" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2347" Parameter: C <- "-47.2347" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4942 TOTAL ENERGY = -82.0159 RDTITL> * VAN DER WAALS = -34.7812 ELECTROSTATIC = -47.2347 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4942" Parameter: CONF_N -> "8002" Comparing "4942" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4943" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758699 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756544 ATOM PAIRS WERE FOUND FOR ATOM LIST 41383 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29709 from a total of 756544 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4943 -78.66330 -3.35260 0.62966 INTE EXTERN> -29.78135 -48.88195 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6633" Parameter: A <- "-78.6633" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7813" Parameter: B <- "-29.7813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.882" Parameter: C <- "-48.882" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4943 TOTAL ENERGY = -78.6633 RDTITL> * VAN DER WAALS = -29.7813 ELECTROSTATIC = -48.882 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4943" Parameter: CONF_N -> "8002" Comparing "4943" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4944" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756544 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756276 ATOM PAIRS WERE FOUND FOR ATOM LIST 41365 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29859 from a total of 756276 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4944 -78.67864 0.01534 0.66128 INTE EXTERN> -30.55579 -48.12285 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6786" Parameter: A <- "-78.6786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5558" Parameter: B <- "-30.5558" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1229" Parameter: C <- "-48.1229" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4944 TOTAL ENERGY = -78.6786 RDTITL> * VAN DER WAALS = -30.5558 ELECTROSTATIC = -48.1229 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4944" Parameter: CONF_N -> "8002" Comparing "4944" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4945" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756276 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759417 ATOM PAIRS WERE FOUND FOR ATOM LIST 41595 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30616 from a total of 759417 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4945 -76.01595 -2.66269 0.60983 INTE EXTERN> -34.30165 -41.71429 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0159" Parameter: A <- "-76.0159" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3017" Parameter: B <- "-34.3017" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7143" Parameter: C <- "-41.7143" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4945 TOTAL ENERGY = -76.0159 RDTITL> * VAN DER WAALS = -34.3017 ELECTROSTATIC = -41.7143 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4945" Parameter: CONF_N -> "8002" Comparing "4945" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4946" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759417 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760187 ATOM PAIRS WERE FOUND FOR ATOM LIST 41823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30255 from a total of 760187 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4946 -80.62017 4.60422 0.75999 INTE EXTERN> -29.67898 -50.94118 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6202" Parameter: A <- "-80.6202" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.679" Parameter: B <- "-29.679" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9412" Parameter: C <- "-50.9412" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4946 TOTAL ENERGY = -80.6202 RDTITL> * VAN DER WAALS = -29.679 ELECTROSTATIC = -50.9412 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4946" Parameter: CONF_N -> "8002" Comparing "4946" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4947" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760187 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764793 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30435 from a total of 764793 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4947 -75.03555 -5.58462 0.62903 INTE EXTERN> -30.53846 -44.49709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0355" Parameter: A <- "-75.0355" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5385" Parameter: B <- "-30.5385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4971" Parameter: C <- "-44.4971" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4947 TOTAL ENERGY = -75.0355 RDTITL> * VAN DER WAALS = -30.5385 ELECTROSTATIC = -44.4971 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4947" Parameter: CONF_N -> "8002" Comparing "4947" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4948" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764793 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757447 ATOM PAIRS WERE FOUND FOR ATOM LIST 41572 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30125 from a total of 757447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4948 -81.57963 6.54408 0.68535 INTE EXTERN> -30.83449 -50.74514 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5796" Parameter: A <- "-81.5796" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8345" Parameter: B <- "-30.8345" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7451" Parameter: C <- "-50.7451" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4948 TOTAL ENERGY = -81.5796 RDTITL> * VAN DER WAALS = -30.8345 ELECTROSTATIC = -50.7451 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4948" Parameter: CONF_N -> "8002" Comparing "4948" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4949" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755616 ATOM PAIRS WERE FOUND FOR ATOM LIST 41367 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30309 from a total of 755616 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4949 -76.82491 -4.75472 0.60312 INTE EXTERN> -32.51467 -44.31024 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8249" Parameter: A <- "-76.8249" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5147" Parameter: B <- "-32.5147" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3102" Parameter: C <- "-44.3102" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4949 TOTAL ENERGY = -76.8249 RDTITL> * VAN DER WAALS = -32.5147 ELECTROSTATIC = -44.3102 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4949" Parameter: CONF_N -> "8002" Comparing "4949" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4950" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755616 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761480 ATOM PAIRS WERE FOUND FOR ATOM LIST 41729 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30336 from a total of 761480 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4950 -84.32720 7.50228 0.70813 INTE EXTERN> -27.32091 -57.00629 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.3272" Parameter: A <- "-84.3272" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3209" Parameter: B <- "-27.3209" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.0063" Parameter: C <- "-57.0063" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4950 TOTAL ENERGY = -84.3272 RDTITL> * VAN DER WAALS = -27.3209 ELECTROSTATIC = -57.0063 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4950" Parameter: CONF_N -> "8002" Comparing "4950" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4951" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761480 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761713 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30322 from a total of 761713 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4951 -80.18323 -4.14397 0.69571 INTE EXTERN> -28.85446 -51.32876 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1832" Parameter: A <- "-80.1832" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8545" Parameter: B <- "-28.8545" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3288" Parameter: C <- "-51.3288" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4951 TOTAL ENERGY = -80.1832 RDTITL> * VAN DER WAALS = -28.8545 ELECTROSTATIC = -51.3288 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4951" Parameter: CONF_N -> "8002" Comparing "4951" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4952" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761713 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759703 ATOM PAIRS WERE FOUND FOR ATOM LIST 41518 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30117 from a total of 759703 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4952 -85.16223 4.97901 0.73278 INTE EXTERN> -29.14743 -56.01481 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.1622" Parameter: A <- "-85.1622" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1474" Parameter: B <- "-29.1474" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.0148" Parameter: C <- "-56.0148" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4952 TOTAL ENERGY = -85.1622 RDTITL> * VAN DER WAALS = -29.1474 ELECTROSTATIC = -56.0148 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4952" Parameter: CONF_N -> "8002" Comparing "4952" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4953" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759703 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762097 ATOM PAIRS WERE FOUND FOR ATOM LIST 41718 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30851 from a total of 762097 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4953 -74.56539 -10.59684 0.74150 INTE EXTERN> -26.05314 -48.51225 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5654" Parameter: A <- "-74.5654" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0531" Parameter: B <- "-26.0531" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5123" Parameter: C <- "-48.5123" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4953 TOTAL ENERGY = -74.5654 RDTITL> * VAN DER WAALS = -26.0531 ELECTROSTATIC = -48.5123 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4953" Parameter: CONF_N -> "8002" Comparing "4953" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4954" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762097 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760579 ATOM PAIRS WERE FOUND FOR ATOM LIST 41575 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30829 from a total of 760579 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4954 -80.68400 6.11861 0.61203 INTE EXTERN> -32.16617 -48.51783 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.684" Parameter: A <- "-80.684" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1662" Parameter: B <- "-32.1662" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5178" Parameter: C <- "-48.5178" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4954 TOTAL ENERGY = -80.684 RDTITL> * VAN DER WAALS = -32.1662 ELECTROSTATIC = -48.5178 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4954" Parameter: CONF_N -> "8002" Comparing "4954" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4955" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760579 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764391 ATOM PAIRS WERE FOUND FOR ATOM LIST 41858 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30921 from a total of 764391 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4955 -83.62465 2.94065 0.74818 INTE EXTERN> -27.45159 -56.17306 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.6247" Parameter: A <- "-83.6247" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4516" Parameter: B <- "-27.4516" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.1731" Parameter: C <- "-56.1731" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4955 TOTAL ENERGY = -83.6247 RDTITL> * VAN DER WAALS = -27.4516 ELECTROSTATIC = -56.1731 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4955" Parameter: CONF_N -> "8002" Comparing "4955" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4956" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764391 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763231 ATOM PAIRS WERE FOUND FOR ATOM LIST 41787 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 31002 from a total of 763231 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4956 -81.87533 -1.74932 0.79513 INTE EXTERN> -25.18298 -56.69235 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8753" Parameter: A <- "-81.8753" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.183" Parameter: B <- "-25.183" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.6923" Parameter: C <- "-56.6923" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4956 TOTAL ENERGY = -81.8753 RDTITL> * VAN DER WAALS = -25.183 ELECTROSTATIC = -56.6923 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4956" Parameter: CONF_N -> "8002" Comparing "4956" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4957" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763231 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757084 ATOM PAIRS WERE FOUND FOR ATOM LIST 41388 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30775 from a total of 757084 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4957 -82.84040 0.96507 0.72566 INTE EXTERN> -29.27831 -53.56209 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.8404" Parameter: A <- "-82.8404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2783" Parameter: B <- "-29.2783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.5621" Parameter: C <- "-53.5621" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4957 TOTAL ENERGY = -82.8404 RDTITL> * VAN DER WAALS = -29.2783 ELECTROSTATIC = -53.5621 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4957" Parameter: CONF_N -> "8002" Comparing "4957" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4958" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757084 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757889 ATOM PAIRS WERE FOUND FOR ATOM LIST 41458 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30637 from a total of 757889 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4958 -81.05452 -1.78588 0.66449 INTE EXTERN> -32.05226 -49.00226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.0545" Parameter: A <- "-81.0545" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0523" Parameter: B <- "-32.0523" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0023" Parameter: C <- "-49.0023" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4958 TOTAL ENERGY = -81.0545 RDTITL> * VAN DER WAALS = -32.0523 ELECTROSTATIC = -49.0023 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4958" Parameter: CONF_N -> "8002" Comparing "4958" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4959" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757889 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760930 ATOM PAIRS WERE FOUND FOR ATOM LIST 41524 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30368 from a total of 760930 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4959 -77.80751 -3.24701 0.66858 INTE EXTERN> -28.83807 -48.96944 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8075" Parameter: A <- "-77.8075" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8381" Parameter: B <- "-28.8381" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9694" Parameter: C <- "-48.9694" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4959 TOTAL ENERGY = -77.8075 RDTITL> * VAN DER WAALS = -28.8381 ELECTROSTATIC = -48.9694 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4959" Parameter: CONF_N -> "8002" Comparing "4959" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4960" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760930 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766661 ATOM PAIRS WERE FOUND FOR ATOM LIST 42089 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30579 from a total of 766661 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4960 -81.13774 3.33023 0.77867 INTE EXTERN> -27.17235 -53.96539 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1377" Parameter: A <- "-81.1377" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1724" Parameter: B <- "-27.1724" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.9654" Parameter: C <- "-53.9654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4960 TOTAL ENERGY = -81.1377 RDTITL> * VAN DER WAALS = -27.1724 ELECTROSTATIC = -53.9654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4960" Parameter: CONF_N -> "8002" Comparing "4960" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4961" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766661 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758801 ATOM PAIRS WERE FOUND FOR ATOM LIST 41622 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30607 from a total of 758801 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4961 -80.17980 -0.95794 0.71397 INTE EXTERN> -28.87589 -51.30391 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1798" Parameter: A <- "-80.1798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8759" Parameter: B <- "-28.8759" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3039" Parameter: C <- "-51.3039" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4961 TOTAL ENERGY = -80.1798 RDTITL> * VAN DER WAALS = -28.8759 ELECTROSTATIC = -51.3039 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4961" Parameter: CONF_N -> "8002" Comparing "4961" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4962" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758801 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761574 ATOM PAIRS WERE FOUND FOR ATOM LIST 41686 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30299 from a total of 761574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4962 -80.78080 0.60100 0.73235 INTE EXTERN> -28.64110 -52.13970 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7808" Parameter: A <- "-80.7808" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6411" Parameter: B <- "-28.6411" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1397" Parameter: C <- "-52.1397" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4962 TOTAL ENERGY = -80.7808 RDTITL> * VAN DER WAALS = -28.6411 ELECTROSTATIC = -52.1397 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4962" Parameter: CONF_N -> "8002" Comparing "4962" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4963" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757839 ATOM PAIRS WERE FOUND FOR ATOM LIST 41572 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30059 from a total of 757839 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4963 -76.09360 -4.68720 0.62835 INTE EXTERN> -32.42247 -43.67113 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0936" Parameter: A <- "-76.0936" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4225" Parameter: B <- "-32.4225" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6711" Parameter: C <- "-43.6711" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4963 TOTAL ENERGY = -76.0936 RDTITL> * VAN DER WAALS = -32.4225 ELECTROSTATIC = -43.6711 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4963" Parameter: CONF_N -> "8002" Comparing "4963" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4964" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757839 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756676 ATOM PAIRS WERE FOUND FOR ATOM LIST 41612 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29980 from a total of 756676 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4964 -81.13393 5.04032 0.69659 INTE EXTERN> -30.76853 -50.36540 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1339" Parameter: A <- "-81.1339" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7685" Parameter: B <- "-30.7685" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3654" Parameter: C <- "-50.3654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4964 TOTAL ENERGY = -81.1339 RDTITL> * VAN DER WAALS = -30.7685 ELECTROSTATIC = -50.3654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4964" Parameter: CONF_N -> "8002" Comparing "4964" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4965" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756676 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758416 ATOM PAIRS WERE FOUND FOR ATOM LIST 41644 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29788 from a total of 758416 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4965 -86.60997 5.47604 0.69768 INTE EXTERN> -32.31244 -54.29753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.61" Parameter: A <- "-86.61" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3124" Parameter: B <- "-32.3124" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2975" Parameter: C <- "-54.2975" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4965 TOTAL ENERGY = -86.61 RDTITL> * VAN DER WAALS = -32.3124 ELECTROSTATIC = -54.2975 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4965" Parameter: CONF_N -> "8002" Comparing "4965" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4966" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758416 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762399 ATOM PAIRS WERE FOUND FOR ATOM LIST 41946 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 31033 from a total of 762399 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4966 -79.13708 -7.47289 0.72243 INTE EXTERN> -27.53788 -51.59920 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1371" Parameter: A <- "-79.1371" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5379" Parameter: B <- "-27.5379" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5992" Parameter: C <- "-51.5992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4966 TOTAL ENERGY = -79.1371 RDTITL> * VAN DER WAALS = -27.5379 ELECTROSTATIC = -51.5992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4966" Parameter: CONF_N -> "8002" Comparing "4966" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4967" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762399 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760556 ATOM PAIRS WERE FOUND FOR ATOM LIST 41705 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30316 from a total of 760556 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4967 -81.69558 2.55850 0.69517 INTE EXTERN> -28.71757 -52.97801 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6956" Parameter: A <- "-81.6956" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7176" Parameter: B <- "-28.7176" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.978" Parameter: C <- "-52.978" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4967 TOTAL ENERGY = -81.6956 RDTITL> * VAN DER WAALS = -28.7176 ELECTROSTATIC = -52.978 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4967" Parameter: CONF_N -> "8002" Comparing "4967" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4968" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760556 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758394 ATOM PAIRS WERE FOUND FOR ATOM LIST 41722 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30123 from a total of 758394 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4968 -78.29839 -3.39719 0.68086 INTE EXTERN> -28.40698 -49.89142 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2984" Parameter: A <- "-78.2984" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.407" Parameter: B <- "-28.407" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8914" Parameter: C <- "-49.8914" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4968 TOTAL ENERGY = -78.2984 RDTITL> * VAN DER WAALS = -28.407 ELECTROSTATIC = -49.8914 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4968" Parameter: CONF_N -> "8002" Comparing "4968" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4969" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758394 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760874 ATOM PAIRS WERE FOUND FOR ATOM LIST 41662 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30239 from a total of 760874 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4969 -77.76722 -0.53117 0.58604 INTE EXTERN> -33.52140 -44.24582 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7672" Parameter: A <- "-77.7672" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5214" Parameter: B <- "-33.5214" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2458" Parameter: C <- "-44.2458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4969 TOTAL ENERGY = -77.7672 RDTITL> * VAN DER WAALS = -33.5214 ELECTROSTATIC = -44.2458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4969" Parameter: CONF_N -> "8002" Comparing "4969" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4970" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760874 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758624 ATOM PAIRS WERE FOUND FOR ATOM LIST 41639 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29320 from a total of 758624 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4970 -79.13017 1.36296 0.68200 INTE EXTERN> -26.97271 -52.15746 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1302" Parameter: A <- "-79.1302" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9727" Parameter: B <- "-26.9727" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1575" Parameter: C <- "-52.1575" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4970 TOTAL ENERGY = -79.1302 RDTITL> * VAN DER WAALS = -26.9727 ELECTROSTATIC = -52.1575 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4970" Parameter: CONF_N -> "8002" Comparing "4970" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4971" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758624 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758528 ATOM PAIRS WERE FOUND FOR ATOM LIST 41657 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29596 from a total of 758528 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4971 -86.34486 7.21468 0.71957 INTE EXTERN> -29.71796 -56.62689 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.3449" Parameter: A <- "-86.3449" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.718" Parameter: B <- "-29.718" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.6269" Parameter: C <- "-56.6269" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4971 TOTAL ENERGY = -86.3449 RDTITL> * VAN DER WAALS = -29.718 ELECTROSTATIC = -56.6269 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4971" Parameter: CONF_N -> "8002" Comparing "4971" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4972" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758528 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758865 ATOM PAIRS WERE FOUND FOR ATOM LIST 41593 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29506 from a total of 758865 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4972 -73.07920 -13.26566 0.68742 INTE EXTERN> -28.31169 -44.76751 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0792" Parameter: A <- "-73.0792" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3117" Parameter: B <- "-28.3117" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7675" Parameter: C <- "-44.7675" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4972 TOTAL ENERGY = -73.0792 RDTITL> * VAN DER WAALS = -28.3117 ELECTROSTATIC = -44.7675 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4972" Parameter: CONF_N -> "8002" Comparing "4972" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4973" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758865 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752093 ATOM PAIRS WERE FOUND FOR ATOM LIST 41314 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29662 from a total of 752093 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4973 -82.28897 9.20977 0.62613 INTE EXTERN> -28.92243 -53.36654 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.289" Parameter: A <- "-82.289" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9224" Parameter: B <- "-28.9224" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3665" Parameter: C <- "-53.3665" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4973 TOTAL ENERGY = -82.289 RDTITL> * VAN DER WAALS = -28.9224 ELECTROSTATIC = -53.3665 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4973" Parameter: CONF_N -> "8002" Comparing "4973" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4974" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752093 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754682 ATOM PAIRS WERE FOUND FOR ATOM LIST 41406 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29847 from a total of 754682 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4974 -79.01704 -3.27193 0.67647 INTE EXTERN> -29.39760 -49.61944 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.017" Parameter: A <- "-79.017" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3976" Parameter: B <- "-29.3976" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6194" Parameter: C <- "-49.6194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4974 TOTAL ENERGY = -79.017 RDTITL> * VAN DER WAALS = -29.3976 ELECTROSTATIC = -49.6194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4974" Parameter: CONF_N -> "8002" Comparing "4974" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4975" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754682 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762430 ATOM PAIRS WERE FOUND FOR ATOM LIST 41753 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29755 from a total of 762430 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4975 -78.98192 -0.03511 0.69812 INTE EXTERN> -28.90454 -50.07739 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9819" Parameter: A <- "-78.9819" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9045" Parameter: B <- "-28.9045" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0774" Parameter: C <- "-50.0774" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4975 TOTAL ENERGY = -78.9819 RDTITL> * VAN DER WAALS = -28.9045 ELECTROSTATIC = -50.0774 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4975" Parameter: CONF_N -> "8002" Comparing "4975" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4976" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762430 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761189 ATOM PAIRS WERE FOUND FOR ATOM LIST 41857 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30456 from a total of 761189 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4976 -77.33622 -1.64570 0.72008 INTE EXTERN> -26.79913 -50.53709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3362" Parameter: A <- "-77.3362" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7991" Parameter: B <- "-26.7991" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5371" Parameter: C <- "-50.5371" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4976 TOTAL ENERGY = -77.3362 RDTITL> * VAN DER WAALS = -26.7991 ELECTROSTATIC = -50.5371 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4976" Parameter: CONF_N -> "8002" Comparing "4976" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4977" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761189 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763036 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30233 from a total of 763036 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4977 -84.66399 7.32777 0.72265 INTE EXTERN> -29.10544 -55.55855 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.664" Parameter: A <- "-84.664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1054" Parameter: B <- "-29.1054" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.5585" Parameter: C <- "-55.5585" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4977 TOTAL ENERGY = -84.664 RDTITL> * VAN DER WAALS = -29.1054 ELECTROSTATIC = -55.5585 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4977" Parameter: CONF_N -> "8002" Comparing "4977" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4978" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763036 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757993 ATOM PAIRS WERE FOUND FOR ATOM LIST 41497 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30497 from a total of 757993 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4978 -83.47075 -1.19324 0.68822 INTE EXTERN> -30.36623 -53.10452 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.4707" Parameter: A <- "-83.4707" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3662" Parameter: B <- "-30.3662" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.1045" Parameter: C <- "-53.1045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4978 TOTAL ENERGY = -83.4707 RDTITL> * VAN DER WAALS = -30.3662 ELECTROSTATIC = -53.1045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4978" Parameter: CONF_N -> "8002" Comparing "4978" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4979" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757993 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760139 ATOM PAIRS WERE FOUND FOR ATOM LIST 41773 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29680 from a total of 760139 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4979 -76.53432 -6.93643 0.61437 INTE EXTERN> -33.24358 -43.29074 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5343" Parameter: A <- "-76.5343" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2436" Parameter: B <- "-33.2436" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2907" Parameter: C <- "-43.2907" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4979 TOTAL ENERGY = -76.5343 RDTITL> * VAN DER WAALS = -33.2436 ELECTROSTATIC = -43.2907 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4979" Parameter: CONF_N -> "8002" Comparing "4979" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4980" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760139 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41861 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30883 from a total of 764422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4980 -83.47708 6.94276 0.64974 INTE EXTERN> -32.78063 -50.69646 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.4771" Parameter: A <- "-83.4771" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7806" Parameter: B <- "-32.7806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6965" Parameter: C <- "-50.6965" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4980 TOTAL ENERGY = -83.4771 RDTITL> * VAN DER WAALS = -32.7806 ELECTROSTATIC = -50.6965 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4980" Parameter: CONF_N -> "8002" Comparing "4980" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4981" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753968 ATOM PAIRS WERE FOUND FOR ATOM LIST 41400 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30243 from a total of 753968 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4981 -79.13830 -4.33879 0.71213 INTE EXTERN> -31.08370 -48.05460 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1383" Parameter: A <- "-79.1383" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0837" Parameter: B <- "-31.0837" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0546" Parameter: C <- "-48.0546" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4981 TOTAL ENERGY = -79.1383 RDTITL> * VAN DER WAALS = -31.0837 ELECTROSTATIC = -48.0546 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4981" Parameter: CONF_N -> "8002" Comparing "4981" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4982" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753968 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752179 ATOM PAIRS WERE FOUND FOR ATOM LIST 41319 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29789 from a total of 752179 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4982 -78.90656 -0.23174 0.59175 INTE EXTERN> -32.78191 -46.12465 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9066" Parameter: A <- "-78.9066" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7819" Parameter: B <- "-32.7819" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1246" Parameter: C <- "-46.1246" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4982 TOTAL ENERGY = -78.9066 RDTITL> * VAN DER WAALS = -32.7819 ELECTROSTATIC = -46.1246 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4982" Parameter: CONF_N -> "8002" Comparing "4982" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4983" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752179 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760938 ATOM PAIRS WERE FOUND FOR ATOM LIST 41723 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30412 from a total of 760938 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4983 -85.00164 6.09508 0.70679 INTE EXTERN> -29.08180 -55.91984 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.0016" Parameter: A <- "-85.0016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0818" Parameter: B <- "-29.0818" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.9198" Parameter: C <- "-55.9198" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4983 TOTAL ENERGY = -85.0016 RDTITL> * VAN DER WAALS = -29.0818 ELECTROSTATIC = -55.9198 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4983" Parameter: CONF_N -> "8002" Comparing "4983" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4984" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760938 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761153 ATOM PAIRS WERE FOUND FOR ATOM LIST 41406 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29520 from a total of 761153 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4984 -79.00137 -6.00027 0.60067 INTE EXTERN> -32.47262 -46.52875 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0014" Parameter: A <- "-79.0014" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4726" Parameter: B <- "-32.4726" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5288" Parameter: C <- "-46.5288" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4984 TOTAL ENERGY = -79.0014 RDTITL> * VAN DER WAALS = -32.4726 ELECTROSTATIC = -46.5288 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4984" Parameter: CONF_N -> "8002" Comparing "4984" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4985" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761153 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752109 ATOM PAIRS WERE FOUND FOR ATOM LIST 41354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29077 from a total of 752109 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4985 -78.80680 -0.19457 0.60741 INTE EXTERN> -31.02549 -47.78131 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8068" Parameter: A <- "-78.8068" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0255" Parameter: B <- "-31.0255" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7813" Parameter: C <- "-47.7813" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4985 TOTAL ENERGY = -78.8068 RDTITL> * VAN DER WAALS = -31.0255 ELECTROSTATIC = -47.7813 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4985" Parameter: CONF_N -> "8002" Comparing "4985" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4986" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752109 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749395 ATOM PAIRS WERE FOUND FOR ATOM LIST 41022 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29258 from a total of 749395 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4986 -72.59328 -6.21352 0.74029 INTE EXTERN> -25.72160 -46.87168 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5933" Parameter: A <- "-72.5933" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7216" Parameter: B <- "-25.7216" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8717" Parameter: C <- "-46.8717" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4986 TOTAL ENERGY = -72.5933 RDTITL> * VAN DER WAALS = -25.7216 ELECTROSTATIC = -46.8717 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4986" Parameter: CONF_N -> "8002" Comparing "4986" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4987" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749395 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751688 ATOM PAIRS WERE FOUND FOR ATOM LIST 41209 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29556 from a total of 751688 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4987 -74.31481 1.72154 0.71970 INTE EXTERN> -28.02036 -46.29445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3148" Parameter: A <- "-74.3148" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0204" Parameter: B <- "-28.0204" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2945" Parameter: C <- "-46.2945" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4987 TOTAL ENERGY = -74.3148 RDTITL> * VAN DER WAALS = -28.0204 ELECTROSTATIC = -46.2945 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4987" Parameter: CONF_N -> "8002" Comparing "4987" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4988" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751688 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756035 ATOM PAIRS WERE FOUND FOR ATOM LIST 41557 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29867 from a total of 756035 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4988 -78.12315 3.80834 0.74285 INTE EXTERN> -26.78732 -51.33584 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1232" Parameter: A <- "-78.1232" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7873" Parameter: B <- "-26.7873" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3358" Parameter: C <- "-51.3358" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4988 TOTAL ENERGY = -78.1232 RDTITL> * VAN DER WAALS = -26.7873 ELECTROSTATIC = -51.3358 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4988" Parameter: CONF_N -> "8002" Comparing "4988" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4989" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756035 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755201 ATOM PAIRS WERE FOUND FOR ATOM LIST 41336 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29785 from a total of 755201 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4989 -79.80541 1.68226 0.71255 INTE EXTERN> -30.62867 -49.17674 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8054" Parameter: A <- "-79.8054" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6287" Parameter: B <- "-30.6287" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1767" Parameter: C <- "-49.1767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4989 TOTAL ENERGY = -79.8054 RDTITL> * VAN DER WAALS = -30.6287 ELECTROSTATIC = -49.1767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4989" Parameter: CONF_N -> "8002" Comparing "4989" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4990" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755201 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754043 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29866 from a total of 754043 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4990 -73.36963 -6.43577 0.66687 INTE EXTERN> -28.88874 -44.48089 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3696" Parameter: A <- "-73.3696" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8887" Parameter: B <- "-28.8887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4809" Parameter: C <- "-44.4809" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4990 TOTAL ENERGY = -73.3696 RDTITL> * VAN DER WAALS = -28.8887 ELECTROSTATIC = -44.4809 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4990" Parameter: CONF_N -> "8002" Comparing "4990" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4991" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754043 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761114 ATOM PAIRS WERE FOUND FOR ATOM LIST 41586 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30494 from a total of 761114 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4991 -73.84020 0.47056 0.58783 INTE EXTERN> -32.04860 -41.79159 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8402" Parameter: A <- "-73.8402" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0486" Parameter: B <- "-32.0486" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7916" Parameter: C <- "-41.7916" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4991 TOTAL ENERGY = -73.8402 RDTITL> * VAN DER WAALS = -32.0486 ELECTROSTATIC = -41.7916 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4991" Parameter: CONF_N -> "8002" Comparing "4991" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4992" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761114 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756697 ATOM PAIRS WERE FOUND FOR ATOM LIST 41603 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29786 from a total of 756697 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4992 -69.16645 -4.67375 0.53236 INTE EXTERN> -30.27363 -38.89282 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1664" Parameter: A <- "-69.1664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2736" Parameter: B <- "-30.2736" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8928" Parameter: C <- "-38.8928" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4992 TOTAL ENERGY = -69.1664 RDTITL> * VAN DER WAALS = -30.2736 ELECTROSTATIC = -38.8928 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4992" Parameter: CONF_N -> "8002" Comparing "4992" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4993" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756697 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751953 ATOM PAIRS WERE FOUND FOR ATOM LIST 41317 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29814 from a total of 751953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4993 -71.58744 2.42100 0.54716 INTE EXTERN> -33.69442 -37.89303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5874" Parameter: A <- "-71.5874" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6944" Parameter: B <- "-33.6944" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.893" Parameter: C <- "-37.893" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4993 TOTAL ENERGY = -71.5874 RDTITL> * VAN DER WAALS = -33.6944 ELECTROSTATIC = -37.893 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4993" Parameter: CONF_N -> "8002" Comparing "4993" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4994" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753431 ATOM PAIRS WERE FOUND FOR ATOM LIST 41362 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29939 from a total of 753431 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4994 -72.61785 1.03041 0.65570 INTE EXTERN> -30.95401 -41.66384 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6179" Parameter: A <- "-72.6179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.954" Parameter: B <- "-30.954" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6638" Parameter: C <- "-41.6638" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4994 TOTAL ENERGY = -72.6179 RDTITL> * VAN DER WAALS = -30.954 ELECTROSTATIC = -41.6638 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4994" Parameter: CONF_N -> "8002" Comparing "4994" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4995" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753431 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761387 ATOM PAIRS WERE FOUND FOR ATOM LIST 41835 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29830 from a total of 761387 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4995 -77.07766 4.45981 0.61415 INTE EXTERN> -33.06755 -44.01011 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0777" Parameter: A <- "-77.0777" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0676" Parameter: B <- "-33.0676" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0101" Parameter: C <- "-44.0101" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4995 TOTAL ENERGY = -77.0777 RDTITL> * VAN DER WAALS = -33.0676 ELECTROSTATIC = -44.0101 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4995" Parameter: CONF_N -> "8002" Comparing "4995" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4996" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761387 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758068 ATOM PAIRS WERE FOUND FOR ATOM LIST 41724 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30160 from a total of 758068 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4996 -77.32247 0.24480 0.63894 INTE EXTERN> -32.32184 -45.00063 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3225" Parameter: A <- "-77.3225" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3218" Parameter: B <- "-32.3218" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0006" Parameter: C <- "-45.0006" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4996 TOTAL ENERGY = -77.3225 RDTITL> * VAN DER WAALS = -32.3218 ELECTROSTATIC = -45.0006 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4996" Parameter: CONF_N -> "8002" Comparing "4996" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4997" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758068 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759445 ATOM PAIRS WERE FOUND FOR ATOM LIST 41679 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29725 from a total of 759445 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4997 -79.40707 2.08460 0.68650 INTE EXTERN> -31.15029 -48.25678 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4071" Parameter: A <- "-79.4071" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1503" Parameter: B <- "-31.1503" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2568" Parameter: C <- "-48.2568" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4997 TOTAL ENERGY = -79.4071 RDTITL> * VAN DER WAALS = -31.1503 ELECTROSTATIC = -48.2568 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4997" Parameter: CONF_N -> "8002" Comparing "4997" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4998" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759445 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753602 ATOM PAIRS WERE FOUND FOR ATOM LIST 41141 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29723 from a total of 753602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4998 -74.54343 -4.86364 0.74782 INTE EXTERN> -26.54639 -47.99704 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5434" Parameter: A <- "-74.5434" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5464" Parameter: B <- "-26.5464" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.997" Parameter: C <- "-47.997" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4998 TOTAL ENERGY = -74.5434 RDTITL> * VAN DER WAALS = -26.5464 ELECTROSTATIC = -47.997 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4998" Parameter: CONF_N -> "8002" Comparing "4998" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "4999" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756091 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29607 from a total of 756091 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 4999 -75.28204 0.73861 0.74623 INTE EXTERN> -28.70496 -46.57709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.282" Parameter: A <- "-75.282" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.705" Parameter: B <- "-28.705" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5771" Parameter: C <- "-46.5771" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 4999 TOTAL ENERGY = -75.282 RDTITL> * VAN DER WAALS = -28.705 ELECTROSTATIC = -46.5771 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "4999" Parameter: CONF_N -> "8002" Comparing "4999" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5000" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756091 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756824 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29800 from a total of 756824 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5000 -78.09372 2.81168 0.65576 INTE EXTERN> -29.52979 -48.56393 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0937" Parameter: A <- "-78.0937" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5298" Parameter: B <- "-29.5298" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5639" Parameter: C <- "-48.5639" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5000 TOTAL ENERGY = -78.0937 RDTITL> * VAN DER WAALS = -29.5298 ELECTROSTATIC = -48.5639 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5000" Parameter: CONF_N -> "8002" Comparing "5000" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5001" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756824 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765025 ATOM PAIRS WERE FOUND FOR ATOM LIST 41837 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29509 from a total of 765025 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5001 -72.01345 -6.08028 0.58006 INTE EXTERN> -32.01685 -39.99659 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0134" Parameter: A <- "-72.0134" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0169" Parameter: B <- "-32.0169" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9966" Parameter: C <- "-39.9966" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5001 TOTAL ENERGY = -72.0134 RDTITL> * VAN DER WAALS = -32.0169 ELECTROSTATIC = -39.9966 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5001" Parameter: CONF_N -> "8002" Comparing "5001" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5002" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765025 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759255 ATOM PAIRS WERE FOUND FOR ATOM LIST 41646 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29082 from a total of 759255 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5002 -72.56488 0.55144 0.67643 INTE EXTERN> -26.59786 -45.96703 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5649" Parameter: A <- "-72.5649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5979" Parameter: B <- "-26.5979" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.967" Parameter: C <- "-45.967" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5002 TOTAL ENERGY = -72.5649 RDTITL> * VAN DER WAALS = -26.5979 ELECTROSTATIC = -45.967 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5002" Parameter: CONF_N -> "8002" Comparing "5002" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5003" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759255 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754288 ATOM PAIRS WERE FOUND FOR ATOM LIST 41346 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29096 from a total of 754288 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5003 -68.58354 -3.98134 0.76405 INTE EXTERN> -21.81240 -46.77114 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5835" Parameter: A <- "-68.5835" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.8124" Parameter: B <- "-21.8124" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7711" Parameter: C <- "-46.7711" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5003 TOTAL ENERGY = -68.5835 RDTITL> * VAN DER WAALS = -21.8124 ELECTROSTATIC = -46.7711 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5003" Parameter: CONF_N -> "8002" Comparing "5003" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5004" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754288 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751588 ATOM PAIRS WERE FOUND FOR ATOM LIST 41237 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28717 from a total of 751588 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5004 -61.69801 -6.88553 0.46516 INTE EXTERN> -30.37926 -31.31875 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.698" Parameter: A <- "-61.698" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3793" Parameter: B <- "-30.3793" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.3187" Parameter: C <- "-31.3187" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5004 TOTAL ENERGY = -61.698 RDTITL> * VAN DER WAALS = -30.3793 ELECTROSTATIC = -31.3187 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5004" Parameter: CONF_N -> "8002" Comparing "5004" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5005" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751588 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759222 ATOM PAIRS WERE FOUND FOR ATOM LIST 41631 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29695 from a total of 759222 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5005 -73.00364 11.30563 0.65307 INTE EXTERN> -29.02967 -43.97397 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0036" Parameter: A <- "-73.0036" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0297" Parameter: B <- "-29.0297" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.974" Parameter: C <- "-43.974" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5005 TOTAL ENERGY = -73.0036 RDTITL> * VAN DER WAALS = -29.0297 ELECTROSTATIC = -43.974 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5005" Parameter: CONF_N -> "8002" Comparing "5005" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5006" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759222 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759592 ATOM PAIRS WERE FOUND FOR ATOM LIST 41712 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29398 from a total of 759592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5006 -80.45322 7.44958 0.68521 INTE EXTERN> -31.08934 -49.36389 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4532" Parameter: A <- "-80.4532" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0893" Parameter: B <- "-31.0893" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3639" Parameter: C <- "-49.3639" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5006 TOTAL ENERGY = -80.4532 RDTITL> * VAN DER WAALS = -31.0893 ELECTROSTATIC = -49.3639 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5006" Parameter: CONF_N -> "8002" Comparing "5006" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5007" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757410 ATOM PAIRS WERE FOUND FOR ATOM LIST 41332 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29286 from a total of 757410 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5007 -74.38089 -6.07233 0.57602 INTE EXTERN> -30.86777 -43.51312 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3809" Parameter: A <- "-74.3809" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8678" Parameter: B <- "-30.8678" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5131" Parameter: C <- "-43.5131" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5007 TOTAL ENERGY = -74.3809 RDTITL> * VAN DER WAALS = -30.8678 ELECTROSTATIC = -43.5131 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5007" Parameter: CONF_N -> "8002" Comparing "5007" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5008" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757410 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755931 ATOM PAIRS WERE FOUND FOR ATOM LIST 41403 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29500 from a total of 755931 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5008 -73.60037 -0.78052 0.66661 INTE EXTERN> -29.47003 -44.13034 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6004" Parameter: A <- "-73.6004" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.47" Parameter: B <- "-29.47" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1303" Parameter: C <- "-44.1303" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5008 TOTAL ENERGY = -73.6004 RDTITL> * VAN DER WAALS = -29.47 ELECTROSTATIC = -44.1303 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5008" Parameter: CONF_N -> "8002" Comparing "5008" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5009" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755931 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753036 ATOM PAIRS WERE FOUND FOR ATOM LIST 41331 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29779 from a total of 753036 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5009 -75.60103 2.00066 0.80754 INTE EXTERN> -25.38770 -50.21333 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.601" Parameter: A <- "-75.601" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3877" Parameter: B <- "-25.3877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2133" Parameter: C <- "-50.2133" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5009 TOTAL ENERGY = -75.601 RDTITL> * VAN DER WAALS = -25.3877 ELECTROSTATIC = -50.2133 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5009" Parameter: CONF_N -> "8002" Comparing "5009" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5010" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753036 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756245 ATOM PAIRS WERE FOUND FOR ATOM LIST 41409 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29337 from a total of 756245 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5010 -77.84098 2.23995 0.63467 INTE EXTERN> -31.99216 -45.84882 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.841" Parameter: A <- "-77.841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9922" Parameter: B <- "-31.9922" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8488" Parameter: C <- "-45.8488" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5010 TOTAL ENERGY = -77.841 RDTITL> * VAN DER WAALS = -31.9922 ELECTROSTATIC = -45.8488 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5010" Parameter: CONF_N -> "8002" Comparing "5010" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5011" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756245 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763776 ATOM PAIRS WERE FOUND FOR ATOM LIST 41814 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29609 from a total of 763776 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5011 -71.40780 -6.43318 0.65048 INTE EXTERN> -30.47097 -40.93683 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4078" Parameter: A <- "-71.4078" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.471" Parameter: B <- "-30.471" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9368" Parameter: C <- "-40.9368" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5011 TOTAL ENERGY = -71.4078 RDTITL> * VAN DER WAALS = -30.471 ELECTROSTATIC = -40.9368 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5011" Parameter: CONF_N -> "8002" Comparing "5011" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5012" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763776 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761765 ATOM PAIRS WERE FOUND FOR ATOM LIST 41785 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29352 from a total of 761765 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5012 -76.22006 4.81226 0.60239 INTE EXTERN> -32.32479 -43.89527 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2201" Parameter: A <- "-76.2201" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3248" Parameter: B <- "-32.3248" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8953" Parameter: C <- "-43.8953" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5012 TOTAL ENERGY = -76.2201 RDTITL> * VAN DER WAALS = -32.3248 ELECTROSTATIC = -43.8953 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5012" Parameter: CONF_N -> "8002" Comparing "5012" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5013" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761765 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759485 ATOM PAIRS WERE FOUND FOR ATOM LIST 41424 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29234 from a total of 759485 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5013 -73.84284 -2.37722 0.62137 INTE EXTERN> -27.89664 -45.94621 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8428" Parameter: A <- "-73.8428" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8966" Parameter: B <- "-27.8966" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9462" Parameter: C <- "-45.9462" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5013 TOTAL ENERGY = -73.8428 RDTITL> * VAN DER WAALS = -27.8966 ELECTROSTATIC = -45.9462 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5013" Parameter: CONF_N -> "8002" Comparing "5013" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5014" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759485 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760433 ATOM PAIRS WERE FOUND FOR ATOM LIST 41761 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29800 from a total of 760433 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5014 -70.89501 -2.94783 0.68311 INTE EXTERN> -26.23465 -44.66036 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.895" Parameter: A <- "-70.895" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2346" Parameter: B <- "-26.2346" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6604" Parameter: C <- "-44.6604" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5014 TOTAL ENERGY = -70.895 RDTITL> * VAN DER WAALS = -26.2346 ELECTROSTATIC = -44.6604 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5014" Parameter: CONF_N -> "8002" Comparing "5014" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5015" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760433 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762259 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28999 from a total of 762259 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5015 -72.68443 1.78942 0.57001 INTE EXTERN> -33.22512 -39.45931 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6844" Parameter: A <- "-72.6844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2251" Parameter: B <- "-33.2251" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4593" Parameter: C <- "-39.4593" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5015 TOTAL ENERGY = -72.6844 RDTITL> * VAN DER WAALS = -33.2251 ELECTROSTATIC = -39.4593 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5015" Parameter: CONF_N -> "8002" Comparing "5015" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5016" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762259 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758108 ATOM PAIRS WERE FOUND FOR ATOM LIST 41664 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29160 from a total of 758108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5016 -78.73815 6.05372 0.75418 INTE EXTERN> -26.76998 -51.96817 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7381" Parameter: A <- "-78.7381" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.77" Parameter: B <- "-26.77" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.9682" Parameter: C <- "-51.9682" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5016 TOTAL ENERGY = -78.7381 RDTITL> * VAN DER WAALS = -26.77 ELECTROSTATIC = -51.9682 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5016" Parameter: CONF_N -> "8002" Comparing "5016" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5017" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758138 ATOM PAIRS WERE FOUND FOR ATOM LIST 41544 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29660 from a total of 758138 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5017 -75.13477 -3.60338 0.63233 INTE EXTERN> -31.47154 -43.66323 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1348" Parameter: A <- "-75.1348" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4715" Parameter: B <- "-31.4715" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6632" Parameter: C <- "-43.6632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5017 TOTAL ENERGY = -75.1348 RDTITL> * VAN DER WAALS = -31.4715 ELECTROSTATIC = -43.6632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5017" Parameter: CONF_N -> "8002" Comparing "5017" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5018" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758138 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759897 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29163 from a total of 759897 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5018 -73.78525 -1.34952 0.63212 INTE EXTERN> -27.66341 -46.12184 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7853" Parameter: A <- "-73.7853" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6634" Parameter: B <- "-27.6634" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1218" Parameter: C <- "-46.1218" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5018 TOTAL ENERGY = -73.7853 RDTITL> * VAN DER WAALS = -27.6634 ELECTROSTATIC = -46.1218 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5018" Parameter: CONF_N -> "8002" Comparing "5018" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5019" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759897 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757108 ATOM PAIRS WERE FOUND FOR ATOM LIST 41392 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30065 from a total of 757108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5019 -67.06346 -6.72180 0.61410 INTE EXTERN> -29.29393 -37.76953 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0635" Parameter: A <- "-67.0635" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2939" Parameter: B <- "-29.2939" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7695" Parameter: C <- "-37.7695" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5019 TOTAL ENERGY = -67.0635 RDTITL> * VAN DER WAALS = -29.2939 ELECTROSTATIC = -37.7695 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5019" Parameter: CONF_N -> "8002" Comparing "5019" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5020" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759214 ATOM PAIRS WERE FOUND FOR ATOM LIST 41441 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29929 from a total of 759214 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5020 -71.33244 4.26898 0.79532 INTE EXTERN> -25.31062 -46.02182 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3324" Parameter: A <- "-71.3324" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3106" Parameter: B <- "-25.3106" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0218" Parameter: C <- "-46.0218" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5020 TOTAL ENERGY = -71.3324 RDTITL> * VAN DER WAALS = -25.3106 ELECTROSTATIC = -46.0218 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5020" Parameter: CONF_N -> "8002" Comparing "5020" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5021" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759214 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753598 ATOM PAIRS WERE FOUND FOR ATOM LIST 41286 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29415 from a total of 753598 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5021 -77.08491 5.75247 0.65993 INTE EXTERN> -28.61451 -48.47040 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0849" Parameter: A <- "-77.0849" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6145" Parameter: B <- "-28.6145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4704" Parameter: C <- "-48.4704" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5021 TOTAL ENERGY = -77.0849 RDTITL> * VAN DER WAALS = -28.6145 ELECTROSTATIC = -48.4704 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5021" Parameter: CONF_N -> "8002" Comparing "5021" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5022" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753598 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755129 ATOM PAIRS WERE FOUND FOR ATOM LIST 41499 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29643 from a total of 755129 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5022 -71.41528 -5.66963 0.68169 INTE EXTERN> -27.61165 -43.80363 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4153" Parameter: A <- "-71.4153" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6117" Parameter: B <- "-27.6117" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8036" Parameter: C <- "-43.8036" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5022 TOTAL ENERGY = -71.4153 RDTITL> * VAN DER WAALS = -27.6117 ELECTROSTATIC = -43.8036 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5022" Parameter: CONF_N -> "8002" Comparing "5022" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5023" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755129 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755820 ATOM PAIRS WERE FOUND FOR ATOM LIST 41669 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29635 from a total of 755820 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5023 -77.67289 6.25760 0.61018 INTE EXTERN> -30.48169 -47.19120 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6729" Parameter: A <- "-77.6729" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4817" Parameter: B <- "-30.4817" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1912" Parameter: C <- "-47.1912" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5023 TOTAL ENERGY = -77.6729 RDTITL> * VAN DER WAALS = -30.4817 ELECTROSTATIC = -47.1912 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5023" Parameter: CONF_N -> "8002" Comparing "5023" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5024" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755820 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757082 ATOM PAIRS WERE FOUND FOR ATOM LIST 41558 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30057 from a total of 757082 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5024 -70.14992 -7.52297 0.57922 INTE EXTERN> -30.97726 -39.17266 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1499" Parameter: A <- "-70.1499" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9773" Parameter: B <- "-30.9773" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1727" Parameter: C <- "-39.1727" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5024 TOTAL ENERGY = -70.1499 RDTITL> * VAN DER WAALS = -30.9773 ELECTROSTATIC = -39.1727 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5024" Parameter: CONF_N -> "8002" Comparing "5024" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5025" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757082 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41427 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29901 from a total of 752422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5025 -75.74812 5.59821 0.63572 INTE EXTERN> -31.78823 -43.95989 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7481" Parameter: A <- "-75.7481" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7882" Parameter: B <- "-31.7882" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9599" Parameter: C <- "-43.9599" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5025 TOTAL ENERGY = -75.7481 RDTITL> * VAN DER WAALS = -31.7882 ELECTROSTATIC = -43.9599 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5025" Parameter: CONF_N -> "8002" Comparing "5025" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5026" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762203 ATOM PAIRS WERE FOUND FOR ATOM LIST 41923 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29780 from a total of 762203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5026 -77.37989 1.63177 0.69486 INTE EXTERN> -26.84664 -50.53325 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3799" Parameter: A <- "-77.3799" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8466" Parameter: B <- "-26.8466" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5332" Parameter: C <- "-50.5332" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5026 TOTAL ENERGY = -77.3799 RDTITL> * VAN DER WAALS = -26.8466 ELECTROSTATIC = -50.5332 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5026" Parameter: CONF_N -> "8002" Comparing "5026" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5027" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761614 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29939 from a total of 761614 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5027 -76.55280 -0.82708 0.64537 INTE EXTERN> -27.19777 -49.35504 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5528" Parameter: A <- "-76.5528" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1978" Parameter: B <- "-27.1978" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.355" Parameter: C <- "-49.355" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5027 TOTAL ENERGY = -76.5528 RDTITL> * VAN DER WAALS = -27.1978 ELECTROSTATIC = -49.355 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5027" Parameter: CONF_N -> "8002" Comparing "5027" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5028" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761614 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756005 ATOM PAIRS WERE FOUND FOR ATOM LIST 41500 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29778 from a total of 756005 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5028 -79.71714 3.16434 0.65711 INTE EXTERN> -29.76994 -49.94720 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7171" Parameter: A <- "-79.7171" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7699" Parameter: B <- "-29.7699" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9472" Parameter: C <- "-49.9472" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5028 TOTAL ENERGY = -79.7171 RDTITL> * VAN DER WAALS = -29.7699 ELECTROSTATIC = -49.9472 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5028" Parameter: CONF_N -> "8002" Comparing "5028" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5029" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756005 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762003 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30289 from a total of 762003 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5029 -76.45120 -3.26594 0.68256 INTE EXTERN> -28.48566 -47.96554 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4512" Parameter: A <- "-76.4512" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4857" Parameter: B <- "-28.4857" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9655" Parameter: C <- "-47.9655" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5029 TOTAL ENERGY = -76.4512 RDTITL> * VAN DER WAALS = -28.4857 ELECTROSTATIC = -47.9655 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5029" Parameter: CONF_N -> "8002" Comparing "5029" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5030" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762003 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760919 ATOM PAIRS WERE FOUND FOR ATOM LIST 41814 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30501 from a total of 760919 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5030 -73.82519 -2.62602 0.68307 INTE EXTERN> -27.94511 -45.88008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8252" Parameter: A <- "-73.8252" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9451" Parameter: B <- "-27.9451" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8801" Parameter: C <- "-45.8801" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5030 TOTAL ENERGY = -73.8252 RDTITL> * VAN DER WAALS = -27.9451 ELECTROSTATIC = -45.8801 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5030" Parameter: CONF_N -> "8002" Comparing "5030" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5031" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760919 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761379 ATOM PAIRS WERE FOUND FOR ATOM LIST 41692 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30217 from a total of 761379 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5031 -78.61634 4.79116 0.61700 INTE EXTERN> -34.19711 -44.41923 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6163" Parameter: A <- "-78.6163" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1971" Parameter: B <- "-34.1971" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4192" Parameter: C <- "-44.4192" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5031 TOTAL ENERGY = -78.6163 RDTITL> * VAN DER WAALS = -34.1971 ELECTROSTATIC = -44.4192 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5031" Parameter: CONF_N -> "8002" Comparing "5031" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5032" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761379 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759743 ATOM PAIRS WERE FOUND FOR ATOM LIST 41494 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29763 from a total of 759743 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5032 -78.17565 -0.44069 0.58103 INTE EXTERN> -33.57153 -44.60412 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1756" Parameter: A <- "-78.1756" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5715" Parameter: B <- "-33.5715" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6041" Parameter: C <- "-44.6041" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5032 TOTAL ENERGY = -78.1756 RDTITL> * VAN DER WAALS = -33.5715 ELECTROSTATIC = -44.6041 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5032" Parameter: CONF_N -> "8002" Comparing "5032" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5033" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759743 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760786 ATOM PAIRS WERE FOUND FOR ATOM LIST 41608 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30460 from a total of 760786 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5033 -77.56223 -0.61341 0.66434 INTE EXTERN> -30.64394 -46.91829 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5622" Parameter: A <- "-77.5622" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6439" Parameter: B <- "-30.6439" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9183" Parameter: C <- "-46.9183" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5033 TOTAL ENERGY = -77.5622 RDTITL> * VAN DER WAALS = -30.6439 ELECTROSTATIC = -46.9183 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5033" Parameter: CONF_N -> "8002" Comparing "5033" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5034" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760786 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761942 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30285 from a total of 761942 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5034 -72.96618 -4.59606 0.59273 INTE EXTERN> -30.48952 -42.47665 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9662" Parameter: A <- "-72.9662" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4895" Parameter: B <- "-30.4895" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4767" Parameter: C <- "-42.4767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5034 TOTAL ENERGY = -72.9662 RDTITL> * VAN DER WAALS = -30.4895 ELECTROSTATIC = -42.4767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5034" Parameter: CONF_N -> "8002" Comparing "5034" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5035" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761942 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757510 ATOM PAIRS WERE FOUND FOR ATOM LIST 41559 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30026 from a total of 757510 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5035 -78.44993 5.48375 0.65896 INTE EXTERN> -28.97827 -49.47166 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4499" Parameter: A <- "-78.4499" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9783" Parameter: B <- "-28.9783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4717" Parameter: C <- "-49.4717" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5035 TOTAL ENERGY = -78.4499 RDTITL> * VAN DER WAALS = -28.9783 ELECTROSTATIC = -49.4717 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5035" Parameter: CONF_N -> "8002" Comparing "5035" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5036" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757510 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759119 ATOM PAIRS WERE FOUND FOR ATOM LIST 41518 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29959 from a total of 759119 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5036 -83.53513 5.08520 0.72466 INTE EXTERN> -29.24800 -54.28713 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.5351" Parameter: A <- "-83.5351" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.248" Parameter: B <- "-29.248" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2871" Parameter: C <- "-54.2871" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5036 TOTAL ENERGY = -83.5351 RDTITL> * VAN DER WAALS = -29.248 ELECTROSTATIC = -54.2871 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5036" Parameter: CONF_N -> "8002" Comparing "5036" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5037" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759119 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762190 ATOM PAIRS WERE FOUND FOR ATOM LIST 41753 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30454 from a total of 762190 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5037 -80.90512 -2.63001 0.71794 INTE EXTERN> -28.26976 -52.63536 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9051" Parameter: A <- "-80.9051" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2698" Parameter: B <- "-28.2698" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6354" Parameter: C <- "-52.6354" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5037 TOTAL ENERGY = -80.9051 RDTITL> * VAN DER WAALS = -28.2698 ELECTROSTATIC = -52.6354 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5037" Parameter: CONF_N -> "8002" Comparing "5037" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5038" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762190 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759256 ATOM PAIRS WERE FOUND FOR ATOM LIST 41621 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29833 from a total of 759256 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5038 -77.38202 -3.52310 0.64540 INTE EXTERN> -29.65908 -47.72294 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.382" Parameter: A <- "-77.382" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6591" Parameter: B <- "-29.6591" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7229" Parameter: C <- "-47.7229" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5038 TOTAL ENERGY = -77.382 RDTITL> * VAN DER WAALS = -29.6591 ELECTROSTATIC = -47.7229 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5038" Parameter: CONF_N -> "8002" Comparing "5038" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5039" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759256 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41440 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30116 from a total of 761009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5039 -78.00433 0.62232 0.64952 INTE EXTERN> -31.76972 -46.23462 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0043" Parameter: A <- "-78.0043" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7697" Parameter: B <- "-31.7697" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2346" Parameter: C <- "-46.2346" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5039 TOTAL ENERGY = -78.0043 RDTITL> * VAN DER WAALS = -31.7697 ELECTROSTATIC = -46.2346 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5039" Parameter: CONF_N -> "8002" Comparing "5039" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5040" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759238 ATOM PAIRS WERE FOUND FOR ATOM LIST 41570 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29066 from a total of 759238 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5040 -70.62999 -7.37435 0.54742 INTE EXTERN> -31.85102 -38.77897 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.63" Parameter: A <- "-70.63" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.851" Parameter: B <- "-31.851" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.779" Parameter: C <- "-38.779" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5040 TOTAL ENERGY = -70.63 RDTITL> * VAN DER WAALS = -31.851 ELECTROSTATIC = -38.779 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5040" Parameter: CONF_N -> "8002" Comparing "5040" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5041" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759238 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767344 ATOM PAIRS WERE FOUND FOR ATOM LIST 41865 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29630 from a total of 767344 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5041 -73.21908 2.58909 0.69313 INTE EXTERN> -28.71316 -44.50592 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2191" Parameter: A <- "-73.2191" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7132" Parameter: B <- "-28.7132" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5059" Parameter: C <- "-44.5059" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5041 TOTAL ENERGY = -73.2191 RDTITL> * VAN DER WAALS = -28.7132 ELECTROSTATIC = -44.5059 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5041" Parameter: CONF_N -> "8002" Comparing "5041" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5042" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767344 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766373 ATOM PAIRS WERE FOUND FOR ATOM LIST 41930 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30365 from a total of 766373 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5042 -77.28002 4.06094 0.64544 INTE EXTERN> -28.58419 -48.69583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.28" Parameter: A <- "-77.28" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5842" Parameter: B <- "-28.5842" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6958" Parameter: C <- "-48.6958" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5042 TOTAL ENERGY = -77.28 RDTITL> * VAN DER WAALS = -28.5842 ELECTROSTATIC = -48.6958 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5042" Parameter: CONF_N -> "8002" Comparing "5042" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5043" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766373 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761519 ATOM PAIRS WERE FOUND FOR ATOM LIST 41899 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29863 from a total of 761519 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5043 -81.19273 3.91272 0.69663 INTE EXTERN> -31.14064 -50.05209 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1927" Parameter: A <- "-81.1927" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1406" Parameter: B <- "-31.1406" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0521" Parameter: C <- "-50.0521" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5043 TOTAL ENERGY = -81.1927 RDTITL> * VAN DER WAALS = -31.1406 ELECTROSTATIC = -50.0521 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5043" Parameter: CONF_N -> "8002" Comparing "5043" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5044" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761519 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763023 ATOM PAIRS WERE FOUND FOR ATOM LIST 41791 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29647 from a total of 763023 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5044 -79.50492 -1.68781 0.75010 INTE EXTERN> -27.02806 -52.47687 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5049" Parameter: A <- "-79.5049" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0281" Parameter: B <- "-27.0281" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.4769" Parameter: C <- "-52.4769" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5044 TOTAL ENERGY = -79.5049 RDTITL> * VAN DER WAALS = -27.0281 ELECTROSTATIC = -52.4769 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5044" Parameter: CONF_N -> "8002" Comparing "5044" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5045" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763023 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761585 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29831 from a total of 761585 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5045 -77.92954 -1.57538 0.75718 INTE EXTERN> -26.23783 -51.69171 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9295" Parameter: A <- "-77.9295" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2378" Parameter: B <- "-26.2378" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6917" Parameter: C <- "-51.6917" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5045 TOTAL ENERGY = -77.9295 RDTITL> * VAN DER WAALS = -26.2378 ELECTROSTATIC = -51.6917 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5045" Parameter: CONF_N -> "8002" Comparing "5045" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5046" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761585 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758642 ATOM PAIRS WERE FOUND FOR ATOM LIST 41585 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29977 from a total of 758642 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5046 -72.06635 -5.86319 0.80799 INTE EXTERN> -22.51435 -49.55200 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0664" Parameter: A <- "-72.0664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.5144" Parameter: B <- "-22.5144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.552" Parameter: C <- "-49.552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5046 TOTAL ENERGY = -72.0664 RDTITL> * VAN DER WAALS = -22.5144 ELECTROSTATIC = -49.552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5046" Parameter: CONF_N -> "8002" Comparing "5046" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5047" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758642 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760644 ATOM PAIRS WERE FOUND FOR ATOM LIST 41543 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28868 from a total of 760644 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5047 -66.19126 -5.87510 0.72950 INTE EXTERN> -22.45255 -43.73871 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1913" Parameter: A <- "-66.1913" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.4525" Parameter: B <- "-22.4525" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7387" Parameter: C <- "-43.7387" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5047 TOTAL ENERGY = -66.1913 RDTITL> * VAN DER WAALS = -22.4525 ELECTROSTATIC = -43.7387 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5047" Parameter: CONF_N -> "8002" Comparing "5047" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5048" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760644 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762138 ATOM PAIRS WERE FOUND FOR ATOM LIST 41635 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29601 from a total of 762138 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5048 -72.32413 6.13288 0.64290 INTE EXTERN> -29.20002 -43.12411 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3241" Parameter: A <- "-72.3241" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2" Parameter: B <- "-29.2" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1241" Parameter: C <- "-43.1241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5048 TOTAL ENERGY = -72.3241 RDTITL> * VAN DER WAALS = -29.2 ELECTROSTATIC = -43.1241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5048" Parameter: CONF_N -> "8002" Comparing "5048" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5049" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762138 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768586 ATOM PAIRS WERE FOUND FOR ATOM LIST 42151 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30405 from a total of 768586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5049 -83.43495 11.11082 0.75569 INTE EXTERN> -28.01277 -55.42218 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.435" Parameter: A <- "-83.435" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0128" Parameter: B <- "-28.0128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.4222" Parameter: C <- "-55.4222" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5049 TOTAL ENERGY = -83.435 RDTITL> * VAN DER WAALS = -28.0128 ELECTROSTATIC = -55.4222 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5049" Parameter: CONF_N -> "8002" Comparing "5049" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5050" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764471 ATOM PAIRS WERE FOUND FOR ATOM LIST 41840 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30359 from a total of 764471 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5050 -80.56994 -2.86501 0.72210 INTE EXTERN> -29.00499 -51.56495 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5699" Parameter: A <- "-80.5699" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.005" Parameter: B <- "-29.005" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.565" Parameter: C <- "-51.565" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5050 TOTAL ENERGY = -80.5699 RDTITL> * VAN DER WAALS = -29.005 ELECTROSTATIC = -51.565 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5050" Parameter: CONF_N -> "8002" Comparing "5050" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5051" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764471 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763812 ATOM PAIRS WERE FOUND FOR ATOM LIST 41730 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29747 from a total of 763812 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5051 -83.01944 2.44950 0.77931 INTE EXTERN> -27.06483 -55.95461 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.0194" Parameter: A <- "-83.0194" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0648" Parameter: B <- "-27.0648" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.9546" Parameter: C <- "-55.9546" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5051 TOTAL ENERGY = -83.0194 RDTITL> * VAN DER WAALS = -27.0648 ELECTROSTATIC = -55.9546 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5051" Parameter: CONF_N -> "8002" Comparing "5051" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5052" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763812 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758906 ATOM PAIRS WERE FOUND FOR ATOM LIST 41526 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29624 from a total of 758906 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5052 -73.97390 -9.04553 0.65499 INTE EXTERN> -29.49780 -44.47610 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9739" Parameter: A <- "-73.9739" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4978" Parameter: B <- "-29.4978" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4761" Parameter: C <- "-44.4761" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5052 TOTAL ENERGY = -73.9739 RDTITL> * VAN DER WAALS = -29.4978 ELECTROSTATIC = -44.4761 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5052" Parameter: CONF_N -> "8002" Comparing "5052" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5053" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758906 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760911 ATOM PAIRS WERE FOUND FOR ATOM LIST 41692 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29374 from a total of 760911 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5053 -68.33756 -5.63635 0.52011 INTE EXTERN> -31.61666 -36.72090 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3376" Parameter: A <- "-68.3376" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6167" Parameter: B <- "-31.6167" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7209" Parameter: C <- "-36.7209" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5053 TOTAL ENERGY = -68.3376 RDTITL> * VAN DER WAALS = -31.6167 ELECTROSTATIC = -36.7209 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5053" Parameter: CONF_N -> "8002" Comparing "5053" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5054" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760911 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760224 ATOM PAIRS WERE FOUND FOR ATOM LIST 41578 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29368 from a total of 760224 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5054 -67.21548 -1.12208 0.53785 INTE EXTERN> -32.56758 -34.64790 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2155" Parameter: A <- "-67.2155" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5676" Parameter: B <- "-32.5676" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.6479" Parameter: C <- "-34.6479" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5054 TOTAL ENERGY = -67.2155 RDTITL> * VAN DER WAALS = -32.5676 ELECTROSTATIC = -34.6479 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5054" Parameter: CONF_N -> "8002" Comparing "5054" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5055" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760224 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759251 ATOM PAIRS WERE FOUND FOR ATOM LIST 41513 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29286 from a total of 759251 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5055 -73.40927 6.19380 0.66132 INTE EXTERN> -29.04677 -44.36250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4093" Parameter: A <- "-73.4093" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0468" Parameter: B <- "-29.0468" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3625" Parameter: C <- "-44.3625" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5055 TOTAL ENERGY = -73.4093 RDTITL> * VAN DER WAALS = -29.0468 ELECTROSTATIC = -44.3625 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5055" Parameter: CONF_N -> "8002" Comparing "5055" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5056" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759251 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759785 ATOM PAIRS WERE FOUND FOR ATOM LIST 41512 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29471 from a total of 759785 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5056 -73.62106 0.21178 0.58750 INTE EXTERN> -31.68825 -41.93281 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6211" Parameter: A <- "-73.6211" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6882" Parameter: B <- "-31.6882" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9328" Parameter: C <- "-41.9328" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5056 TOTAL ENERGY = -73.6211 RDTITL> * VAN DER WAALS = -31.6882 ELECTROSTATIC = -41.9328 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5056" Parameter: CONF_N -> "8002" Comparing "5056" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5057" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759785 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754157 ATOM PAIRS WERE FOUND FOR ATOM LIST 41168 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29112 from a total of 754157 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5057 -81.53411 7.91305 0.74481 INTE EXTERN> -27.50527 -54.02883 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5341" Parameter: A <- "-81.5341" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5053" Parameter: B <- "-27.5053" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0288" Parameter: C <- "-54.0288" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5057 TOTAL ENERGY = -81.5341 RDTITL> * VAN DER WAALS = -27.5053 ELECTROSTATIC = -54.0288 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5057" Parameter: CONF_N -> "8002" Comparing "5057" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5058" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754157 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757894 ATOM PAIRS WERE FOUND FOR ATOM LIST 41431 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28547 from a total of 757894 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5058 -76.96979 -4.56432 0.65473 INTE EXTERN> -29.69720 -47.27258 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9698" Parameter: A <- "-76.9698" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6972" Parameter: B <- "-29.6972" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2726" Parameter: C <- "-47.2726" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5058 TOTAL ENERGY = -76.9698 RDTITL> * VAN DER WAALS = -29.6972 ELECTROSTATIC = -47.2726 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5058" Parameter: CONF_N -> "8002" Comparing "5058" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5059" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757894 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753258 ATOM PAIRS WERE FOUND FOR ATOM LIST 41217 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28949 from a total of 753258 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5059 -78.07814 1.10835 0.69661 INTE EXTERN> -27.93523 -50.14290 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0781" Parameter: A <- "-78.0781" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9352" Parameter: B <- "-27.9352" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1429" Parameter: C <- "-50.1429" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5059 TOTAL ENERGY = -78.0781 RDTITL> * VAN DER WAALS = -27.9352 ELECTROSTATIC = -50.1429 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5059" Parameter: CONF_N -> "8002" Comparing "5059" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5060" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753258 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756561 ATOM PAIRS WERE FOUND FOR ATOM LIST 41349 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30135 from a total of 756561 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5060 -79.49854 1.42040 0.68605 INTE EXTERN> -29.52970 -49.96883 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4985" Parameter: A <- "-79.4985" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5297" Parameter: B <- "-29.5297" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9688" Parameter: C <- "-49.9688" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5060 TOTAL ENERGY = -79.4985 RDTITL> * VAN DER WAALS = -29.5297 ELECTROSTATIC = -49.9688 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5060" Parameter: CONF_N -> "8002" Comparing "5060" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5061" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756561 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763394 ATOM PAIRS WERE FOUND FOR ATOM LIST 41659 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29759 from a total of 763394 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5061 -77.55149 -1.94705 0.67603 INTE EXTERN> -30.30384 -47.24764 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5515" Parameter: A <- "-77.5515" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3038" Parameter: B <- "-30.3038" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2476" Parameter: C <- "-47.2476" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5061 TOTAL ENERGY = -77.5515 RDTITL> * VAN DER WAALS = -30.3038 ELECTROSTATIC = -47.2476 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5061" Parameter: CONF_N -> "8002" Comparing "5061" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5062" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763394 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761596 ATOM PAIRS WERE FOUND FOR ATOM LIST 41838 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30045 from a total of 761596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5062 -69.33256 -8.21893 0.56014 INTE EXTERN> -32.78532 -36.54724 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3326" Parameter: A <- "-69.3326" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7853" Parameter: B <- "-32.7853" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5472" Parameter: C <- "-36.5472" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5062 TOTAL ENERGY = -69.3326 RDTITL> * VAN DER WAALS = -32.7853 ELECTROSTATIC = -36.5472 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5062" Parameter: CONF_N -> "8002" Comparing "5062" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5063" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760143 ATOM PAIRS WERE FOUND FOR ATOM LIST 41649 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29887 from a total of 760143 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5063 -73.42186 4.08930 0.74441 INTE EXTERN> -28.50603 -44.91583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4219" Parameter: A <- "-73.4219" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.506" Parameter: B <- "-28.506" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9158" Parameter: C <- "-44.9158" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5063 TOTAL ENERGY = -73.4219 RDTITL> * VAN DER WAALS = -28.506 ELECTROSTATIC = -44.9158 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5063" Parameter: CONF_N -> "8002" Comparing "5063" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5064" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760143 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761417 ATOM PAIRS WERE FOUND FOR ATOM LIST 41752 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29630 from a total of 761417 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5064 -74.97231 1.55045 0.69035 INTE EXTERN> -30.78917 -44.18314 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9723" Parameter: A <- "-74.9723" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7892" Parameter: B <- "-30.7892" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1831" Parameter: C <- "-44.1831" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5064 TOTAL ENERGY = -74.9723 RDTITL> * VAN DER WAALS = -30.7892 ELECTROSTATIC = -44.1831 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5064" Parameter: CONF_N -> "8002" Comparing "5064" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5065" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761417 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755217 ATOM PAIRS WERE FOUND FOR ATOM LIST 41534 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29777 from a total of 755217 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5065 -62.08758 -12.88472 0.60961 INTE EXTERN> -31.84702 -30.24056 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.0876" Parameter: A <- "-62.0876" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.847" Parameter: B <- "-31.847" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.2406" Parameter: C <- "-30.2406" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5065 TOTAL ENERGY = -62.0876 RDTITL> * VAN DER WAALS = -31.847 ELECTROSTATIC = -30.2406 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5065" Parameter: CONF_N -> "8002" Comparing "5065" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5066" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755217 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752531 ATOM PAIRS WERE FOUND FOR ATOM LIST 41228 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30202 from a total of 752531 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5066 -67.48280 5.39522 0.77594 INTE EXTERN> -24.65418 -42.82862 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4828" Parameter: A <- "-67.4828" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6542" Parameter: B <- "-24.6542" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8286" Parameter: C <- "-42.8286" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5066 TOTAL ENERGY = -67.4828 RDTITL> * VAN DER WAALS = -24.6542 ELECTROSTATIC = -42.8286 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5066" Parameter: CONF_N -> "8002" Comparing "5066" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5067" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752531 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41797 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30670 from a total of 759601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5067 -68.70404 1.22124 0.63206 INTE EXTERN> -30.91035 -37.79370 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.704" Parameter: A <- "-68.704" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9103" Parameter: B <- "-30.9103" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7937" Parameter: C <- "-37.7937" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5067 TOTAL ENERGY = -68.704 RDTITL> * VAN DER WAALS = -30.9103 ELECTROSTATIC = -37.7937 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5067" Parameter: CONF_N -> "8002" Comparing "5067" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5068" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761393 ATOM PAIRS WERE FOUND FOR ATOM LIST 41784 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30365 from a total of 761393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5068 -61.13376 -7.57028 0.65438 INTE EXTERN> -31.02334 -30.11042 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.1338" Parameter: A <- "-61.1338" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0233" Parameter: B <- "-31.0233" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.1104" Parameter: C <- "-30.1104" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5068 TOTAL ENERGY = -61.1338 RDTITL> * VAN DER WAALS = -31.0233 ELECTROSTATIC = -30.1104 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5068" Parameter: CONF_N -> "8002" Comparing "5068" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5069" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757712 ATOM PAIRS WERE FOUND FOR ATOM LIST 41599 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29759 from a total of 757712 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5069 -69.89421 8.76045 0.64814 INTE EXTERN> -32.00600 -37.88821 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8942" Parameter: A <- "-69.8942" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.006" Parameter: B <- "-32.006" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8882" Parameter: C <- "-37.8882" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5069 TOTAL ENERGY = -69.8942 RDTITL> * VAN DER WAALS = -32.006 ELECTROSTATIC = -37.8882 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5069" Parameter: CONF_N -> "8002" Comparing "5069" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5070" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757712 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764176 ATOM PAIRS WERE FOUND FOR ATOM LIST 41897 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30787 from a total of 764176 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5070 -75.56577 5.67156 0.78495 INTE EXTERN> -29.38148 -46.18429 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5658" Parameter: A <- "-75.5658" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3815" Parameter: B <- "-29.3815" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1843" Parameter: C <- "-46.1843" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5070 TOTAL ENERGY = -75.5658 RDTITL> * VAN DER WAALS = -29.3815 ELECTROSTATIC = -46.1843 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5070" Parameter: CONF_N -> "8002" Comparing "5070" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5071" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764176 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757305 ATOM PAIRS WERE FOUND FOR ATOM LIST 41565 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29978 from a total of 757305 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5071 -72.87546 -2.69031 0.59994 INTE EXTERN> -30.96637 -41.90908 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8755" Parameter: A <- "-72.8755" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9664" Parameter: B <- "-30.9664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9091" Parameter: C <- "-41.9091" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5071 TOTAL ENERGY = -72.8755 RDTITL> * VAN DER WAALS = -30.9664 ELECTROSTATIC = -41.9091 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5071" Parameter: CONF_N -> "8002" Comparing "5071" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5072" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757305 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758870 ATOM PAIRS WERE FOUND FOR ATOM LIST 41497 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30213 from a total of 758870 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5072 -80.82543 7.94997 0.66263 INTE EXTERN> -30.82400 -50.00142 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.8254" Parameter: A <- "-80.8254" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.824" Parameter: B <- "-30.824" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0014" Parameter: C <- "-50.0014" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5072 TOTAL ENERGY = -80.8254 RDTITL> * VAN DER WAALS = -30.824 ELECTROSTATIC = -50.0014 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5072" Parameter: CONF_N -> "8002" Comparing "5072" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5073" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758870 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759993 ATOM PAIRS WERE FOUND FOR ATOM LIST 41747 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30588 from a total of 759993 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5073 -79.91132 -0.91411 0.60284 INTE EXTERN> -34.47610 -45.43522 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9113" Parameter: A <- "-79.9113" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.4761" Parameter: B <- "-34.4761" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4352" Parameter: C <- "-45.4352" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5073 TOTAL ENERGY = -79.9113 RDTITL> * VAN DER WAALS = -34.4761 ELECTROSTATIC = -45.4352 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5073" Parameter: CONF_N -> "8002" Comparing "5073" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5074" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759993 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754922 ATOM PAIRS WERE FOUND FOR ATOM LIST 41461 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29958 from a total of 754922 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5074 -69.55207 -10.35924 0.71215 INTE EXTERN> -27.89860 -41.65348 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5521" Parameter: A <- "-69.5521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8986" Parameter: B <- "-27.8986" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6535" Parameter: C <- "-41.6535" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5074 TOTAL ENERGY = -69.5521 RDTITL> * VAN DER WAALS = -27.8986 ELECTROSTATIC = -41.6535 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5074" Parameter: CONF_N -> "8002" Comparing "5074" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5075" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754922 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758090 ATOM PAIRS WERE FOUND FOR ATOM LIST 41499 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29892 from a total of 758090 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5075 -72.59212 3.04005 0.68805 INTE EXTERN> -27.62441 -44.96771 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5921" Parameter: A <- "-72.5921" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6244" Parameter: B <- "-27.6244" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9677" Parameter: C <- "-44.9677" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5075 TOTAL ENERGY = -72.5921 RDTITL> * VAN DER WAALS = -27.6244 ELECTROSTATIC = -44.9677 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5075" Parameter: CONF_N -> "8002" Comparing "5075" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5076" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758090 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753353 ATOM PAIRS WERE FOUND FOR ATOM LIST 41118 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30006 from a total of 753353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5076 -74.79386 2.20174 0.64316 INTE EXTERN> -33.41439 -41.37947 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7939" Parameter: A <- "-74.7939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4144" Parameter: B <- "-33.4144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3795" Parameter: C <- "-41.3795" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5076 TOTAL ENERGY = -74.7939 RDTITL> * VAN DER WAALS = -33.4144 ELECTROSTATIC = -41.3795 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5076" Parameter: CONF_N -> "8002" Comparing "5076" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5077" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752122 ATOM PAIRS WERE FOUND FOR ATOM LIST 41083 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29688 from a total of 752122 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5077 -66.11452 -8.67934 0.66708 INTE EXTERN> -29.44412 -36.67040 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1145" Parameter: A <- "-66.1145" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4441" Parameter: B <- "-29.4441" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6704" Parameter: C <- "-36.6704" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5077 TOTAL ENERGY = -66.1145 RDTITL> * VAN DER WAALS = -29.4441 ELECTROSTATIC = -36.6704 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5077" Parameter: CONF_N -> "8002" Comparing "5077" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5078" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752122 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752081 ATOM PAIRS WERE FOUND FOR ATOM LIST 41186 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29468 from a total of 752081 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5078 -64.70994 -1.40458 0.63812 INTE EXTERN> -27.48134 -37.22860 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7099" Parameter: A <- "-64.7099" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4813" Parameter: B <- "-27.4813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2286" Parameter: C <- "-37.2286" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5078 TOTAL ENERGY = -64.7099 RDTITL> * VAN DER WAALS = -27.4813 ELECTROSTATIC = -37.2286 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5078" Parameter: CONF_N -> "8002" Comparing "5078" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5079" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752081 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749691 ATOM PAIRS WERE FOUND FOR ATOM LIST 41138 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29541 from a total of 749691 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5079 -79.75736 15.04742 0.68055 INTE EXTERN> -33.09850 -46.65886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7574" Parameter: A <- "-79.7574" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0985" Parameter: B <- "-33.0985" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6589" Parameter: C <- "-46.6589" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5079 TOTAL ENERGY = -79.7574 RDTITL> * VAN DER WAALS = -33.0985 ELECTROSTATIC = -46.6589 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5079" Parameter: CONF_N -> "8002" Comparing "5079" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5080" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749691 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753000 ATOM PAIRS WERE FOUND FOR ATOM LIST 41151 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29290 from a total of 753000 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5080 -71.39800 -8.35936 0.62405 INTE EXTERN> -32.08962 -39.30837 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.398" Parameter: A <- "-71.398" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0896" Parameter: B <- "-32.0896" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3084" Parameter: C <- "-39.3084" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5080 TOTAL ENERGY = -71.398 RDTITL> * VAN DER WAALS = -32.0896 ELECTROSTATIC = -39.3084 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5080" Parameter: CONF_N -> "8002" Comparing "5080" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5081" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753000 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759159 ATOM PAIRS WERE FOUND FOR ATOM LIST 41330 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29823 from a total of 759159 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5081 -71.21119 -0.18681 0.64892 INTE EXTERN> -27.76490 -43.44629 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2112" Parameter: A <- "-71.2112" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7649" Parameter: B <- "-27.7649" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4463" Parameter: C <- "-43.4463" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5081 TOTAL ENERGY = -71.2112 RDTITL> * VAN DER WAALS = -27.7649 ELECTROSTATIC = -43.4463 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5081" Parameter: CONF_N -> "8002" Comparing "5081" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5082" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759159 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755621 ATOM PAIRS WERE FOUND FOR ATOM LIST 41532 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29397 from a total of 755621 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5082 -75.75090 4.53972 0.66751 INTE EXTERN> -31.15482 -44.59608 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7509" Parameter: A <- "-75.7509" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1548" Parameter: B <- "-31.1548" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5961" Parameter: C <- "-44.5961" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5082 TOTAL ENERGY = -75.7509 RDTITL> * VAN DER WAALS = -31.1548 ELECTROSTATIC = -44.5961 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5082" Parameter: CONF_N -> "8002" Comparing "5082" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5083" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755621 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762507 ATOM PAIRS WERE FOUND FOR ATOM LIST 41729 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30051 from a total of 762507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5083 -75.95012 0.19921 0.74328 INTE EXTERN> -25.83000 -50.12012 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9501" Parameter: A <- "-75.9501" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.83" Parameter: B <- "-25.83" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1201" Parameter: C <- "-50.1201" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5083 TOTAL ENERGY = -75.9501 RDTITL> * VAN DER WAALS = -25.83 ELECTROSTATIC = -50.1201 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5083" Parameter: CONF_N -> "8002" Comparing "5083" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5084" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759069 ATOM PAIRS WERE FOUND FOR ATOM LIST 41439 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29675 from a total of 759069 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5084 -70.36420 -5.58591 0.62372 INTE EXTERN> -31.43064 -38.93357 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3642" Parameter: A <- "-70.3642" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4306" Parameter: B <- "-31.4306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9336" Parameter: C <- "-38.9336" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5084 TOTAL ENERGY = -70.3642 RDTITL> * VAN DER WAALS = -31.4306 ELECTROSTATIC = -38.9336 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5084" Parameter: CONF_N -> "8002" Comparing "5084" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5085" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759069 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758024 ATOM PAIRS WERE FOUND FOR ATOM LIST 41481 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29747 from a total of 758024 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5085 -60.28124 -10.08296 0.61677 INTE EXTERN> -27.15617 -33.12507 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.2812" Parameter: A <- "-60.2812" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1562" Parameter: B <- "-27.1562" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1251" Parameter: C <- "-33.1251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5085 TOTAL ENERGY = -60.2812 RDTITL> * VAN DER WAALS = -27.1562 ELECTROSTATIC = -33.1251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5085" Parameter: CONF_N -> "8002" Comparing "5085" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5086" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758024 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760539 ATOM PAIRS WERE FOUND FOR ATOM LIST 41738 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29359 from a total of 760539 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5086 -68.90561 8.62437 0.72069 INTE EXTERN> -28.31631 -40.58930 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9056" Parameter: A <- "-68.9056" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3163" Parameter: B <- "-28.3163" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5893" Parameter: C <- "-40.5893" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5086 TOTAL ENERGY = -68.9056 RDTITL> * VAN DER WAALS = -28.3163 ELECTROSTATIC = -40.5893 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5086" Parameter: CONF_N -> "8002" Comparing "5086" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5087" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760539 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758971 ATOM PAIRS WERE FOUND FOR ATOM LIST 41509 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29728 from a total of 758971 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5087 -69.02732 0.12171 0.62856 INTE EXTERN> -33.54178 -35.48554 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0273" Parameter: A <- "-69.0273" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5418" Parameter: B <- "-33.5418" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4855" Parameter: C <- "-35.4855" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5087 TOTAL ENERGY = -69.0273 RDTITL> * VAN DER WAALS = -33.5418 ELECTROSTATIC = -35.4855 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5087" Parameter: CONF_N -> "8002" Comparing "5087" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5088" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758971 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756913 ATOM PAIRS WERE FOUND FOR ATOM LIST 41596 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30385 from a total of 756913 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5088 -76.37320 7.34588 0.84097 INTE EXTERN> -27.60197 -48.77123 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3732" Parameter: A <- "-76.3732" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.602" Parameter: B <- "-27.602" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7712" Parameter: C <- "-48.7712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5088 TOTAL ENERGY = -76.3732 RDTITL> * VAN DER WAALS = -27.602 ELECTROSTATIC = -48.7712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5088" Parameter: CONF_N -> "8002" Comparing "5088" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5089" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756913 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763281 ATOM PAIRS WERE FOUND FOR ATOM LIST 41923 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30064 from a total of 763281 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5089 -70.52534 -5.84786 0.73764 INTE EXTERN> -26.32933 -44.19601 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5253" Parameter: A <- "-70.5253" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3293" Parameter: B <- "-26.3293" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.196" Parameter: C <- "-44.196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5089 TOTAL ENERGY = -70.5253 RDTITL> * VAN DER WAALS = -26.3293 ELECTROSTATIC = -44.196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5089" Parameter: CONF_N -> "8002" Comparing "5089" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5090" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763281 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760002 ATOM PAIRS WERE FOUND FOR ATOM LIST 41549 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29948 from a total of 760002 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5090 -73.20958 2.68424 0.74723 INTE EXTERN> -25.94868 -47.26089 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2096" Parameter: A <- "-73.2096" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9487" Parameter: B <- "-25.9487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2609" Parameter: C <- "-47.2609" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5090 TOTAL ENERGY = -73.2096 RDTITL> * VAN DER WAALS = -25.9487 ELECTROSTATIC = -47.2609 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5090" Parameter: CONF_N -> "8002" Comparing "5090" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5091" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760002 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758591 ATOM PAIRS WERE FOUND FOR ATOM LIST 41468 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29786 from a total of 758591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5091 -74.30811 1.09853 0.60001 INTE EXTERN> -32.19261 -42.11550 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3081" Parameter: A <- "-74.3081" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1926" Parameter: B <- "-32.1926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1155" Parameter: C <- "-42.1155" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5091 TOTAL ENERGY = -74.3081 RDTITL> * VAN DER WAALS = -32.1926 ELECTROSTATIC = -42.1155 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5091" Parameter: CONF_N -> "8002" Comparing "5091" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5092" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752051 ATOM PAIRS WERE FOUND FOR ATOM LIST 41226 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30004 from a total of 752051 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5092 -77.69453 3.38642 0.65540 INTE EXTERN> -31.06427 -46.63026 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6945" Parameter: A <- "-77.6945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0643" Parameter: B <- "-31.0643" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6303" Parameter: C <- "-46.6303" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5092 TOTAL ENERGY = -77.6945 RDTITL> * VAN DER WAALS = -31.0643 ELECTROSTATIC = -46.6303 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5092" Parameter: CONF_N -> "8002" Comparing "5092" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5093" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752051 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757898 ATOM PAIRS WERE FOUND FOR ATOM LIST 41524 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30654 from a total of 757898 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5093 -79.28839 1.59387 0.77950 INTE EXTERN> -26.70259 -52.58581 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2884" Parameter: A <- "-79.2884" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7026" Parameter: B <- "-26.7026" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5858" Parameter: C <- "-52.5858" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5093 TOTAL ENERGY = -79.2884 RDTITL> * VAN DER WAALS = -26.7026 ELECTROSTATIC = -52.5858 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5093" Parameter: CONF_N -> "8002" Comparing "5093" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5094" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757898 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764132 ATOM PAIRS WERE FOUND FOR ATOM LIST 41707 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30285 from a total of 764132 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5094 -73.46489 -5.82351 0.64917 INTE EXTERN> -31.12085 -42.34404 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4649" Parameter: A <- "-73.4649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1209" Parameter: B <- "-31.1209" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.344" Parameter: C <- "-42.344" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5094 TOTAL ENERGY = -73.4649 RDTITL> * VAN DER WAALS = -31.1209 ELECTROSTATIC = -42.344 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5094" Parameter: CONF_N -> "8002" Comparing "5094" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5095" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764132 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761447 ATOM PAIRS WERE FOUND FOR ATOM LIST 41837 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30266 from a total of 761447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5095 -70.20926 -3.25563 0.78016 INTE EXTERN> -27.84644 -42.36282 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2093" Parameter: A <- "-70.2093" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8464" Parameter: B <- "-27.8464" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3628" Parameter: C <- "-42.3628" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5095 TOTAL ENERGY = -70.2093 RDTITL> * VAN DER WAALS = -27.8464 ELECTROSTATIC = -42.3628 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5095" Parameter: CONF_N -> "8002" Comparing "5095" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5096" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753328 ATOM PAIRS WERE FOUND FOR ATOM LIST 41313 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29448 from a total of 753328 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5096 -70.85200 0.64275 0.57982 INTE EXTERN> -30.36132 -40.49068 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.852" Parameter: A <- "-70.852" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3613" Parameter: B <- "-30.3613" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4907" Parameter: C <- "-40.4907" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5096 TOTAL ENERGY = -70.852 RDTITL> * VAN DER WAALS = -30.3613 ELECTROSTATIC = -40.4907 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5096" Parameter: CONF_N -> "8002" Comparing "5096" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5097" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753328 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766899 ATOM PAIRS WERE FOUND FOR ATOM LIST 41966 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30592 from a total of 766899 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5097 -77.41822 6.56622 0.72811 INTE EXTERN> -30.22867 -47.18955 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4182" Parameter: A <- "-77.4182" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2287" Parameter: B <- "-30.2287" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1895" Parameter: C <- "-47.1895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5097 TOTAL ENERGY = -77.4182 RDTITL> * VAN DER WAALS = -30.2287 ELECTROSTATIC = -47.1895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5097" Parameter: CONF_N -> "8002" Comparing "5097" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5098" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766899 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759263 ATOM PAIRS WERE FOUND FOR ATOM LIST 41773 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30659 from a total of 759263 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5098 -71.02972 -6.38851 0.74083 INTE EXTERN> -28.80690 -42.22282 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0297" Parameter: A <- "-71.0297" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8069" Parameter: B <- "-28.8069" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2228" Parameter: C <- "-42.2228" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5098 TOTAL ENERGY = -71.0297 RDTITL> * VAN DER WAALS = -28.8069 ELECTROSTATIC = -42.2228 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5098" Parameter: CONF_N -> "8002" Comparing "5098" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5099" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759263 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761984 ATOM PAIRS WERE FOUND FOR ATOM LIST 41776 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30171 from a total of 761984 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5099 -74.48392 3.45420 0.65907 INTE EXTERN> -29.20230 -45.28162 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4839" Parameter: A <- "-74.4839" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2023" Parameter: B <- "-29.2023" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2816" Parameter: C <- "-45.2816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5099 TOTAL ENERGY = -74.4839 RDTITL> * VAN DER WAALS = -29.2023 ELECTROSTATIC = -45.2816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5099" Parameter: CONF_N -> "8002" Comparing "5099" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5100" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761984 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767156 ATOM PAIRS WERE FOUND FOR ATOM LIST 41884 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30434 from a total of 767156 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5100 -82.56669 8.08277 0.72651 INTE EXTERN> -30.91337 -51.65332 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5667" Parameter: A <- "-82.5667" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9134" Parameter: B <- "-30.9134" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6533" Parameter: C <- "-51.6533" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5100 TOTAL ENERGY = -82.5667 RDTITL> * VAN DER WAALS = -30.9134 ELECTROSTATIC = -51.6533 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5100" Parameter: CONF_N -> "8002" Comparing "5100" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5101" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767156 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756189 ATOM PAIRS WERE FOUND FOR ATOM LIST 41378 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29738 from a total of 756189 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5101 -74.50010 -8.06659 0.66612 INTE EXTERN> -31.13938 -43.36072 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5001" Parameter: A <- "-74.5001" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1394" Parameter: B <- "-31.1394" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3607" Parameter: C <- "-43.3607" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5101 TOTAL ENERGY = -74.5001 RDTITL> * VAN DER WAALS = -31.1394 ELECTROSTATIC = -43.3607 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5101" Parameter: CONF_N -> "8002" Comparing "5101" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5102" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756189 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761300 ATOM PAIRS WERE FOUND FOR ATOM LIST 41728 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29824 from a total of 761300 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5102 -69.73320 -4.76690 0.65928 INTE EXTERN> -30.29039 -39.44280 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7332" Parameter: A <- "-69.7332" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2904" Parameter: B <- "-30.2904" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4428" Parameter: C <- "-39.4428" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5102 TOTAL ENERGY = -69.7332 RDTITL> * VAN DER WAALS = -30.2904 ELECTROSTATIC = -39.4428 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5102" Parameter: CONF_N -> "8002" Comparing "5102" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5103" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761300 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760115 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29849 from a total of 760115 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5103 -73.15404 3.42084 0.60434 INTE EXTERN> -33.01195 -40.14209 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.154" Parameter: A <- "-73.154" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.012" Parameter: B <- "-33.012" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1421" Parameter: C <- "-40.1421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5103 TOTAL ENERGY = -73.154 RDTITL> * VAN DER WAALS = -33.012 ELECTROSTATIC = -40.1421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5103" Parameter: CONF_N -> "8002" Comparing "5103" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5104" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760115 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758655 ATOM PAIRS WERE FOUND FOR ATOM LIST 41504 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30292 from a total of 758655 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5104 -73.89556 0.74152 0.72956 INTE EXTERN> -26.84034 -47.05522 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8956" Parameter: A <- "-73.8956" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8403" Parameter: B <- "-26.8403" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0552" Parameter: C <- "-47.0552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5104 TOTAL ENERGY = -73.8956 RDTITL> * VAN DER WAALS = -26.8403 ELECTROSTATIC = -47.0552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5104" Parameter: CONF_N -> "8002" Comparing "5104" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5105" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758655 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754541 ATOM PAIRS WERE FOUND FOR ATOM LIST 41504 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29498 from a total of 754541 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5105 -73.16266 -0.73290 0.65041 INTE EXTERN> -31.75163 -41.41103 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1627" Parameter: A <- "-73.1627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7516" Parameter: B <- "-31.7516" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.411" Parameter: C <- "-41.411" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5105 TOTAL ENERGY = -73.1627 RDTITL> * VAN DER WAALS = -31.7516 ELECTROSTATIC = -41.411 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5105" Parameter: CONF_N -> "8002" Comparing "5105" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5106" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754541 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763981 ATOM PAIRS WERE FOUND FOR ATOM LIST 41728 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30419 from a total of 763981 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5106 -71.50873 -1.65393 0.65621 INTE EXTERN> -29.16698 -42.34175 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5087" Parameter: A <- "-71.5087" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.167" Parameter: B <- "-29.167" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3417" Parameter: C <- "-42.3417" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5106 TOTAL ENERGY = -71.5087 RDTITL> * VAN DER WAALS = -29.167 ELECTROSTATIC = -42.3417 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5106" Parameter: CONF_N -> "8002" Comparing "5106" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5107" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763981 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759633 ATOM PAIRS WERE FOUND FOR ATOM LIST 41716 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29692 from a total of 759633 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5107 -67.36573 -4.14299 0.71177 INTE EXTERN> -30.44081 -36.92492 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3657" Parameter: A <- "-67.3657" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4408" Parameter: B <- "-30.4408" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9249" Parameter: C <- "-36.9249" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5107 TOTAL ENERGY = -67.3657 RDTITL> * VAN DER WAALS = -30.4408 ELECTROSTATIC = -36.9249 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5107" Parameter: CONF_N -> "8002" Comparing "5107" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5108" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759633 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757894 ATOM PAIRS WERE FOUND FOR ATOM LIST 41625 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30006 from a total of 757894 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5108 -72.08653 4.72080 0.68720 INTE EXTERN> -30.22264 -41.86389 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0865" Parameter: A <- "-72.0865" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2226" Parameter: B <- "-30.2226" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8639" Parameter: C <- "-41.8639" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5108 TOTAL ENERGY = -72.0865 RDTITL> * VAN DER WAALS = -30.2226 ELECTROSTATIC = -41.8639 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5108" Parameter: CONF_N -> "8002" Comparing "5108" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5109" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757894 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754381 ATOM PAIRS WERE FOUND FOR ATOM LIST 41498 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30613 from a total of 754381 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5109 -64.79984 -7.28669 0.66445 INTE EXTERN> -26.00642 -38.79343 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7998" Parameter: A <- "-64.7998" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0064" Parameter: B <- "-26.0064" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7934" Parameter: C <- "-38.7934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5109 TOTAL ENERGY = -64.7998 RDTITL> * VAN DER WAALS = -26.0064 ELECTROSTATIC = -38.7934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5109" Parameter: CONF_N -> "8002" Comparing "5109" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5110" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754381 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762069 ATOM PAIRS WERE FOUND FOR ATOM LIST 41625 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30269 from a total of 762069 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5110 -74.03343 9.23358 0.64315 INTE EXTERN> -32.40856 -41.62487 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0334" Parameter: A <- "-74.0334" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4086" Parameter: B <- "-32.4086" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6249" Parameter: C <- "-41.6249" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5110 TOTAL ENERGY = -74.0334 RDTITL> * VAN DER WAALS = -32.4086 ELECTROSTATIC = -41.6249 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5110" Parameter: CONF_N -> "8002" Comparing "5110" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5111" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762069 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763919 ATOM PAIRS WERE FOUND FOR ATOM LIST 42088 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30189 from a total of 763919 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5111 -83.75030 9.71687 0.71056 INTE EXTERN> -28.87953 -54.87077 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.7503" Parameter: A <- "-83.7503" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8795" Parameter: B <- "-28.8795" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8708" Parameter: C <- "-54.8708" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5111 TOTAL ENERGY = -83.7503 RDTITL> * VAN DER WAALS = -28.8795 ELECTROSTATIC = -54.8708 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5111" Parameter: CONF_N -> "8002" Comparing "5111" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5112" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763919 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760883 ATOM PAIRS WERE FOUND FOR ATOM LIST 41720 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30387 from a total of 760883 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5112 -78.18138 -5.56892 0.63893 INTE EXTERN> -32.58249 -45.59888 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1814" Parameter: A <- "-78.1814" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5825" Parameter: B <- "-32.5825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5989" Parameter: C <- "-45.5989" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5112 TOTAL ENERGY = -78.1814 RDTITL> * VAN DER WAALS = -32.5825 ELECTROSTATIC = -45.5989 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5112" Parameter: CONF_N -> "8002" Comparing "5112" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5113" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760883 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756804 ATOM PAIRS WERE FOUND FOR ATOM LIST 41392 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29591 from a total of 756804 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5113 -75.21772 -2.96366 0.67582 INTE EXTERN> -27.73442 -47.48330 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2177" Parameter: A <- "-75.2177" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7344" Parameter: B <- "-27.7344" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4833" Parameter: C <- "-47.4833" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5113 TOTAL ENERGY = -75.2177 RDTITL> * VAN DER WAALS = -27.7344 ELECTROSTATIC = -47.4833 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5113" Parameter: CONF_N -> "8002" Comparing "5113" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5114" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756804 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755222 ATOM PAIRS WERE FOUND FOR ATOM LIST 41443 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29989 from a total of 755222 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5114 -75.92839 0.71067 0.64926 INTE EXTERN> -30.92289 -45.00550 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9284" Parameter: A <- "-75.9284" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9229" Parameter: B <- "-30.9229" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0055" Parameter: C <- "-45.0055" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5114 TOTAL ENERGY = -75.9284 RDTITL> * VAN DER WAALS = -30.9229 ELECTROSTATIC = -45.0055 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5114" Parameter: CONF_N -> "8002" Comparing "5114" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5115" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755222 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757136 ATOM PAIRS WERE FOUND FOR ATOM LIST 41578 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29971 from a total of 757136 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5115 -74.27862 -1.64977 0.62243 INTE EXTERN> -31.98689 -42.29173 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2786" Parameter: A <- "-74.2786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9869" Parameter: B <- "-31.9869" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2917" Parameter: C <- "-42.2917" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5115 TOTAL ENERGY = -74.2786 RDTITL> * VAN DER WAALS = -31.9869 ELECTROSTATIC = -42.2917 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5115" Parameter: CONF_N -> "8002" Comparing "5115" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5116" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757136 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751756 ATOM PAIRS WERE FOUND FOR ATOM LIST 41319 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29099 from a total of 751756 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5116 -78.26964 3.99102 0.62024 INTE EXTERN> -31.75091 -46.51873 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2696" Parameter: A <- "-78.2696" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7509" Parameter: B <- "-31.7509" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5187" Parameter: C <- "-46.5187" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5116 TOTAL ENERGY = -78.2696 RDTITL> * VAN DER WAALS = -31.7509 ELECTROSTATIC = -46.5187 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5116" Parameter: CONF_N -> "8002" Comparing "5116" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5117" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751756 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754790 ATOM PAIRS WERE FOUND FOR ATOM LIST 41467 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29604 from a total of 754790 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5117 -80.07223 1.80259 0.74070 INTE EXTERN> -27.90418 -52.16805 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0722" Parameter: A <- "-80.0722" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9042" Parameter: B <- "-27.9042" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1681" Parameter: C <- "-52.1681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5117 TOTAL ENERGY = -80.0722 RDTITL> * VAN DER WAALS = -27.9042 ELECTROSTATIC = -52.1681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5117" Parameter: CONF_N -> "8002" Comparing "5117" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5118" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754790 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751126 ATOM PAIRS WERE FOUND FOR ATOM LIST 41477 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29329 from a total of 751126 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5118 -76.27825 -3.79398 0.67277 INTE EXTERN> -29.87491 -46.40334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2782" Parameter: A <- "-76.2782" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8749" Parameter: B <- "-29.8749" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4033" Parameter: C <- "-46.4033" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5118 TOTAL ENERGY = -76.2782 RDTITL> * VAN DER WAALS = -29.8749 ELECTROSTATIC = -46.4033 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5118" Parameter: CONF_N -> "8002" Comparing "5118" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5119" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751126 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756271 ATOM PAIRS WERE FOUND FOR ATOM LIST 41539 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29281 from a total of 756271 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5119 -69.91919 -6.35906 0.72555 INTE EXTERN> -27.66065 -42.25853 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9192" Parameter: A <- "-69.9192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6607" Parameter: B <- "-27.6607" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2585" Parameter: C <- "-42.2585" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5119 TOTAL ENERGY = -69.9192 RDTITL> * VAN DER WAALS = -27.6607 ELECTROSTATIC = -42.2585 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5119" Parameter: CONF_N -> "8002" Comparing "5119" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5120" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756271 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751713 ATOM PAIRS WERE FOUND FOR ATOM LIST 41304 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29349 from a total of 751713 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5120 -75.48850 5.56931 0.57227 INTE EXTERN> -33.92692 -41.56158 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4885" Parameter: A <- "-75.4885" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9269" Parameter: B <- "-33.9269" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5616" Parameter: C <- "-41.5616" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5120 TOTAL ENERGY = -75.4885 RDTITL> * VAN DER WAALS = -33.9269 ELECTROSTATIC = -41.5616 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5120" Parameter: CONF_N -> "8002" Comparing "5120" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5121" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751713 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754738 ATOM PAIRS WERE FOUND FOR ATOM LIST 41264 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29401 from a total of 754738 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5121 -73.84178 -1.64673 0.73618 INTE EXTERN> -26.06913 -47.77265 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8418" Parameter: A <- "-73.8418" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0691" Parameter: B <- "-26.0691" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7726" Parameter: C <- "-47.7726" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5121 TOTAL ENERGY = -73.8418 RDTITL> * VAN DER WAALS = -26.0691 ELECTROSTATIC = -47.7726 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5121" Parameter: CONF_N -> "8002" Comparing "5121" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5122" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754738 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755741 ATOM PAIRS WERE FOUND FOR ATOM LIST 41316 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29738 from a total of 755741 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5122 -70.54659 -3.29519 0.73564 INTE EXTERN> -23.53218 -47.01440 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5466" Parameter: A <- "-70.5466" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.5322" Parameter: B <- "-23.5322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0144" Parameter: C <- "-47.0144" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5122 TOTAL ENERGY = -70.5466 RDTITL> * VAN DER WAALS = -23.5322 ELECTROSTATIC = -47.0144 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5122" Parameter: CONF_N -> "8002" Comparing "5122" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5123" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755741 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754938 ATOM PAIRS WERE FOUND FOR ATOM LIST 41395 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28962 from a total of 754938 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5123 -67.60759 -2.93900 0.63679 INTE EXTERN> -28.19718 -39.41041 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6076" Parameter: A <- "-67.6076" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1972" Parameter: B <- "-28.1972" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4104" Parameter: C <- "-39.4104" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5123 TOTAL ENERGY = -67.6076 RDTITL> * VAN DER WAALS = -28.1972 ELECTROSTATIC = -39.4104 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5123" Parameter: CONF_N -> "8002" Comparing "5123" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5124" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754938 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757512 ATOM PAIRS WERE FOUND FOR ATOM LIST 41453 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30118 from a total of 757512 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5124 -70.42098 2.81339 0.67234 INTE EXTERN> -28.10717 -42.31382 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.421" Parameter: A <- "-70.421" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1072" Parameter: B <- "-28.1072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3138" Parameter: C <- "-42.3138" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5124 TOTAL ENERGY = -70.421 RDTITL> * VAN DER WAALS = -28.1072 ELECTROSTATIC = -42.3138 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5124" Parameter: CONF_N -> "8002" Comparing "5124" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5125" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757512 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758823 ATOM PAIRS WERE FOUND FOR ATOM LIST 41717 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29969 from a total of 758823 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5125 -76.02124 5.60026 0.78281 INTE EXTERN> -27.79906 -48.22218 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0212" Parameter: A <- "-76.0212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7991" Parameter: B <- "-27.7991" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2222" Parameter: C <- "-48.2222" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5125 TOTAL ENERGY = -76.0212 RDTITL> * VAN DER WAALS = -27.7991 ELECTROSTATIC = -48.2222 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5125" Parameter: CONF_N -> "8002" Comparing "5125" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5126" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758823 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757297 ATOM PAIRS WERE FOUND FOR ATOM LIST 41585 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29916 from a total of 757297 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5126 -77.54247 1.52123 0.81375 INTE EXTERN> -25.45471 -52.08776 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5425" Parameter: A <- "-77.5425" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4547" Parameter: B <- "-25.4547" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0878" Parameter: C <- "-52.0878" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5126 TOTAL ENERGY = -77.5425 RDTITL> * VAN DER WAALS = -25.4547 ELECTROSTATIC = -52.0878 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5126" Parameter: CONF_N -> "8002" Comparing "5126" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5127" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757297 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760122 ATOM PAIRS WERE FOUND FOR ATOM LIST 41746 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29895 from a total of 760122 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5127 -71.51288 -6.02959 0.62102 INTE EXTERN> -29.18921 -42.32367 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5129" Parameter: A <- "-71.5129" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1892" Parameter: B <- "-29.1892" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3237" Parameter: C <- "-42.3237" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5127 TOTAL ENERGY = -71.5129 RDTITL> * VAN DER WAALS = -29.1892 ELECTROSTATIC = -42.3237 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5127" Parameter: CONF_N -> "8002" Comparing "5127" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5128" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760122 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760835 ATOM PAIRS WERE FOUND FOR ATOM LIST 41818 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29288 from a total of 760835 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5128 -61.82321 -9.68967 0.77995 INTE EXTERN> -24.28886 -37.53436 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.8232" Parameter: A <- "-61.8232" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2889" Parameter: B <- "-24.2889" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5344" Parameter: C <- "-37.5344" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5128 TOTAL ENERGY = -61.8232 RDTITL> * VAN DER WAALS = -24.2889 ELECTROSTATIC = -37.5344 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5128" Parameter: CONF_N -> "8002" Comparing "5128" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5129" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760835 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759982 ATOM PAIRS WERE FOUND FOR ATOM LIST 41697 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29846 from a total of 759982 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5129 -75.14029 13.31708 0.64179 INTE EXTERN> -30.25046 -44.88983 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1403" Parameter: A <- "-75.1403" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2505" Parameter: B <- "-30.2505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8898" Parameter: C <- "-44.8898" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5129 TOTAL ENERGY = -75.1403 RDTITL> * VAN DER WAALS = -30.2505 ELECTROSTATIC = -44.8898 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5129" Parameter: CONF_N -> "8002" Comparing "5129" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5130" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759982 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757688 ATOM PAIRS WERE FOUND FOR ATOM LIST 41434 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30191 from a total of 757688 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5130 -76.10112 0.96083 0.61845 INTE EXTERN> -31.79436 -44.30676 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1011" Parameter: A <- "-76.1011" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7944" Parameter: B <- "-31.7944" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3068" Parameter: C <- "-44.3068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5130 TOTAL ENERGY = -76.1011 RDTITL> * VAN DER WAALS = -31.7944 ELECTROSTATIC = -44.3068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5130" Parameter: CONF_N -> "8002" Comparing "5130" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5131" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757688 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755988 ATOM PAIRS WERE FOUND FOR ATOM LIST 41512 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29378 from a total of 755988 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5131 -73.06814 -3.03298 0.65937 INTE EXTERN> -27.38446 -45.68368 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0681" Parameter: A <- "-73.0681" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3845" Parameter: B <- "-27.3845" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6837" Parameter: C <- "-45.6837" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5131 TOTAL ENERGY = -73.0681 RDTITL> * VAN DER WAALS = -27.3845 ELECTROSTATIC = -45.6837 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5131" Parameter: CONF_N -> "8002" Comparing "5131" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5132" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755988 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762508 ATOM PAIRS WERE FOUND FOR ATOM LIST 41709 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29901 from a total of 762508 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5132 -75.72882 2.66068 0.66491 INTE EXTERN> -30.13978 -45.58904 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7288" Parameter: A <- "-75.7288" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1398" Parameter: B <- "-30.1398" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.589" Parameter: C <- "-45.589" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5132 TOTAL ENERGY = -75.7288 RDTITL> * VAN DER WAALS = -30.1398 ELECTROSTATIC = -45.589 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5132" Parameter: CONF_N -> "8002" Comparing "5132" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5133" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762508 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755521 ATOM PAIRS WERE FOUND FOR ATOM LIST 41455 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29603 from a total of 755521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5133 -80.56638 4.83756 0.65288 INTE EXTERN> -30.25783 -50.30856 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5664" Parameter: A <- "-80.5664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2578" Parameter: B <- "-30.2578" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3086" Parameter: C <- "-50.3086" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5133 TOTAL ENERGY = -80.5664 RDTITL> * VAN DER WAALS = -30.2578 ELECTROSTATIC = -50.3086 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5133" Parameter: CONF_N -> "8002" Comparing "5133" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5134" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758376 ATOM PAIRS WERE FOUND FOR ATOM LIST 41609 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30402 from a total of 758376 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5134 -77.64256 -2.92382 0.69252 INTE EXTERN> -27.01755 -50.62501 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6426" Parameter: A <- "-77.6426" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0175" Parameter: B <- "-27.0175" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.625" Parameter: C <- "-50.625" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5134 TOTAL ENERGY = -77.6426 RDTITL> * VAN DER WAALS = -27.0175 ELECTROSTATIC = -50.625 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5134" Parameter: CONF_N -> "8002" Comparing "5134" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5135" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758376 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759330 ATOM PAIRS WERE FOUND FOR ATOM LIST 41762 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30236 from a total of 759330 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5135 -72.87936 -4.76320 0.59834 INTE EXTERN> -32.28055 -40.59881 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8794" Parameter: A <- "-72.8794" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2805" Parameter: B <- "-32.2805" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5988" Parameter: C <- "-40.5988" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5135 TOTAL ENERGY = -72.8794 RDTITL> * VAN DER WAALS = -32.2805 ELECTROSTATIC = -40.5988 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5135" Parameter: CONF_N -> "8002" Comparing "5135" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5136" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759330 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756153 ATOM PAIRS WERE FOUND FOR ATOM LIST 41592 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29961 from a total of 756153 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5136 -71.65608 -1.22328 0.62295 INTE EXTERN> -28.84868 -42.80740 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6561" Parameter: A <- "-71.6561" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8487" Parameter: B <- "-28.8487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8074" Parameter: C <- "-42.8074" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5136 TOTAL ENERGY = -71.6561 RDTITL> * VAN DER WAALS = -28.8487 ELECTROSTATIC = -42.8074 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5136" Parameter: CONF_N -> "8002" Comparing "5136" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5137" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756153 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754428 ATOM PAIRS WERE FOUND FOR ATOM LIST 41399 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30155 from a total of 754428 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5137 -76.72159 5.06551 0.64599 INTE EXTERN> -30.24571 -46.47588 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7216" Parameter: A <- "-76.7216" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2457" Parameter: B <- "-30.2457" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4759" Parameter: C <- "-46.4759" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5137 TOTAL ENERGY = -76.7216 RDTITL> * VAN DER WAALS = -30.2457 ELECTROSTATIC = -46.4759 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5137" Parameter: CONF_N -> "8002" Comparing "5137" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5138" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754428 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756961 ATOM PAIRS WERE FOUND FOR ATOM LIST 41361 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29851 from a total of 756961 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5138 -78.42769 1.70609 0.65772 INTE EXTERN> -31.30077 -47.12691 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4277" Parameter: A <- "-78.4277" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3008" Parameter: B <- "-31.3008" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1269" Parameter: C <- "-47.1269" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5138 TOTAL ENERGY = -78.4277 RDTITL> * VAN DER WAALS = -31.3008 ELECTROSTATIC = -47.1269 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5138" Parameter: CONF_N -> "8002" Comparing "5138" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5139" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756961 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757651 ATOM PAIRS WERE FOUND FOR ATOM LIST 41560 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30542 from a total of 757651 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5139 -76.37440 -2.05328 0.59109 INTE EXTERN> -32.90511 -43.46929 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3744" Parameter: A <- "-76.3744" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9051" Parameter: B <- "-32.9051" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4693" Parameter: C <- "-43.4693" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5139 TOTAL ENERGY = -76.3744 RDTITL> * VAN DER WAALS = -32.9051 ELECTROSTATIC = -43.4693 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5139" Parameter: CONF_N -> "8002" Comparing "5139" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5140" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757651 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756770 ATOM PAIRS WERE FOUND FOR ATOM LIST 41446 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29565 from a total of 756770 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5140 -72.29357 -4.08083 0.77874 INTE EXTERN> -25.65072 -46.64285 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2936" Parameter: A <- "-72.2936" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6507" Parameter: B <- "-25.6507" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6429" Parameter: C <- "-46.6429" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5140 TOTAL ENERGY = -72.2936 RDTITL> * VAN DER WAALS = -25.6507 ELECTROSTATIC = -46.6429 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5140" Parameter: CONF_N -> "8002" Comparing "5140" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5141" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756770 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754425 ATOM PAIRS WERE FOUND FOR ATOM LIST 41424 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29932 from a total of 754425 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5141 -78.51698 6.22341 0.67465 INTE EXTERN> -31.40127 -47.11571 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.517" Parameter: A <- "-78.517" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4013" Parameter: B <- "-31.4013" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1157" Parameter: C <- "-47.1157" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5141 TOTAL ENERGY = -78.517 RDTITL> * VAN DER WAALS = -31.4013 ELECTROSTATIC = -47.1157 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5141" Parameter: CONF_N -> "8002" Comparing "5141" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5142" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754425 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760157 ATOM PAIRS WERE FOUND FOR ATOM LIST 41623 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30277 from a total of 760157 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5142 -82.32980 3.81282 0.75983 INTE EXTERN> -27.38079 -54.94901 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3298" Parameter: A <- "-82.3298" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3808" Parameter: B <- "-27.3808" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.949" Parameter: C <- "-54.949" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5142 TOTAL ENERGY = -82.3298 RDTITL> * VAN DER WAALS = -27.3808 ELECTROSTATIC = -54.949 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5142" Parameter: CONF_N -> "8002" Comparing "5142" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5143" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760157 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753079 ATOM PAIRS WERE FOUND FOR ATOM LIST 41349 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29830 from a total of 753079 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5143 -70.68988 -11.63992 0.57329 INTE EXTERN> -31.89469 -38.79519 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6899" Parameter: A <- "-70.6899" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8947" Parameter: B <- "-31.8947" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7952" Parameter: C <- "-38.7952" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5143 TOTAL ENERGY = -70.6899 RDTITL> * VAN DER WAALS = -31.8947 ELECTROSTATIC = -38.7952 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5143" Parameter: CONF_N -> "8002" Comparing "5143" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5144" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753079 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759512 ATOM PAIRS WERE FOUND FOR ATOM LIST 41458 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30220 from a total of 759512 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5144 -75.95709 5.26720 0.69052 INTE EXTERN> -26.85716 -49.09992 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9571" Parameter: A <- "-75.9571" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8572" Parameter: B <- "-26.8572" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0999" Parameter: C <- "-49.0999" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5144 TOTAL ENERGY = -75.9571 RDTITL> * VAN DER WAALS = -26.8572 ELECTROSTATIC = -49.0999 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5144" Parameter: CONF_N -> "8002" Comparing "5144" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5145" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759512 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759820 ATOM PAIRS WERE FOUND FOR ATOM LIST 41456 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29984 from a total of 759820 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5145 -79.93307 3.97599 0.65513 INTE EXTERN> -30.88183 -49.05125 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9331" Parameter: A <- "-79.9331" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8818" Parameter: B <- "-30.8818" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0512" Parameter: C <- "-49.0512" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5145 TOTAL ENERGY = -79.9331 RDTITL> * VAN DER WAALS = -30.8818 ELECTROSTATIC = -49.0512 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5145" Parameter: CONF_N -> "8002" Comparing "5145" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5146" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759820 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754941 ATOM PAIRS WERE FOUND FOR ATOM LIST 41354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29311 from a total of 754941 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5146 -77.49086 -2.44221 0.75699 INTE EXTERN> -27.11565 -50.37521 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4909" Parameter: A <- "-77.4909" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1156" Parameter: B <- "-27.1156" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3752" Parameter: C <- "-50.3752" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5146 TOTAL ENERGY = -77.4909 RDTITL> * VAN DER WAALS = -27.1156 ELECTROSTATIC = -50.3752 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5146" Parameter: CONF_N -> "8002" Comparing "5146" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5147" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754941 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757252 ATOM PAIRS WERE FOUND FOR ATOM LIST 41403 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29638 from a total of 757252 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5147 -75.83075 -1.66011 0.62472 INTE EXTERN> -30.38720 -45.44355 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8307" Parameter: A <- "-75.8307" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3872" Parameter: B <- "-30.3872" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4436" Parameter: C <- "-45.4436" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5147 TOTAL ENERGY = -75.8307 RDTITL> * VAN DER WAALS = -30.3872 ELECTROSTATIC = -45.4436 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5147" Parameter: CONF_N -> "8002" Comparing "5147" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5148" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757252 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760889 ATOM PAIRS WERE FOUND FOR ATOM LIST 41520 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30066 from a total of 760889 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5148 -75.68240 -0.14834 0.73928 INTE EXTERN> -27.02432 -48.65809 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6824" Parameter: A <- "-75.6824" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0243" Parameter: B <- "-27.0243" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6581" Parameter: C <- "-48.6581" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5148 TOTAL ENERGY = -75.6824 RDTITL> * VAN DER WAALS = -27.0243 ELECTROSTATIC = -48.6581 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5148" Parameter: CONF_N -> "8002" Comparing "5148" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5149" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760889 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758106 ATOM PAIRS WERE FOUND FOR ATOM LIST 41517 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29806 from a total of 758106 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5149 -73.32280 -2.35960 0.55711 INTE EXTERN> -32.21565 -41.10715 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3228" Parameter: A <- "-73.3228" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2157" Parameter: B <- "-32.2157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1071" Parameter: C <- "-41.1071" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5149 TOTAL ENERGY = -73.3228 RDTITL> * VAN DER WAALS = -32.2157 ELECTROSTATIC = -41.1071 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5149" Parameter: CONF_N -> "8002" Comparing "5149" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5150" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758106 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750937 ATOM PAIRS WERE FOUND FOR ATOM LIST 41231 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29894 from a total of 750937 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5150 -75.42771 2.10491 0.61804 INTE EXTERN> -31.99297 -43.43473 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4277" Parameter: A <- "-75.4277" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.993" Parameter: B <- "-31.993" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4347" Parameter: C <- "-43.4347" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5150 TOTAL ENERGY = -75.4277 RDTITL> * VAN DER WAALS = -31.993 ELECTROSTATIC = -43.4347 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5150" Parameter: CONF_N -> "8002" Comparing "5150" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5151" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750937 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755508 ATOM PAIRS WERE FOUND FOR ATOM LIST 41475 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29318 from a total of 755508 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5151 -77.54381 2.11610 0.59451 INTE EXTERN> -30.35805 -47.18576 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5438" Parameter: A <- "-77.5438" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.358" Parameter: B <- "-30.358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1858" Parameter: C <- "-47.1858" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5151 TOTAL ENERGY = -77.5438 RDTITL> * VAN DER WAALS = -30.358 ELECTROSTATIC = -47.1858 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5151" Parameter: CONF_N -> "8002" Comparing "5151" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5152" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755508 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751207 ATOM PAIRS WERE FOUND FOR ATOM LIST 41351 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29440 from a total of 751207 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5152 -74.27150 -3.27231 0.60639 INTE EXTERN> -30.20724 -44.06426 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2715" Parameter: A <- "-74.2715" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2072" Parameter: B <- "-30.2072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0643" Parameter: C <- "-44.0643" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5152 TOTAL ENERGY = -74.2715 RDTITL> * VAN DER WAALS = -30.2072 ELECTROSTATIC = -44.0643 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5152" Parameter: CONF_N -> "8002" Comparing "5152" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5153" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751207 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756687 ATOM PAIRS WERE FOUND FOR ATOM LIST 41562 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30240 from a total of 756687 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5153 -74.90880 0.63730 0.76335 INTE EXTERN> -27.55726 -47.35154 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9088" Parameter: A <- "-74.9088" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5573" Parameter: B <- "-27.5573" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3515" Parameter: C <- "-47.3515" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5153 TOTAL ENERGY = -74.9088 RDTITL> * VAN DER WAALS = -27.5573 ELECTROSTATIC = -47.3515 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5153" Parameter: CONF_N -> "8002" Comparing "5153" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5154" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756687 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754398 ATOM PAIRS WERE FOUND FOR ATOM LIST 41282 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29918 from a total of 754398 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5154 -79.61180 4.70300 0.71759 INTE EXTERN> -28.07185 -51.53995 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6118" Parameter: A <- "-79.6118" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0719" Parameter: B <- "-28.0719" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5399" Parameter: C <- "-51.5399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5154 TOTAL ENERGY = -79.6118 RDTITL> * VAN DER WAALS = -28.0719 ELECTROSTATIC = -51.5399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5154" Parameter: CONF_N -> "8002" Comparing "5154" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5155" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754398 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750814 ATOM PAIRS WERE FOUND FOR ATOM LIST 41249 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29730 from a total of 750814 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5155 -74.53700 -5.07480 0.68536 INTE EXTERN> -28.17778 -46.35921 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.537" Parameter: A <- "-74.537" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1778" Parameter: B <- "-28.1778" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3592" Parameter: C <- "-46.3592" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5155 TOTAL ENERGY = -74.537 RDTITL> * VAN DER WAALS = -28.1778 ELECTROSTATIC = -46.3592 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5155" Parameter: CONF_N -> "8002" Comparing "5155" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5156" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750814 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753214 ATOM PAIRS WERE FOUND FOR ATOM LIST 41481 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29989 from a total of 753214 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5156 -71.11655 -3.42045 0.80681 INTE EXTERN> -21.86697 -49.24958 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1165" Parameter: A <- "-71.1165" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.867" Parameter: B <- "-21.867" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2496" Parameter: C <- "-49.2496" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5156 TOTAL ENERGY = -71.1165 RDTITL> * VAN DER WAALS = -21.867 ELECTROSTATIC = -49.2496 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5156" Parameter: CONF_N -> "8002" Comparing "5156" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5157" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753214 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755727 ATOM PAIRS WERE FOUND FOR ATOM LIST 41548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30011 from a total of 755727 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5157 -73.44206 2.32551 0.57655 INTE EXTERN> -32.83810 -40.60396 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4421" Parameter: A <- "-73.4421" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8381" Parameter: B <- "-32.8381" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.604" Parameter: C <- "-40.604" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5157 TOTAL ENERGY = -73.4421 RDTITL> * VAN DER WAALS = -32.8381 ELECTROSTATIC = -40.604 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5157" Parameter: CONF_N -> "8002" Comparing "5157" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5158" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755727 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763453 ATOM PAIRS WERE FOUND FOR ATOM LIST 41895 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30278 from a total of 763453 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5158 -71.62835 -1.81371 0.77999 INTE EXTERN> -25.87831 -45.75004 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6283" Parameter: A <- "-71.6283" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8783" Parameter: B <- "-25.8783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.75" Parameter: C <- "-45.75" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5158 TOTAL ENERGY = -71.6283 RDTITL> * VAN DER WAALS = -25.8783 ELECTROSTATIC = -45.75 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5158" Parameter: CONF_N -> "8002" Comparing "5158" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5159" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763453 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758337 ATOM PAIRS WERE FOUND FOR ATOM LIST 41447 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30561 from a total of 758337 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5159 -72.90887 1.28052 0.60588 INTE EXTERN> -29.45330 -43.45556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9089" Parameter: A <- "-72.9089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4533" Parameter: B <- "-29.4533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4556" Parameter: C <- "-43.4556" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5159 TOTAL ENERGY = -72.9089 RDTITL> * VAN DER WAALS = -29.4533 ELECTROSTATIC = -43.4556 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5159" Parameter: CONF_N -> "8002" Comparing "5159" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5160" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758337 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762403 ATOM PAIRS WERE FOUND FOR ATOM LIST 41932 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30517 from a total of 762403 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5160 -77.26886 4.36000 0.66040 INTE EXTERN> -29.66221 -47.60665 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2689" Parameter: A <- "-77.2689" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6622" Parameter: B <- "-29.6622" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6066" Parameter: C <- "-47.6066" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5160 TOTAL ENERGY = -77.2689 RDTITL> * VAN DER WAALS = -29.6622 ELECTROSTATIC = -47.6066 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5160" Parameter: CONF_N -> "8002" Comparing "5160" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5161" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762403 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767046 ATOM PAIRS WERE FOUND FOR ATOM LIST 42192 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29820 from a total of 767046 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5161 -74.07037 -3.19849 0.56375 INTE EXTERN> -30.39210 -43.67827 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0704" Parameter: A <- "-74.0704" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3921" Parameter: B <- "-30.3921" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6783" Parameter: C <- "-43.6783" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5161 TOTAL ENERGY = -74.0704 RDTITL> * VAN DER WAALS = -30.3921 ELECTROSTATIC = -43.6783 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5161" Parameter: CONF_N -> "8002" Comparing "5161" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5162" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767046 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759440 ATOM PAIRS WERE FOUND FOR ATOM LIST 41837 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29931 from a total of 759440 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5162 -78.17689 4.10652 0.72977 INTE EXTERN> -26.59725 -51.57963 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1769" Parameter: A <- "-78.1769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5973" Parameter: B <- "-26.5973" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5796" Parameter: C <- "-51.5796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5162 TOTAL ENERGY = -78.1769 RDTITL> * VAN DER WAALS = -26.5973 ELECTROSTATIC = -51.5796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5162" Parameter: CONF_N -> "8002" Comparing "5162" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5163" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759440 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755500 ATOM PAIRS WERE FOUND FOR ATOM LIST 41397 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30072 from a total of 755500 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5163 -74.63680 -3.54009 0.52555 INTE EXTERN> -31.92930 -42.70750 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6368" Parameter: A <- "-74.6368" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9293" Parameter: B <- "-31.9293" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7075" Parameter: C <- "-42.7075" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5163 TOTAL ENERGY = -74.6368 RDTITL> * VAN DER WAALS = -31.9293 ELECTROSTATIC = -42.7075 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5163" Parameter: CONF_N -> "8002" Comparing "5163" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5164" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755500 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752044 ATOM PAIRS WERE FOUND FOR ATOM LIST 41360 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29752 from a total of 752044 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5164 -66.04935 -8.58745 0.46344 INTE EXTERN> -35.13108 -30.91827 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0493" Parameter: A <- "-66.0493" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.1311" Parameter: B <- "-35.1311" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.9183" Parameter: C <- "-30.9183" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5164 TOTAL ENERGY = -66.0493 RDTITL> * VAN DER WAALS = -35.1311 ELECTROSTATIC = -30.9183 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5164" Parameter: CONF_N -> "8002" Comparing "5164" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5165" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752044 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758937 ATOM PAIRS WERE FOUND FOR ATOM LIST 41626 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30205 from a total of 758937 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5165 -71.04984 5.00049 0.58444 INTE EXTERN> -31.90730 -39.14254 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0498" Parameter: A <- "-71.0498" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9073" Parameter: B <- "-31.9073" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1425" Parameter: C <- "-39.1425" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5165 TOTAL ENERGY = -71.0498 RDTITL> * VAN DER WAALS = -31.9073 ELECTROSTATIC = -39.1425 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5165" Parameter: CONF_N -> "8002" Comparing "5165" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5166" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758937 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755842 ATOM PAIRS WERE FOUND FOR ATOM LIST 41633 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29938 from a total of 755842 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5166 -77.45140 6.40155 0.66699 INTE EXTERN> -30.71644 -46.73495 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4514" Parameter: A <- "-77.4514" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7164" Parameter: B <- "-30.7164" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.735" Parameter: C <- "-46.735" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5166 TOTAL ENERGY = -77.4514 RDTITL> * VAN DER WAALS = -30.7164 ELECTROSTATIC = -46.735 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5166" Parameter: CONF_N -> "8002" Comparing "5166" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5167" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755842 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759071 ATOM PAIRS WERE FOUND FOR ATOM LIST 41515 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29726 from a total of 759071 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5167 -77.13967 -0.31172 0.64301 INTE EXTERN> -30.40834 -46.73134 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1397" Parameter: A <- "-77.1397" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4083" Parameter: B <- "-30.4083" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7313" Parameter: C <- "-46.7313" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5167 TOTAL ENERGY = -77.1397 RDTITL> * VAN DER WAALS = -30.4083 ELECTROSTATIC = -46.7313 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5167" Parameter: CONF_N -> "8002" Comparing "5167" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5168" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759071 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751956 ATOM PAIRS WERE FOUND FOR ATOM LIST 41276 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29581 from a total of 751956 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5168 -71.66567 -5.47400 0.55888 INTE EXTERN> -32.26204 -39.40363 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6657" Parameter: A <- "-71.6657" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.262" Parameter: B <- "-32.262" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4036" Parameter: C <- "-39.4036" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5168 TOTAL ENERGY = -71.6657 RDTITL> * VAN DER WAALS = -32.262 ELECTROSTATIC = -39.4036 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5168" Parameter: CONF_N -> "8002" Comparing "5168" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5169" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751956 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761294 ATOM PAIRS WERE FOUND FOR ATOM LIST 41810 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29543 from a total of 761294 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5169 -74.90322 3.23754 0.65361 INTE EXTERN> -31.04148 -43.86173 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9032" Parameter: A <- "-74.9032" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0415" Parameter: B <- "-31.0415" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8617" Parameter: C <- "-43.8617" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5169 TOTAL ENERGY = -74.9032 RDTITL> * VAN DER WAALS = -31.0415 ELECTROSTATIC = -43.8617 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5169" Parameter: CONF_N -> "8002" Comparing "5169" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5170" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761294 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754388 ATOM PAIRS WERE FOUND FOR ATOM LIST 41473 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29413 from a total of 754388 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5170 -74.98414 0.08093 0.61636 INTE EXTERN> -31.74340 -43.24074 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9841" Parameter: A <- "-74.9841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7434" Parameter: B <- "-31.7434" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2407" Parameter: C <- "-43.2407" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5170 TOTAL ENERGY = -74.9841 RDTITL> * VAN DER WAALS = -31.7434 ELECTROSTATIC = -43.2407 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5170" Parameter: CONF_N -> "8002" Comparing "5170" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5171" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754388 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759457 ATOM PAIRS WERE FOUND FOR ATOM LIST 41460 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29624 from a total of 759457 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5171 -71.48961 -3.49453 0.70874 INTE EXTERN> -28.08869 -43.40092 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4896" Parameter: A <- "-71.4896" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0887" Parameter: B <- "-28.0887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4009" Parameter: C <- "-43.4009" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5171 TOTAL ENERGY = -71.4896 RDTITL> * VAN DER WAALS = -28.0887 ELECTROSTATIC = -43.4009 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5171" Parameter: CONF_N -> "8002" Comparing "5171" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5172" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759457 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755425 ATOM PAIRS WERE FOUND FOR ATOM LIST 41507 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30182 from a total of 755425 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5172 -72.18124 0.69163 0.56969 INTE EXTERN> -30.53793 -41.64331 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1812" Parameter: A <- "-72.1812" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5379" Parameter: B <- "-30.5379" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6433" Parameter: C <- "-41.6433" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5172 TOTAL ENERGY = -72.1812 RDTITL> * VAN DER WAALS = -30.5379 ELECTROSTATIC = -41.6433 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5172" Parameter: CONF_N -> "8002" Comparing "5172" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5173" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755425 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757111 ATOM PAIRS WERE FOUND FOR ATOM LIST 41606 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30240 from a total of 757111 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5173 -73.07409 0.89285 0.69165 INTE EXTERN> -26.67036 -46.40373 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0741" Parameter: A <- "-73.0741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6704" Parameter: B <- "-26.6704" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4037" Parameter: C <- "-46.4037" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5173 TOTAL ENERGY = -73.0741 RDTITL> * VAN DER WAALS = -26.6704 ELECTROSTATIC = -46.4037 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5173" Parameter: CONF_N -> "8002" Comparing "5173" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5174" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757111 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754120 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29653 from a total of 754120 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5174 -68.61394 -4.46015 0.55834 INTE EXTERN> -32.41238 -36.20156 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6139" Parameter: A <- "-68.6139" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4124" Parameter: B <- "-32.4124" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2016" Parameter: C <- "-36.2016" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5174 TOTAL ENERGY = -68.6139 RDTITL> * VAN DER WAALS = -32.4124 ELECTROSTATIC = -36.2016 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5174" Parameter: CONF_N -> "8002" Comparing "5174" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5175" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754120 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761245 ATOM PAIRS WERE FOUND FOR ATOM LIST 41695 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29888 from a total of 761245 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5175 -74.53187 5.91793 0.59996 INTE EXTERN> -32.02549 -42.50638 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5319" Parameter: A <- "-74.5319" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0255" Parameter: B <- "-32.0255" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5064" Parameter: C <- "-42.5064" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5175 TOTAL ENERGY = -74.5319 RDTITL> * VAN DER WAALS = -32.0255 ELECTROSTATIC = -42.5064 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5175" Parameter: CONF_N -> "8002" Comparing "5175" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5176" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761245 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754007 ATOM PAIRS WERE FOUND FOR ATOM LIST 41230 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29172 from a total of 754007 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5176 -71.35568 -3.17619 0.61222 INTE EXTERN> -29.54339 -41.81228 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3557" Parameter: A <- "-71.3557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5434" Parameter: B <- "-29.5434" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8123" Parameter: C <- "-41.8123" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5176 TOTAL ENERGY = -71.3557 RDTITL> * VAN DER WAALS = -29.5434 ELECTROSTATIC = -41.8123 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5176" Parameter: CONF_N -> "8002" Comparing "5176" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5177" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754007 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754255 ATOM PAIRS WERE FOUND FOR ATOM LIST 41441 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29694 from a total of 754255 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5177 -73.47386 2.11818 0.73395 INTE EXTERN> -28.00489 -45.46897 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4739" Parameter: A <- "-73.4739" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0049" Parameter: B <- "-28.0049" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.469" Parameter: C <- "-45.469" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5177 TOTAL ENERGY = -73.4739 RDTITL> * VAN DER WAALS = -28.0049 ELECTROSTATIC = -45.469 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5177" Parameter: CONF_N -> "8002" Comparing "5177" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5178" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754255 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755311 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29782 from a total of 755311 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5178 -73.27278 -0.20107 0.75599 INTE EXTERN> -24.39863 -48.87415 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2728" Parameter: A <- "-73.2728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3986" Parameter: B <- "-24.3986" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8742" Parameter: C <- "-48.8742" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5178 TOTAL ENERGY = -73.2728 RDTITL> * VAN DER WAALS = -24.3986 ELECTROSTATIC = -48.8742 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5178" Parameter: CONF_N -> "8002" Comparing "5178" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5179" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755311 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758811 ATOM PAIRS WERE FOUND FOR ATOM LIST 41586 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29655 from a total of 758811 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5179 -70.02002 -3.25277 0.66156 INTE EXTERN> -29.82694 -40.19308 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.02" Parameter: A <- "-70.02" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8269" Parameter: B <- "-29.8269" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1931" Parameter: C <- "-40.1931" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5179 TOTAL ENERGY = -70.02 RDTITL> * VAN DER WAALS = -29.8269 ELECTROSTATIC = -40.1931 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5179" Parameter: CONF_N -> "8002" Comparing "5179" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5180" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758811 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750638 ATOM PAIRS WERE FOUND FOR ATOM LIST 41370 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29741 from a total of 750638 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5180 -76.87056 6.85054 0.59588 INTE EXTERN> -31.61321 -45.25735 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8706" Parameter: A <- "-76.8706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6132" Parameter: B <- "-31.6132" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2574" Parameter: C <- "-45.2574" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5180 TOTAL ENERGY = -76.8706 RDTITL> * VAN DER WAALS = -31.6132 ELECTROSTATIC = -45.2574 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5180" Parameter: CONF_N -> "8002" Comparing "5180" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5181" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750638 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750864 ATOM PAIRS WERE FOUND FOR ATOM LIST 41134 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29617 from a total of 750864 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5181 -82.55824 5.68768 0.73060 INTE EXTERN> -28.07485 -54.48340 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5582" Parameter: A <- "-82.5582" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0748" Parameter: B <- "-28.0748" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.4834" Parameter: C <- "-54.4834" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5181 TOTAL ENERGY = -82.5582 RDTITL> * VAN DER WAALS = -28.0748 ELECTROSTATIC = -54.4834 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5181" Parameter: CONF_N -> "8002" Comparing "5181" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5182" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750864 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758266 ATOM PAIRS WERE FOUND FOR ATOM LIST 41634 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30425 from a total of 758266 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5182 -75.87097 -6.68728 0.71798 INTE EXTERN> -25.67692 -50.19404 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.871" Parameter: A <- "-75.871" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6769" Parameter: B <- "-25.6769" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.194" Parameter: C <- "-50.194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5182 TOTAL ENERGY = -75.871 RDTITL> * VAN DER WAALS = -25.6769 ELECTROSTATIC = -50.194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5182" Parameter: CONF_N -> "8002" Comparing "5182" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5183" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758266 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756634 ATOM PAIRS WERE FOUND FOR ATOM LIST 41542 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29789 from a total of 756634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5183 -66.35235 -9.51862 0.63427 INTE EXTERN> -26.20467 -40.14768 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3523" Parameter: A <- "-66.3523" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2047" Parameter: B <- "-26.2047" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1477" Parameter: C <- "-40.1477" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5183 TOTAL ENERGY = -66.3523 RDTITL> * VAN DER WAALS = -26.2047 ELECTROSTATIC = -40.1477 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5183" Parameter: CONF_N -> "8002" Comparing "5183" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5184" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763701 ATOM PAIRS WERE FOUND FOR ATOM LIST 42000 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30187 from a total of 763701 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5184 -72.64921 6.29686 0.61961 INTE EXTERN> -32.82616 -39.82306 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6492" Parameter: A <- "-72.6492" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8262" Parameter: B <- "-32.8262" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8231" Parameter: C <- "-39.8231" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5184 TOTAL ENERGY = -72.6492 RDTITL> * VAN DER WAALS = -32.8262 ELECTROSTATIC = -39.8231 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5184" Parameter: CONF_N -> "8002" Comparing "5184" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5185" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763701 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756807 ATOM PAIRS WERE FOUND FOR ATOM LIST 41667 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30207 from a total of 756807 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5185 -74.51727 1.86806 0.58947 INTE EXTERN> -33.34686 -41.17041 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5173" Parameter: A <- "-74.5173" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3469" Parameter: B <- "-33.3469" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1704" Parameter: C <- "-41.1704" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5185 TOTAL ENERGY = -74.5173 RDTITL> * VAN DER WAALS = -33.3469 ELECTROSTATIC = -41.1704 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5185" Parameter: CONF_N -> "8002" Comparing "5185" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5186" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756807 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756764 ATOM PAIRS WERE FOUND FOR ATOM LIST 41579 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30240 from a total of 756764 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5186 -70.41480 -4.10247 0.65215 INTE EXTERN> -27.96049 -42.45431 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4148" Parameter: A <- "-70.4148" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9605" Parameter: B <- "-27.9605" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4543" Parameter: C <- "-42.4543" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5186 TOTAL ENERGY = -70.4148 RDTITL> * VAN DER WAALS = -27.9605 ELECTROSTATIC = -42.4543 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5186" Parameter: CONF_N -> "8002" Comparing "5186" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5187" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756764 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752953 ATOM PAIRS WERE FOUND FOR ATOM LIST 41307 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30148 from a total of 752953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5187 -66.50329 -3.91152 0.63195 INTE EXTERN> -28.30822 -38.19507 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5033" Parameter: A <- "-66.5033" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3082" Parameter: B <- "-28.3082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1951" Parameter: C <- "-38.1951" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5187 TOTAL ENERGY = -66.5033 RDTITL> * VAN DER WAALS = -28.3082 ELECTROSTATIC = -38.1951 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5187" Parameter: CONF_N -> "8002" Comparing "5187" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5188" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752648 ATOM PAIRS WERE FOUND FOR ATOM LIST 41432 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29917 from a total of 752648 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5188 -81.71962 15.21633 0.74898 INTE EXTERN> -26.97906 -54.74056 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.7196" Parameter: A <- "-81.7196" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9791" Parameter: B <- "-26.9791" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.7406" Parameter: C <- "-54.7406" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5188 TOTAL ENERGY = -81.7196 RDTITL> * VAN DER WAALS = -26.9791 ELECTROSTATIC = -54.7406 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5188" Parameter: CONF_N -> "8002" Comparing "5188" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5189" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752648 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749272 ATOM PAIRS WERE FOUND FOR ATOM LIST 41032 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29647 from a total of 749272 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5189 -74.31005 -7.40957 0.61089 INTE EXTERN> -32.41440 -41.89565 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.31" Parameter: A <- "-74.31" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4144" Parameter: B <- "-32.4144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8956" Parameter: C <- "-41.8956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5189 TOTAL ENERGY = -74.31 RDTITL> * VAN DER WAALS = -32.4144 ELECTROSTATIC = -41.8956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5189" Parameter: CONF_N -> "8002" Comparing "5189" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5190" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749272 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759396 ATOM PAIRS WERE FOUND FOR ATOM LIST 41671 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30517 from a total of 759396 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5190 -77.41409 3.10405 0.63444 INTE EXTERN> -34.37937 -43.03472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4141" Parameter: A <- "-77.4141" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3794" Parameter: B <- "-34.3794" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0347" Parameter: C <- "-43.0347" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5190 TOTAL ENERGY = -77.4141 RDTITL> * VAN DER WAALS = -34.3794 ELECTROSTATIC = -43.0347 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5190" Parameter: CONF_N -> "8002" Comparing "5190" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5191" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759396 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759889 ATOM PAIRS WERE FOUND FOR ATOM LIST 41717 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30097 from a total of 759889 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5191 -77.97535 0.56125 0.59686 INTE EXTERN> -34.12690 -43.84844 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9753" Parameter: A <- "-77.9753" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1269" Parameter: B <- "-34.1269" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8484" Parameter: C <- "-43.8484" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5191 TOTAL ENERGY = -77.9753 RDTITL> * VAN DER WAALS = -34.1269 ELECTROSTATIC = -43.8484 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5191" Parameter: CONF_N -> "8002" Comparing "5191" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5192" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759889 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760031 ATOM PAIRS WERE FOUND FOR ATOM LIST 41739 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29784 from a total of 760031 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5192 -73.26398 -4.71137 0.70794 INTE EXTERN> -26.30391 -46.96006 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.264" Parameter: A <- "-73.264" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3039" Parameter: B <- "-26.3039" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9601" Parameter: C <- "-46.9601" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5192 TOTAL ENERGY = -73.264 RDTITL> * VAN DER WAALS = -26.3039 ELECTROSTATIC = -46.9601 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5192" Parameter: CONF_N -> "8002" Comparing "5192" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5193" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760031 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755937 ATOM PAIRS WERE FOUND FOR ATOM LIST 41708 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30027 from a total of 755937 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5193 -75.12563 1.86166 0.64286 INTE EXTERN> -32.30922 -42.81641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1256" Parameter: A <- "-75.1256" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3092" Parameter: B <- "-32.3092" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8164" Parameter: C <- "-42.8164" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5193 TOTAL ENERGY = -75.1256 RDTITL> * VAN DER WAALS = -32.3092 ELECTROSTATIC = -42.8164 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5193" Parameter: CONF_N -> "8002" Comparing "5193" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5194" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755937 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760008 ATOM PAIRS WERE FOUND FOR ATOM LIST 41747 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30437 from a total of 760008 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5194 -83.01909 7.89345 0.77243 INTE EXTERN> -28.50672 -54.51237 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.0191" Parameter: A <- "-83.0191" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5067" Parameter: B <- "-28.5067" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.5124" Parameter: C <- "-54.5124" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5194 TOTAL ENERGY = -83.0191 RDTITL> * VAN DER WAALS = -28.5067 ELECTROSTATIC = -54.5124 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5194" Parameter: CONF_N -> "8002" Comparing "5194" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5195" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760008 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762942 ATOM PAIRS WERE FOUND FOR ATOM LIST 41764 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30135 from a total of 762942 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5195 -73.41701 -9.60207 0.67568 INTE EXTERN> -32.09858 -41.31844 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.417" Parameter: A <- "-73.417" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0986" Parameter: B <- "-32.0986" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3184" Parameter: C <- "-41.3184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5195 TOTAL ENERGY = -73.417 RDTITL> * VAN DER WAALS = -32.0986 ELECTROSTATIC = -41.3184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5195" Parameter: CONF_N -> "8002" Comparing "5195" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5196" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762942 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763529 ATOM PAIRS WERE FOUND FOR ATOM LIST 41862 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30106 from a total of 763529 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5196 -76.87763 3.46062 0.71867 INTE EXTERN> -28.97845 -47.89918 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8776" Parameter: A <- "-76.8776" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9785" Parameter: B <- "-28.9785" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8992" Parameter: C <- "-47.8992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5196 TOTAL ENERGY = -76.8776 RDTITL> * VAN DER WAALS = -28.9785 ELECTROSTATIC = -47.8992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5196" Parameter: CONF_N -> "8002" Comparing "5196" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5197" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763529 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756971 ATOM PAIRS WERE FOUND FOR ATOM LIST 41503 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29926 from a total of 756971 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5197 -73.67370 -3.20393 0.64815 INTE EXTERN> -32.68837 -40.98532 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6737" Parameter: A <- "-73.6737" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6884" Parameter: B <- "-32.6884" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9853" Parameter: C <- "-40.9853" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5197 TOTAL ENERGY = -73.6737 RDTITL> * VAN DER WAALS = -32.6884 ELECTROSTATIC = -40.9853 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5197" Parameter: CONF_N -> "8002" Comparing "5197" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5198" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756971 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755874 ATOM PAIRS WERE FOUND FOR ATOM LIST 41538 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 755874 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5198 -73.91556 0.24186 0.71690 INTE EXTERN> -30.20515 -43.71040 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9156" Parameter: A <- "-73.9156" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2052" Parameter: B <- "-30.2052" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7104" Parameter: C <- "-43.7104" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5198 TOTAL ENERGY = -73.9156 RDTITL> * VAN DER WAALS = -30.2052 ELECTROSTATIC = -43.7104 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5198" Parameter: CONF_N -> "8002" Comparing "5198" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5199" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755874 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761331 ATOM PAIRS WERE FOUND FOR ATOM LIST 41840 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29775 from a total of 761331 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5199 -76.69792 2.78237 0.78894 INTE EXTERN> -24.69872 -51.99920 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6979" Parameter: A <- "-76.6979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6987" Parameter: B <- "-24.6987" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.9992" Parameter: C <- "-51.9992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5199 TOTAL ENERGY = -76.6979 RDTITL> * VAN DER WAALS = -24.6987 ELECTROSTATIC = -51.9992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5199" Parameter: CONF_N -> "8002" Comparing "5199" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5200" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761331 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755142 ATOM PAIRS WERE FOUND FOR ATOM LIST 41551 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30221 from a total of 755142 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5200 -78.53269 1.83476 0.69386 INTE EXTERN> -29.94751 -48.58518 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5327" Parameter: A <- "-78.5327" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9475" Parameter: B <- "-29.9475" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5852" Parameter: C <- "-48.5852" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5200 TOTAL ENERGY = -78.5327 RDTITL> * VAN DER WAALS = -29.9475 ELECTROSTATIC = -48.5852 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5200" Parameter: CONF_N -> "8002" Comparing "5200" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5201" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755142 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758189 ATOM PAIRS WERE FOUND FOR ATOM LIST 41633 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29670 from a total of 758189 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5201 -81.91839 3.38570 0.61791 INTE EXTERN> -33.52396 -48.39443 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9184" Parameter: A <- "-81.9184" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.524" Parameter: B <- "-33.524" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3944" Parameter: C <- "-48.3944" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5201 TOTAL ENERGY = -81.9184 RDTITL> * VAN DER WAALS = -33.524 ELECTROSTATIC = -48.3944 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5201" Parameter: CONF_N -> "8002" Comparing "5201" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5202" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758189 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752193 ATOM PAIRS WERE FOUND FOR ATOM LIST 41540 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29733 from a total of 752193 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5202 -81.91117 -0.00722 0.69006 INTE EXTERN> -31.36932 -50.54185 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9112" Parameter: A <- "-81.9112" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3693" Parameter: B <- "-31.3693" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5419" Parameter: C <- "-50.5419" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5202 TOTAL ENERGY = -81.9112 RDTITL> * VAN DER WAALS = -31.3693 ELECTROSTATIC = -50.5419 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5202" Parameter: CONF_N -> "8002" Comparing "5202" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5203" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752193 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755752 ATOM PAIRS WERE FOUND FOR ATOM LIST 41371 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28760 from a total of 755752 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5203 -75.55146 -6.35971 0.67294 INTE EXTERN> -28.31577 -47.23569 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5515" Parameter: A <- "-75.5515" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3158" Parameter: B <- "-28.3158" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2357" Parameter: C <- "-47.2357" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5203 TOTAL ENERGY = -75.5515 RDTITL> * VAN DER WAALS = -28.3158 ELECTROSTATIC = -47.2357 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5203" Parameter: CONF_N -> "8002" Comparing "5203" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5204" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755752 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760852 ATOM PAIRS WERE FOUND FOR ATOM LIST 41653 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29786 from a total of 760852 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5204 -79.16541 3.61395 0.73363 INTE EXTERN> -28.07805 -51.08736 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1654" Parameter: A <- "-79.1654" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.078" Parameter: B <- "-28.078" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0874" Parameter: C <- "-51.0874" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5204 TOTAL ENERGY = -79.1654 RDTITL> * VAN DER WAALS = -28.078 ELECTROSTATIC = -51.0874 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5204" Parameter: CONF_N -> "8002" Comparing "5204" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5205" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760852 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761182 ATOM PAIRS WERE FOUND FOR ATOM LIST 41909 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29734 from a total of 761182 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5205 -74.72087 -4.44454 0.77227 INTE EXTERN> -29.55655 -45.16432 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7209" Parameter: A <- "-74.7209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5566" Parameter: B <- "-29.5566" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1643" Parameter: C <- "-45.1643" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5205 TOTAL ENERGY = -74.7209 RDTITL> * VAN DER WAALS = -29.5566 ELECTROSTATIC = -45.1643 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5205" Parameter: CONF_N -> "8002" Comparing "5205" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5206" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761182 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757218 ATOM PAIRS WERE FOUND FOR ATOM LIST 41583 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29976 from a total of 757218 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5206 -75.56723 0.84635 0.61167 INTE EXTERN> -33.22063 -42.34659 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5672" Parameter: A <- "-75.5672" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2206" Parameter: B <- "-33.2206" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3466" Parameter: C <- "-42.3466" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5206 TOTAL ENERGY = -75.5672 RDTITL> * VAN DER WAALS = -33.2206 ELECTROSTATIC = -42.3466 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5206" Parameter: CONF_N -> "8002" Comparing "5206" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5207" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757218 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758266 ATOM PAIRS WERE FOUND FOR ATOM LIST 41559 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30115 from a total of 758266 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5207 -71.76862 -3.79860 0.63094 INTE EXTERN> -35.41662 -36.35200 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7686" Parameter: A <- "-71.7686" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.4166" Parameter: B <- "-35.4166" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.352" Parameter: C <- "-36.352" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5207 TOTAL ENERGY = -71.7686 RDTITL> * VAN DER WAALS = -35.4166 ELECTROSTATIC = -36.352 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5207" Parameter: CONF_N -> "8002" Comparing "5207" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5208" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758266 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758227 ATOM PAIRS WERE FOUND FOR ATOM LIST 41679 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30296 from a total of 758227 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5208 -71.62761 -0.14101 0.82552 INTE EXTERN> -25.50977 -46.11784 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6276" Parameter: A <- "-71.6276" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5098" Parameter: B <- "-25.5098" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1178" Parameter: C <- "-46.1178" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5208 TOTAL ENERGY = -71.6276 RDTITL> * VAN DER WAALS = -25.5098 ELECTROSTATIC = -46.1178 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5208" Parameter: CONF_N -> "8002" Comparing "5208" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5209" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758227 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758502 ATOM PAIRS WERE FOUND FOR ATOM LIST 41695 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30072 from a total of 758502 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5209 -67.55670 -4.07091 0.68618 INTE EXTERN> -29.73706 -37.81964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5567" Parameter: A <- "-67.5567" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7371" Parameter: B <- "-29.7371" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8196" Parameter: C <- "-37.8196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5209 TOTAL ENERGY = -67.5567 RDTITL> * VAN DER WAALS = -29.7371 ELECTROSTATIC = -37.8196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5209" Parameter: CONF_N -> "8002" Comparing "5209" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5210" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758502 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760165 ATOM PAIRS WERE FOUND FOR ATOM LIST 41740 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29849 from a total of 760165 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5210 -71.10477 3.54807 0.60197 INTE EXTERN> -33.42745 -37.67731 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1048" Parameter: A <- "-71.1048" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4275" Parameter: B <- "-33.4275" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6773" Parameter: C <- "-37.6773" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5210 TOTAL ENERGY = -71.1048 RDTITL> * VAN DER WAALS = -33.4275 ELECTROSTATIC = -37.6773 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5210" Parameter: CONF_N -> "8002" Comparing "5210" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5211" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760165 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759523 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29853 from a total of 759523 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5211 -73.81941 2.71465 0.73693 INTE EXTERN> -27.69282 -46.12659 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8194" Parameter: A <- "-73.8194" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6928" Parameter: B <- "-27.6928" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1266" Parameter: C <- "-46.1266" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5211 TOTAL ENERGY = -73.8194 RDTITL> * VAN DER WAALS = -27.6928 ELECTROSTATIC = -46.1266 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5211" Parameter: CONF_N -> "8002" Comparing "5211" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5212" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759523 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757646 ATOM PAIRS WERE FOUND FOR ATOM LIST 41675 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29393 from a total of 757646 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5212 -69.64533 -4.17408 0.64345 INTE EXTERN> -32.18414 -37.46120 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6453" Parameter: A <- "-69.6453" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1841" Parameter: B <- "-32.1841" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4612" Parameter: C <- "-37.4612" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5212 TOTAL ENERGY = -69.6453 RDTITL> * VAN DER WAALS = -32.1841 ELECTROSTATIC = -37.4612 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5212" Parameter: CONF_N -> "8002" Comparing "5212" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5213" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757646 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754906 ATOM PAIRS WERE FOUND FOR ATOM LIST 41254 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29420 from a total of 754906 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5213 -68.72483 -0.92050 0.66210 INTE EXTERN> -29.62910 -39.09573 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7248" Parameter: A <- "-68.7248" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6291" Parameter: B <- "-29.6291" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0957" Parameter: C <- "-39.0957" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5213 TOTAL ENERGY = -68.7248 RDTITL> * VAN DER WAALS = -29.6291 ELECTROSTATIC = -39.0957 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5213" Parameter: CONF_N -> "8002" Comparing "5213" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5214" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754906 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761525 ATOM PAIRS WERE FOUND FOR ATOM LIST 41909 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29404 from a total of 761525 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5214 -73.15403 4.42919 0.66980 INTE EXTERN> -29.82726 -43.32677 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.154" Parameter: A <- "-73.154" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8273" Parameter: B <- "-29.8273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3268" Parameter: C <- "-43.3268" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5214 TOTAL ENERGY = -73.154 RDTITL> * VAN DER WAALS = -29.8273 ELECTROSTATIC = -43.3268 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5214" Parameter: CONF_N -> "8002" Comparing "5214" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5215" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761525 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754243 ATOM PAIRS WERE FOUND FOR ATOM LIST 41510 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29100 from a total of 754243 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5215 -72.01896 -1.13506 0.62756 INTE EXTERN> -30.82652 -41.19244 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.019" Parameter: A <- "-72.019" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8265" Parameter: B <- "-30.8265" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1924" Parameter: C <- "-41.1924" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5215 TOTAL ENERGY = -72.019 RDTITL> * VAN DER WAALS = -30.8265 ELECTROSTATIC = -41.1924 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5215" Parameter: CONF_N -> "8002" Comparing "5215" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5216" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754243 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753587 ATOM PAIRS WERE FOUND FOR ATOM LIST 41364 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28971 from a total of 753587 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5216 -71.36459 -0.65437 0.65646 INTE EXTERN> -29.24196 -42.12263 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3646" Parameter: A <- "-71.3646" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.242" Parameter: B <- "-29.242" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1226" Parameter: C <- "-42.1226" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5216 TOTAL ENERGY = -71.3646 RDTITL> * VAN DER WAALS = -29.242 ELECTROSTATIC = -42.1226 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5216" Parameter: CONF_N -> "8002" Comparing "5216" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5217" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753587 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750680 ATOM PAIRS WERE FOUND FOR ATOM LIST 41240 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28143 from a total of 750680 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5217 -69.15306 -2.21153 0.60069 INTE EXTERN> -28.62919 -40.52387 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1531" Parameter: A <- "-69.1531" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6292" Parameter: B <- "-28.6292" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5239" Parameter: C <- "-40.5239" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5217 TOTAL ENERGY = -69.1531 RDTITL> * VAN DER WAALS = -28.6292 ELECTROSTATIC = -40.5239 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5217" Parameter: CONF_N -> "8002" Comparing "5217" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5218" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750680 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753241 ATOM PAIRS WERE FOUND FOR ATOM LIST 41276 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28171 from a total of 753241 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5218 -62.94121 -6.21185 0.64182 INTE EXTERN> -24.86003 -38.08118 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9412" Parameter: A <- "-62.9412" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.86" Parameter: B <- "-24.86" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0812" Parameter: C <- "-38.0812" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5218 TOTAL ENERGY = -62.9412 RDTITL> * VAN DER WAALS = -24.86 ELECTROSTATIC = -38.0812 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5218" Parameter: CONF_N -> "8002" Comparing "5218" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5219" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753241 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750200 ATOM PAIRS WERE FOUND FOR ATOM LIST 41328 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28688 from a total of 750200 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5219 -69.41740 6.47619 0.62150 INTE EXTERN> -28.11490 -41.30250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4174" Parameter: A <- "-69.4174" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1149" Parameter: B <- "-28.1149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3025" Parameter: C <- "-41.3025" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5219 TOTAL ENERGY = -69.4174 RDTITL> * VAN DER WAALS = -28.1149 ELECTROSTATIC = -41.3025 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5219" Parameter: CONF_N -> "8002" Comparing "5219" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5220" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750200 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751041 ATOM PAIRS WERE FOUND FOR ATOM LIST 41211 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28408 from a total of 751041 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5220 -64.52115 -4.89625 0.49471 INTE EXTERN> -31.21061 -33.31054 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5211" Parameter: A <- "-64.5211" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2106" Parameter: B <- "-31.2106" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.3105" Parameter: C <- "-33.3105" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5220 TOTAL ENERGY = -64.5211 RDTITL> * VAN DER WAALS = -31.2106 ELECTROSTATIC = -33.3105 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5220" Parameter: CONF_N -> "8002" Comparing "5220" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5221" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751041 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751104 ATOM PAIRS WERE FOUND FOR ATOM LIST 41237 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28187 from a total of 751104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5221 -62.94878 -1.57237 0.69412 INTE EXTERN> -25.09833 -37.85044 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9488" Parameter: A <- "-62.9488" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0983" Parameter: B <- "-25.0983" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8504" Parameter: C <- "-37.8504" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5221 TOTAL ENERGY = -62.9488 RDTITL> * VAN DER WAALS = -25.0983 ELECTROSTATIC = -37.8504 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5221" Parameter: CONF_N -> "8002" Comparing "5221" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5222" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756787 ATOM PAIRS WERE FOUND FOR ATOM LIST 41679 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29422 from a total of 756787 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5222 -72.09925 9.15047 0.56123 INTE EXTERN> -32.98214 -39.11711 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0993" Parameter: A <- "-72.0993" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9821" Parameter: B <- "-32.9821" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1171" Parameter: C <- "-39.1171" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5222 TOTAL ENERGY = -72.0993 RDTITL> * VAN DER WAALS = -32.9821 ELECTROSTATIC = -39.1171 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5222" Parameter: CONF_N -> "8002" Comparing "5222" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5223" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756787 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757380 ATOM PAIRS WERE FOUND FOR ATOM LIST 41522 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29074 from a total of 757380 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5223 -68.93309 -3.16616 0.57844 INTE EXTERN> -31.12148 -37.81161 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9331" Parameter: A <- "-68.9331" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1215" Parameter: B <- "-31.1215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8116" Parameter: C <- "-37.8116" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5223 TOTAL ENERGY = -68.9331 RDTITL> * VAN DER WAALS = -31.1215 ELECTROSTATIC = -37.8116 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5223" Parameter: CONF_N -> "8002" Comparing "5223" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5224" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757380 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752226 ATOM PAIRS WERE FOUND FOR ATOM LIST 41203 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28785 from a total of 752226 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5224 -60.99494 -7.93816 0.57380 INTE EXTERN> -27.27304 -33.72190 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.9949" Parameter: A <- "-60.9949" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.273" Parameter: B <- "-27.273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7219" Parameter: C <- "-33.7219" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5224 TOTAL ENERGY = -60.9949 RDTITL> * VAN DER WAALS = -27.273 ELECTROSTATIC = -33.7219 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5224" Parameter: CONF_N -> "8002" Comparing "5224" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5225" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752226 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755390 ATOM PAIRS WERE FOUND FOR ATOM LIST 41306 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29156 from a total of 755390 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5225 -70.53655 9.54161 0.62062 INTE EXTERN> -29.69072 -40.84583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5365" Parameter: A <- "-70.5365" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6907" Parameter: B <- "-29.6907" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8458" Parameter: C <- "-40.8458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5225 TOTAL ENERGY = -70.5365 RDTITL> * VAN DER WAALS = -29.6907 ELECTROSTATIC = -40.8458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5225" Parameter: CONF_N -> "8002" Comparing "5225" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5226" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755390 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753109 ATOM PAIRS WERE FOUND FOR ATOM LIST 41378 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28717 from a total of 753109 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5226 -64.07486 -6.46169 0.56605 INTE EXTERN> -28.74740 -35.32746 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0749" Parameter: A <- "-64.0749" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7474" Parameter: B <- "-28.7474" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3275" Parameter: C <- "-35.3275" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5226 TOTAL ENERGY = -64.0749 RDTITL> * VAN DER WAALS = -28.7474 ELECTROSTATIC = -35.3275 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5226" Parameter: CONF_N -> "8002" Comparing "5226" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5227" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753109 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758549 ATOM PAIRS WERE FOUND FOR ATOM LIST 41613 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29404 from a total of 758549 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5227 -60.55025 -3.52461 0.56688 INTE EXTERN> -29.27318 -31.27707 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.5503" Parameter: A <- "-60.5503" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2732" Parameter: B <- "-29.2732" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.2771" Parameter: C <- "-31.2771" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5227 TOTAL ENERGY = -60.5503 RDTITL> * VAN DER WAALS = -29.2732 ELECTROSTATIC = -31.2771 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5227" Parameter: CONF_N -> "8002" Comparing "5227" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5228" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758549 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753104 ATOM PAIRS WERE FOUND FOR ATOM LIST 41183 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28884 from a total of 753104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5228 -68.64953 8.09928 0.45853 INTE EXTERN> -33.71293 -34.93660 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6495" Parameter: A <- "-68.6495" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7129" Parameter: B <- "-33.7129" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9366" Parameter: C <- "-34.9366" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5228 TOTAL ENERGY = -68.6495 RDTITL> * VAN DER WAALS = -33.7129 ELECTROSTATIC = -34.9366 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5228" Parameter: CONF_N -> "8002" Comparing "5228" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5229" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753608 ATOM PAIRS WERE FOUND FOR ATOM LIST 41344 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29644 from a total of 753608 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5229 -62.25669 -6.39284 0.65843 INTE EXTERN> -26.23259 -36.02410 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.2567" Parameter: A <- "-62.2567" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2326" Parameter: B <- "-26.2326" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0241" Parameter: C <- "-36.0241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5229 TOTAL ENERGY = -62.2567 RDTITL> * VAN DER WAALS = -26.2326 ELECTROSTATIC = -36.0241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5229" Parameter: CONF_N -> "8002" Comparing "5229" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5230" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753608 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753031 ATOM PAIRS WERE FOUND FOR ATOM LIST 41418 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29090 from a total of 753031 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5230 -64.24028 1.98359 0.52187 INTE EXTERN> -30.41241 -33.82787 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2403" Parameter: A <- "-64.2403" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4124" Parameter: B <- "-30.4124" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8279" Parameter: C <- "-33.8279" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5230 TOTAL ENERGY = -64.2403 RDTITL> * VAN DER WAALS = -30.4124 ELECTROSTATIC = -33.8279 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5230" Parameter: CONF_N -> "8002" Comparing "5230" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5231" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753031 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750877 ATOM PAIRS WERE FOUND FOR ATOM LIST 41209 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28783 from a total of 750877 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5231 -76.06635 11.82607 0.57748 INTE EXTERN> -32.09349 -43.97286 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0663" Parameter: A <- "-76.0663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0935" Parameter: B <- "-32.0935" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9729" Parameter: C <- "-43.9729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5231 TOTAL ENERGY = -76.0663 RDTITL> * VAN DER WAALS = -32.0935 ELECTROSTATIC = -43.9729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5231" Parameter: CONF_N -> "8002" Comparing "5231" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5232" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750877 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750831 ATOM PAIRS WERE FOUND FOR ATOM LIST 41241 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29126 from a total of 750831 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5232 -67.81633 -8.25002 0.60525 INTE EXTERN> -28.94865 -38.86768 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8163" Parameter: A <- "-67.8163" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9487" Parameter: B <- "-28.9487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8677" Parameter: C <- "-38.8677" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5232 TOTAL ENERGY = -67.8163 RDTITL> * VAN DER WAALS = -28.9487 ELECTROSTATIC = -38.8677 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5232" Parameter: CONF_N -> "8002" Comparing "5232" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5233" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750831 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749858 ATOM PAIRS WERE FOUND FOR ATOM LIST 41255 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28979 from a total of 749858 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5233 -68.20747 0.39114 0.55984 INTE EXTERN> -30.75017 -37.45730 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2075" Parameter: A <- "-68.2075" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7502" Parameter: B <- "-30.7502" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4573" Parameter: C <- "-37.4573" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5233 TOTAL ENERGY = -68.2075 RDTITL> * VAN DER WAALS = -30.7502 ELECTROSTATIC = -37.4573 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5233" Parameter: CONF_N -> "8002" Comparing "5233" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5234" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749858 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752930 ATOM PAIRS WERE FOUND FOR ATOM LIST 41387 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29331 from a total of 752930 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5234 -61.06179 -7.14568 0.65718 INTE EXTERN> -26.74512 -34.31667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.0618" Parameter: A <- "-61.0618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7451" Parameter: B <- "-26.7451" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3167" Parameter: C <- "-34.3167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5234 TOTAL ENERGY = -61.0618 RDTITL> * VAN DER WAALS = -26.7451 ELECTROSTATIC = -34.3167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5234" Parameter: CONF_N -> "8002" Comparing "5234" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5235" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752930 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754936 ATOM PAIRS WERE FOUND FOR ATOM LIST 41365 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29863 from a total of 754936 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5235 -72.91213 11.85034 0.63955 INTE EXTERN> -28.80773 -44.10439 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9121" Parameter: A <- "-72.9121" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8077" Parameter: B <- "-28.8077" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1044" Parameter: C <- "-44.1044" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5235 TOTAL ENERGY = -72.9121 RDTITL> * VAN DER WAALS = -28.8077 ELECTROSTATIC = -44.1044 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5235" Parameter: CONF_N -> "8002" Comparing "5235" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5236" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754936 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753458 ATOM PAIRS WERE FOUND FOR ATOM LIST 41408 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29948 from a total of 753458 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5236 -71.14524 -1.76689 0.53684 INTE EXTERN> -32.47119 -38.67405 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1452" Parameter: A <- "-71.1452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4712" Parameter: B <- "-32.4712" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.674" Parameter: C <- "-38.674" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5236 TOTAL ENERGY = -71.1452 RDTITL> * VAN DER WAALS = -32.4712 ELECTROSTATIC = -38.674 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5236" Parameter: CONF_N -> "8002" Comparing "5236" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5237" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753458 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754199 ATOM PAIRS WERE FOUND FOR ATOM LIST 41358 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29254 from a total of 754199 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5237 -66.56034 -4.58490 0.61790 INTE EXTERN> -29.71266 -36.84767 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5603" Parameter: A <- "-66.5603" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7127" Parameter: B <- "-29.7127" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8477" Parameter: C <- "-36.8477" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5237 TOTAL ENERGY = -66.5603 RDTITL> * VAN DER WAALS = -29.7127 ELECTROSTATIC = -36.8477 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5237" Parameter: CONF_N -> "8002" Comparing "5237" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5238" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754199 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753522 ATOM PAIRS WERE FOUND FOR ATOM LIST 41375 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29184 from a total of 753522 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5238 -68.52688 1.96654 0.52887 INTE EXTERN> -30.81592 -37.71096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5269" Parameter: A <- "-68.5269" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8159" Parameter: B <- "-30.8159" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.711" Parameter: C <- "-37.711" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5238 TOTAL ENERGY = -68.5269 RDTITL> * VAN DER WAALS = -30.8159 ELECTROSTATIC = -37.711 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5238" Parameter: CONF_N -> "8002" Comparing "5238" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5239" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753522 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752770 ATOM PAIRS WERE FOUND FOR ATOM LIST 41316 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29160 from a total of 752770 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5239 -69.05324 0.52635 0.66232 INTE EXTERN> -24.80288 -44.25036 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0532" Parameter: A <- "-69.0532" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8029" Parameter: B <- "-24.8029" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2504" Parameter: C <- "-44.2504" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5239 TOTAL ENERGY = -69.0532 RDTITL> * VAN DER WAALS = -24.8029 ELECTROSTATIC = -44.2504 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5239" Parameter: CONF_N -> "8002" Comparing "5239" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5240" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752770 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750284 ATOM PAIRS WERE FOUND FOR ATOM LIST 41109 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28949 from a total of 750284 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5240 -66.49712 -2.55611 0.49497 INTE EXTERN> -32.70703 -33.79010 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4971" Parameter: A <- "-66.4971" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.707" Parameter: B <- "-32.707" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7901" Parameter: C <- "-33.7901" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5240 TOTAL ENERGY = -66.4971 RDTITL> * VAN DER WAALS = -32.707 ELECTROSTATIC = -33.7901 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5240" Parameter: CONF_N -> "8002" Comparing "5240" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5241" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750284 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758554 ATOM PAIRS WERE FOUND FOR ATOM LIST 41787 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30001 from a total of 758554 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5241 -71.53675 5.03963 0.52972 INTE EXTERN> -32.64715 -38.88960 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5368" Parameter: A <- "-71.5368" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6471" Parameter: B <- "-32.6471" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8896" Parameter: C <- "-38.8896" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5241 TOTAL ENERGY = -71.5368 RDTITL> * VAN DER WAALS = -32.6471 ELECTROSTATIC = -38.8896 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5241" Parameter: CONF_N -> "8002" Comparing "5241" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5242" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758554 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755019 ATOM PAIRS WERE FOUND FOR ATOM LIST 41507 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30128 from a total of 755019 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5242 -77.26604 5.72929 0.62800 INTE EXTERN> -29.83204 -47.43400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.266" Parameter: A <- "-77.266" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.832" Parameter: B <- "-29.832" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.434" Parameter: C <- "-47.434" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5242 TOTAL ENERGY = -77.266 RDTITL> * VAN DER WAALS = -29.832 ELECTROSTATIC = -47.434 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5242" Parameter: CONF_N -> "8002" Comparing "5242" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5243" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755019 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752150 ATOM PAIRS WERE FOUND FOR ATOM LIST 41102 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29878 from a total of 752150 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5243 -70.51804 -6.74801 0.65254 INTE EXTERN> -26.74131 -43.77672 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.518" Parameter: A <- "-70.518" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7413" Parameter: B <- "-26.7413" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7767" Parameter: C <- "-43.7767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5243 TOTAL ENERGY = -70.518 RDTITL> * VAN DER WAALS = -26.7413 ELECTROSTATIC = -43.7767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5243" Parameter: CONF_N -> "8002" Comparing "5243" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5244" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752150 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754386 ATOM PAIRS WERE FOUND FOR ATOM LIST 41329 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29834 from a total of 754386 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5244 -74.83174 4.31370 0.85874 INTE EXTERN> -23.91337 -50.91837 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8317" Parameter: A <- "-74.8317" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9134" Parameter: B <- "-23.9134" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9184" Parameter: C <- "-50.9184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5244 TOTAL ENERGY = -74.8317 RDTITL> * VAN DER WAALS = -23.9134 ELECTROSTATIC = -50.9184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5244" Parameter: CONF_N -> "8002" Comparing "5244" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5245" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754386 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753522 ATOM PAIRS WERE FOUND FOR ATOM LIST 41259 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29623 from a total of 753522 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5245 -74.84932 0.01759 0.69941 INTE EXTERN> -28.80182 -46.04751 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8493" Parameter: A <- "-74.8493" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8018" Parameter: B <- "-28.8018" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0475" Parameter: C <- "-46.0475" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5245 TOTAL ENERGY = -74.8493 RDTITL> * VAN DER WAALS = -28.8018 ELECTROSTATIC = -46.0475 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5245" Parameter: CONF_N -> "8002" Comparing "5245" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5246" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753522 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758264 ATOM PAIRS WERE FOUND FOR ATOM LIST 41484 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29535 from a total of 758264 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5246 -75.61078 0.76146 0.65861 INTE EXTERN> -30.44869 -45.16209 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6108" Parameter: A <- "-75.6108" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4487" Parameter: B <- "-30.4487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1621" Parameter: C <- "-45.1621" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5246 TOTAL ENERGY = -75.6108 RDTITL> * VAN DER WAALS = -30.4487 ELECTROSTATIC = -45.1621 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5246" Parameter: CONF_N -> "8002" Comparing "5246" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5247" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758264 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756248 ATOM PAIRS WERE FOUND FOR ATOM LIST 41387 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29960 from a total of 756248 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5247 -73.54841 -2.06238 0.65262 INTE EXTERN> -29.75557 -43.79284 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5484" Parameter: A <- "-73.5484" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7556" Parameter: B <- "-29.7556" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7928" Parameter: C <- "-43.7928" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5247 TOTAL ENERGY = -73.5484 RDTITL> * VAN DER WAALS = -29.7556 ELECTROSTATIC = -43.7928 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5247" Parameter: CONF_N -> "8002" Comparing "5247" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5248" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756248 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758395 ATOM PAIRS WERE FOUND FOR ATOM LIST 41428 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29786 from a total of 758395 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5248 -82.53830 8.98989 0.68541 INTE EXTERN> -30.23827 -52.30003 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5383" Parameter: A <- "-82.5383" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2383" Parameter: B <- "-30.2383" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3" Parameter: C <- "-52.3" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5248 TOTAL ENERGY = -82.5383 RDTITL> * VAN DER WAALS = -30.2383 ELECTROSTATIC = -52.3 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5248" Parameter: CONF_N -> "8002" Comparing "5248" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5249" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758395 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754392 ATOM PAIRS WERE FOUND FOR ATOM LIST 41368 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29627 from a total of 754392 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5249 -75.38243 -7.15586 0.63270 INTE EXTERN> -31.31267 -44.06976 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3824" Parameter: A <- "-75.3824" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3127" Parameter: B <- "-31.3127" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0698" Parameter: C <- "-44.0698" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5249 TOTAL ENERGY = -75.3824 RDTITL> * VAN DER WAALS = -31.3127 ELECTROSTATIC = -44.0698 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5249" Parameter: CONF_N -> "8002" Comparing "5249" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5250" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754392 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756656 ATOM PAIRS WERE FOUND FOR ATOM LIST 41321 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30245 from a total of 756656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5250 -77.93531 2.55288 0.76814 INTE EXTERN> -28.38923 -49.54608 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9353" Parameter: A <- "-77.9353" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3892" Parameter: B <- "-28.3892" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5461" Parameter: C <- "-49.5461" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5250 TOTAL ENERGY = -77.9353 RDTITL> * VAN DER WAALS = -28.3892 ELECTROSTATIC = -49.5461 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5250" Parameter: CONF_N -> "8002" Comparing "5250" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5251" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750442 ATOM PAIRS WERE FOUND FOR ATOM LIST 41143 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29913 from a total of 750442 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5251 -78.53058 0.59526 0.72806 INTE EXTERN> -31.14786 -47.38272 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5306" Parameter: A <- "-78.5306" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1479" Parameter: B <- "-31.1479" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3827" Parameter: C <- "-47.3827" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5251 TOTAL ENERGY = -78.5306 RDTITL> * VAN DER WAALS = -31.1479 ELECTROSTATIC = -47.3827 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5251" Parameter: CONF_N -> "8002" Comparing "5251" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5252" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750442 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760807 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29941 from a total of 760807 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5252 -73.35777 -5.17281 0.58991 INTE EXTERN> -32.05918 -41.29859 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3578" Parameter: A <- "-73.3578" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0592" Parameter: B <- "-32.0592" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2986" Parameter: C <- "-41.2986" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5252 TOTAL ENERGY = -73.3578 RDTITL> * VAN DER WAALS = -32.0592 ELECTROSTATIC = -41.2986 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5252" Parameter: CONF_N -> "8002" Comparing "5252" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5253" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760807 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757375 ATOM PAIRS WERE FOUND FOR ATOM LIST 41440 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29438 from a total of 757375 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5253 -74.85709 1.49933 0.78998 INTE EXTERN> -23.44748 -51.40961 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8571" Parameter: A <- "-74.8571" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4475" Parameter: B <- "-23.4475" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4096" Parameter: C <- "-51.4096" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5253 TOTAL ENERGY = -74.8571 RDTITL> * VAN DER WAALS = -23.4475 ELECTROSTATIC = -51.4096 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5253" Parameter: CONF_N -> "8002" Comparing "5253" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5254" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757375 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41274 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29138 from a total of 755794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5254 -66.79949 -8.05761 0.57778 INTE EXTERN> -29.69657 -37.10292 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7995" Parameter: A <- "-66.7995" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6966" Parameter: B <- "-29.6966" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1029" Parameter: C <- "-37.1029" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5254 TOTAL ENERGY = -66.7995 RDTITL> * VAN DER WAALS = -29.6966 ELECTROSTATIC = -37.1029 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5254" Parameter: CONF_N -> "8002" Comparing "5254" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5255" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757735 ATOM PAIRS WERE FOUND FOR ATOM LIST 41546 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29544 from a total of 757735 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5255 -79.01592 12.21644 0.61069 INTE EXTERN> -31.81845 -47.19748 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0159" Parameter: A <- "-79.0159" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8184" Parameter: B <- "-31.8184" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1975" Parameter: C <- "-47.1975" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5255 TOTAL ENERGY = -79.0159 RDTITL> * VAN DER WAALS = -31.8184 ELECTROSTATIC = -47.1975 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5255" Parameter: CONF_N -> "8002" Comparing "5255" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5256" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757735 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754077 ATOM PAIRS WERE FOUND FOR ATOM LIST 41305 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28860 from a total of 754077 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5256 -75.54561 -3.47031 0.62676 INTE EXTERN> -30.95290 -44.59271 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5456" Parameter: A <- "-75.5456" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9529" Parameter: B <- "-30.9529" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5927" Parameter: C <- "-44.5927" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5256 TOTAL ENERGY = -75.5456 RDTITL> * VAN DER WAALS = -30.9529 ELECTROSTATIC = -44.5927 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5256" Parameter: CONF_N -> "8002" Comparing "5256" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5257" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754077 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749464 ATOM PAIRS WERE FOUND FOR ATOM LIST 41213 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28439 from a total of 749464 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5257 -68.16514 -7.38047 0.52260 INTE EXTERN> -32.22971 -35.93543 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1651" Parameter: A <- "-68.1651" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2297" Parameter: B <- "-32.2297" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9354" Parameter: C <- "-35.9354" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5257 TOTAL ENERGY = -68.1651 RDTITL> * VAN DER WAALS = -32.2297 ELECTROSTATIC = -35.9354 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5257" Parameter: CONF_N -> "8002" Comparing "5257" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5258" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749464 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748353 ATOM PAIRS WERE FOUND FOR ATOM LIST 41062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28819 from a total of 748353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5258 -68.08805 -0.07709 0.62057 INTE EXTERN> -25.95114 -42.13691 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.088" Parameter: A <- "-68.088" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9511" Parameter: B <- "-25.9511" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1369" Parameter: C <- "-42.1369" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5258 TOTAL ENERGY = -68.088 RDTITL> * VAN DER WAALS = -25.9511 ELECTROSTATIC = -42.1369 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5258" Parameter: CONF_N -> "8002" Comparing "5258" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5259" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754996 ATOM PAIRS WERE FOUND FOR ATOM LIST 41156 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29779 from a total of 754996 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5259 -74.16522 6.07717 0.60404 INTE EXTERN> -30.08364 -44.08158 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1652" Parameter: A <- "-74.1652" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0836" Parameter: B <- "-30.0836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0816" Parameter: C <- "-44.0816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5259 TOTAL ENERGY = -74.1652 RDTITL> * VAN DER WAALS = -30.0836 ELECTROSTATIC = -44.0816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5259" Parameter: CONF_N -> "8002" Comparing "5259" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5260" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754996 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759362 ATOM PAIRS WERE FOUND FOR ATOM LIST 41782 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29587 from a total of 759362 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5260 -69.12770 -5.03752 0.69194 INTE EXTERN> -25.30863 -43.81907 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1277" Parameter: A <- "-69.1277" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3086" Parameter: B <- "-25.3086" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8191" Parameter: C <- "-43.8191" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5260 TOTAL ENERGY = -69.1277 RDTITL> * VAN DER WAALS = -25.3086 ELECTROSTATIC = -43.8191 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5260" Parameter: CONF_N -> "8002" Comparing "5260" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5261" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759362 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757607 ATOM PAIRS WERE FOUND FOR ATOM LIST 41379 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28945 from a total of 757607 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5261 -72.68618 3.55849 0.64615 INTE EXTERN> -29.68677 -42.99942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6862" Parameter: A <- "-72.6862" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6868" Parameter: B <- "-29.6868" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9994" Parameter: C <- "-42.9994" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5261 TOTAL ENERGY = -72.6862 RDTITL> * VAN DER WAALS = -29.6868 ELECTROSTATIC = -42.9994 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5261" Parameter: CONF_N -> "8002" Comparing "5261" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5262" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757607 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759512 ATOM PAIRS WERE FOUND FOR ATOM LIST 41555 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29409 from a total of 759512 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5262 -64.03733 -8.64885 0.57074 INTE EXTERN> -32.51848 -31.51885 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0373" Parameter: A <- "-64.0373" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5185" Parameter: B <- "-32.5185" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.5188" Parameter: C <- "-31.5188" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5262 TOTAL ENERGY = -64.0373 RDTITL> * VAN DER WAALS = -32.5185 ELECTROSTATIC = -31.5188 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5262" Parameter: CONF_N -> "8002" Comparing "5262" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5263" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759512 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760333 ATOM PAIRS WERE FOUND FOR ATOM LIST 41557 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28849 from a total of 760333 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5263 -76.63862 12.60129 0.78357 INTE EXTERN> -26.92011 -49.71851 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6386" Parameter: A <- "-76.6386" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9201" Parameter: B <- "-26.9201" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7185" Parameter: C <- "-49.7185" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5263 TOTAL ENERGY = -76.6386 RDTITL> * VAN DER WAALS = -26.9201 ELECTROSTATIC = -49.7185 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5263" Parameter: CONF_N -> "8002" Comparing "5263" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5264" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760333 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757019 ATOM PAIRS WERE FOUND FOR ATOM LIST 41663 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29094 from a total of 757019 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5264 -80.63684 3.99822 0.63543 INTE EXTERN> -32.11826 -48.51858 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6368" Parameter: A <- "-80.6368" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1183" Parameter: B <- "-32.1183" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5186" Parameter: C <- "-48.5186" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5264 TOTAL ENERGY = -80.6368 RDTITL> * VAN DER WAALS = -32.1183 ELECTROSTATIC = -48.5186 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5264" Parameter: CONF_N -> "8002" Comparing "5264" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5265" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757019 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754436 ATOM PAIRS WERE FOUND FOR ATOM LIST 41604 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29397 from a total of 754436 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5265 -70.23494 -10.40191 0.57815 INTE EXTERN> -29.97650 -40.25844 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2349" Parameter: A <- "-70.2349" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9765" Parameter: B <- "-29.9765" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2584" Parameter: C <- "-40.2584" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5265 TOTAL ENERGY = -70.2349 RDTITL> * VAN DER WAALS = -29.9765 ELECTROSTATIC = -40.2584 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5265" Parameter: CONF_N -> "8002" Comparing "5265" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5266" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754436 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758993 ATOM PAIRS WERE FOUND FOR ATOM LIST 41517 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29779 from a total of 758993 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5266 -69.81674 -0.41819 0.57850 INTE EXTERN> -32.80848 -37.00826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8167" Parameter: A <- "-69.8167" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8085" Parameter: B <- "-32.8085" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0083" Parameter: C <- "-37.0083" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5266 TOTAL ENERGY = -69.8167 RDTITL> * VAN DER WAALS = -32.8085 ELECTROSTATIC = -37.0083 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5266" Parameter: CONF_N -> "8002" Comparing "5266" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5267" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758993 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752865 ATOM PAIRS WERE FOUND FOR ATOM LIST 41224 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29437 from a total of 752865 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5267 -77.72668 7.90993 0.70762 INTE EXTERN> -26.72644 -51.00024 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7267" Parameter: A <- "-77.7267" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7264" Parameter: B <- "-26.7264" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0002" Parameter: C <- "-51.0002" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5267 TOTAL ENERGY = -77.7267 RDTITL> * VAN DER WAALS = -26.7264 ELECTROSTATIC = -51.0002 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5267" Parameter: CONF_N -> "8002" Comparing "5267" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5268" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752865 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755656 ATOM PAIRS WERE FOUND FOR ATOM LIST 41405 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29777 from a total of 755656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5268 -83.79426 6.06758 0.74264 INTE EXTERN> -28.16705 -55.62720 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.7943" Parameter: A <- "-83.7943" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1671" Parameter: B <- "-28.1671" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.6272" Parameter: C <- "-55.6272" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5268 TOTAL ENERGY = -83.7943 RDTITL> * VAN DER WAALS = -28.1671 ELECTROSTATIC = -55.6272 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5268" Parameter: CONF_N -> "8002" Comparing "5268" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5269" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750755 ATOM PAIRS WERE FOUND FOR ATOM LIST 41374 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30270 from a total of 750755 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5269 -78.68928 -5.10497 0.62497 INTE EXTERN> -33.47208 -45.21720 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6893" Parameter: A <- "-78.6893" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4721" Parameter: B <- "-33.4721" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2172" Parameter: C <- "-45.2172" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5269 TOTAL ENERGY = -78.6893 RDTITL> * VAN DER WAALS = -33.4721 ELECTROSTATIC = -45.2172 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5269" Parameter: CONF_N -> "8002" Comparing "5269" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5270" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750755 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759847 ATOM PAIRS WERE FOUND FOR ATOM LIST 41678 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30884 from a total of 759847 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5270 -89.87607 11.18679 0.74712 INTE EXTERN> -31.60940 -58.26667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-89.8761" Parameter: A <- "-89.8761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6094" Parameter: B <- "-31.6094" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.2667" Parameter: C <- "-58.2667" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5270 TOTAL ENERGY = -89.8761 RDTITL> * VAN DER WAALS = -31.6094 ELECTROSTATIC = -58.2667 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5270" Parameter: CONF_N -> "8002" Comparing "5270" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5271" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759847 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761293 ATOM PAIRS WERE FOUND FOR ATOM LIST 41826 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30278 from a total of 761293 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5271 -83.81308 -6.06299 0.78923 INTE EXTERN> -29.95841 -53.85467 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.8131" Parameter: A <- "-83.8131" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9584" Parameter: B <- "-29.9584" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8547" Parameter: C <- "-53.8547" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5271 TOTAL ENERGY = -83.8131 RDTITL> * VAN DER WAALS = -29.9584 ELECTROSTATIC = -53.8547 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5271" Parameter: CONF_N -> "8002" Comparing "5271" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5272" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761293 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761341 ATOM PAIRS WERE FOUND FOR ATOM LIST 41816 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30520 from a total of 761341 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5272 -85.88127 2.06819 0.70797 INTE EXTERN> -31.83458 -54.04669 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.8813" Parameter: A <- "-85.8813" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8346" Parameter: B <- "-31.8346" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0467" Parameter: C <- "-54.0467" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5272 TOTAL ENERGY = -85.8813 RDTITL> * VAN DER WAALS = -31.8346 ELECTROSTATIC = -54.0467 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5272" Parameter: CONF_N -> "8002" Comparing "5272" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5273" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761341 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761187 ATOM PAIRS WERE FOUND FOR ATOM LIST 41737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30775 from a total of 761187 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5273 -89.00330 3.12204 0.69164 INTE EXTERN> -32.20733 -56.79597 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-89.0033" Parameter: A <- "-89.0033" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2073" Parameter: B <- "-32.2073" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.796" Parameter: C <- "-56.796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5273 TOTAL ENERGY = -89.0033 RDTITL> * VAN DER WAALS = -32.2073 ELECTROSTATIC = -56.796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5273" Parameter: CONF_N -> "8002" Comparing "5273" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5274" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761187 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756452 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30708 from a total of 756452 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5274 -81.77603 -7.22727 0.68644 INTE EXTERN> -32.83616 -48.93987 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.776" Parameter: A <- "-81.776" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8362" Parameter: B <- "-32.8362" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9399" Parameter: C <- "-48.9399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5274 TOTAL ENERGY = -81.776 RDTITL> * VAN DER WAALS = -32.8362 ELECTROSTATIC = -48.9399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5274" Parameter: CONF_N -> "8002" Comparing "5274" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5275" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756452 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764424 ATOM PAIRS WERE FOUND FOR ATOM LIST 42005 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30708 from a total of 764424 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5275 -72.09371 -9.68233 0.68977 INTE EXTERN> -31.65153 -40.44217 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0937" Parameter: A <- "-72.0937" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6515" Parameter: B <- "-31.6515" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4422" Parameter: C <- "-40.4422" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5275 TOTAL ENERGY = -72.0937 RDTITL> * VAN DER WAALS = -31.6515 ELECTROSTATIC = -40.4422 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5275" Parameter: CONF_N -> "8002" Comparing "5275" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5276" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764424 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751947 ATOM PAIRS WERE FOUND FOR ATOM LIST 41210 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30178 from a total of 751947 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5276 -85.04242 12.94871 0.72350 INTE EXTERN> -31.84797 -53.19445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.0424" Parameter: A <- "-85.0424" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.848" Parameter: B <- "-31.848" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.1945" Parameter: C <- "-53.1945" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5276 TOTAL ENERGY = -85.0424 RDTITL> * VAN DER WAALS = -31.848 ELECTROSTATIC = -53.1945 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5276" Parameter: CONF_N -> "8002" Comparing "5276" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5277" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751947 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748562 ATOM PAIRS WERE FOUND FOR ATOM LIST 41109 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29517 from a total of 748562 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5277 -70.37712 -14.66530 0.67993 INTE EXTERN> -27.93214 -42.44497 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3771" Parameter: A <- "-70.3771" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9321" Parameter: B <- "-27.9321" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.445" Parameter: C <- "-42.445" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5277 TOTAL ENERGY = -70.3771 RDTITL> * VAN DER WAALS = -27.9321 ELECTROSTATIC = -42.445 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5277" Parameter: CONF_N -> "8002" Comparing "5277" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5278" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748562 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747371 ATOM PAIRS WERE FOUND FOR ATOM LIST 41158 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29741 from a total of 747371 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5278 -71.67084 1.29373 0.69381 INTE EXTERN> -31.47504 -40.19580 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6708" Parameter: A <- "-71.6708" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.475" Parameter: B <- "-31.475" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1958" Parameter: C <- "-40.1958" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5278 TOTAL ENERGY = -71.6708 RDTITL> * VAN DER WAALS = -31.475 ELECTROSTATIC = -40.1958 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5278" Parameter: CONF_N -> "8002" Comparing "5278" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5279" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747371 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760825 ATOM PAIRS WERE FOUND FOR ATOM LIST 41886 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30655 from a total of 760825 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5279 -81.69271 10.02186 0.68953 INTE EXTERN> -33.75231 -47.94040 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6927" Parameter: A <- "-81.6927" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7523" Parameter: B <- "-33.7523" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9404" Parameter: C <- "-47.9404" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5279 TOTAL ENERGY = -81.6927 RDTITL> * VAN DER WAALS = -33.7523 ELECTROSTATIC = -47.9404 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5279" Parameter: CONF_N -> "8002" Comparing "5279" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5280" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760825 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755147 ATOM PAIRS WERE FOUND FOR ATOM LIST 41311 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29646 from a total of 755147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5280 -85.65591 3.96320 0.70191 INTE EXTERN> -31.96639 -53.68951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.6559" Parameter: A <- "-85.6559" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9664" Parameter: B <- "-31.9664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6895" Parameter: C <- "-53.6895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5280 TOTAL ENERGY = -85.6559 RDTITL> * VAN DER WAALS = -31.9664 ELECTROSTATIC = -53.6895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5280" Parameter: CONF_N -> "8002" Comparing "5280" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5281" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754410 ATOM PAIRS WERE FOUND FOR ATOM LIST 41405 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29730 from a total of 754410 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5281 -73.77856 -11.87735 0.72566 INTE EXTERN> -28.09559 -45.68297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7786" Parameter: A <- "-73.7786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0956" Parameter: B <- "-28.0956" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.683" Parameter: C <- "-45.683" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5281 TOTAL ENERGY = -73.7786 RDTITL> * VAN DER WAALS = -28.0956 ELECTROSTATIC = -45.683 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5281" Parameter: CONF_N -> "8002" Comparing "5281" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5282" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754410 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756902 ATOM PAIRS WERE FOUND FOR ATOM LIST 41294 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30318 from a total of 756902 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5282 -76.55427 2.77571 0.61287 INTE EXTERN> -33.76126 -42.79301 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5543" Parameter: A <- "-76.5543" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7613" Parameter: B <- "-33.7613" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.793" Parameter: C <- "-42.793" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5282 TOTAL ENERGY = -76.5543 RDTITL> * VAN DER WAALS = -33.7613 ELECTROSTATIC = -42.793 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5282" Parameter: CONF_N -> "8002" Comparing "5282" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5283" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756902 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758825 ATOM PAIRS WERE FOUND FOR ATOM LIST 41587 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29728 from a total of 758825 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5283 -81.87825 5.32398 0.69706 INTE EXTERN> -30.55994 -51.31832 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8783" Parameter: A <- "-81.8783" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5599" Parameter: B <- "-30.5599" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3183" Parameter: C <- "-51.3183" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5283 TOTAL ENERGY = -81.8783 RDTITL> * VAN DER WAALS = -30.5599 ELECTROSTATIC = -51.3183 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5283" Parameter: CONF_N -> "8002" Comparing "5283" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5284" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758825 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756442 ATOM PAIRS WERE FOUND FOR ATOM LIST 41445 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29796 from a total of 756442 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5284 -77.63202 -4.24623 0.79065 INTE EXTERN> -28.02079 -49.61124 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.632" Parameter: A <- "-77.632" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0208" Parameter: B <- "-28.0208" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6112" Parameter: C <- "-49.6112" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5284 TOTAL ENERGY = -77.632 RDTITL> * VAN DER WAALS = -28.0208 ELECTROSTATIC = -49.6112 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5284" Parameter: CONF_N -> "8002" Comparing "5284" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5285" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756442 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760342 ATOM PAIRS WERE FOUND FOR ATOM LIST 41741 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29944 from a total of 760342 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5285 -75.48413 -2.14789 0.61540 INTE EXTERN> -30.43177 -45.05236 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4841" Parameter: A <- "-75.4841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4318" Parameter: B <- "-30.4318" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0524" Parameter: C <- "-45.0524" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5285 TOTAL ENERGY = -75.4841 RDTITL> * VAN DER WAALS = -30.4318 ELECTROSTATIC = -45.0524 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5285" Parameter: CONF_N -> "8002" Comparing "5285" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5286" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760342 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758473 ATOM PAIRS WERE FOUND FOR ATOM LIST 41352 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30275 from a total of 758473 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5286 -74.52228 -0.96185 0.60551 INTE EXTERN> -34.47192 -40.05036 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5223" Parameter: A <- "-74.5223" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.4719" Parameter: B <- "-34.4719" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0504" Parameter: C <- "-40.0504" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5286 TOTAL ENERGY = -74.5223 RDTITL> * VAN DER WAALS = -34.4719 ELECTROSTATIC = -40.0504 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5286" Parameter: CONF_N -> "8002" Comparing "5286" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5287" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758473 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751654 ATOM PAIRS WERE FOUND FOR ATOM LIST 41412 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29615 from a total of 751654 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5287 -70.52840 -3.99388 0.57172 INTE EXTERN> -34.83904 -35.68936 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5284" Parameter: A <- "-70.5284" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.839" Parameter: B <- "-34.839" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6894" Parameter: C <- "-35.6894" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5287 TOTAL ENERGY = -70.5284 RDTITL> * VAN DER WAALS = -34.839 ELECTROSTATIC = -35.6894 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5287" Parameter: CONF_N -> "8002" Comparing "5287" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5288" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751654 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756903 ATOM PAIRS WERE FOUND FOR ATOM LIST 41574 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30111 from a total of 756903 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5288 -81.14008 10.61168 0.74843 INTE EXTERN> -27.50081 -53.63927 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1401" Parameter: A <- "-81.1401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5008" Parameter: B <- "-27.5008" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6393" Parameter: C <- "-53.6393" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5288 TOTAL ENERGY = -81.1401 RDTITL> * VAN DER WAALS = -27.5008 ELECTROSTATIC = -53.6393 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5288" Parameter: CONF_N -> "8002" Comparing "5288" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5289" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756903 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757934 ATOM PAIRS WERE FOUND FOR ATOM LIST 41677 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30243 from a total of 757934 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5289 -79.79935 -1.34073 0.66441 INTE EXTERN> -33.49072 -46.30863 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7993" Parameter: A <- "-79.7993" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4907" Parameter: B <- "-33.4907" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3086" Parameter: C <- "-46.3086" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5289 TOTAL ENERGY = -79.7993 RDTITL> * VAN DER WAALS = -33.4907 ELECTROSTATIC = -46.3086 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5289" Parameter: CONF_N -> "8002" Comparing "5289" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5290" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757934 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760809 ATOM PAIRS WERE FOUND FOR ATOM LIST 41722 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30132 from a total of 760809 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5290 -81.73216 1.93281 0.61546 INTE EXTERN> -32.20046 -49.53169 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.7322" Parameter: A <- "-81.7322" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2005" Parameter: B <- "-32.2005" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5317" Parameter: C <- "-49.5317" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5290 TOTAL ENERGY = -81.7322 RDTITL> * VAN DER WAALS = -32.2005 ELECTROSTATIC = -49.5317 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5290" Parameter: CONF_N -> "8002" Comparing "5290" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5291" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760809 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761486 ATOM PAIRS WERE FOUND FOR ATOM LIST 41676 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30221 from a total of 761486 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5291 -88.26030 6.52814 0.79093 INTE EXTERN> -27.54644 -60.71386 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.2603" Parameter: A <- "-88.2603" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5464" Parameter: B <- "-27.5464" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-60.7139" Parameter: C <- "-60.7139" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5291 TOTAL ENERGY = -88.2603 RDTITL> * VAN DER WAALS = -27.5464 ELECTROSTATIC = -60.7139 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5291" Parameter: CONF_N -> "8002" Comparing "5291" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5292" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761486 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30556 from a total of 762422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5292 -74.89469 -13.36561 0.65374 INTE EXTERN> -32.94841 -41.94628 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8947" Parameter: A <- "-74.8947" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9484" Parameter: B <- "-32.9484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9463" Parameter: C <- "-41.9463" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5292 TOTAL ENERGY = -74.8947 RDTITL> * VAN DER WAALS = -32.9484 ELECTROSTATIC = -41.9463 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5292" Parameter: CONF_N -> "8002" Comparing "5292" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5293" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761946 ATOM PAIRS WERE FOUND FOR ATOM LIST 41940 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29812 from a total of 761946 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5293 -71.46824 -3.42645 0.52651 INTE EXTERN> -32.47258 -38.99566 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4682" Parameter: A <- "-71.4682" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4726" Parameter: B <- "-32.4726" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9957" Parameter: C <- "-38.9957" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5293 TOTAL ENERGY = -71.4682 RDTITL> * VAN DER WAALS = -32.4726 ELECTROSTATIC = -38.9957 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5293" Parameter: CONF_N -> "8002" Comparing "5293" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5294" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761946 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761894 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30792 from a total of 761894 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5294 -76.36202 4.89378 0.63655 INTE EXTERN> -33.05938 -43.30263 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.362" Parameter: A <- "-76.362" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0594" Parameter: B <- "-33.0594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3026" Parameter: C <- "-43.3026" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5294 TOTAL ENERGY = -76.362 RDTITL> * VAN DER WAALS = -33.0594 ELECTROSTATIC = -43.3026 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5294" Parameter: CONF_N -> "8002" Comparing "5294" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5295" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761894 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759164 ATOM PAIRS WERE FOUND FOR ATOM LIST 41680 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29805 from a total of 759164 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5295 -79.62399 3.26197 0.65302 INTE EXTERN> -31.54198 -48.08201 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.624" Parameter: A <- "-79.624" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.542" Parameter: B <- "-31.542" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.082" Parameter: C <- "-48.082" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5295 TOTAL ENERGY = -79.624 RDTITL> * VAN DER WAALS = -31.542 ELECTROSTATIC = -48.082 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5295" Parameter: CONF_N -> "8002" Comparing "5295" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5296" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759164 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757416 ATOM PAIRS WERE FOUND FOR ATOM LIST 41479 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29511 from a total of 757416 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5296 -76.61446 -3.00953 0.74869 INTE EXTERN> -25.92347 -50.69100 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6145" Parameter: A <- "-76.6145" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9235" Parameter: B <- "-25.9235" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.691" Parameter: C <- "-50.691" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5296 TOTAL ENERGY = -76.6145 RDTITL> * VAN DER WAALS = -25.9235 ELECTROSTATIC = -50.691 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5296" Parameter: CONF_N -> "8002" Comparing "5296" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5297" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757416 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756727 ATOM PAIRS WERE FOUND FOR ATOM LIST 41461 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29450 from a total of 756727 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5297 -81.84159 5.22713 0.74827 INTE EXTERN> -28.15631 -53.68528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8416" Parameter: A <- "-81.8416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1563" Parameter: B <- "-28.1563" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6853" Parameter: C <- "-53.6853" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5297 TOTAL ENERGY = -81.8416 RDTITL> * VAN DER WAALS = -28.1563 ELECTROSTATIC = -53.6853 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5297" Parameter: CONF_N -> "8002" Comparing "5297" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5298" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756727 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755772 ATOM PAIRS WERE FOUND FOR ATOM LIST 41644 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29825 from a total of 755772 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5298 -72.20703 -9.63456 0.68915 INTE EXTERN> -30.84729 -41.35974 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.207" Parameter: A <- "-72.207" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8473" Parameter: B <- "-30.8473" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3597" Parameter: C <- "-41.3597" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5298 TOTAL ENERGY = -72.207 RDTITL> * VAN DER WAALS = -30.8473 ELECTROSTATIC = -41.3597 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5298" Parameter: CONF_N -> "8002" Comparing "5298" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5299" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755772 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41651 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29736 from a total of 760118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5299 -80.01455 7.80752 0.65884 INTE EXTERN> -30.66492 -49.34964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0146" Parameter: A <- "-80.0146" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6649" Parameter: B <- "-30.6649" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3496" Parameter: C <- "-49.3496" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5299 TOTAL ENERGY = -80.0146 RDTITL> * VAN DER WAALS = -30.6649 ELECTROSTATIC = -49.3496 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5299" Parameter: CONF_N -> "8002" Comparing "5299" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5300" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760639 ATOM PAIRS WERE FOUND FOR ATOM LIST 41690 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29187 from a total of 760639 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5300 -77.03089 -2.98366 0.58621 INTE EXTERN> -32.16178 -44.86911 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0309" Parameter: A <- "-77.0309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1618" Parameter: B <- "-32.1618" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8691" Parameter: C <- "-44.8691" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5300 TOTAL ENERGY = -77.0309 RDTITL> * VAN DER WAALS = -32.1618 ELECTROSTATIC = -44.8691 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5300" Parameter: CONF_N -> "8002" Comparing "5300" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5301" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760639 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752945 ATOM PAIRS WERE FOUND FOR ATOM LIST 41403 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29354 from a total of 752945 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5301 -70.80515 -6.22574 0.67003 INTE EXTERN> -27.46713 -43.33803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8052" Parameter: A <- "-70.8052" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4671" Parameter: B <- "-27.4671" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.338" Parameter: C <- "-43.338" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5301 TOTAL ENERGY = -70.8052 RDTITL> * VAN DER WAALS = -27.4671 ELECTROSTATIC = -43.338 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5301" Parameter: CONF_N -> "8002" Comparing "5301" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5302" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752945 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752774 ATOM PAIRS WERE FOUND FOR ATOM LIST 41324 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29461 from a total of 752774 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5302 -72.64258 1.83743 0.56148 INTE EXTERN> -32.86892 -39.77366 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6426" Parameter: A <- "-72.6426" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8689" Parameter: B <- "-32.8689" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7737" Parameter: C <- "-39.7737" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5302 TOTAL ENERGY = -72.6426 RDTITL> * VAN DER WAALS = -32.8689 ELECTROSTATIC = -39.7737 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5302" Parameter: CONF_N -> "8002" Comparing "5302" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5303" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752774 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755060 ATOM PAIRS WERE FOUND FOR ATOM LIST 41378 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29899 from a total of 755060 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5303 -72.83546 0.19288 0.69063 INTE EXTERN> -28.97009 -43.86537 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8355" Parameter: A <- "-72.8355" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9701" Parameter: B <- "-28.9701" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8654" Parameter: C <- "-43.8654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5303 TOTAL ENERGY = -72.8355 RDTITL> * VAN DER WAALS = -28.9701 ELECTROSTATIC = -43.8654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5303" Parameter: CONF_N -> "8002" Comparing "5303" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5304" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755060 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752719 ATOM PAIRS WERE FOUND FOR ATOM LIST 41429 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29205 from a total of 752719 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5304 -69.35889 -3.47658 0.60324 INTE EXTERN> -31.36323 -37.99565 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3589" Parameter: A <- "-69.3589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3632" Parameter: B <- "-31.3632" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9957" Parameter: C <- "-37.9957" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5304 TOTAL ENERGY = -69.3589 RDTITL> * VAN DER WAALS = -31.3632 ELECTROSTATIC = -37.9957 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5304" Parameter: CONF_N -> "8002" Comparing "5304" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5305" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752719 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758441 ATOM PAIRS WERE FOUND FOR ATOM LIST 41687 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30231 from a total of 758441 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5305 -69.80375 0.44486 0.63617 INTE EXTERN> -32.58748 -37.21627 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8037" Parameter: A <- "-69.8037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5875" Parameter: B <- "-32.5875" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2163" Parameter: C <- "-37.2163" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5305 TOTAL ENERGY = -69.8037 RDTITL> * VAN DER WAALS = -32.5875 ELECTROSTATIC = -37.2163 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5305" Parameter: CONF_N -> "8002" Comparing "5305" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5306" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758441 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750539 ATOM PAIRS WERE FOUND FOR ATOM LIST 41226 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29441 from a total of 750539 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5306 -70.15627 0.35252 0.62920 INTE EXTERN> -33.77995 -36.37632 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1563" Parameter: A <- "-70.1563" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7799" Parameter: B <- "-33.7799" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3763" Parameter: C <- "-36.3763" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5306 TOTAL ENERGY = -70.1563 RDTITL> * VAN DER WAALS = -33.7799 ELECTROSTATIC = -36.3763 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5306" Parameter: CONF_N -> "8002" Comparing "5306" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5307" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750539 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758398 ATOM PAIRS WERE FOUND FOR ATOM LIST 41624 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29737 from a total of 758398 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5307 -77.21059 7.05432 0.69460 INTE EXTERN> -30.18085 -47.02975 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2106" Parameter: A <- "-77.2106" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1808" Parameter: B <- "-30.1808" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0297" Parameter: C <- "-47.0297" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5307 TOTAL ENERGY = -77.2106 RDTITL> * VAN DER WAALS = -30.1808 ELECTROSTATIC = -47.0297 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5307" Parameter: CONF_N -> "8002" Comparing "5307" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5308" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758398 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754250 ATOM PAIRS WERE FOUND FOR ATOM LIST 41465 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30069 from a total of 754250 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5308 -81.89393 4.68334 0.74554 INTE EXTERN> -30.28646 -51.60747 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8939" Parameter: A <- "-81.8939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2865" Parameter: B <- "-30.2865" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6075" Parameter: C <- "-51.6075" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5308 TOTAL ENERGY = -81.8939 RDTITL> * VAN DER WAALS = -30.2865 ELECTROSTATIC = -51.6075 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5308" Parameter: CONF_N -> "8002" Comparing "5308" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5309" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754250 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754448 ATOM PAIRS WERE FOUND FOR ATOM LIST 41422 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30251 from a total of 754448 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5309 -74.83272 -7.06121 0.66939 INTE EXTERN> -30.73537 -44.09736 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8327" Parameter: A <- "-74.8327" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7354" Parameter: B <- "-30.7354" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0974" Parameter: C <- "-44.0974" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5309 TOTAL ENERGY = -74.8327 RDTITL> * VAN DER WAALS = -30.7354 ELECTROSTATIC = -44.0974 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5309" Parameter: CONF_N -> "8002" Comparing "5309" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5310" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754448 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41515 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30304 from a total of 757794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5310 -75.95096 1.11823 0.68668 INTE EXTERN> -31.01042 -44.94054 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.951" Parameter: A <- "-75.951" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0104" Parameter: B <- "-31.0104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9405" Parameter: C <- "-44.9405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5310 TOTAL ENERGY = -75.951 RDTITL> * VAN DER WAALS = -31.0104 ELECTROSTATIC = -44.9405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5310" Parameter: CONF_N -> "8002" Comparing "5310" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5311" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758179 ATOM PAIRS WERE FOUND FOR ATOM LIST 41580 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29600 from a total of 758179 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5311 -80.27078 4.31982 0.72264 INTE EXTERN> -29.80314 -50.46764 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2708" Parameter: A <- "-80.2708" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8031" Parameter: B <- "-29.8031" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4676" Parameter: C <- "-50.4676" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5311 TOTAL ENERGY = -80.2708 RDTITL> * VAN DER WAALS = -29.8031 ELECTROSTATIC = -50.4676 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5311" Parameter: CONF_N -> "8002" Comparing "5311" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5312" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758179 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756717 ATOM PAIRS WERE FOUND FOR ATOM LIST 41523 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29607 from a total of 756717 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5312 -80.11100 -0.15978 0.72971 INTE EXTERN> -28.49052 -51.62048 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.111" Parameter: A <- "-80.111" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4905" Parameter: B <- "-28.4905" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6205" Parameter: C <- "-51.6205" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5312 TOTAL ENERGY = -80.111 RDTITL> * VAN DER WAALS = -28.4905 ELECTROSTATIC = -51.6205 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5312" Parameter: CONF_N -> "8002" Comparing "5312" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5313" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756717 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757385 ATOM PAIRS WERE FOUND FOR ATOM LIST 41601 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30338 from a total of 757385 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5313 -70.39590 -9.71510 0.72008 INTE EXTERN> -27.47810 -42.91780 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3959" Parameter: A <- "-70.3959" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4781" Parameter: B <- "-27.4781" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9178" Parameter: C <- "-42.9178" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5313 TOTAL ENERGY = -70.3959 RDTITL> * VAN DER WAALS = -27.4781 ELECTROSTATIC = -42.9178 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5313" Parameter: CONF_N -> "8002" Comparing "5313" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5314" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757385 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758384 ATOM PAIRS WERE FOUND FOR ATOM LIST 41761 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30369 from a total of 758384 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5314 -84.11148 13.71558 0.70001 INTE EXTERN> -31.58678 -52.52470 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.1115" Parameter: A <- "-84.1115" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5868" Parameter: B <- "-31.5868" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5247" Parameter: C <- "-52.5247" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5314 TOTAL ENERGY = -84.1115 RDTITL> * VAN DER WAALS = -31.5868 ELECTROSTATIC = -52.5247 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5314" Parameter: CONF_N -> "8002" Comparing "5314" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5315" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758384 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758616 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29759 from a total of 758616 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5315 -79.05470 -5.05678 0.67041 INTE EXTERN> -30.32942 -48.72528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0547" Parameter: A <- "-79.0547" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3294" Parameter: B <- "-30.3294" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7253" Parameter: C <- "-48.7253" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5315 TOTAL ENERGY = -79.0547 RDTITL> * VAN DER WAALS = -30.3294 ELECTROSTATIC = -48.7253 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5315" Parameter: CONF_N -> "8002" Comparing "5315" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5316" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758616 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763365 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29867 from a total of 763365 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5316 -81.76035 2.70564 0.68734 INTE EXTERN> -32.55097 -49.20938 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.7603" Parameter: A <- "-81.7603" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.551" Parameter: B <- "-32.551" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2094" Parameter: C <- "-49.2094" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5316 TOTAL ENERGY = -81.7603 RDTITL> * VAN DER WAALS = -32.551 ELECTROSTATIC = -49.2094 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5316" Parameter: CONF_N -> "8002" Comparing "5316" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5317" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763365 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758166 ATOM PAIRS WERE FOUND FOR ATOM LIST 41662 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30135 from a total of 758166 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5317 -74.35858 -7.40176 0.72926 INTE EXTERN> -30.29981 -44.05877 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3586" Parameter: A <- "-74.3586" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2998" Parameter: B <- "-30.2998" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0588" Parameter: C <- "-44.0588" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5317 TOTAL ENERGY = -74.3586 RDTITL> * VAN DER WAALS = -30.2998 ELECTROSTATIC = -44.0588 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5317" Parameter: CONF_N -> "8002" Comparing "5317" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5318" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758166 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755541 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29463 from a total of 755541 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5318 -71.45477 -2.90381 0.50711 INTE EXTERN> -32.92840 -38.52637 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4548" Parameter: A <- "-71.4548" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9284" Parameter: B <- "-32.9284" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5264" Parameter: C <- "-38.5264" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5318 TOTAL ENERGY = -71.4548 RDTITL> * VAN DER WAALS = -32.9284 ELECTROSTATIC = -38.5264 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5318" Parameter: CONF_N -> "8002" Comparing "5318" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5319" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755541 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758228 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29622 from a total of 758228 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5319 -78.18722 6.73245 0.67225 INTE EXTERN> -29.91986 -48.26736 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1872" Parameter: A <- "-78.1872" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9199" Parameter: B <- "-29.9199" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2674" Parameter: C <- "-48.2674" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5319 TOTAL ENERGY = -78.1872 RDTITL> * VAN DER WAALS = -29.9199 ELECTROSTATIC = -48.2674 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5319" Parameter: CONF_N -> "8002" Comparing "5319" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5320" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758228 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757345 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29370 from a total of 757345 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5320 -71.59863 -6.58859 0.60939 INTE EXTERN> -30.82870 -40.76992 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5986" Parameter: A <- "-71.5986" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8287" Parameter: B <- "-30.8287" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7699" Parameter: C <- "-40.7699" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5320 TOTAL ENERGY = -71.5986 RDTITL> * VAN DER WAALS = -30.8287 ELECTROSTATIC = -40.7699 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5320" Parameter: CONF_N -> "8002" Comparing "5320" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5321" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757345 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760917 ATOM PAIRS WERE FOUND FOR ATOM LIST 41449 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29729 from a total of 760917 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5321 -72.58284 0.98421 0.60683 INTE EXTERN> -30.19414 -42.38870 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5828" Parameter: A <- "-72.5828" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1941" Parameter: B <- "-30.1941" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3887" Parameter: C <- "-42.3887" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5321 TOTAL ENERGY = -72.5828 RDTITL> * VAN DER WAALS = -30.1941 ELECTROSTATIC = -42.3887 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5321" Parameter: CONF_N -> "8002" Comparing "5321" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5322" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760917 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760078 ATOM PAIRS WERE FOUND FOR ATOM LIST 41614 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29475 from a total of 760078 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5322 -76.48964 3.90680 0.61244 INTE EXTERN> -32.19039 -44.29925 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4896" Parameter: A <- "-76.4896" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1904" Parameter: B <- "-32.1904" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2992" Parameter: C <- "-44.2992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5322 TOTAL ENERGY = -76.4896 RDTITL> * VAN DER WAALS = -32.1904 ELECTROSTATIC = -44.2992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5322" Parameter: CONF_N -> "8002" Comparing "5322" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5323" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760078 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756378 ATOM PAIRS WERE FOUND FOR ATOM LIST 41485 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29739 from a total of 756378 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5323 -67.44000 -9.04964 0.63554 INTE EXTERN> -29.74693 -37.69308 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.44" Parameter: A <- "-67.44" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7469" Parameter: B <- "-29.7469" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6931" Parameter: C <- "-37.6931" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5323 TOTAL ENERGY = -67.44 RDTITL> * VAN DER WAALS = -29.7469 ELECTROSTATIC = -37.6931 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5323" Parameter: CONF_N -> "8002" Comparing "5323" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5324" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756378 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759193 ATOM PAIRS WERE FOUND FOR ATOM LIST 41744 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29812 from a total of 759193 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5324 -68.62072 1.18072 0.61626 INTE EXTERN> -29.59016 -39.03056 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6207" Parameter: A <- "-68.6207" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5902" Parameter: B <- "-29.5902" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0306" Parameter: C <- "-39.0306" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5324 TOTAL ENERGY = -68.6207 RDTITL> * VAN DER WAALS = -29.5902 ELECTROSTATIC = -39.0306 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5324" Parameter: CONF_N -> "8002" Comparing "5324" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5325" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759193 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761443 ATOM PAIRS WERE FOUND FOR ATOM LIST 41925 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29804 from a total of 761443 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5325 -75.09436 6.47364 0.77958 INTE EXTERN> -25.14383 -49.95053 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0944" Parameter: A <- "-75.0944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1438" Parameter: B <- "-25.1438" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9505" Parameter: C <- "-49.9505" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5325 TOTAL ENERGY = -75.0944 RDTITL> * VAN DER WAALS = -25.1438 ELECTROSTATIC = -49.9505 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5325" Parameter: CONF_N -> "8002" Comparing "5325" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5326" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761443 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757357 ATOM PAIRS WERE FOUND FOR ATOM LIST 41342 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29825 from a total of 757357 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5326 -72.91665 -2.17771 0.62602 INTE EXTERN> -28.57833 -44.33832 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9166" Parameter: A <- "-72.9166" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5783" Parameter: B <- "-28.5783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3383" Parameter: C <- "-44.3383" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5326 TOTAL ENERGY = -72.9166 RDTITL> * VAN DER WAALS = -28.5783 ELECTROSTATIC = -44.3383 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5326" Parameter: CONF_N -> "8002" Comparing "5326" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5327" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757357 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763622 ATOM PAIRS WERE FOUND FOR ATOM LIST 41664 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30657 from a total of 763622 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5327 -73.53155 0.61490 0.62606 INTE EXTERN> -30.30995 -43.22160 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5316" Parameter: A <- "-73.5316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3099" Parameter: B <- "-30.3099" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2216" Parameter: C <- "-43.2216" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5327 TOTAL ENERGY = -73.5316 RDTITL> * VAN DER WAALS = -30.3099 ELECTROSTATIC = -43.2216 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5327" Parameter: CONF_N -> "8002" Comparing "5327" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5328" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763622 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759409 ATOM PAIRS WERE FOUND FOR ATOM LIST 41484 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29895 from a total of 759409 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5328 -63.93600 -9.59556 0.60852 INTE EXTERN> -29.68143 -34.25456 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.936" Parameter: A <- "-63.936" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6814" Parameter: B <- "-29.6814" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2546" Parameter: C <- "-34.2546" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5328 TOTAL ENERGY = -63.936 RDTITL> * VAN DER WAALS = -29.6814 ELECTROSTATIC = -34.2546 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5328" Parameter: CONF_N -> "8002" Comparing "5328" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5329" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759409 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756173 ATOM PAIRS WERE FOUND FOR ATOM LIST 41472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29330 from a total of 756173 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5329 -71.62891 7.69291 0.72198 INTE EXTERN> -27.38028 -44.24863 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6289" Parameter: A <- "-71.6289" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3803" Parameter: B <- "-27.3803" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2486" Parameter: C <- "-44.2486" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5329 TOTAL ENERGY = -71.6289 RDTITL> * VAN DER WAALS = -27.3803 ELECTROSTATIC = -44.2486 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5329" Parameter: CONF_N -> "8002" Comparing "5329" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5330" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756173 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757963 ATOM PAIRS WERE FOUND FOR ATOM LIST 41447 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29772 from a total of 757963 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5330 -70.74654 -0.88237 0.59131 INTE EXTERN> -31.85208 -38.89447 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7465" Parameter: A <- "-70.7465" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8521" Parameter: B <- "-31.8521" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8945" Parameter: C <- "-38.8945" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5330 TOTAL ENERGY = -70.7465 RDTITL> * VAN DER WAALS = -31.8521 ELECTROSTATIC = -38.8945 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5330" Parameter: CONF_N -> "8002" Comparing "5330" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5331" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757963 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759159 ATOM PAIRS WERE FOUND FOR ATOM LIST 41519 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30061 from a total of 759159 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5331 -72.09437 1.34782 0.61374 INTE EXTERN> -32.26746 -39.82690 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0944" Parameter: A <- "-72.0944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2675" Parameter: B <- "-32.2675" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8269" Parameter: C <- "-39.8269" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5331 TOTAL ENERGY = -72.0944 RDTITL> * VAN DER WAALS = -32.2675 ELECTROSTATIC = -39.8269 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5331" Parameter: CONF_N -> "8002" Comparing "5331" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5332" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759159 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758243 ATOM PAIRS WERE FOUND FOR ATOM LIST 41655 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30238 from a total of 758243 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5332 -71.18799 -0.90637 0.64886 INTE EXTERN> -28.43013 -42.75786 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.188" Parameter: A <- "-71.188" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4301" Parameter: B <- "-28.4301" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7579" Parameter: C <- "-42.7579" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5332 TOTAL ENERGY = -71.188 RDTITL> * VAN DER WAALS = -28.4301 ELECTROSTATIC = -42.7579 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5332" Parameter: CONF_N -> "8002" Comparing "5332" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5333" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758243 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762910 ATOM PAIRS WERE FOUND FOR ATOM LIST 42062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29947 from a total of 762910 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5333 -71.95162 0.76362 0.68108 INTE EXTERN> -29.53029 -42.42133 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9516" Parameter: A <- "-71.9516" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5303" Parameter: B <- "-29.5303" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4213" Parameter: C <- "-42.4213" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5333 TOTAL ENERGY = -71.9516 RDTITL> * VAN DER WAALS = -29.5303 ELECTROSTATIC = -42.4213 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5333" Parameter: CONF_N -> "8002" Comparing "5333" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5334" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762910 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758929 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29738 from a total of 758929 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5334 -75.12798 3.17636 0.75180 INTE EXTERN> -25.97364 -49.15433 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.128" Parameter: A <- "-75.128" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9736" Parameter: B <- "-25.9736" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1543" Parameter: C <- "-49.1543" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5334 TOTAL ENERGY = -75.128 RDTITL> * VAN DER WAALS = -25.9736 ELECTROSTATIC = -49.1543 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5334" Parameter: CONF_N -> "8002" Comparing "5334" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5335" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758929 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758552 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30303 from a total of 758552 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5335 -69.08877 -6.03921 0.60393 INTE EXTERN> -32.00676 -37.08201 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0888" Parameter: A <- "-69.0888" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0068" Parameter: B <- "-32.0068" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.082" Parameter: C <- "-37.082" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5335 TOTAL ENERGY = -69.0888 RDTITL> * VAN DER WAALS = -32.0068 ELECTROSTATIC = -37.082 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5335" Parameter: CONF_N -> "8002" Comparing "5335" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5336" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758552 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757540 ATOM PAIRS WERE FOUND FOR ATOM LIST 41548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29932 from a total of 757540 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5336 -71.33565 2.24688 0.76094 INTE EXTERN> -25.46146 -45.87419 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3357" Parameter: A <- "-71.3357" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4615" Parameter: B <- "-25.4615" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8742" Parameter: C <- "-45.8742" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5336 TOTAL ENERGY = -71.3357 RDTITL> * VAN DER WAALS = -25.4615 ELECTROSTATIC = -45.8742 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5336" Parameter: CONF_N -> "8002" Comparing "5336" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5337" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757540 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758500 ATOM PAIRS WERE FOUND FOR ATOM LIST 41647 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29408 from a total of 758500 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5337 -70.46626 -0.86940 0.66078 INTE EXTERN> -29.40422 -41.06203 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4663" Parameter: A <- "-70.4663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4042" Parameter: B <- "-29.4042" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.062" Parameter: C <- "-41.062" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5337 TOTAL ENERGY = -70.4663 RDTITL> * VAN DER WAALS = -29.4042 ELECTROSTATIC = -41.062 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5337" Parameter: CONF_N -> "8002" Comparing "5337" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5338" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758500 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758776 ATOM PAIRS WERE FOUND FOR ATOM LIST 41764 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30087 from a total of 758776 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5338 -67.28211 -3.18414 0.69003 INTE EXTERN> -26.93849 -40.34362 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2821" Parameter: A <- "-67.2821" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9385" Parameter: B <- "-26.9385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3436" Parameter: C <- "-40.3436" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5338 TOTAL ENERGY = -67.2821 RDTITL> * VAN DER WAALS = -26.9385 ELECTROSTATIC = -40.3436 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5338" Parameter: CONF_N -> "8002" Comparing "5338" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5339" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758776 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764886 ATOM PAIRS WERE FOUND FOR ATOM LIST 41971 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30352 from a total of 764886 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5339 -76.81523 9.53312 0.63723 INTE EXTERN> -30.85369 -45.96153 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8152" Parameter: A <- "-76.8152" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8537" Parameter: B <- "-30.8537" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9615" Parameter: C <- "-45.9615" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5339 TOTAL ENERGY = -76.8152 RDTITL> * VAN DER WAALS = -30.8537 ELECTROSTATIC = -45.9615 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5339" Parameter: CONF_N -> "8002" Comparing "5339" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5340" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764886 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762299 ATOM PAIRS WERE FOUND FOR ATOM LIST 41830 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29803 from a total of 762299 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5340 -75.75983 -1.05540 0.61945 INTE EXTERN> -32.75439 -43.00544 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7598" Parameter: A <- "-75.7598" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7544" Parameter: B <- "-32.7544" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0054" Parameter: C <- "-43.0054" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5340 TOTAL ENERGY = -75.7598 RDTITL> * VAN DER WAALS = -32.7544 ELECTROSTATIC = -43.0054 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5340" Parameter: CONF_N -> "8002" Comparing "5340" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5341" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762299 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760828 ATOM PAIRS WERE FOUND FOR ATOM LIST 41773 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30233 from a total of 760828 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5341 -75.26051 -0.49933 0.64437 INTE EXTERN> -30.41748 -44.84302 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2605" Parameter: A <- "-75.2605" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4175" Parameter: B <- "-30.4175" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.843" Parameter: C <- "-44.843" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5341 TOTAL ENERGY = -75.2605 RDTITL> * VAN DER WAALS = -30.4175 ELECTROSTATIC = -44.843 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5341" Parameter: CONF_N -> "8002" Comparing "5341" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5342" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760828 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764954 ATOM PAIRS WERE FOUND FOR ATOM LIST 41960 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30413 from a total of 764954 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5342 -74.44935 -0.81115 0.63816 INTE EXTERN> -31.44049 -43.00886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4494" Parameter: A <- "-74.4494" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4405" Parameter: B <- "-31.4405" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0089" Parameter: C <- "-43.0089" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5342 TOTAL ENERGY = -74.4494 RDTITL> * VAN DER WAALS = -31.4405 ELECTROSTATIC = -43.0089 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5342" Parameter: CONF_N -> "8002" Comparing "5342" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5343" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764954 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757397 ATOM PAIRS WERE FOUND FOR ATOM LIST 41392 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30473 from a total of 757397 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5343 -76.80774 2.35839 0.61265 INTE EXTERN> -35.44253 -41.36521 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8077" Parameter: A <- "-76.8077" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.4425" Parameter: B <- "-35.4425" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3652" Parameter: C <- "-41.3652" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5343 TOTAL ENERGY = -76.8077 RDTITL> * VAN DER WAALS = -35.4425 ELECTROSTATIC = -41.3652 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5343" Parameter: CONF_N -> "8002" Comparing "5343" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5344" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757397 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755307 ATOM PAIRS WERE FOUND FOR ATOM LIST 41205 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30225 from a total of 755307 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5344 -71.89562 -4.91212 0.63873 INTE EXTERN> -29.76879 -42.12683 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8956" Parameter: A <- "-71.8956" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7688" Parameter: B <- "-29.7688" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1268" Parameter: C <- "-42.1268" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5344 TOTAL ENERGY = -71.8956 RDTITL> * VAN DER WAALS = -29.7688 ELECTROSTATIC = -42.1268 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5344" Parameter: CONF_N -> "8002" Comparing "5344" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5345" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755307 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760447 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30435 from a total of 760447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5345 -74.87624 2.98061 0.66538 INTE EXTERN> -30.81080 -44.06544 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8762" Parameter: A <- "-74.8762" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8108" Parameter: B <- "-30.8108" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0654" Parameter: C <- "-44.0654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5345 TOTAL ENERGY = -74.8762 RDTITL> * VAN DER WAALS = -30.8108 ELECTROSTATIC = -44.0654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5345" Parameter: CONF_N -> "8002" Comparing "5345" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5346" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754715 ATOM PAIRS WERE FOUND FOR ATOM LIST 41192 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30115 from a total of 754715 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5346 -71.99675 -2.87949 0.61427 INTE EXTERN> -33.76865 -38.22810 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9968" Parameter: A <- "-71.9968" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7687" Parameter: B <- "-33.7687" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2281" Parameter: C <- "-38.2281" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5346 TOTAL ENERGY = -71.9968 RDTITL> * VAN DER WAALS = -33.7687 ELECTROSTATIC = -38.2281 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5346" Parameter: CONF_N -> "8002" Comparing "5346" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5347" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754715 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754889 ATOM PAIRS WERE FOUND FOR ATOM LIST 41505 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30228 from a total of 754889 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5347 -73.31988 1.32313 0.74055 INTE EXTERN> -29.07877 -44.24111 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3199" Parameter: A <- "-73.3199" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0788" Parameter: B <- "-29.0788" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2411" Parameter: C <- "-44.2411" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5347 TOTAL ENERGY = -73.3199 RDTITL> * VAN DER WAALS = -29.0788 ELECTROSTATIC = -44.2411 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5347" Parameter: CONF_N -> "8002" Comparing "5347" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5348" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754889 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755064 ATOM PAIRS WERE FOUND FOR ATOM LIST 41385 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29919 from a total of 755064 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5348 -75.56675 2.24688 0.71819 INTE EXTERN> -30.41976 -45.14699 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5668" Parameter: A <- "-75.5668" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4198" Parameter: B <- "-30.4198" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.147" Parameter: C <- "-45.147" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5348 TOTAL ENERGY = -75.5668 RDTITL> * VAN DER WAALS = -30.4198 ELECTROSTATIC = -45.147 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5348" Parameter: CONF_N -> "8002" Comparing "5348" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5349" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755064 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760363 ATOM PAIRS WERE FOUND FOR ATOM LIST 41760 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30346 from a total of 760363 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5349 -76.14131 0.57456 0.70637 INTE EXTERN> -31.33559 -44.80572 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1413" Parameter: A <- "-76.1413" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3356" Parameter: B <- "-31.3356" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8057" Parameter: C <- "-44.8057" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5349 TOTAL ENERGY = -76.1413 RDTITL> * VAN DER WAALS = -31.3356 ELECTROSTATIC = -44.8057 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5349" Parameter: CONF_N -> "8002" Comparing "5349" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5350" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760363 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762664 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 31169 from a total of 762664 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5350 -76.76266 0.62135 0.67829 INTE EXTERN> -29.03835 -47.72431 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7627" Parameter: A <- "-76.7627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0384" Parameter: B <- "-29.0384" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7243" Parameter: C <- "-47.7243" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5350 TOTAL ENERGY = -76.7627 RDTITL> * VAN DER WAALS = -29.0384 ELECTROSTATIC = -47.7243 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5350" Parameter: CONF_N -> "8002" Comparing "5350" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5351" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762664 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762453 ATOM PAIRS WERE FOUND FOR ATOM LIST 41537 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30751 from a total of 762453 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5351 -76.23034 -0.53232 0.67605 INTE EXTERN> -33.34718 -42.88316 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2303" Parameter: A <- "-76.2303" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3472" Parameter: B <- "-33.3472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8832" Parameter: C <- "-42.8832" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5351 TOTAL ENERGY = -76.2303 RDTITL> * VAN DER WAALS = -33.3472 ELECTROSTATIC = -42.8832 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5351" Parameter: CONF_N -> "8002" Comparing "5351" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5352" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762453 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756992 ATOM PAIRS WERE FOUND FOR ATOM LIST 41552 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30759 from a total of 756992 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5352 -73.79927 -2.43108 0.68772 INTE EXTERN> -28.94328 -44.85599 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7993" Parameter: A <- "-73.7993" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9433" Parameter: B <- "-28.9433" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.856" Parameter: C <- "-44.856" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5352 TOTAL ENERGY = -73.7993 RDTITL> * VAN DER WAALS = -28.9433 ELECTROSTATIC = -44.856 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5352" Parameter: CONF_N -> "8002" Comparing "5352" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5353" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756992 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757866 ATOM PAIRS WERE FOUND FOR ATOM LIST 41570 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30413 from a total of 757866 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5353 -68.89729 -4.90198 0.61770 INTE EXTERN> -34.28227 -34.61502 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8973" Parameter: A <- "-68.8973" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.2823" Parameter: B <- "-34.2823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.615" Parameter: C <- "-34.615" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5353 TOTAL ENERGY = -68.8973 RDTITL> * VAN DER WAALS = -34.2823 ELECTROSTATIC = -34.615 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5353" Parameter: CONF_N -> "8002" Comparing "5353" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5354" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757866 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760609 ATOM PAIRS WERE FOUND FOR ATOM LIST 41722 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30880 from a total of 760609 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5354 -73.74041 4.84312 0.67260 INTE EXTERN> -28.50319 -45.23721 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7404" Parameter: A <- "-73.7404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5032" Parameter: B <- "-28.5032" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2372" Parameter: C <- "-45.2372" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5354 TOTAL ENERGY = -73.7404 RDTITL> * VAN DER WAALS = -28.5032 ELECTROSTATIC = -45.2372 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5354" Parameter: CONF_N -> "8002" Comparing "5354" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5355" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760609 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760122 ATOM PAIRS WERE FOUND FOR ATOM LIST 41583 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30644 from a total of 760122 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5355 -64.58506 -9.15535 0.68729 INTE EXTERN> -32.74707 -31.83799 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5851" Parameter: A <- "-64.5851" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7471" Parameter: B <- "-32.7471" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.838" Parameter: C <- "-31.838" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5355 TOTAL ENERGY = -64.5851 RDTITL> * VAN DER WAALS = -32.7471 ELECTROSTATIC = -31.838 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5355" Parameter: CONF_N -> "8002" Comparing "5355" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5356" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760122 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762420 ATOM PAIRS WERE FOUND FOR ATOM LIST 41746 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30889 from a total of 762420 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5356 -73.05062 8.46556 0.77140 INTE EXTERN> -31.47885 -41.57176 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0506" Parameter: A <- "-73.0506" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4789" Parameter: B <- "-31.4789" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5718" Parameter: C <- "-41.5718" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5356 TOTAL ENERGY = -73.0506 RDTITL> * VAN DER WAALS = -31.4789 ELECTROSTATIC = -41.5718 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5356" Parameter: CONF_N -> "8002" Comparing "5356" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5357" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762420 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757568 ATOM PAIRS WERE FOUND FOR ATOM LIST 41568 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30516 from a total of 757568 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5357 -71.78946 -1.26116 0.58005 INTE EXTERN> -34.45241 -37.33705 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7895" Parameter: A <- "-71.7895" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.4524" Parameter: B <- "-34.4524" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.337" Parameter: C <- "-37.337" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5357 TOTAL ENERGY = -71.7895 RDTITL> * VAN DER WAALS = -34.4524 ELECTROSTATIC = -37.337 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5357" Parameter: CONF_N -> "8002" Comparing "5357" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5358" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757568 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755575 ATOM PAIRS WERE FOUND FOR ATOM LIST 41474 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29821 from a total of 755575 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5358 -70.06305 -1.72641 0.65915 INTE EXTERN> -30.99188 -39.07117 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0631" Parameter: A <- "-70.0631" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9919" Parameter: B <- "-30.9919" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0712" Parameter: C <- "-39.0712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5358 TOTAL ENERGY = -70.0631 RDTITL> * VAN DER WAALS = -30.9919 ELECTROSTATIC = -39.0712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5358" Parameter: CONF_N -> "8002" Comparing "5358" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5359" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755575 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755317 ATOM PAIRS WERE FOUND FOR ATOM LIST 41381 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29476 from a total of 755317 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5359 -64.52285 -5.54020 0.57280 INTE EXTERN> -33.97159 -30.55126 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5229" Parameter: A <- "-64.5229" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9716" Parameter: B <- "-33.9716" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.5513" Parameter: C <- "-30.5513" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5359 TOTAL ENERGY = -64.5229 RDTITL> * VAN DER WAALS = -33.9716 ELECTROSTATIC = -30.5513 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5359" Parameter: CONF_N -> "8002" Comparing "5359" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5360" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755317 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756563 ATOM PAIRS WERE FOUND FOR ATOM LIST 41330 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29942 from a total of 756563 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5360 -72.45370 7.93085 0.68634 INTE EXTERN> -30.20363 -42.25008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4537" Parameter: A <- "-72.4537" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2036" Parameter: B <- "-30.2036" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2501" Parameter: C <- "-42.2501" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5360 TOTAL ENERGY = -72.4537 RDTITL> * VAN DER WAALS = -30.2036 ELECTROSTATIC = -42.2501 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5360" Parameter: CONF_N -> "8002" Comparing "5360" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5361" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756563 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41308 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29129 from a total of 756958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5361 -66.41059 -6.04311 0.69784 INTE EXTERN> -25.27828 -41.13231 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4106" Parameter: A <- "-66.4106" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2783" Parameter: B <- "-25.2783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1323" Parameter: C <- "-41.1323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5361 TOTAL ENERGY = -66.4106 RDTITL> * VAN DER WAALS = -25.2783 ELECTROSTATIC = -41.1323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5361" Parameter: CONF_N -> "8002" Comparing "5361" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5362" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757613 ATOM PAIRS WERE FOUND FOR ATOM LIST 41689 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29787 from a total of 757613 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5362 -67.40404 0.99345 0.70853 INTE EXTERN> -28.05396 -39.35008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.404" Parameter: A <- "-67.404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.054" Parameter: B <- "-28.054" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3501" Parameter: C <- "-39.3501" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5362 TOTAL ENERGY = -67.404 RDTITL> * VAN DER WAALS = -28.054 ELECTROSTATIC = -39.3501 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5362" Parameter: CONF_N -> "8002" Comparing "5362" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5363" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757613 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759914 ATOM PAIRS WERE FOUND FOR ATOM LIST 41671 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29877 from a total of 759914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5363 -70.47435 3.07031 0.66815 INTE EXTERN> -29.62541 -40.84895 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4744" Parameter: A <- "-70.4744" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6254" Parameter: B <- "-29.6254" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8489" Parameter: C <- "-40.8489" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5363 TOTAL ENERGY = -70.4744 RDTITL> * VAN DER WAALS = -29.6254 ELECTROSTATIC = -40.8489 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5363" Parameter: CONF_N -> "8002" Comparing "5363" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5364" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760685 ATOM PAIRS WERE FOUND FOR ATOM LIST 41639 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29500 from a total of 760685 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5364 -69.31200 -1.16236 0.67603 INTE EXTERN> -27.31121 -42.00078 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.312" Parameter: A <- "-69.312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3112" Parameter: B <- "-27.3112" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0008" Parameter: C <- "-42.0008" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5364 TOTAL ENERGY = -69.312 RDTITL> * VAN DER WAALS = -27.3112 ELECTROSTATIC = -42.0008 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5364" Parameter: CONF_N -> "8002" Comparing "5364" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5365" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760685 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761227 ATOM PAIRS WERE FOUND FOR ATOM LIST 41770 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29613 from a total of 761227 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5365 -78.09495 8.78296 0.64697 INTE EXTERN> -32.25508 -45.83987 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.095" Parameter: A <- "-78.095" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2551" Parameter: B <- "-32.2551" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8399" Parameter: C <- "-45.8399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5365 TOTAL ENERGY = -78.095 RDTITL> * VAN DER WAALS = -32.2551 ELECTROSTATIC = -45.8399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5365" Parameter: CONF_N -> "8002" Comparing "5365" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5366" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761227 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756713 ATOM PAIRS WERE FOUND FOR ATOM LIST 41683 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29707 from a total of 756713 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5366 -73.06490 -5.03005 0.72555 INTE EXTERN> -26.56664 -46.49826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0649" Parameter: A <- "-73.0649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5666" Parameter: B <- "-26.5666" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4983" Parameter: C <- "-46.4983" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5366 TOTAL ENERGY = -73.0649 RDTITL> * VAN DER WAALS = -26.5666 ELECTROSTATIC = -46.4983 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5366" Parameter: CONF_N -> "8002" Comparing "5366" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5367" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756713 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760677 ATOM PAIRS WERE FOUND FOR ATOM LIST 41770 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29817 from a total of 760677 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5367 -70.42945 -2.63544 0.60242 INTE EXTERN> -32.82110 -37.60835 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4295" Parameter: A <- "-70.4295" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8211" Parameter: B <- "-32.8211" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6083" Parameter: C <- "-37.6083" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5367 TOTAL ENERGY = -70.4295 RDTITL> * VAN DER WAALS = -32.8211 ELECTROSTATIC = -37.6083 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5367" Parameter: CONF_N -> "8002" Comparing "5367" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5368" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760677 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763536 ATOM PAIRS WERE FOUND FOR ATOM LIST 41624 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29468 from a total of 763536 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5368 -70.60772 0.17827 0.58554 INTE EXTERN> -33.08869 -37.51903 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6077" Parameter: A <- "-70.6077" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0887" Parameter: B <- "-33.0887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.519" Parameter: C <- "-37.519" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5368 TOTAL ENERGY = -70.6077 RDTITL> * VAN DER WAALS = -33.0887 ELECTROSTATIC = -37.519 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5368" Parameter: CONF_N -> "8002" Comparing "5368" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5369" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763536 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762465 ATOM PAIRS WERE FOUND FOR ATOM LIST 41739 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28998 from a total of 762465 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5369 -66.97153 -3.63619 0.49711 INTE EXTERN> -31.60718 -35.36435 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9715" Parameter: A <- "-66.9715" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6072" Parameter: B <- "-31.6072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3643" Parameter: C <- "-35.3643" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5369 TOTAL ENERGY = -66.9715 RDTITL> * VAN DER WAALS = -31.6072 ELECTROSTATIC = -35.3643 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5369" Parameter: CONF_N -> "8002" Comparing "5369" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5370" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762465 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758892 ATOM PAIRS WERE FOUND FOR ATOM LIST 41625 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29247 from a total of 758892 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5370 -68.09181 1.12028 0.49310 INTE EXTERN> -34.62407 -33.46774 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0918" Parameter: A <- "-68.0918" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6241" Parameter: B <- "-34.6241" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.4677" Parameter: C <- "-33.4677" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5370 TOTAL ENERGY = -68.0918 RDTITL> * VAN DER WAALS = -34.6241 ELECTROSTATIC = -33.4677 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5370" Parameter: CONF_N -> "8002" Comparing "5370" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5371" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758892 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769557 ATOM PAIRS WERE FOUND FOR ATOM LIST 42037 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30656 from a total of 769557 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5371 -83.70836 15.61655 0.67505 INTE EXTERN> -31.69024 -52.01812 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.7084" Parameter: A <- "-83.7084" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6902" Parameter: B <- "-31.6902" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0181" Parameter: C <- "-52.0181" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5371 TOTAL ENERGY = -83.7084 RDTITL> * VAN DER WAALS = -31.6902 ELECTROSTATIC = -52.0181 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5371" Parameter: CONF_N -> "8002" Comparing "5371" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5372" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769557 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767554 ATOM PAIRS WERE FOUND FOR ATOM LIST 42056 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30620 from a total of 767554 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5372 -74.76414 -8.94422 0.68614 INTE EXTERN> -27.71607 -47.04807 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7641" Parameter: A <- "-74.7641" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7161" Parameter: B <- "-27.7161" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0481" Parameter: C <- "-47.0481" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5372 TOTAL ENERGY = -74.7641 RDTITL> * VAN DER WAALS = -27.7161 ELECTROSTATIC = -47.0481 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5372" Parameter: CONF_N -> "8002" Comparing "5372" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5373" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767554 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763685 ATOM PAIRS WERE FOUND FOR ATOM LIST 41806 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29738 from a total of 763685 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5373 -67.27718 -7.48696 0.68179 INTE EXTERN> -26.84113 -40.43605 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2772" Parameter: A <- "-67.2772" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8411" Parameter: B <- "-26.8411" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4361" Parameter: C <- "-40.4361" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5373 TOTAL ENERGY = -67.2772 RDTITL> * VAN DER WAALS = -26.8411 ELECTROSTATIC = -40.4361 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5373" Parameter: CONF_N -> "8002" Comparing "5373" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5374" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763685 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759370 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29543 from a total of 759370 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5374 -77.95272 10.67554 0.65612 INTE EXTERN> -31.10824 -46.84447 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9527" Parameter: A <- "-77.9527" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1082" Parameter: B <- "-31.1082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8445" Parameter: C <- "-46.8445" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5374 TOTAL ENERGY = -77.9527 RDTITL> * VAN DER WAALS = -31.1082 ELECTROSTATIC = -46.8445 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5374" Parameter: CONF_N -> "8002" Comparing "5374" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5375" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759370 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756149 ATOM PAIRS WERE FOUND FOR ATOM LIST 41316 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29292 from a total of 756149 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5375 -72.64661 -5.30611 0.72167 INTE EXTERN> -27.95631 -44.69029 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6466" Parameter: A <- "-72.6466" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9563" Parameter: B <- "-27.9563" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6903" Parameter: C <- "-44.6903" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5375 TOTAL ENERGY = -72.6466 RDTITL> * VAN DER WAALS = -27.9563 ELECTROSTATIC = -44.6903 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5375" Parameter: CONF_N -> "8002" Comparing "5375" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5376" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756149 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762220 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29004 from a total of 762220 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5376 -74.63532 1.98871 0.69278 INTE EXTERN> -29.17740 -45.45792 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6353" Parameter: A <- "-74.6353" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1774" Parameter: B <- "-29.1774" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4579" Parameter: C <- "-45.4579" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5376 TOTAL ENERGY = -74.6353 RDTITL> * VAN DER WAALS = -29.1774 ELECTROSTATIC = -45.4579 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5376" Parameter: CONF_N -> "8002" Comparing "5376" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5377" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762220 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765717 ATOM PAIRS WERE FOUND FOR ATOM LIST 41914 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29039 from a total of 765717 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5377 -76.99609 2.36078 0.65574 INTE EXTERN> -30.65981 -46.33628 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9961" Parameter: A <- "-76.9961" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6598" Parameter: B <- "-30.6598" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3363" Parameter: C <- "-46.3363" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5377 TOTAL ENERGY = -76.9961 RDTITL> * VAN DER WAALS = -30.6598 ELECTROSTATIC = -46.3363 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5377" Parameter: CONF_N -> "8002" Comparing "5377" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5378" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765717 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760400 ATOM PAIRS WERE FOUND FOR ATOM LIST 41690 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28986 from a total of 760400 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5378 -69.22935 -7.76675 0.68990 INTE EXTERN> -24.11745 -45.11189 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2293" Parameter: A <- "-69.2293" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1175" Parameter: B <- "-24.1175" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1119" Parameter: C <- "-45.1119" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5378 TOTAL ENERGY = -69.2293 RDTITL> * VAN DER WAALS = -24.1175 ELECTROSTATIC = -45.1119 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5378" Parameter: CONF_N -> "8002" Comparing "5378" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5379" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760400 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759846 ATOM PAIRS WERE FOUND FOR ATOM LIST 41677 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29537 from a total of 759846 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5379 -83.12842 13.89907 0.65316 INTE EXTERN> -33.15461 -49.97381 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.1284" Parameter: A <- "-83.1284" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1546" Parameter: B <- "-33.1546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9738" Parameter: C <- "-49.9738" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5379 TOTAL ENERGY = -83.1284 RDTITL> * VAN DER WAALS = -33.1546 ELECTROSTATIC = -49.9738 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5379" Parameter: CONF_N -> "8002" Comparing "5379" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5380" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759846 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765645 ATOM PAIRS WERE FOUND FOR ATOM LIST 41887 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30235 from a total of 765645 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5380 -71.61873 -11.50969 0.66949 INTE EXTERN> -31.26987 -40.34886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6187" Parameter: A <- "-71.6187" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2699" Parameter: B <- "-31.2699" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3489" Parameter: C <- "-40.3489" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5380 TOTAL ENERGY = -71.6187 RDTITL> * VAN DER WAALS = -31.2699 ELECTROSTATIC = -40.3489 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5380" Parameter: CONF_N -> "8002" Comparing "5380" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5381" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765645 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766469 ATOM PAIRS WERE FOUND FOR ATOM LIST 42012 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30455 from a total of 766469 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5381 -73.82570 2.20696 0.75501 INTE EXTERN> -28.41193 -45.41377 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8257" Parameter: A <- "-73.8257" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4119" Parameter: B <- "-28.4119" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4138" Parameter: C <- "-45.4138" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5381 TOTAL ENERGY = -73.8257 RDTITL> * VAN DER WAALS = -28.4119 ELECTROSTATIC = -45.4138 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5381" Parameter: CONF_N -> "8002" Comparing "5381" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5382" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766469 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768275 ATOM PAIRS WERE FOUND FOR ATOM LIST 42129 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30433 from a total of 768275 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5382 -72.71295 -1.11275 0.58138 INTE EXTERN> -34.33386 -38.37908 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7129" Parameter: A <- "-72.7129" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3339" Parameter: B <- "-34.3339" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3791" Parameter: C <- "-38.3791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5382 TOTAL ENERGY = -72.7129 RDTITL> * VAN DER WAALS = -34.3339 ELECTROSTATIC = -38.3791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5382" Parameter: CONF_N -> "8002" Comparing "5382" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5383" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768275 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760853 ATOM PAIRS WERE FOUND FOR ATOM LIST 41578 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29696 from a total of 760853 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5383 -77.70488 4.99193 0.61828 INTE EXTERN> -30.32571 -47.37917 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7049" Parameter: A <- "-77.7049" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3257" Parameter: B <- "-30.3257" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3792" Parameter: C <- "-47.3792" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5383 TOTAL ENERGY = -77.7049 RDTITL> * VAN DER WAALS = -30.3257 ELECTROSTATIC = -47.3792 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5383" Parameter: CONF_N -> "8002" Comparing "5383" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5384" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760853 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756710 ATOM PAIRS WERE FOUND FOR ATOM LIST 41497 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29622 from a total of 756710 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5384 -69.92436 -7.78052 0.56754 INTE EXTERN> -29.62363 -40.30074 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9244" Parameter: A <- "-69.9244" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6236" Parameter: B <- "-29.6236" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3007" Parameter: C <- "-40.3007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5384 TOTAL ENERGY = -69.9244 RDTITL> * VAN DER WAALS = -29.6236 ELECTROSTATIC = -40.3007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5384" Parameter: CONF_N -> "8002" Comparing "5384" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5385" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756710 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770187 ATOM PAIRS WERE FOUND FOR ATOM LIST 42275 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30024 from a total of 770187 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5385 -79.04384 9.11947 0.56290 INTE EXTERN> -34.70933 -44.33451 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0438" Parameter: A <- "-79.0438" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.7093" Parameter: B <- "-34.7093" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3345" Parameter: C <- "-44.3345" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5385 TOTAL ENERGY = -79.0438 RDTITL> * VAN DER WAALS = -34.7093 ELECTROSTATIC = -44.3345 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5385" Parameter: CONF_N -> "8002" Comparing "5385" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5386" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770187 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761209 ATOM PAIRS WERE FOUND FOR ATOM LIST 41726 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 761209 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5386 -68.45481 -10.58902 0.66474 INTE EXTERN> -27.93883 -40.51598 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4548" Parameter: A <- "-68.4548" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9388" Parameter: B <- "-27.9388" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.516" Parameter: C <- "-40.516" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5386 TOTAL ENERGY = -68.4548 RDTITL> * VAN DER WAALS = -27.9388 ELECTROSTATIC = -40.516 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5386" Parameter: CONF_N -> "8002" Comparing "5386" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5387" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761209 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762590 ATOM PAIRS WERE FOUND FOR ATOM LIST 41727 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30037 from a total of 762590 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5387 -72.24606 3.79125 0.59056 INTE EXTERN> -33.17752 -39.06854 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2461" Parameter: A <- "-72.2461" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1775" Parameter: B <- "-33.1775" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0685" Parameter: C <- "-39.0685" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5387 TOTAL ENERGY = -72.2461 RDTITL> * VAN DER WAALS = -33.1775 ELECTROSTATIC = -39.0685 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5387" Parameter: CONF_N -> "8002" Comparing "5387" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5388" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762590 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768225 ATOM PAIRS WERE FOUND FOR ATOM LIST 42013 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30128 from a total of 768225 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5388 -72.94871 0.70265 0.77669 INTE EXTERN> -26.17388 -46.77483 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9487" Parameter: A <- "-72.9487" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1739" Parameter: B <- "-26.1739" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7748" Parameter: C <- "-46.7748" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5388 TOTAL ENERGY = -72.9487 RDTITL> * VAN DER WAALS = -26.1739 ELECTROSTATIC = -46.7748 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5388" Parameter: CONF_N -> "8002" Comparing "5388" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5389" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768225 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764510 ATOM PAIRS WERE FOUND FOR ATOM LIST 42098 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29732 from a total of 764510 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5389 -72.53092 -0.41779 0.63790 INTE EXTERN> -32.41056 -40.12036 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5309" Parameter: A <- "-72.5309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4106" Parameter: B <- "-32.4106" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1204" Parameter: C <- "-40.1204" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5389 TOTAL ENERGY = -72.5309 RDTITL> * VAN DER WAALS = -32.4106 ELECTROSTATIC = -40.1204 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5389" Parameter: CONF_N -> "8002" Comparing "5389" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5390" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764510 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763073 ATOM PAIRS WERE FOUND FOR ATOM LIST 41747 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29841 from a total of 763073 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5390 -77.76811 5.23719 0.64712 INTE EXTERN> -29.36720 -48.40091 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7681" Parameter: A <- "-77.7681" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3672" Parameter: B <- "-29.3672" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4009" Parameter: C <- "-48.4009" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5390 TOTAL ENERGY = -77.7681 RDTITL> * VAN DER WAALS = -29.3672 ELECTROSTATIC = -48.4009 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5390" Parameter: CONF_N -> "8002" Comparing "5390" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5391" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763073 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764583 ATOM PAIRS WERE FOUND FOR ATOM LIST 42037 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30543 from a total of 764583 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5391 -72.39107 -5.37704 0.67726 INTE EXTERN> -28.91397 -43.47710 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3911" Parameter: A <- "-72.3911" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.914" Parameter: B <- "-28.914" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4771" Parameter: C <- "-43.4771" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5391 TOTAL ENERGY = -72.3911 RDTITL> * VAN DER WAALS = -28.914 ELECTROSTATIC = -43.4771 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5391" Parameter: CONF_N -> "8002" Comparing "5391" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5392" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764583 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756989 ATOM PAIRS WERE FOUND FOR ATOM LIST 41450 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30083 from a total of 756989 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5392 -78.26097 5.86990 0.66319 INTE EXTERN> -30.63303 -47.62794 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.261" Parameter: A <- "-78.261" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.633" Parameter: B <- "-30.633" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6279" Parameter: C <- "-47.6279" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5392 TOTAL ENERGY = -78.261 RDTITL> * VAN DER WAALS = -30.633 ELECTROSTATIC = -47.6279 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5392" Parameter: CONF_N -> "8002" Comparing "5392" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5393" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756989 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760436 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30132 from a total of 760436 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5393 -72.13754 -6.12342 0.68543 INTE EXTERN> -27.59964 -44.53790 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1375" Parameter: A <- "-72.1375" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5996" Parameter: B <- "-27.5996" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5379" Parameter: C <- "-44.5379" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5393 TOTAL ENERGY = -72.1375 RDTITL> * VAN DER WAALS = -27.5996 ELECTROSTATIC = -44.5379 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5393" Parameter: CONF_N -> "8002" Comparing "5393" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5394" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760436 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761577 ATOM PAIRS WERE FOUND FOR ATOM LIST 41758 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30066 from a total of 761577 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5394 -72.39492 0.25738 0.59343 INTE EXTERN> -30.59650 -41.79842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3949" Parameter: A <- "-72.3949" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5965" Parameter: B <- "-30.5965" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7984" Parameter: C <- "-41.7984" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5394 TOTAL ENERGY = -72.3949 RDTITL> * VAN DER WAALS = -30.5965 ELECTROSTATIC = -41.7984 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5394" Parameter: CONF_N -> "8002" Comparing "5394" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5395" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761577 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30007 from a total of 759422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5395 -74.31738 1.92246 0.69826 INTE EXTERN> -27.65326 -46.66412 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3174" Parameter: A <- "-74.3174" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6533" Parameter: B <- "-27.6533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6641" Parameter: C <- "-46.6641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5395 TOTAL ENERGY = -74.3174 RDTITL> * VAN DER WAALS = -27.6533 ELECTROSTATIC = -46.6641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5395" Parameter: CONF_N -> "8002" Comparing "5395" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5396" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756664 ATOM PAIRS WERE FOUND FOR ATOM LIST 41391 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30314 from a total of 756664 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5396 -68.09054 -6.22684 0.65389 INTE EXTERN> -26.58132 -41.50922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0905" Parameter: A <- "-68.0905" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5813" Parameter: B <- "-26.5813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5092" Parameter: C <- "-41.5092" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5396 TOTAL ENERGY = -68.0905 RDTITL> * VAN DER WAALS = -26.5813 ELECTROSTATIC = -41.5092 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5396" Parameter: CONF_N -> "8002" Comparing "5396" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5397" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756664 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753243 ATOM PAIRS WERE FOUND FOR ATOM LIST 41164 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29885 from a total of 753243 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5397 -67.23239 -0.85815 0.57362 INTE EXTERN> -30.42168 -36.81071 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2324" Parameter: A <- "-67.2324" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4217" Parameter: B <- "-30.4217" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8107" Parameter: C <- "-36.8107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5397 TOTAL ENERGY = -67.2324 RDTITL> * VAN DER WAALS = -30.4217 ELECTROSTATIC = -36.8107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5397" Parameter: CONF_N -> "8002" Comparing "5397" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5398" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753243 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766358 ATOM PAIRS WERE FOUND FOR ATOM LIST 42016 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30181 from a total of 766358 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5398 -70.88407 3.65168 0.55123 INTE EXTERN> -33.13208 -37.75198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8841" Parameter: A <- "-70.8841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1321" Parameter: B <- "-33.1321" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.752" Parameter: C <- "-37.752" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5398 TOTAL ENERGY = -70.8841 RDTITL> * VAN DER WAALS = -33.1321 ELECTROSTATIC = -37.752 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5398" Parameter: CONF_N -> "8002" Comparing "5398" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5399" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766358 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759090 ATOM PAIRS WERE FOUND FOR ATOM LIST 41682 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30308 from a total of 759090 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5399 -74.93574 4.05167 0.66955 INTE EXTERN> -29.17370 -45.76203 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9357" Parameter: A <- "-74.9357" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1737" Parameter: B <- "-29.1737" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.762" Parameter: C <- "-45.762" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5399 TOTAL ENERGY = -74.9357 RDTITL> * VAN DER WAALS = -29.1737 ELECTROSTATIC = -45.762 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5399" Parameter: CONF_N -> "8002" Comparing "5399" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5400" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759090 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759188 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30148 from a total of 759188 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5400 -81.51747 6.58173 0.64481 INTE EXTERN> -30.34603 -51.17144 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5175" Parameter: A <- "-81.5175" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.346" Parameter: B <- "-30.346" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1714" Parameter: C <- "-51.1714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5400 TOTAL ENERGY = -81.5175 RDTITL> * VAN DER WAALS = -30.346 ELECTROSTATIC = -51.1714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5400" Parameter: CONF_N -> "8002" Comparing "5400" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5401" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759188 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759354 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30049 from a total of 759354 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5401 -69.89441 -11.62306 0.61973 INTE EXTERN> -30.29566 -39.59875 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8944" Parameter: A <- "-69.8944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2957" Parameter: B <- "-30.2957" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5987" Parameter: C <- "-39.5987" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5401 TOTAL ENERGY = -69.8944 RDTITL> * VAN DER WAALS = -30.2957 ELECTROSTATIC = -39.5987 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5401" Parameter: CONF_N -> "8002" Comparing "5401" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5402" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759354 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757984 ATOM PAIRS WERE FOUND FOR ATOM LIST 41589 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30394 from a total of 757984 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5402 -74.69317 4.79876 0.63789 INTE EXTERN> -32.65506 -42.03811 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6932" Parameter: A <- "-74.6932" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6551" Parameter: B <- "-32.6551" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0381" Parameter: C <- "-42.0381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5402 TOTAL ENERGY = -74.6932 RDTITL> * VAN DER WAALS = -32.6551 ELECTROSTATIC = -42.0381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5402" Parameter: CONF_N -> "8002" Comparing "5402" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5403" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757984 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761004 ATOM PAIRS WERE FOUND FOR ATOM LIST 41592 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30138 from a total of 761004 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5403 -72.10979 -2.58338 0.61300 INTE EXTERN> -29.64287 -42.46693 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1098" Parameter: A <- "-72.1098" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6429" Parameter: B <- "-29.6429" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4669" Parameter: C <- "-42.4669" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5403 TOTAL ENERGY = -72.1098 RDTITL> * VAN DER WAALS = -29.6429 ELECTROSTATIC = -42.4669 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5403" Parameter: CONF_N -> "8002" Comparing "5403" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5404" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761004 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758229 ATOM PAIRS WERE FOUND FOR ATOM LIST 41610 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30398 from a total of 758229 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5404 -74.86624 2.75645 0.73664 INTE EXTERN> -25.80775 -49.05848 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8662" Parameter: A <- "-74.8662" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8078" Parameter: B <- "-25.8078" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0585" Parameter: C <- "-49.0585" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5404 TOTAL ENERGY = -74.8662 RDTITL> * VAN DER WAALS = -25.8078 ELECTROSTATIC = -49.0585 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5404" Parameter: CONF_N -> "8002" Comparing "5404" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5405" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758229 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763544 ATOM PAIRS WERE FOUND FOR ATOM LIST 41736 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30654 from a total of 763544 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5405 -72.79737 -2.06887 0.73882 INTE EXTERN> -26.61523 -46.18214 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7974" Parameter: A <- "-72.7974" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6152" Parameter: B <- "-26.6152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1821" Parameter: C <- "-46.1821" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5405 TOTAL ENERGY = -72.7974 RDTITL> * VAN DER WAALS = -26.6152 ELECTROSTATIC = -46.1821 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5405" Parameter: CONF_N -> "8002" Comparing "5405" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5406" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763544 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760375 ATOM PAIRS WERE FOUND FOR ATOM LIST 41777 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29174 from a total of 760375 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5406 -68.47610 -4.32127 0.62896 INTE EXTERN> -26.70304 -41.77306 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4761" Parameter: A <- "-68.4761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.703" Parameter: B <- "-26.703" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7731" Parameter: C <- "-41.7731" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5406 TOTAL ENERGY = -68.4761 RDTITL> * VAN DER WAALS = -26.703 ELECTROSTATIC = -41.7731 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5406" Parameter: CONF_N -> "8002" Comparing "5406" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5407" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760375 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765524 ATOM PAIRS WERE FOUND FOR ATOM LIST 41914 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29913 from a total of 765524 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5407 -70.41338 1.93728 0.64336 INTE EXTERN> -30.42070 -39.99268 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4134" Parameter: A <- "-70.4134" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4207" Parameter: B <- "-30.4207" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9927" Parameter: C <- "-39.9927" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5407 TOTAL ENERGY = -70.4134 RDTITL> * VAN DER WAALS = -30.4207 ELECTROSTATIC = -39.9927 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5407" Parameter: CONF_N -> "8002" Comparing "5407" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5408" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765524 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757113 ATOM PAIRS WERE FOUND FOR ATOM LIST 41386 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29866 from a total of 757113 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5408 -69.40512 -1.00826 0.62824 INTE EXTERN> -33.04752 -36.35760 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4051" Parameter: A <- "-69.4051" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0475" Parameter: B <- "-33.0475" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3576" Parameter: C <- "-36.3576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5408 TOTAL ENERGY = -69.4051 RDTITL> * VAN DER WAALS = -33.0475 ELECTROSTATIC = -36.3576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5408" Parameter: CONF_N -> "8002" Comparing "5408" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5409" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757113 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758511 ATOM PAIRS WERE FOUND FOR ATOM LIST 41442 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30213 from a total of 758511 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5409 -74.90595 5.50083 0.70085 INTE EXTERN> -28.05337 -46.85258 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.906" Parameter: A <- "-74.906" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0534" Parameter: B <- "-28.0534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8526" Parameter: C <- "-46.8526" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5409 TOTAL ENERGY = -74.906 RDTITL> * VAN DER WAALS = -28.0534 ELECTROSTATIC = -46.8526 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5409" Parameter: CONF_N -> "8002" Comparing "5409" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5410" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758511 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758743 ATOM PAIRS WERE FOUND FOR ATOM LIST 41346 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29648 from a total of 758743 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5410 -66.72423 -8.18172 0.72611 INTE EXTERN> -28.78158 -37.94266 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7242" Parameter: A <- "-66.7242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7816" Parameter: B <- "-28.7816" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9427" Parameter: C <- "-37.9427" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5410 TOTAL ENERGY = -66.7242 RDTITL> * VAN DER WAALS = -28.7816 ELECTROSTATIC = -37.9427 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5410" Parameter: CONF_N -> "8002" Comparing "5410" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5411" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758743 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757596 ATOM PAIRS WERE FOUND FOR ATOM LIST 41551 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29062 from a total of 757596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5411 -74.54558 7.82134 0.65959 INTE EXTERN> -30.95498 -43.59060 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5456" Parameter: A <- "-74.5456" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.955" Parameter: B <- "-30.955" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5906" Parameter: C <- "-43.5906" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5411 TOTAL ENERGY = -74.5456 RDTITL> * VAN DER WAALS = -30.955 ELECTROSTATIC = -43.5906 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5411" Parameter: CONF_N -> "8002" Comparing "5411" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5412" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760720 ATOM PAIRS WERE FOUND FOR ATOM LIST 41759 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29894 from a total of 760720 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5412 -67.00338 -7.54220 0.57453 INTE EXTERN> -30.65721 -36.34617 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0034" Parameter: A <- "-67.0034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6572" Parameter: B <- "-30.6572" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3462" Parameter: C <- "-36.3462" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5412 TOTAL ENERGY = -67.0034 RDTITL> * VAN DER WAALS = -30.6572 ELECTROSTATIC = -36.3462 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5412" Parameter: CONF_N -> "8002" Comparing "5412" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5413" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760720 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758733 ATOM PAIRS WERE FOUND FOR ATOM LIST 41683 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29255 from a total of 758733 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5413 -70.63510 3.63172 0.71014 INTE EXTERN> -29.41284 -41.22227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6351" Parameter: A <- "-70.6351" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4128" Parameter: B <- "-29.4128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2223" Parameter: C <- "-41.2223" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5413 TOTAL ENERGY = -70.6351 RDTITL> * VAN DER WAALS = -29.4128 ELECTROSTATIC = -41.2223 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5413" Parameter: CONF_N -> "8002" Comparing "5413" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5414" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758733 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758145 ATOM PAIRS WERE FOUND FOR ATOM LIST 41504 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29565 from a total of 758145 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5414 -70.24381 -0.39129 0.61648 INTE EXTERN> -31.51488 -38.72893 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2438" Parameter: A <- "-70.2438" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5149" Parameter: B <- "-31.5149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7289" Parameter: C <- "-38.7289" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5414 TOTAL ENERGY = -70.2438 RDTITL> * VAN DER WAALS = -31.5149 ELECTROSTATIC = -38.7289 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5414" Parameter: CONF_N -> "8002" Comparing "5414" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5415" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758145 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758277 ATOM PAIRS WERE FOUND FOR ATOM LIST 41586 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28767 from a total of 758277 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5415 -69.88367 -0.36014 0.62882 INTE EXTERN> -28.53903 -41.34464 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8837" Parameter: A <- "-69.8837" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.539" Parameter: B <- "-28.539" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3446" Parameter: C <- "-41.3446" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5415 TOTAL ENERGY = -69.8837 RDTITL> * VAN DER WAALS = -28.539 ELECTROSTATIC = -41.3446 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5415" Parameter: CONF_N -> "8002" Comparing "5415" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5416" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758277 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763826 ATOM PAIRS WERE FOUND FOR ATOM LIST 41704 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29819 from a total of 763826 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5416 -71.63820 1.75453 0.60201 INTE EXTERN> -31.74717 -39.89104 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6382" Parameter: A <- "-71.6382" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7472" Parameter: B <- "-31.7472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.891" Parameter: C <- "-39.891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5416 TOTAL ENERGY = -71.6382 RDTITL> * VAN DER WAALS = -31.7472 ELECTROSTATIC = -39.891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5416" Parameter: CONF_N -> "8002" Comparing "5416" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5417" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763826 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763978 ATOM PAIRS WERE FOUND FOR ATOM LIST 41937 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29739 from a total of 763978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5417 -70.42277 -1.21543 0.62207 INTE EXTERN> -28.30027 -42.12250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4228" Parameter: A <- "-70.4228" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3003" Parameter: B <- "-28.3003" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1225" Parameter: C <- "-42.1225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5417 TOTAL ENERGY = -70.4228 RDTITL> * VAN DER WAALS = -28.3003 ELECTROSTATIC = -42.1225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5417" Parameter: CONF_N -> "8002" Comparing "5417" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5418" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765691 ATOM PAIRS WERE FOUND FOR ATOM LIST 42067 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30424 from a total of 765691 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5418 -71.21624 0.79347 0.67258 INTE EXTERN> -28.09115 -43.12509 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2162" Parameter: A <- "-71.2162" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0912" Parameter: B <- "-28.0912" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1251" Parameter: C <- "-43.1251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5418 TOTAL ENERGY = -71.2162 RDTITL> * VAN DER WAALS = -28.0912 ELECTROSTATIC = -43.1251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5418" Parameter: CONF_N -> "8002" Comparing "5418" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5419" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765691 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763014 ATOM PAIRS WERE FOUND FOR ATOM LIST 41751 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29616 from a total of 763014 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5419 -77.70728 6.49104 0.67977 INTE EXTERN> -28.28137 -49.42591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7073" Parameter: A <- "-77.7073" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2814" Parameter: B <- "-28.2814" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4259" Parameter: C <- "-49.4259" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5419 TOTAL ENERGY = -77.7073 RDTITL> * VAN DER WAALS = -28.2814 ELECTROSTATIC = -49.4259 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5419" Parameter: CONF_N -> "8002" Comparing "5419" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5420" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763014 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760048 ATOM PAIRS WERE FOUND FOR ATOM LIST 41706 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29451 from a total of 760048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5420 -75.78437 -1.92290 0.61488 INTE EXTERN> -31.74539 -44.03898 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7844" Parameter: A <- "-75.7844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7454" Parameter: B <- "-31.7454" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.039" Parameter: C <- "-44.039" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5420 TOTAL ENERGY = -75.7844 RDTITL> * VAN DER WAALS = -31.7454 ELECTROSTATIC = -44.039 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5420" Parameter: CONF_N -> "8002" Comparing "5420" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5421" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762257 ATOM PAIRS WERE FOUND FOR ATOM LIST 41723 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29520 from a total of 762257 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5421 -65.74630 -10.03808 0.61582 INTE EXTERN> -27.09367 -38.65263 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7463" Parameter: A <- "-65.7463" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0937" Parameter: B <- "-27.0937" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6526" Parameter: C <- "-38.6526" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5421 TOTAL ENERGY = -65.7463 RDTITL> * VAN DER WAALS = -27.0937 ELECTROSTATIC = -38.6526 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5421" Parameter: CONF_N -> "8002" Comparing "5421" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5422" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762257 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766560 ATOM PAIRS WERE FOUND FOR ATOM LIST 42061 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29801 from a total of 766560 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5422 -73.25453 7.50823 0.63901 INTE EXTERN> -29.61203 -43.64250 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2545" Parameter: A <- "-73.2545" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.612" Parameter: B <- "-29.612" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6425" Parameter: C <- "-43.6425" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5422 TOTAL ENERGY = -73.2545 RDTITL> * VAN DER WAALS = -29.612 ELECTROSTATIC = -43.6425 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5422" Parameter: CONF_N -> "8002" Comparing "5422" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5423" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766560 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758819 ATOM PAIRS WERE FOUND FOR ATOM LIST 41572 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29588 from a total of 758819 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5423 -75.47440 2.21987 0.62276 INTE EXTERN> -31.56285 -43.91155 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4744" Parameter: A <- "-75.4744" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5629" Parameter: B <- "-31.5629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9115" Parameter: C <- "-43.9115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5423 TOTAL ENERGY = -75.4744 RDTITL> * VAN DER WAALS = -31.5629 ELECTROSTATIC = -43.9115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5423" Parameter: CONF_N -> "8002" Comparing "5423" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5424" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758819 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761668 ATOM PAIRS WERE FOUND FOR ATOM LIST 41580 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30057 from a total of 761668 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5424 -71.19423 -4.28017 0.61358 INTE EXTERN> -33.25399 -37.94025 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1942" Parameter: A <- "-71.1942" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.254" Parameter: B <- "-33.254" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9402" Parameter: C <- "-37.9402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5424 TOTAL ENERGY = -71.1942 RDTITL> * VAN DER WAALS = -33.254 ELECTROSTATIC = -37.9402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5424" Parameter: CONF_N -> "8002" Comparing "5424" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5425" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761668 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757522 ATOM PAIRS WERE FOUND FOR ATOM LIST 41492 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29895 from a total of 757522 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5425 -69.68262 -1.51161 0.67602 INTE EXTERN> -30.83390 -38.84872 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6826" Parameter: A <- "-69.6826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8339" Parameter: B <- "-30.8339" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8487" Parameter: C <- "-38.8487" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5425 TOTAL ENERGY = -69.6826 RDTITL> * VAN DER WAALS = -30.8339 ELECTROSTATIC = -38.8487 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5425" Parameter: CONF_N -> "8002" Comparing "5425" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5426" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757522 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763447 ATOM PAIRS WERE FOUND FOR ATOM LIST 41884 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29562 from a total of 763447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5426 -76.43157 6.74895 0.68916 INTE EXTERN> -32.14239 -44.28918 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4316" Parameter: A <- "-76.4316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1424" Parameter: B <- "-32.1424" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2892" Parameter: C <- "-44.2892" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5426 TOTAL ENERGY = -76.4316 RDTITL> * VAN DER WAALS = -32.1424 ELECTROSTATIC = -44.2892 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5426" Parameter: CONF_N -> "8002" Comparing "5426" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5427" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753972 ATOM PAIRS WERE FOUND FOR ATOM LIST 41562 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29259 from a total of 753972 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5427 -69.09918 -7.33239 0.71418 INTE EXTERN> -27.04534 -42.05384 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0992" Parameter: A <- "-69.0992" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0453" Parameter: B <- "-27.0453" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0538" Parameter: C <- "-42.0538" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5427 TOTAL ENERGY = -69.0992 RDTITL> * VAN DER WAALS = -27.0453 ELECTROSTATIC = -42.0538 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5427" Parameter: CONF_N -> "8002" Comparing "5427" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5428" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753972 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765262 ATOM PAIRS WERE FOUND FOR ATOM LIST 41937 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30325 from a total of 765262 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5428 -74.15960 5.06042 0.69051 INTE EXTERN> -29.21621 -44.94339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1596" Parameter: A <- "-74.1596" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2162" Parameter: B <- "-29.2162" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9434" Parameter: C <- "-44.9434" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5428 TOTAL ENERGY = -74.1596 RDTITL> * VAN DER WAALS = -29.2162 ELECTROSTATIC = -44.9434 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5428" Parameter: CONF_N -> "8002" Comparing "5428" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5429" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765262 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769022 ATOM PAIRS WERE FOUND FOR ATOM LIST 41869 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30083 from a total of 769022 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5429 -70.24117 -3.91844 0.70350 INTE EXTERN> -28.72961 -41.51155 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2412" Parameter: A <- "-70.2412" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7296" Parameter: B <- "-28.7296" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5116" Parameter: C <- "-41.5116" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5429 TOTAL ENERGY = -70.2412 RDTITL> * VAN DER WAALS = -28.7296 ELECTROSTATIC = -41.5116 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5429" Parameter: CONF_N -> "8002" Comparing "5429" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5430" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769022 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768105 ATOM PAIRS WERE FOUND FOR ATOM LIST 42023 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29902 from a total of 768105 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5430 -71.70220 1.46104 0.78035 INTE EXTERN> -26.68262 -45.01958 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7022" Parameter: A <- "-71.7022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6826" Parameter: B <- "-26.6826" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0196" Parameter: C <- "-45.0196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5430 TOTAL ENERGY = -71.7022 RDTITL> * VAN DER WAALS = -26.6826 ELECTROSTATIC = -45.0196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5430" Parameter: CONF_N -> "8002" Comparing "5430" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5431" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768105 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761640 ATOM PAIRS WERE FOUND FOR ATOM LIST 41545 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30092 from a total of 761640 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5431 -63.15149 -8.55072 0.63788 INTE EXTERN> -27.68781 -35.46367 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1515" Parameter: A <- "-63.1515" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6878" Parameter: B <- "-27.6878" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4637" Parameter: C <- "-35.4637" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5431 TOTAL ENERGY = -63.1515 RDTITL> * VAN DER WAALS = -27.6878 ELECTROSTATIC = -35.4637 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5431" Parameter: CONF_N -> "8002" Comparing "5431" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5432" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761640 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762736 ATOM PAIRS WERE FOUND FOR ATOM LIST 41486 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30379 from a total of 762736 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5432 -67.75272 4.60123 0.57794 INTE EXTERN> -32.25085 -35.50187 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7527" Parameter: A <- "-67.7527" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2508" Parameter: B <- "-32.2508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5019" Parameter: C <- "-35.5019" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5432 TOTAL ENERGY = -67.7527 RDTITL> * VAN DER WAALS = -32.2508 ELECTROSTATIC = -35.5019 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5432" Parameter: CONF_N -> "8002" Comparing "5432" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5433" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762736 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762442 ATOM PAIRS WERE FOUND FOR ATOM LIST 41623 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30163 from a total of 762442 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5433 -70.07138 2.31867 0.54753 INTE EXTERN> -34.10252 -35.96886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0714" Parameter: A <- "-70.0714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1025" Parameter: B <- "-34.1025" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9689" Parameter: C <- "-35.9689" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5433 TOTAL ENERGY = -70.0714 RDTITL> * VAN DER WAALS = -34.1025 ELECTROSTATIC = -35.9689 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5433" Parameter: CONF_N -> "8002" Comparing "5433" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5434" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762442 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763678 ATOM PAIRS WERE FOUND FOR ATOM LIST 41627 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30127 from a total of 763678 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5434 -66.06524 -4.00614 0.76905 INTE EXTERN> -26.38436 -39.68088 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0652" Parameter: A <- "-66.0652" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3844" Parameter: B <- "-26.3844" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6809" Parameter: C <- "-39.6809" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5434 TOTAL ENERGY = -66.0652 RDTITL> * VAN DER WAALS = -26.3844 ELECTROSTATIC = -39.6809 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5434" Parameter: CONF_N -> "8002" Comparing "5434" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5435" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763678 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769444 ATOM PAIRS WERE FOUND FOR ATOM LIST 41856 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30381 from a total of 769444 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5435 -69.24309 3.17785 0.60013 INTE EXTERN> -31.94264 -37.30045 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2431" Parameter: A <- "-69.2431" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9426" Parameter: B <- "-31.9426" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3004" Parameter: C <- "-37.3004" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5435 TOTAL ENERGY = -69.2431 RDTITL> * VAN DER WAALS = -31.9426 ELECTROSTATIC = -37.3004 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5435" Parameter: CONF_N -> "8002" Comparing "5435" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5436" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769444 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41803 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30072 from a total of 763526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5436 -71.30505 2.06196 0.51021 INTE EXTERN> -31.49305 -39.81201 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3051" Parameter: A <- "-71.3051" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.493" Parameter: B <- "-31.493" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.812" Parameter: C <- "-39.812" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5436 TOTAL ENERGY = -71.3051 RDTITL> * VAN DER WAALS = -31.493 ELECTROSTATIC = -39.812 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5436" Parameter: CONF_N -> "8002" Comparing "5436" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5437" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761878 ATOM PAIRS WERE FOUND FOR ATOM LIST 41583 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29840 from a total of 761878 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5437 -68.10173 -3.20332 0.58667 INTE EXTERN> -30.25394 -37.84779 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1017" Parameter: A <- "-68.1017" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2539" Parameter: B <- "-30.2539" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8478" Parameter: C <- "-37.8478" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5437 TOTAL ENERGY = -68.1017 RDTITL> * VAN DER WAALS = -30.2539 ELECTROSTATIC = -37.8478 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5437" Parameter: CONF_N -> "8002" Comparing "5437" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5438" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761878 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762044 ATOM PAIRS WERE FOUND FOR ATOM LIST 41657 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29747 from a total of 762044 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5438 -70.70136 2.59963 0.59516 INTE EXTERN> -30.13019 -40.57117 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7014" Parameter: A <- "-70.7014" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1302" Parameter: B <- "-30.1302" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5712" Parameter: C <- "-40.5712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5438 TOTAL ENERGY = -70.7014 RDTITL> * VAN DER WAALS = -30.1302 ELECTROSTATIC = -40.5712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5438" Parameter: CONF_N -> "8002" Comparing "5438" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5439" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762044 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763367 ATOM PAIRS WERE FOUND FOR ATOM LIST 41617 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29554 from a total of 763367 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5439 -68.88632 -1.81504 0.68288 INTE EXTERN> -29.52673 -39.35959 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8863" Parameter: A <- "-68.8863" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5267" Parameter: B <- "-29.5267" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3596" Parameter: C <- "-39.3596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5439 TOTAL ENERGY = -68.8863 RDTITL> * VAN DER WAALS = -29.5267 ELECTROSTATIC = -39.3596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5439" Parameter: CONF_N -> "8002" Comparing "5439" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5440" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763367 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756697 ATOM PAIRS WERE FOUND FOR ATOM LIST 41390 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28974 from a total of 756697 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5440 -71.71115 2.82483 0.66482 INTE EXTERN> -28.45043 -43.26072 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7112" Parameter: A <- "-71.7112" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4504" Parameter: B <- "-28.4504" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2607" Parameter: C <- "-43.2607" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5440 TOTAL ENERGY = -71.7112 RDTITL> * VAN DER WAALS = -28.4504 ELECTROSTATIC = -43.2607 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5440" Parameter: CONF_N -> "8002" Comparing "5440" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5441" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756697 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764456 ATOM PAIRS WERE FOUND FOR ATOM LIST 41937 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30037 from a total of 764456 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5441 -67.61450 -4.09666 0.72697 INTE EXTERN> -23.82012 -43.79438 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6145" Parameter: A <- "-67.6145" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8201" Parameter: B <- "-23.8201" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7944" Parameter: C <- "-43.7944" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5441 TOTAL ENERGY = -67.6145 RDTITL> * VAN DER WAALS = -23.8201 ELECTROSTATIC = -43.7944 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5441" Parameter: CONF_N -> "8002" Comparing "5441" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5442" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764456 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769715 ATOM PAIRS WERE FOUND FOR ATOM LIST 42162 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30602 from a total of 769715 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5442 -68.69719 1.08269 0.69352 INTE EXTERN> -29.64019 -39.05700 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6972" Parameter: A <- "-68.6972" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6402" Parameter: B <- "-29.6402" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.057" Parameter: C <- "-39.057" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5442 TOTAL ENERGY = -68.6972 RDTITL> * VAN DER WAALS = -29.6402 ELECTROSTATIC = -39.057 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5442" Parameter: CONF_N -> "8002" Comparing "5442" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5443" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769715 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759226 ATOM PAIRS WERE FOUND FOR ATOM LIST 41544 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30194 from a total of 759226 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5443 -73.02195 4.32477 0.76262 INTE EXTERN> -24.81282 -48.20914 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.022" Parameter: A <- "-73.022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8128" Parameter: B <- "-24.8128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2091" Parameter: C <- "-48.2091" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5443 TOTAL ENERGY = -73.022 RDTITL> * VAN DER WAALS = -24.8128 ELECTROSTATIC = -48.2091 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5443" Parameter: CONF_N -> "8002" Comparing "5443" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5444" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759226 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30701 from a total of 762118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5444 -69.04734 -3.97462 0.57030 INTE EXTERN> -33.88215 -35.16519 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0473" Parameter: A <- "-69.0473" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8821" Parameter: B <- "-33.8821" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1652" Parameter: C <- "-35.1652" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5444 TOTAL ENERGY = -69.0473 RDTITL> * VAN DER WAALS = -33.8821 ELECTROSTATIC = -35.1652 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5444" Parameter: CONF_N -> "8002" Comparing "5444" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5445" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763549 ATOM PAIRS WERE FOUND FOR ATOM LIST 41989 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29726 from a total of 763549 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5445 -75.11142 6.06408 0.68940 INTE EXTERN> -29.94380 -45.16762 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1114" Parameter: A <- "-75.1114" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9438" Parameter: B <- "-29.9438" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1676" Parameter: C <- "-45.1676" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5445 TOTAL ENERGY = -75.1114 RDTITL> * VAN DER WAALS = -29.9438 ELECTROSTATIC = -45.1676 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5445" Parameter: CONF_N -> "8002" Comparing "5445" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5446" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763549 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763409 ATOM PAIRS WERE FOUND FOR ATOM LIST 41759 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30186 from a total of 763409 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5446 -69.18719 -5.92423 0.67996 INTE EXTERN> -28.34135 -40.84584 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1872" Parameter: A <- "-69.1872" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3413" Parameter: B <- "-28.3413" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8458" Parameter: C <- "-40.8458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5446 TOTAL ENERGY = -69.1872 RDTITL> * VAN DER WAALS = -28.3413 ELECTROSTATIC = -40.8458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5446" Parameter: CONF_N -> "8002" Comparing "5446" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5447" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763409 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761039 ATOM PAIRS WERE FOUND FOR ATOM LIST 41669 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29961 from a total of 761039 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5447 -75.77518 6.58799 0.64641 INTE EXTERN> -31.29952 -44.47566 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7752" Parameter: A <- "-75.7752" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2995" Parameter: B <- "-31.2995" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4757" Parameter: C <- "-44.4757" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5447 TOTAL ENERGY = -75.7752 RDTITL> * VAN DER WAALS = -31.2995 ELECTROSTATIC = -44.4757 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5447" Parameter: CONF_N -> "8002" Comparing "5447" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5448" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761039 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764639 ATOM PAIRS WERE FOUND FOR ATOM LIST 41786 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29772 from a total of 764639 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5448 -64.32741 -11.44776 0.57563 INTE EXTERN> -28.05402 -36.27340 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3274" Parameter: A <- "-64.3274" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.054" Parameter: B <- "-28.054" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2734" Parameter: C <- "-36.2734" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5448 TOTAL ENERGY = -64.3274 RDTITL> * VAN DER WAALS = -28.054 ELECTROSTATIC = -36.2734 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5448" Parameter: CONF_N -> "8002" Comparing "5448" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5449" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764639 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759797 ATOM PAIRS WERE FOUND FOR ATOM LIST 41661 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29873 from a total of 759797 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5449 -69.15054 4.82313 0.68941 INTE EXTERN> -26.45129 -42.69925 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1505" Parameter: A <- "-69.1505" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4513" Parameter: B <- "-26.4513" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6993" Parameter: C <- "-42.6993" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5449 TOTAL ENERGY = -69.1505 RDTITL> * VAN DER WAALS = -26.4513 ELECTROSTATIC = -42.6993 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5449" Parameter: CONF_N -> "8002" Comparing "5449" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5450" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759797 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767605 ATOM PAIRS WERE FOUND FOR ATOM LIST 41970 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30410 from a total of 767605 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5450 -72.90697 3.75643 0.59785 INTE EXTERN> -27.34482 -45.56215 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.907" Parameter: A <- "-72.907" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3448" Parameter: B <- "-27.3448" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5621" Parameter: C <- "-45.5621" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5450 TOTAL ENERGY = -72.907 RDTITL> * VAN DER WAALS = -27.3448 ELECTROSTATIC = -45.5621 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5450" Parameter: CONF_N -> "8002" Comparing "5450" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5451" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767605 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763820 ATOM PAIRS WERE FOUND FOR ATOM LIST 41649 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30127 from a total of 763820 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5451 -65.69302 -7.21395 0.64803 INTE EXTERN> -26.71491 -38.97811 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.693" Parameter: A <- "-65.693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7149" Parameter: B <- "-26.7149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9781" Parameter: C <- "-38.9781" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5451 TOTAL ENERGY = -65.693 RDTITL> * VAN DER WAALS = -26.7149 ELECTROSTATIC = -38.9781 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5451" Parameter: CONF_N -> "8002" Comparing "5451" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5452" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763820 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764815 ATOM PAIRS WERE FOUND FOR ATOM LIST 41725 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30492 from a total of 764815 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5452 -65.76090 0.06788 0.54985 INTE EXTERN> -30.62285 -35.13805 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7609" Parameter: A <- "-65.7609" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6228" Parameter: B <- "-30.6228" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.138" Parameter: C <- "-35.138" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5452 TOTAL ENERGY = -65.7609 RDTITL> * VAN DER WAALS = -30.6228 ELECTROSTATIC = -35.138 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5452" Parameter: CONF_N -> "8002" Comparing "5452" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5453" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764815 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765558 ATOM PAIRS WERE FOUND FOR ATOM LIST 41896 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30261 from a total of 765558 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5453 -74.97613 9.21523 0.62142 INTE EXTERN> -30.34795 -44.62817 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9761" Parameter: A <- "-74.9761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.348" Parameter: B <- "-30.348" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6282" Parameter: C <- "-44.6282" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5453 TOTAL ENERGY = -74.9761 RDTITL> * VAN DER WAALS = -30.348 ELECTROSTATIC = -44.6282 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5453" Parameter: CONF_N -> "8002" Comparing "5453" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5454" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765558 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41439 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29489 from a total of 755110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5454 -70.61370 -4.36243 0.69029 INTE EXTERN> -26.09465 -44.51905 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6137" Parameter: A <- "-70.6137" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0946" Parameter: B <- "-26.0946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5191" Parameter: C <- "-44.5191" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5454 TOTAL ENERGY = -70.6137 RDTITL> * VAN DER WAALS = -26.0946 ELECTROSTATIC = -44.5191 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5454" Parameter: CONF_N -> "8002" Comparing "5454" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5455" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759014 ATOM PAIRS WERE FOUND FOR ATOM LIST 41606 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29513 from a total of 759014 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5455 -69.94668 -0.66702 0.55359 INTE EXTERN> -32.13646 -37.81021 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9467" Parameter: A <- "-69.9467" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1365" Parameter: B <- "-32.1365" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8102" Parameter: C <- "-37.8102" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5455 TOTAL ENERGY = -69.9467 RDTITL> * VAN DER WAALS = -32.1365 ELECTROSTATIC = -37.8102 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5455" Parameter: CONF_N -> "8002" Comparing "5455" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5456" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759014 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760244 ATOM PAIRS WERE FOUND FOR ATOM LIST 41489 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29552 from a total of 760244 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5456 -65.20896 -4.73772 0.83715 INTE EXTERN> -26.10566 -39.10330 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.209" Parameter: A <- "-65.209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1057" Parameter: B <- "-26.1057" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1033" Parameter: C <- "-39.1033" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5456 TOTAL ENERGY = -65.209 RDTITL> * VAN DER WAALS = -26.1057 ELECTROSTATIC = -39.1033 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5456" Parameter: CONF_N -> "8002" Comparing "5456" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5457" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760244 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758437 ATOM PAIRS WERE FOUND FOR ATOM LIST 41688 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29925 from a total of 758437 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5457 -70.36188 5.15292 0.60595 INTE EXTERN> -29.52854 -40.83334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3619" Parameter: A <- "-70.3619" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5285" Parameter: B <- "-29.5285" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8333" Parameter: C <- "-40.8333" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5457 TOTAL ENERGY = -70.3619 RDTITL> * VAN DER WAALS = -29.5285 ELECTROSTATIC = -40.8333 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5457" Parameter: CONF_N -> "8002" Comparing "5457" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5458" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758437 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757771 ATOM PAIRS WERE FOUND FOR ATOM LIST 41382 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29629 from a total of 757771 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5458 -75.91690 5.55502 0.68272 INTE EXTERN> -27.31063 -48.60627 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9169" Parameter: A <- "-75.9169" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3106" Parameter: B <- "-27.3106" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6063" Parameter: C <- "-48.6063" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5458 TOTAL ENERGY = -75.9169 RDTITL> * VAN DER WAALS = -27.3106 ELECTROSTATIC = -48.6063 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5458" Parameter: CONF_N -> "8002" Comparing "5458" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5459" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757771 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761500 ATOM PAIRS WERE FOUND FOR ATOM LIST 41836 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29877 from a total of 761500 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5459 -70.41602 -5.50088 0.60655 INTE EXTERN> -27.82424 -42.59177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.416" Parameter: A <- "-70.416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8242" Parameter: B <- "-27.8242" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5918" Parameter: C <- "-42.5918" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5459 TOTAL ENERGY = -70.416 RDTITL> * VAN DER WAALS = -27.8242 ELECTROSTATIC = -42.5918 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5459" Parameter: CONF_N -> "8002" Comparing "5459" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5460" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761500 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755655 ATOM PAIRS WERE FOUND FOR ATOM LIST 41409 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29364 from a total of 755655 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5460 -72.77614 2.36013 0.62684 INTE EXTERN> -29.21059 -43.56556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7761" Parameter: A <- "-72.7761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2106" Parameter: B <- "-29.2106" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5656" Parameter: C <- "-43.5656" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5460 TOTAL ENERGY = -72.7761 RDTITL> * VAN DER WAALS = -29.2106 ELECTROSTATIC = -43.5656 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5460" Parameter: CONF_N -> "8002" Comparing "5460" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5461" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755655 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756300 ATOM PAIRS WERE FOUND FOR ATOM LIST 41361 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29854 from a total of 756300 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5461 -59.19101 -13.58513 0.55202 INTE EXTERN> -28.64760 -30.54341 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.191" Parameter: A <- "-59.191" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6476" Parameter: B <- "-28.6476" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.5434" Parameter: C <- "-30.5434" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5461 TOTAL ENERGY = -59.191 RDTITL> * VAN DER WAALS = -28.6476 ELECTROSTATIC = -30.5434 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5461" Parameter: CONF_N -> "8002" Comparing "5461" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5462" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756300 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761654 ATOM PAIRS WERE FOUND FOR ATOM LIST 41643 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30336 from a total of 761654 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5462 -71.07767 11.88666 0.65888 INTE EXTERN> -28.62769 -42.44998 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0777" Parameter: A <- "-71.0777" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6277" Parameter: B <- "-28.6277" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.45" Parameter: C <- "-42.45" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5462 TOTAL ENERGY = -71.0777 RDTITL> * VAN DER WAALS = -28.6277 ELECTROSTATIC = -42.45 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5462" Parameter: CONF_N -> "8002" Comparing "5462" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5463" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761654 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757551 ATOM PAIRS WERE FOUND FOR ATOM LIST 41448 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29088 from a total of 757551 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5463 -64.56705 -6.51061 0.49156 INTE EXTERN> -29.87981 -34.68724 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5671" Parameter: A <- "-64.5671" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8798" Parameter: B <- "-29.8798" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.6872" Parameter: C <- "-34.6872" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5463 TOTAL ENERGY = -64.5671 RDTITL> * VAN DER WAALS = -29.8798 ELECTROSTATIC = -34.6872 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5463" Parameter: CONF_N -> "8002" Comparing "5463" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5464" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757551 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760831 ATOM PAIRS WERE FOUND FOR ATOM LIST 41629 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29181 from a total of 760831 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5464 -73.03355 8.46650 0.61580 INTE EXTERN> -32.13850 -40.89505 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0336" Parameter: A <- "-73.0336" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1385" Parameter: B <- "-32.1385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8951" Parameter: C <- "-40.8951" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5464 TOTAL ENERGY = -73.0336 RDTITL> * VAN DER WAALS = -32.1385 ELECTROSTATIC = -40.8951 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5464" Parameter: CONF_N -> "8002" Comparing "5464" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5465" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760831 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760747 ATOM PAIRS WERE FOUND FOR ATOM LIST 41783 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29202 from a total of 760747 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5465 -75.68398 2.65043 0.65778 INTE EXTERN> -27.97624 -47.70774 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.684" Parameter: A <- "-75.684" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9762" Parameter: B <- "-27.9762" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7077" Parameter: C <- "-47.7077" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5465 TOTAL ENERGY = -75.684 RDTITL> * VAN DER WAALS = -27.9762 ELECTROSTATIC = -47.7077 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5465" Parameter: CONF_N -> "8002" Comparing "5465" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5466" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760747 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760477 ATOM PAIRS WERE FOUND FOR ATOM LIST 41809 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29210 from a total of 760477 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5466 -70.29675 -5.38723 0.65183 INTE EXTERN> -29.64091 -40.65584 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2967" Parameter: A <- "-70.2967" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6409" Parameter: B <- "-29.6409" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6558" Parameter: C <- "-40.6558" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5466 TOTAL ENERGY = -70.2967 RDTITL> * VAN DER WAALS = -29.6409 ELECTROSTATIC = -40.6558 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5466" Parameter: CONF_N -> "8002" Comparing "5466" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5467" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760477 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764289 ATOM PAIRS WERE FOUND FOR ATOM LIST 41875 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29532 from a total of 764289 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5467 -76.98856 6.69182 0.72564 INTE EXTERN> -27.05772 -49.93085 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9886" Parameter: A <- "-76.9886" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0577" Parameter: B <- "-27.0577" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9308" Parameter: C <- "-49.9308" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5467 TOTAL ENERGY = -76.9886 RDTITL> * VAN DER WAALS = -27.0577 ELECTROSTATIC = -49.9308 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5467" Parameter: CONF_N -> "8002" Comparing "5467" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5468" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764289 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759642 ATOM PAIRS WERE FOUND FOR ATOM LIST 41593 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29549 from a total of 759642 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5468 -72.43050 -4.55806 0.59050 INTE EXTERN> -29.52830 -42.90220 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4305" Parameter: A <- "-72.4305" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5283" Parameter: B <- "-29.5283" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9022" Parameter: C <- "-42.9022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5468 TOTAL ENERGY = -72.4305 RDTITL> * VAN DER WAALS = -29.5283 ELECTROSTATIC = -42.9022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5468" Parameter: CONF_N -> "8002" Comparing "5468" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5469" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759642 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758750 ATOM PAIRS WERE FOUND FOR ATOM LIST 41384 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29914 from a total of 758750 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5469 -70.76336 -1.66714 0.63092 INTE EXTERN> -29.34688 -41.41648 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7634" Parameter: A <- "-70.7634" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3469" Parameter: B <- "-29.3469" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4165" Parameter: C <- "-41.4165" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5469 TOTAL ENERGY = -70.7634 RDTITL> * VAN DER WAALS = -29.3469 ELECTROSTATIC = -41.4165 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5469" Parameter: CONF_N -> "8002" Comparing "5469" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5470" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758750 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763284 ATOM PAIRS WERE FOUND FOR ATOM LIST 41848 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29548 from a total of 763284 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5470 -72.88169 2.11833 0.62982 INTE EXTERN> -31.03047 -41.85122 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8817" Parameter: A <- "-72.8817" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0305" Parameter: B <- "-31.0305" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8512" Parameter: C <- "-41.8512" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5470 TOTAL ENERGY = -72.8817 RDTITL> * VAN DER WAALS = -31.0305 ELECTROSTATIC = -41.8512 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5470" Parameter: CONF_N -> "8002" Comparing "5470" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5471" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763284 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759749 ATOM PAIRS WERE FOUND FOR ATOM LIST 41588 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30064 from a total of 759749 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5471 -77.89808 5.01639 0.58725 INTE EXTERN> -33.96227 -43.93581 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8981" Parameter: A <- "-77.8981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9623" Parameter: B <- "-33.9623" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9358" Parameter: C <- "-43.9358" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5471 TOTAL ENERGY = -77.8981 RDTITL> * VAN DER WAALS = -33.9623 ELECTROSTATIC = -43.9358 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5471" Parameter: CONF_N -> "8002" Comparing "5471" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5472" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759749 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756718 ATOM PAIRS WERE FOUND FOR ATOM LIST 41433 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29272 from a total of 756718 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5472 -63.78544 -14.11265 0.59883 INTE EXTERN> -27.30215 -36.48329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7854" Parameter: A <- "-63.7854" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3021" Parameter: B <- "-27.3021" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4833" Parameter: C <- "-36.4833" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5472 TOTAL ENERGY = -63.7854 RDTITL> * VAN DER WAALS = -27.3021 ELECTROSTATIC = -36.4833 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5472" Parameter: CONF_N -> "8002" Comparing "5472" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5473" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756718 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758054 ATOM PAIRS WERE FOUND FOR ATOM LIST 41401 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29884 from a total of 758054 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5473 -74.65905 10.87361 0.58338 INTE EXTERN> -32.97102 -41.68803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.659" Parameter: A <- "-74.659" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.971" Parameter: B <- "-32.971" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.688" Parameter: C <- "-41.688" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5473 TOTAL ENERGY = -74.659 RDTITL> * VAN DER WAALS = -32.971 ELECTROSTATIC = -41.688 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5473" Parameter: CONF_N -> "8002" Comparing "5473" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5474" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758054 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750358 ATOM PAIRS WERE FOUND FOR ATOM LIST 41106 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29732 from a total of 750358 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5474 -73.05726 -1.60179 0.57313 INTE EXTERN> -31.13668 -41.92057 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0573" Parameter: A <- "-73.0573" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1367" Parameter: B <- "-31.1367" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9206" Parameter: C <- "-41.9206" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5474 TOTAL ENERGY = -73.0573 RDTITL> * VAN DER WAALS = -31.1367 ELECTROSTATIC = -41.9206 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5474" Parameter: CONF_N -> "8002" Comparing "5474" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5475" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750358 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758161 ATOM PAIRS WERE FOUND FOR ATOM LIST 41490 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29416 from a total of 758161 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5475 -67.93148 -5.12578 0.65994 INTE EXTERN> -27.48774 -40.44374 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9315" Parameter: A <- "-67.9315" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4877" Parameter: B <- "-27.4877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4437" Parameter: C <- "-40.4437" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5475 TOTAL ENERGY = -67.9315 RDTITL> * VAN DER WAALS = -27.4877 ELECTROSTATIC = -40.4437 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5475" Parameter: CONF_N -> "8002" Comparing "5475" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5476" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758161 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757687 ATOM PAIRS WERE FOUND FOR ATOM LIST 41685 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29492 from a total of 757687 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5476 -68.47388 0.54241 0.54336 INTE EXTERN> -31.13863 -37.33525 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4739" Parameter: A <- "-68.4739" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1386" Parameter: B <- "-31.1386" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3352" Parameter: C <- "-37.3352" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5476 TOTAL ENERGY = -68.4739 RDTITL> * VAN DER WAALS = -31.1386 ELECTROSTATIC = -37.3352 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5476" Parameter: CONF_N -> "8002" Comparing "5476" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5477" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757687 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762176 ATOM PAIRS WERE FOUND FOR ATOM LIST 41701 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29726 from a total of 762176 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5477 -65.86443 -2.60945 0.58348 INTE EXTERN> -28.25232 -37.61211 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8644" Parameter: A <- "-65.8644" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2523" Parameter: B <- "-28.2523" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6121" Parameter: C <- "-37.6121" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5477 TOTAL ENERGY = -65.8644 RDTITL> * VAN DER WAALS = -28.2523 ELECTROSTATIC = -37.6121 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5477" Parameter: CONF_N -> "8002" Comparing "5477" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5478" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762176 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760372 ATOM PAIRS WERE FOUND FOR ATOM LIST 41602 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30183 from a total of 760372 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5478 -73.62053 7.75610 0.69098 INTE EXTERN> -25.26383 -48.35670 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6205" Parameter: A <- "-73.6205" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2638" Parameter: B <- "-25.2638" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3567" Parameter: C <- "-48.3567" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5478 TOTAL ENERGY = -73.6205 RDTITL> * VAN DER WAALS = -25.2638 ELECTROSTATIC = -48.3567 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5478" Parameter: CONF_N -> "8002" Comparing "5478" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5479" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760372 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768219 ATOM PAIRS WERE FOUND FOR ATOM LIST 42205 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30392 from a total of 768219 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5479 -73.89709 0.27656 0.66503 INTE EXTERN> -29.48950 -44.40759 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8971" Parameter: A <- "-73.8971" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4895" Parameter: B <- "-29.4895" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4076" Parameter: C <- "-44.4076" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5479 TOTAL ENERGY = -73.8971 RDTITL> * VAN DER WAALS = -29.4895 ELECTROSTATIC = -44.4076 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5479" Parameter: CONF_N -> "8002" Comparing "5479" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5480" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768219 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 771177 ATOM PAIRS WERE FOUND FOR ATOM LIST 42108 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30153 from a total of 771177 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5480 -74.48726 0.59017 0.64140 INTE EXTERN> -28.17243 -46.31482 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4873" Parameter: A <- "-74.4873" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1724" Parameter: B <- "-28.1724" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3148" Parameter: C <- "-46.3148" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5480 TOTAL ENERGY = -74.4873 RDTITL> * VAN DER WAALS = -28.1724 ELECTROSTATIC = -46.3148 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5480" Parameter: CONF_N -> "8002" Comparing "5480" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5481" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 771177 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760365 ATOM PAIRS WERE FOUND FOR ATOM LIST 41491 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29713 from a total of 760365 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5481 -73.45983 -1.02743 0.53349 INTE EXTERN> -32.18341 -41.27642 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4598" Parameter: A <- "-73.4598" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1834" Parameter: B <- "-32.1834" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2764" Parameter: C <- "-41.2764" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5481 TOTAL ENERGY = -73.4598 RDTITL> * VAN DER WAALS = -32.1834 ELECTROSTATIC = -41.2764 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5481" Parameter: CONF_N -> "8002" Comparing "5481" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5482" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760365 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764609 ATOM PAIRS WERE FOUND FOR ATOM LIST 41680 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30118 from a total of 764609 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5482 -64.61513 -8.84470 0.53865 INTE EXTERN> -32.25259 -32.36254 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6151" Parameter: A <- "-64.6151" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2526" Parameter: B <- "-32.2526" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.3625" Parameter: C <- "-32.3625" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5482 TOTAL ENERGY = -64.6151 RDTITL> * VAN DER WAALS = -32.2526 ELECTROSTATIC = -32.3625 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5482" Parameter: CONF_N -> "8002" Comparing "5482" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5483" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764609 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764001 ATOM PAIRS WERE FOUND FOR ATOM LIST 41667 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30847 from a total of 764001 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5483 -68.76098 4.14586 0.66489 INTE EXTERN> -29.57672 -39.18426 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.761" Parameter: A <- "-68.761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5767" Parameter: B <- "-29.5767" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1843" Parameter: C <- "-39.1843" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5483 TOTAL ENERGY = -68.761 RDTITL> * VAN DER WAALS = -29.5767 ELECTROSTATIC = -39.1843 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5483" Parameter: CONF_N -> "8002" Comparing "5483" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5484" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764001 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758113 ATOM PAIRS WERE FOUND FOR ATOM LIST 41803 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30614 from a total of 758113 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5484 -75.82703 7.06605 0.61957 INTE EXTERN> -32.76377 -43.06326 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.827" Parameter: A <- "-75.827" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7638" Parameter: B <- "-32.7638" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0633" Parameter: C <- "-43.0633" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5484 TOTAL ENERGY = -75.827 RDTITL> * VAN DER WAALS = -32.7638 ELECTROSTATIC = -43.0633 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5484" Parameter: CONF_N -> "8002" Comparing "5484" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5485" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758113 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761199 ATOM PAIRS WERE FOUND FOR ATOM LIST 41662 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30857 from a total of 761199 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5485 -68.51127 -7.31576 0.52048 INTE EXTERN> -32.24176 -36.26951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5113" Parameter: A <- "-68.5113" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2418" Parameter: B <- "-32.2418" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2695" Parameter: C <- "-36.2695" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5485 TOTAL ENERGY = -68.5113 RDTITL> * VAN DER WAALS = -32.2418 ELECTROSTATIC = -36.2695 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5485" Parameter: CONF_N -> "8002" Comparing "5485" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5486" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761199 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758236 ATOM PAIRS WERE FOUND FOR ATOM LIST 41600 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30132 from a total of 758236 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5486 -66.66202 -1.84925 0.56542 INTE EXTERN> -31.29884 -35.36318 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.662" Parameter: A <- "-66.662" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2988" Parameter: B <- "-31.2988" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3632" Parameter: C <- "-35.3632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5486 TOTAL ENERGY = -66.662 RDTITL> * VAN DER WAALS = -31.2988 ELECTROSTATIC = -35.3632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5486" Parameter: CONF_N -> "8002" Comparing "5486" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5487" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758236 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763115 ATOM PAIRS WERE FOUND FOR ATOM LIST 41591 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30233 from a total of 763115 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5487 -64.65975 -2.00227 0.66932 INTE EXTERN> -26.47368 -38.18607 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6597" Parameter: A <- "-64.6597" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4737" Parameter: B <- "-26.4737" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1861" Parameter: C <- "-38.1861" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5487 TOTAL ENERGY = -64.6597 RDTITL> * VAN DER WAALS = -26.4737 ELECTROSTATIC = -38.1861 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5487" Parameter: CONF_N -> "8002" Comparing "5487" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5488" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763115 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765173 ATOM PAIRS WERE FOUND FOR ATOM LIST 41749 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30937 from a total of 765173 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5488 -75.02641 10.36667 0.63034 INTE EXTERN> -34.29194 -40.73447 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0264" Parameter: A <- "-75.0264" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.2919" Parameter: B <- "-34.2919" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7345" Parameter: C <- "-40.7345" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5488 TOTAL ENERGY = -75.0264 RDTITL> * VAN DER WAALS = -34.2919 ELECTROSTATIC = -40.7345 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5488" Parameter: CONF_N -> "8002" Comparing "5488" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5489" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765173 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763497 ATOM PAIRS WERE FOUND FOR ATOM LIST 41860 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30415 from a total of 763497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5489 -69.31943 -5.70699 0.63637 INTE EXTERN> -29.57866 -39.74076 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3194" Parameter: A <- "-69.3194" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5787" Parameter: B <- "-29.5787" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7408" Parameter: C <- "-39.7408" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5489 TOTAL ENERGY = -69.3194 RDTITL> * VAN DER WAALS = -29.5787 ELECTROSTATIC = -39.7408 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5489" Parameter: CONF_N -> "8002" Comparing "5489" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5490" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764497 ATOM PAIRS WERE FOUND FOR ATOM LIST 41813 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30257 from a total of 764497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5490 -72.24962 2.93019 0.57203 INTE EXTERN> -33.31203 -38.93759 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2496" Parameter: A <- "-72.2496" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.312" Parameter: B <- "-33.312" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9376" Parameter: C <- "-38.9376" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5490 TOTAL ENERGY = -72.2496 RDTITL> * VAN DER WAALS = -33.312 ELECTROSTATIC = -38.9376 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5490" Parameter: CONF_N -> "8002" Comparing "5490" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5491" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766488 ATOM PAIRS WERE FOUND FOR ATOM LIST 42020 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 31060 from a total of 766488 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5491 -65.33765 -6.91197 0.58287 INTE EXTERN> -30.76369 -34.57396 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3376" Parameter: A <- "-65.3376" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7637" Parameter: B <- "-30.7637" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.574" Parameter: C <- "-34.574" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5491 TOTAL ENERGY = -65.3376 RDTITL> * VAN DER WAALS = -30.7637 ELECTROSTATIC = -34.574 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5491" Parameter: CONF_N -> "8002" Comparing "5491" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5492" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766488 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767646 ATOM PAIRS WERE FOUND FOR ATOM LIST 42017 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30496 from a total of 767646 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5492 -69.42041 4.08276 0.81422 INTE EXTERN> -23.88297 -45.53744 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4204" Parameter: A <- "-69.4204" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.883" Parameter: B <- "-23.883" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5374" Parameter: C <- "-45.5374" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5492 TOTAL ENERGY = -69.4204 RDTITL> * VAN DER WAALS = -23.883 ELECTROSTATIC = -45.5374 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5492" Parameter: CONF_N -> "8002" Comparing "5492" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5493" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767646 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41583 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30173 from a total of 761526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5493 -67.26008 -2.16033 0.48531 INTE EXTERN> -36.51164 -30.74844 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2601" Parameter: A <- "-67.2601" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.5116" Parameter: B <- "-36.5116" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.7484" Parameter: C <- "-30.7484" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5493 TOTAL ENERGY = -67.2601 RDTITL> * VAN DER WAALS = -36.5116 ELECTROSTATIC = -30.7484 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5493" Parameter: CONF_N -> "8002" Comparing "5493" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5494" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763474 ATOM PAIRS WERE FOUND FOR ATOM LIST 41879 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30101 from a total of 763474 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5494 -71.96648 4.70640 0.52873 INTE EXTERN> -33.08321 -38.88328 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9665" Parameter: A <- "-71.9665" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0832" Parameter: B <- "-33.0832" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8833" Parameter: C <- "-38.8833" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5494 TOTAL ENERGY = -71.9665 RDTITL> * VAN DER WAALS = -33.0832 ELECTROSTATIC = -38.8833 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5494" Parameter: CONF_N -> "8002" Comparing "5494" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5495" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763474 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764039 ATOM PAIRS WERE FOUND FOR ATOM LIST 41818 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29787 from a total of 764039 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5495 -66.91410 -5.05238 0.57653 INTE EXTERN> -31.07681 -35.83729 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9141" Parameter: A <- "-66.9141" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0768" Parameter: B <- "-31.0768" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8373" Parameter: C <- "-35.8373" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5495 TOTAL ENERGY = -66.9141 RDTITL> * VAN DER WAALS = -31.0768 ELECTROSTATIC = -35.8373 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5495" Parameter: CONF_N -> "8002" Comparing "5495" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5496" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764039 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759887 ATOM PAIRS WERE FOUND FOR ATOM LIST 41771 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30334 from a total of 759887 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5496 -70.87831 3.96421 0.52817 INTE EXTERN> -32.24800 -38.63031 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8783" Parameter: A <- "-70.8783" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.248" Parameter: B <- "-32.248" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6303" Parameter: C <- "-38.6303" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5496 TOTAL ENERGY = -70.8783 RDTITL> * VAN DER WAALS = -32.248 ELECTROSTATIC = -38.6303 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5496" Parameter: CONF_N -> "8002" Comparing "5496" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5497" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759887 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759644 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29914 from a total of 759644 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5497 -68.83958 -2.03873 0.54781 INTE EXTERN> -31.69193 -37.14765 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8396" Parameter: A <- "-68.8396" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6919" Parameter: B <- "-31.6919" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1476" Parameter: C <- "-37.1476" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5497 TOTAL ENERGY = -68.8396 RDTITL> * VAN DER WAALS = -31.6919 ELECTROSTATIC = -37.1476 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5497" Parameter: CONF_N -> "8002" Comparing "5497" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5498" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759644 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761521 ATOM PAIRS WERE FOUND FOR ATOM LIST 41833 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30350 from a total of 761521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5498 -71.20097 2.36139 0.61104 INTE EXTERN> -30.57428 -40.62669 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.201" Parameter: A <- "-71.201" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5743" Parameter: B <- "-30.5743" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6267" Parameter: C <- "-40.6267" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5498 TOTAL ENERGY = -71.201 RDTITL> * VAN DER WAALS = -30.5743 ELECTROSTATIC = -40.6267 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5498" Parameter: CONF_N -> "8002" Comparing "5498" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5499" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755864 ATOM PAIRS WERE FOUND FOR ATOM LIST 41480 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29892 from a total of 755864 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5499 -68.73881 -2.46216 0.66945 INTE EXTERN> -30.09919 -38.63962 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7388" Parameter: A <- "-68.7388" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0992" Parameter: B <- "-30.0992" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6396" Parameter: C <- "-38.6396" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5499 TOTAL ENERGY = -68.7388 RDTITL> * VAN DER WAALS = -30.0992 ELECTROSTATIC = -38.6396 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5499" Parameter: CONF_N -> "8002" Comparing "5499" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5500" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755864 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754012 ATOM PAIRS WERE FOUND FOR ATOM LIST 41416 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29579 from a total of 754012 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5500 -70.22011 1.48130 0.62583 INTE EXTERN> -30.62180 -39.59831 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2201" Parameter: A <- "-70.2201" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6218" Parameter: B <- "-30.6218" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5983" Parameter: C <- "-39.5983" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5500 TOTAL ENERGY = -70.2201 RDTITL> * VAN DER WAALS = -30.6218 ELECTROSTATIC = -39.5983 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5500" Parameter: CONF_N -> "8002" Comparing "5500" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5501" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754012 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757062 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29684 from a total of 757062 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5501 -72.41953 2.19942 0.55599 INTE EXTERN> -32.41044 -40.00909 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4195" Parameter: A <- "-72.4195" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4104" Parameter: B <- "-32.4104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0091" Parameter: C <- "-40.0091" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5501 TOTAL ENERGY = -72.4195 RDTITL> * VAN DER WAALS = -32.4104 ELECTROSTATIC = -40.0091 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5501" Parameter: CONF_N -> "8002" Comparing "5501" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5502" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757062 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755706 ATOM PAIRS WERE FOUND FOR ATOM LIST 41258 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30046 from a total of 755706 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5502 -69.29925 -3.12028 0.67660 INTE EXTERN> -29.81632 -39.48293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2993" Parameter: A <- "-69.2993" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8163" Parameter: B <- "-29.8163" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4829" Parameter: C <- "-39.4829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5502 TOTAL ENERGY = -69.2993 RDTITL> * VAN DER WAALS = -29.8163 ELECTROSTATIC = -39.4829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5502" Parameter: CONF_N -> "8002" Comparing "5502" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5503" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755706 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754040 ATOM PAIRS WERE FOUND FOR ATOM LIST 41465 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29871 from a total of 754040 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5503 -61.84968 -7.44957 0.78380 INTE EXTERN> -25.55672 -36.29296 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.8497" Parameter: A <- "-61.8497" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5567" Parameter: B <- "-25.5567" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.293" Parameter: C <- "-36.293" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5503 TOTAL ENERGY = -61.8497 RDTITL> * VAN DER WAALS = -25.5567 ELECTROSTATIC = -36.293 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5503" Parameter: CONF_N -> "8002" Comparing "5503" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5504" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754040 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757821 ATOM PAIRS WERE FOUND FOR ATOM LIST 41499 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29977 from a total of 757821 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5504 -73.92467 12.07499 0.67075 INTE EXTERN> -28.55995 -45.36472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9247" Parameter: A <- "-73.9247" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5599" Parameter: B <- "-28.5599" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3647" Parameter: C <- "-45.3647" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5504 TOTAL ENERGY = -73.9247 RDTITL> * VAN DER WAALS = -28.5599 ELECTROSTATIC = -45.3647 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5504" Parameter: CONF_N -> "8002" Comparing "5504" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5505" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757821 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748592 ATOM PAIRS WERE FOUND FOR ATOM LIST 41079 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29795 from a total of 748592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5505 -68.29597 -5.62870 0.58735 INTE EXTERN> -32.36331 -35.93266 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.296" Parameter: A <- "-68.296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3633" Parameter: B <- "-32.3633" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9327" Parameter: C <- "-35.9327" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5505 TOTAL ENERGY = -68.296 RDTITL> * VAN DER WAALS = -32.3633 ELECTROSTATIC = -35.9327 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5505" Parameter: CONF_N -> "8002" Comparing "5505" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5506" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757360 ATOM PAIRS WERE FOUND FOR ATOM LIST 41519 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30364 from a total of 757360 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5506 -71.10117 2.80520 0.68569 INTE EXTERN> -29.00630 -42.09487 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1012" Parameter: A <- "-71.1012" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0063" Parameter: B <- "-29.0063" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0949" Parameter: C <- "-42.0949" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5506 TOTAL ENERGY = -71.1012 RDTITL> * VAN DER WAALS = -29.0063 ELECTROSTATIC = -42.0949 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5506" Parameter: CONF_N -> "8002" Comparing "5506" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5507" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757360 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751763 ATOM PAIRS WERE FOUND FOR ATOM LIST 41287 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30059 from a total of 751763 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5507 -74.16062 3.05945 0.53129 INTE EXTERN> -33.22656 -40.93405 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1606" Parameter: A <- "-74.1606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2266" Parameter: B <- "-33.2266" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9341" Parameter: C <- "-40.9341" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5507 TOTAL ENERGY = -74.1606 RDTITL> * VAN DER WAALS = -33.2266 ELECTROSTATIC = -40.9341 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5507" Parameter: CONF_N -> "8002" Comparing "5507" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5508" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751763 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756038 ATOM PAIRS WERE FOUND FOR ATOM LIST 41404 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30286 from a total of 756038 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5508 -69.03697 -5.12364 0.59348 INTE EXTERN> -31.71924 -37.31773 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.037" Parameter: A <- "-69.037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7192" Parameter: B <- "-31.7192" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3177" Parameter: C <- "-37.3177" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5508 TOTAL ENERGY = -69.037 RDTITL> * VAN DER WAALS = -31.7192 ELECTROSTATIC = -37.3177 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5508" Parameter: CONF_N -> "8002" Comparing "5508" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5509" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756038 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757221 ATOM PAIRS WERE FOUND FOR ATOM LIST 41547 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29934 from a total of 757221 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5509 -74.88973 5.85276 0.66892 INTE EXTERN> -30.56065 -44.32908 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8897" Parameter: A <- "-74.8897" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5606" Parameter: B <- "-30.5606" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3291" Parameter: C <- "-44.3291" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5509 TOTAL ENERGY = -74.8897 RDTITL> * VAN DER WAALS = -30.5606 ELECTROSTATIC = -44.3291 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5509" Parameter: CONF_N -> "8002" Comparing "5509" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5510" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757221 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756600 ATOM PAIRS WERE FOUND FOR ATOM LIST 41497 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29921 from a total of 756600 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5510 -73.73901 -1.15072 0.59453 INTE EXTERN> -32.19897 -41.54004 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.739" Parameter: A <- "-73.739" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.199" Parameter: B <- "-32.199" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.54" Parameter: C <- "-41.54" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5510 TOTAL ENERGY = -73.739 RDTITL> * VAN DER WAALS = -32.199 ELECTROSTATIC = -41.54 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5510" Parameter: CONF_N -> "8002" Comparing "5510" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5511" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756600 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755303 ATOM PAIRS WERE FOUND FOR ATOM LIST 41514 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29974 from a total of 755303 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5511 -66.50856 -7.23045 0.47596 INTE EXTERN> -33.88035 -32.62821 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5086" Parameter: A <- "-66.5086" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8804" Parameter: B <- "-33.8804" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.6282" Parameter: C <- "-32.6282" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5511 TOTAL ENERGY = -66.5086 RDTITL> * VAN DER WAALS = -33.8804 ELECTROSTATIC = -32.6282 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5511" Parameter: CONF_N -> "8002" Comparing "5511" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5512" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755303 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761146 ATOM PAIRS WERE FOUND FOR ATOM LIST 41766 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30153 from a total of 761146 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5512 -75.38783 8.87927 0.63909 INTE EXTERN> -31.02132 -44.36651 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3878" Parameter: A <- "-75.3878" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0213" Parameter: B <- "-31.0213" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3665" Parameter: C <- "-44.3665" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5512 TOTAL ENERGY = -75.3878 RDTITL> * VAN DER WAALS = -31.0213 ELECTROSTATIC = -44.3665 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5512" Parameter: CONF_N -> "8002" Comparing "5512" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5513" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761146 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757875 ATOM PAIRS WERE FOUND FOR ATOM LIST 41616 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30411 from a total of 757875 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5513 -76.68788 1.30005 0.58803 INTE EXTERN> -33.16519 -43.52269 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6879" Parameter: A <- "-76.6879" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1652" Parameter: B <- "-33.1652" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5227" Parameter: C <- "-43.5227" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5513 TOTAL ENERGY = -76.6879 RDTITL> * VAN DER WAALS = -33.1652 ELECTROSTATIC = -43.5227 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5513" Parameter: CONF_N -> "8002" Comparing "5513" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5514" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757875 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756013 ATOM PAIRS WERE FOUND FOR ATOM LIST 41443 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30077 from a total of 756013 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5514 -79.72517 3.03729 0.51411 INTE EXTERN> -33.78824 -45.93693 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7252" Parameter: A <- "-79.7252" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7882" Parameter: B <- "-33.7882" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9369" Parameter: C <- "-45.9369" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5514 TOTAL ENERGY = -79.7252 RDTITL> * VAN DER WAALS = -33.7882 ELECTROSTATIC = -45.9369 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5514" Parameter: CONF_N -> "8002" Comparing "5514" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5515" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756013 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756326 ATOM PAIRS WERE FOUND FOR ATOM LIST 41478 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29816 from a total of 756326 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5515 -74.22288 -5.50229 0.55998 INTE EXTERN> -32.58941 -41.63346 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2229" Parameter: A <- "-74.2229" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5894" Parameter: B <- "-32.5894" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6335" Parameter: C <- "-41.6335" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5515 TOTAL ENERGY = -74.2229 RDTITL> * VAN DER WAALS = -32.5894 ELECTROSTATIC = -41.6335 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5515" Parameter: CONF_N -> "8002" Comparing "5515" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5516" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756326 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758689 ATOM PAIRS WERE FOUND FOR ATOM LIST 41520 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30158 from a total of 758689 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5516 -71.79318 -2.42969 0.61998 INTE EXTERN> -29.60909 -42.18409 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7932" Parameter: A <- "-71.7932" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6091" Parameter: B <- "-29.6091" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1841" Parameter: C <- "-42.1841" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5516 TOTAL ENERGY = -71.7932 RDTITL> * VAN DER WAALS = -29.6091 ELECTROSTATIC = -42.1841 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5516" Parameter: CONF_N -> "8002" Comparing "5516" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5517" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758689 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753193 ATOM PAIRS WERE FOUND FOR ATOM LIST 41416 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29786 from a total of 753193 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5517 -76.79893 5.00575 0.55343 INTE EXTERN> -33.84044 -42.95849 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7989" Parameter: A <- "-76.7989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8404" Parameter: B <- "-33.8404" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9585" Parameter: C <- "-42.9585" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5517 TOTAL ENERGY = -76.7989 RDTITL> * VAN DER WAALS = -33.8404 ELECTROSTATIC = -42.9585 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5517" Parameter: CONF_N -> "8002" Comparing "5517" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5518" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753193 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749475 ATOM PAIRS WERE FOUND FOR ATOM LIST 41144 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29636 from a total of 749475 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5518 -72.57725 -4.22169 0.74020 INTE EXTERN> -28.30782 -44.26942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5772" Parameter: A <- "-72.5772" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3078" Parameter: B <- "-28.3078" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2694" Parameter: C <- "-44.2694" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5518 TOTAL ENERGY = -72.5772 RDTITL> * VAN DER WAALS = -28.3078 ELECTROSTATIC = -44.2694 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5518" Parameter: CONF_N -> "8002" Comparing "5518" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5519" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749475 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756481 ATOM PAIRS WERE FOUND FOR ATOM LIST 41293 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30108 from a total of 756481 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5519 -76.25173 3.67449 0.57522 INTE EXTERN> -28.90193 -47.34981 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2517" Parameter: A <- "-76.2517" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9019" Parameter: B <- "-28.9019" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3498" Parameter: C <- "-47.3498" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5519 TOTAL ENERGY = -76.2517 RDTITL> * VAN DER WAALS = -28.9019 ELECTROSTATIC = -47.3498 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5519" Parameter: CONF_N -> "8002" Comparing "5519" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5520" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756481 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760758 ATOM PAIRS WERE FOUND FOR ATOM LIST 41513 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29867 from a total of 760758 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5520 -72.12409 -4.12765 0.65718 INTE EXTERN> -29.69151 -42.43258 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1241" Parameter: A <- "-72.1241" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6915" Parameter: B <- "-29.6915" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4326" Parameter: C <- "-42.4326" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5520 TOTAL ENERGY = -72.1241 RDTITL> * VAN DER WAALS = -29.6915 ELECTROSTATIC = -42.4326 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5520" Parameter: CONF_N -> "8002" Comparing "5520" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5521" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760758 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756901 ATOM PAIRS WERE FOUND FOR ATOM LIST 41609 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29608 from a total of 756901 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5521 -67.29110 -4.83299 0.59733 INTE EXTERN> -30.51387 -36.77722 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2911" Parameter: A <- "-67.2911" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5139" Parameter: B <- "-30.5139" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7772" Parameter: C <- "-36.7772" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5521 TOTAL ENERGY = -67.2911 RDTITL> * VAN DER WAALS = -30.5139 ELECTROSTATIC = -36.7772 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5521" Parameter: CONF_N -> "8002" Comparing "5521" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5522" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756901 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754643 ATOM PAIRS WERE FOUND FOR ATOM LIST 41410 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29877 from a total of 754643 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5522 -71.57391 4.28281 0.65809 INTE EXTERN> -26.39452 -45.17940 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5739" Parameter: A <- "-71.5739" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3945" Parameter: B <- "-26.3945" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1794" Parameter: C <- "-45.1794" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5522 TOTAL ENERGY = -71.5739 RDTITL> * VAN DER WAALS = -26.3945 ELECTROSTATIC = -45.1794 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5522" Parameter: CONF_N -> "8002" Comparing "5522" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5523" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754643 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757122 ATOM PAIRS WERE FOUND FOR ATOM LIST 41397 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29985 from a total of 757122 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5523 -70.00555 -1.56836 0.58334 INTE EXTERN> -32.10413 -37.90142 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0056" Parameter: A <- "-70.0056" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1041" Parameter: B <- "-32.1041" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9014" Parameter: C <- "-37.9014" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5523 TOTAL ENERGY = -70.0056 RDTITL> * VAN DER WAALS = -32.1041 ELECTROSTATIC = -37.9014 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5523" Parameter: CONF_N -> "8002" Comparing "5523" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5524" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757122 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760718 ATOM PAIRS WERE FOUND FOR ATOM LIST 41607 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29856 from a total of 760718 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5524 -71.04416 1.03861 0.54723 INTE EXTERN> -32.54380 -38.50036 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0442" Parameter: A <- "-71.0442" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5438" Parameter: B <- "-32.5438" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5004" Parameter: C <- "-38.5004" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5524 TOTAL ENERGY = -71.0442 RDTITL> * VAN DER WAALS = -32.5438 ELECTROSTATIC = -38.5004 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5524" Parameter: CONF_N -> "8002" Comparing "5524" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5525" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760718 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758841 ATOM PAIRS WERE FOUND FOR ATOM LIST 41623 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29778 from a total of 758841 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5525 -72.67720 1.63304 0.56944 INTE EXTERN> -31.18809 -41.48911 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6772" Parameter: A <- "-72.6772" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1881" Parameter: B <- "-31.1881" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4891" Parameter: C <- "-41.4891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5525 TOTAL ENERGY = -72.6772 RDTITL> * VAN DER WAALS = -31.1881 ELECTROSTATIC = -41.4891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5525" Parameter: CONF_N -> "8002" Comparing "5525" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5526" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758841 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756174 ATOM PAIRS WERE FOUND FOR ATOM LIST 41493 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29517 from a total of 756174 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5526 -68.83117 -3.84603 0.61824 INTE EXTERN> -26.63218 -42.19899 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8312" Parameter: A <- "-68.8312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6322" Parameter: B <- "-26.6322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.199" Parameter: C <- "-42.199" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5526 TOTAL ENERGY = -68.8312 RDTITL> * VAN DER WAALS = -26.6322 ELECTROSTATIC = -42.199 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5526" Parameter: CONF_N -> "8002" Comparing "5526" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5527" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756174 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754906 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30383 from a total of 754906 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5527 -71.16177 2.33060 0.54218 INTE EXTERN> -34.75034 -36.41143 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1618" Parameter: A <- "-71.1618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.7503" Parameter: B <- "-34.7503" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4114" Parameter: C <- "-36.4114" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5527 TOTAL ENERGY = -71.1618 RDTITL> * VAN DER WAALS = -34.7503 ELECTROSTATIC = -36.4114 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5527" Parameter: CONF_N -> "8002" Comparing "5527" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5528" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754906 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749084 ATOM PAIRS WERE FOUND FOR ATOM LIST 41143 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29774 from a total of 749084 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5528 -68.50497 -2.65680 0.59708 INTE EXTERN> -30.21528 -38.28969 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.505" Parameter: A <- "-68.505" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2153" Parameter: B <- "-30.2153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2897" Parameter: C <- "-38.2897" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5528 TOTAL ENERGY = -68.505 RDTITL> * VAN DER WAALS = -30.2153 ELECTROSTATIC = -38.2897 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5528" Parameter: CONF_N -> "8002" Comparing "5528" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5529" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749084 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41497 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29350 from a total of 755794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5529 -72.85310 4.34813 0.60268 INTE EXTERN> -31.13740 -41.71570 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8531" Parameter: A <- "-72.8531" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1374" Parameter: B <- "-31.1374" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7157" Parameter: C <- "-41.7157" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5529 TOTAL ENERGY = -72.8531 RDTITL> * VAN DER WAALS = -31.1374 ELECTROSTATIC = -41.7157 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5529" Parameter: CONF_N -> "8002" Comparing "5529" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5530" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754816 ATOM PAIRS WERE FOUND FOR ATOM LIST 41435 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29945 from a total of 754816 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5530 -69.35024 -3.50286 0.58943 INTE EXTERN> -30.51732 -38.83292 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3502" Parameter: A <- "-69.3502" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5173" Parameter: B <- "-30.5173" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8329" Parameter: C <- "-38.8329" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5530 TOTAL ENERGY = -69.3502 RDTITL> * VAN DER WAALS = -30.5173 ELECTROSTATIC = -38.8329 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5530" Parameter: CONF_N -> "8002" Comparing "5530" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5531" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754816 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755914 ATOM PAIRS WERE FOUND FOR ATOM LIST 41512 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30051 from a total of 755914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5531 -70.27829 0.92805 0.57320 INTE EXTERN> -30.19528 -40.08301 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2783" Parameter: A <- "-70.2783" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1953" Parameter: B <- "-30.1953" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.083" Parameter: C <- "-40.083" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5531 TOTAL ENERGY = -70.2783 RDTITL> * VAN DER WAALS = -30.1953 ELECTROSTATIC = -40.083 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5531" Parameter: CONF_N -> "8002" Comparing "5531" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5532" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757738 ATOM PAIRS WERE FOUND FOR ATOM LIST 41625 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30433 from a total of 757738 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5532 -72.12088 1.84258 0.71573 INTE EXTERN> -27.69851 -44.42237 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1209" Parameter: A <- "-72.1209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6985" Parameter: B <- "-27.6985" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4224" Parameter: C <- "-44.4224" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5532 TOTAL ENERGY = -72.1209 RDTITL> * VAN DER WAALS = -27.6985 ELECTROSTATIC = -44.4224 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5532" Parameter: CONF_N -> "8002" Comparing "5532" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5533" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757738 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755740 ATOM PAIRS WERE FOUND FOR ATOM LIST 41424 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30563 from a total of 755740 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5533 -72.03703 -0.08385 0.59652 INTE EXTERN> -28.91102 -43.12600 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.037" Parameter: A <- "-72.037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.911" Parameter: B <- "-28.911" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.126" Parameter: C <- "-43.126" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5533 TOTAL ENERGY = -72.037 RDTITL> * VAN DER WAALS = -28.911 ELECTROSTATIC = -43.126 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5533" Parameter: CONF_N -> "8002" Comparing "5533" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5534" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755740 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753059 ATOM PAIRS WERE FOUND FOR ATOM LIST 41326 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30088 from a total of 753059 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5534 -71.45276 -0.58427 0.60752 INTE EXTERN> -30.23835 -41.21441 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4528" Parameter: A <- "-71.4528" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2384" Parameter: B <- "-30.2384" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2144" Parameter: C <- "-41.2144" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5534 TOTAL ENERGY = -71.4528 RDTITL> * VAN DER WAALS = -30.2384 ELECTROSTATIC = -41.2144 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5534" Parameter: CONF_N -> "8002" Comparing "5534" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5535" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753059 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757418 ATOM PAIRS WERE FOUND FOR ATOM LIST 41461 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30162 from a total of 757418 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5535 -74.97329 3.52052 0.61218 INTE EXTERN> -30.30816 -44.66512 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9733" Parameter: A <- "-74.9733" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3082" Parameter: B <- "-30.3082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6651" Parameter: C <- "-44.6651" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5535 TOTAL ENERGY = -74.9733 RDTITL> * VAN DER WAALS = -30.3082 ELECTROSTATIC = -44.6651 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5535" Parameter: CONF_N -> "8002" Comparing "5535" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5536" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757418 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764691 ATOM PAIRS WERE FOUND FOR ATOM LIST 41832 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30455 from a total of 764691 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5536 -69.56390 -5.40939 0.54102 INTE EXTERN> -33.26622 -36.29768 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5639" Parameter: A <- "-69.5639" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2662" Parameter: B <- "-33.2662" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2977" Parameter: C <- "-36.2977" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5536 TOTAL ENERGY = -69.5639 RDTITL> * VAN DER WAALS = -33.2662 ELECTROSTATIC = -36.2977 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5536" Parameter: CONF_N -> "8002" Comparing "5536" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5537" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764691 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760022 ATOM PAIRS WERE FOUND FOR ATOM LIST 41633 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29943 from a total of 760022 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5537 -68.86563 -0.69827 0.55700 INTE EXTERN> -28.72777 -40.13785 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8656" Parameter: A <- "-68.8656" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7278" Parameter: B <- "-28.7278" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1379" Parameter: C <- "-40.1379" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5537 TOTAL ENERGY = -68.8656 RDTITL> * VAN DER WAALS = -28.7278 ELECTROSTATIC = -40.1379 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5537" Parameter: CONF_N -> "8002" Comparing "5537" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5538" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760022 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761649 ATOM PAIRS WERE FOUND FOR ATOM LIST 41716 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29652 from a total of 761649 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5538 -79.92138 11.05576 0.57738 INTE EXTERN> -31.97686 -47.94452 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9214" Parameter: A <- "-79.9214" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9769" Parameter: B <- "-31.9769" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9445" Parameter: C <- "-47.9445" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5538 TOTAL ENERGY = -79.9214 RDTITL> * VAN DER WAALS = -31.9769 ELECTROSTATIC = -47.9445 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5538" Parameter: CONF_N -> "8002" Comparing "5538" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5539" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761649 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760860 ATOM PAIRS WERE FOUND FOR ATOM LIST 41940 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29312 from a total of 760860 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5539 -63.67480 -16.24659 0.53588 INTE EXTERN> -31.24206 -32.43274 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6748" Parameter: A <- "-63.6748" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2421" Parameter: B <- "-31.2421" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.4327" Parameter: C <- "-32.4327" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5539 TOTAL ENERGY = -63.6748 RDTITL> * VAN DER WAALS = -31.2421 ELECTROSTATIC = -32.4327 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5539" Parameter: CONF_N -> "8002" Comparing "5539" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5540" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760860 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755868 ATOM PAIRS WERE FOUND FOR ATOM LIST 41317 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29937 from a total of 755868 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5540 -66.01170 2.33690 0.59089 INTE EXTERN> -28.39462 -37.61708 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0117" Parameter: A <- "-66.0117" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3946" Parameter: B <- "-28.3946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6171" Parameter: C <- "-37.6171" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5540 TOTAL ENERGY = -66.0117 RDTITL> * VAN DER WAALS = -28.3946 ELECTROSTATIC = -37.6171 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5540" Parameter: CONF_N -> "8002" Comparing "5540" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5541" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755868 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758928 ATOM PAIRS WERE FOUND FOR ATOM LIST 41571 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30569 from a total of 758928 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5541 -70.07149 4.05979 0.64488 INTE EXTERN> -27.80372 -42.26777 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0715" Parameter: A <- "-70.0715" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8037" Parameter: B <- "-27.8037" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2678" Parameter: C <- "-42.2678" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5541 TOTAL ENERGY = -70.0715 RDTITL> * VAN DER WAALS = -27.8037 ELECTROSTATIC = -42.2678 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5541" Parameter: CONF_N -> "8002" Comparing "5541" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5542" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758928 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762431 ATOM PAIRS WERE FOUND FOR ATOM LIST 41788 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30267 from a total of 762431 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5542 -70.22421 0.15272 0.64931 INTE EXTERN> -30.91099 -39.31321 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2242" Parameter: A <- "-70.2242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.911" Parameter: B <- "-30.911" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3132" Parameter: C <- "-39.3132" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5542 TOTAL ENERGY = -70.2242 RDTITL> * VAN DER WAALS = -30.911 ELECTROSTATIC = -39.3132 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5542" Parameter: CONF_N -> "8002" Comparing "5542" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5543" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762431 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754582 ATOM PAIRS WERE FOUND FOR ATOM LIST 41311 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29767 from a total of 754582 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5543 -69.86315 -0.36105 0.53061 INTE EXTERN> -33.90097 -35.96218 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8632" Parameter: A <- "-69.8632" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.901" Parameter: B <- "-33.901" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9622" Parameter: C <- "-35.9622" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5543 TOTAL ENERGY = -69.8632 RDTITL> * VAN DER WAALS = -33.901 ELECTROSTATIC = -35.9622 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5543" Parameter: CONF_N -> "8002" Comparing "5543" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5544" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754582 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759617 ATOM PAIRS WERE FOUND FOR ATOM LIST 41799 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30131 from a total of 759617 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5544 -76.55364 6.69049 0.58939 INTE EXTERN> -32.86948 -43.68417 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5536" Parameter: A <- "-76.5536" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8695" Parameter: B <- "-32.8695" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6842" Parameter: C <- "-43.6842" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5544 TOTAL ENERGY = -76.5536 RDTITL> * VAN DER WAALS = -32.8695 ELECTROSTATIC = -43.6842 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5544" Parameter: CONF_N -> "8002" Comparing "5544" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5545" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759617 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758145 ATOM PAIRS WERE FOUND FOR ATOM LIST 41740 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29520 from a total of 758145 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5545 -61.52871 -15.02494 0.72886 INTE EXTERN> -27.06123 -34.46748 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.5287" Parameter: A <- "-61.5287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0612" Parameter: B <- "-27.0612" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4675" Parameter: C <- "-34.4675" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5545 TOTAL ENERGY = -61.5287 RDTITL> * VAN DER WAALS = -27.0612 ELECTROSTATIC = -34.4675 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5545" Parameter: CONF_N -> "8002" Comparing "5545" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5546" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758145 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762047 ATOM PAIRS WERE FOUND FOR ATOM LIST 41918 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30120 from a total of 762047 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5546 -68.15141 6.62270 0.54686 INTE EXTERN> -31.34370 -36.80771 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1514" Parameter: A <- "-68.1514" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3437" Parameter: B <- "-31.3437" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8077" Parameter: C <- "-36.8077" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5546 TOTAL ENERGY = -68.1514 RDTITL> * VAN DER WAALS = -31.3437 ELECTROSTATIC = -36.8077 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5546" Parameter: CONF_N -> "8002" Comparing "5546" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5547" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762047 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750615 ATOM PAIRS WERE FOUND FOR ATOM LIST 41136 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29906 from a total of 750615 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5547 -77.59305 9.44165 0.54835 INTE EXTERN> -33.85005 -43.74300 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5931" Parameter: A <- "-77.5931" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.85" Parameter: B <- "-33.85" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.743" Parameter: C <- "-43.743" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5547 TOTAL ENERGY = -77.5931 RDTITL> * VAN DER WAALS = -33.85 ELECTROSTATIC = -43.743 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5547" Parameter: CONF_N -> "8002" Comparing "5547" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5548" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750615 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753068 ATOM PAIRS WERE FOUND FOR ATOM LIST 41360 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29464 from a total of 753068 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5548 -68.29945 -9.29360 0.61044 INTE EXTERN> -29.20798 -39.09147 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2994" Parameter: A <- "-68.2994" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.208" Parameter: B <- "-29.208" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0915" Parameter: C <- "-39.0915" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5548 TOTAL ENERGY = -68.2994 RDTITL> * VAN DER WAALS = -29.208 ELECTROSTATIC = -39.0915 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5548" Parameter: CONF_N -> "8002" Comparing "5548" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5549" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753068 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760851 ATOM PAIRS WERE FOUND FOR ATOM LIST 41510 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30084 from a total of 760851 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5549 -71.27172 2.97228 0.47202 INTE EXTERN> -35.33129 -35.94044 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2717" Parameter: A <- "-71.2717" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.3313" Parameter: B <- "-35.3313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9404" Parameter: C <- "-35.9404" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5549 TOTAL ENERGY = -71.2717 RDTITL> * VAN DER WAALS = -35.3313 ELECTROSTATIC = -35.9404 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5549" Parameter: CONF_N -> "8002" Comparing "5549" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5550" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760851 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763577 ATOM PAIRS WERE FOUND FOR ATOM LIST 41837 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30552 from a total of 763577 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5550 -74.04518 2.77345 0.47974 INTE EXTERN> -36.41897 -37.62621 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0452" Parameter: A <- "-74.0452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.419" Parameter: B <- "-36.419" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6262" Parameter: C <- "-37.6262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5550 TOTAL ENERGY = -74.0452 RDTITL> * VAN DER WAALS = -36.419 ELECTROSTATIC = -37.6262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5550" Parameter: CONF_N -> "8002" Comparing "5550" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5551" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763577 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760685 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29970 from a total of 760685 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5551 -74.13520 0.09002 0.59661 INTE EXTERN> -31.80498 -42.33021 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1352" Parameter: A <- "-74.1352" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.805" Parameter: B <- "-31.805" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3302" Parameter: C <- "-42.3302" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5551 TOTAL ENERGY = -74.1352 RDTITL> * VAN DER WAALS = -31.805 ELECTROSTATIC = -42.3302 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5551" Parameter: CONF_N -> "8002" Comparing "5551" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5552" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760685 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759853 ATOM PAIRS WERE FOUND FOR ATOM LIST 41774 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29886 from a total of 759853 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5552 -63.87198 -10.26322 0.63476 INTE EXTERN> -28.43579 -35.43619 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.872" Parameter: A <- "-63.872" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4358" Parameter: B <- "-28.4358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4362" Parameter: C <- "-35.4362" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5552 TOTAL ENERGY = -63.872 RDTITL> * VAN DER WAALS = -28.4358 ELECTROSTATIC = -35.4362 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5552" Parameter: CONF_N -> "8002" Comparing "5552" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5553" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759853 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758625 ATOM PAIRS WERE FOUND FOR ATOM LIST 41539 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29679 from a total of 758625 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5553 -70.69315 6.82117 0.57388 INTE EXTERN> -32.89610 -37.79705 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6931" Parameter: A <- "-70.6931" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8961" Parameter: B <- "-32.8961" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7971" Parameter: C <- "-37.7971" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5553 TOTAL ENERGY = -70.6931 RDTITL> * VAN DER WAALS = -32.8961 ELECTROSTATIC = -37.7971 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5553" Parameter: CONF_N -> "8002" Comparing "5553" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5554" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758625 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761552 ATOM PAIRS WERE FOUND FOR ATOM LIST 41555 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29989 from a total of 761552 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5554 -70.83876 0.14562 0.60538 INTE EXTERN> -29.08989 -41.74887 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8388" Parameter: A <- "-70.8388" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0899" Parameter: B <- "-29.0899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7489" Parameter: C <- "-41.7489" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5554 TOTAL ENERGY = -70.8388 RDTITL> * VAN DER WAALS = -29.0899 ELECTROSTATIC = -41.7489 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5554" Parameter: CONF_N -> "8002" Comparing "5554" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5555" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761552 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760699 ATOM PAIRS WERE FOUND FOR ATOM LIST 41670 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30001 from a total of 760699 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5555 -65.10236 -5.73641 0.64554 INTE EXTERN> -27.98224 -37.12011 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1024" Parameter: A <- "-65.1024" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9822" Parameter: B <- "-27.9822" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1201" Parameter: C <- "-37.1201" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5555 TOTAL ENERGY = -65.1024 RDTITL> * VAN DER WAALS = -27.9822 ELECTROSTATIC = -37.1201 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5555" Parameter: CONF_N -> "8002" Comparing "5555" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5556" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760699 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760905 ATOM PAIRS WERE FOUND FOR ATOM LIST 41777 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30201 from a total of 760905 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5556 -71.49103 6.38868 0.69630 INTE EXTERN> -29.28041 -42.21062 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.491" Parameter: A <- "-71.491" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2804" Parameter: B <- "-29.2804" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2106" Parameter: C <- "-42.2106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5556 TOTAL ENERGY = -71.491 RDTITL> * VAN DER WAALS = -29.2804 ELECTROSTATIC = -42.2106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5556" Parameter: CONF_N -> "8002" Comparing "5556" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5557" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760905 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765789 ATOM PAIRS WERE FOUND FOR ATOM LIST 42117 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30175 from a total of 765789 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5557 -70.46805 -1.02298 0.59233 INTE EXTERN> -29.25522 -41.21284 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4681" Parameter: A <- "-70.4681" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2552" Parameter: B <- "-29.2552" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2128" Parameter: C <- "-41.2128" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5557 TOTAL ENERGY = -70.4681 RDTITL> * VAN DER WAALS = -29.2552 ELECTROSTATIC = -41.2128 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5557" Parameter: CONF_N -> "8002" Comparing "5557" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5558" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765789 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762192 ATOM PAIRS WERE FOUND FOR ATOM LIST 41916 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30236 from a total of 762192 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5558 -71.47279 1.00474 0.56692 INTE EXTERN> -32.41706 -39.05573 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4728" Parameter: A <- "-71.4728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4171" Parameter: B <- "-32.4171" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0557" Parameter: C <- "-39.0557" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5558 TOTAL ENERGY = -71.4728 RDTITL> * VAN DER WAALS = -32.4171 ELECTROSTATIC = -39.0557 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5558" Parameter: CONF_N -> "8002" Comparing "5558" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5559" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762192 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761758 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30202 from a total of 761758 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5559 -66.93046 -4.54233 0.56989 INTE EXTERN> -31.97421 -34.95625 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9305" Parameter: A <- "-66.9305" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9742" Parameter: B <- "-31.9742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9562" Parameter: C <- "-34.9562" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5559 TOTAL ENERGY = -66.9305 RDTITL> * VAN DER WAALS = -31.9742 ELECTROSTATIC = -34.9562 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5559" Parameter: CONF_N -> "8002" Comparing "5559" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5560" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761758 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754254 ATOM PAIRS WERE FOUND FOR ATOM LIST 41437 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30058 from a total of 754254 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5560 -65.58849 -1.34196 0.69258 INTE EXTERN> -28.00843 -37.58007 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5885" Parameter: A <- "-65.5885" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0084" Parameter: B <- "-28.0084" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5801" Parameter: C <- "-37.5801" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5560 TOTAL ENERGY = -65.5885 RDTITL> * VAN DER WAALS = -28.0084 ELECTROSTATIC = -37.5801 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5560" Parameter: CONF_N -> "8002" Comparing "5560" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5561" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754254 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755703 ATOM PAIRS WERE FOUND FOR ATOM LIST 41633 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30412 from a total of 755703 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5561 -68.91044 3.32195 0.66098 INTE EXTERN> -28.77381 -40.13663 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9104" Parameter: A <- "-68.9104" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7738" Parameter: B <- "-28.7738" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1366" Parameter: C <- "-40.1366" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5561 TOTAL ENERGY = -68.9104 RDTITL> * VAN DER WAALS = -28.7738 ELECTROSTATIC = -40.1366 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5561" Parameter: CONF_N -> "8002" Comparing "5561" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5562" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755703 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751961 ATOM PAIRS WERE FOUND FOR ATOM LIST 41383 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29989 from a total of 751961 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5562 -72.93007 4.01963 0.65589 INTE EXTERN> -29.05490 -43.87517 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9301" Parameter: A <- "-72.9301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0549" Parameter: B <- "-29.0549" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8752" Parameter: C <- "-43.8752" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5562 TOTAL ENERGY = -72.9301 RDTITL> * VAN DER WAALS = -29.0549 ELECTROSTATIC = -43.8752 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5562" Parameter: CONF_N -> "8002" Comparing "5562" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5563" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751961 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750308 ATOM PAIRS WERE FOUND FOR ATOM LIST 41255 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30350 from a total of 750308 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5563 -77.43421 4.50414 0.65681 INTE EXTERN> -31.48509 -45.94912 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4342" Parameter: A <- "-77.4342" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4851" Parameter: B <- "-31.4851" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9491" Parameter: C <- "-45.9491" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5563 TOTAL ENERGY = -77.4342 RDTITL> * VAN DER WAALS = -31.4851 ELECTROSTATIC = -45.9491 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5563" Parameter: CONF_N -> "8002" Comparing "5563" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5564" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750308 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751886 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30505 from a total of 751886 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5564 -70.21974 -7.21448 0.67900 INTE EXTERN> -28.32423 -41.89550 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2197" Parameter: A <- "-70.2197" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3242" Parameter: B <- "-28.3242" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8955" Parameter: C <- "-41.8955" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5564 TOTAL ENERGY = -70.2197 RDTITL> * VAN DER WAALS = -28.3242 ELECTROSTATIC = -41.8955 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5564" Parameter: CONF_N -> "8002" Comparing "5564" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5565" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751886 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755077 ATOM PAIRS WERE FOUND FOR ATOM LIST 41408 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30207 from a total of 755077 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5565 -67.04225 -3.17749 0.59027 INTE EXTERN> -31.78141 -35.26084 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0422" Parameter: A <- "-67.0422" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7814" Parameter: B <- "-31.7814" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2608" Parameter: C <- "-35.2608" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5565 TOTAL ENERGY = -67.0422 RDTITL> * VAN DER WAALS = -31.7814 ELECTROSTATIC = -35.2608 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5565" Parameter: CONF_N -> "8002" Comparing "5565" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5566" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755077 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756446 ATOM PAIRS WERE FOUND FOR ATOM LIST 41606 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29736 from a total of 756446 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5566 -70.56976 3.52752 0.63977 INTE EXTERN> -28.65063 -41.91914 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5698" Parameter: A <- "-70.5698" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6506" Parameter: B <- "-28.6506" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9191" Parameter: C <- "-41.9191" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5566 TOTAL ENERGY = -70.5698 RDTITL> * VAN DER WAALS = -28.6506 ELECTROSTATIC = -41.9191 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5566" Parameter: CONF_N -> "8002" Comparing "5566" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5567" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756446 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755134 ATOM PAIRS WERE FOUND FOR ATOM LIST 41448 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30085 from a total of 755134 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5567 -71.35325 0.78349 0.65346 INTE EXTERN> -32.19532 -39.15793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3533" Parameter: A <- "-71.3533" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1953" Parameter: B <- "-32.1953" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1579" Parameter: C <- "-39.1579" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5567 TOTAL ENERGY = -71.3533 RDTITL> * VAN DER WAALS = -32.1953 ELECTROSTATIC = -39.1579 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5567" Parameter: CONF_N -> "8002" Comparing "5567" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5568" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755134 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753117 ATOM PAIRS WERE FOUND FOR ATOM LIST 41377 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30306 from a total of 753117 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5568 -72.58648 1.23323 0.74550 INTE EXTERN> -24.34722 -48.23926 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5865" Parameter: A <- "-72.5865" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3472" Parameter: B <- "-24.3472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2393" Parameter: C <- "-48.2393" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5568 TOTAL ENERGY = -72.5865 RDTITL> * VAN DER WAALS = -24.3472 ELECTROSTATIC = -48.2393 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5568" Parameter: CONF_N -> "8002" Comparing "5568" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5569" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753117 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751941 ATOM PAIRS WERE FOUND FOR ATOM LIST 41219 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29912 from a total of 751941 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5569 -70.21821 -2.36828 0.71414 INTE EXTERN> -27.18332 -43.03489 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2182" Parameter: A <- "-70.2182" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1833" Parameter: B <- "-27.1833" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0349" Parameter: C <- "-43.0349" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5569 TOTAL ENERGY = -70.2182 RDTITL> * VAN DER WAALS = -27.1833 ELECTROSTATIC = -43.0349 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5569" Parameter: CONF_N -> "8002" Comparing "5569" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5570" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751941 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755124 ATOM PAIRS WERE FOUND FOR ATOM LIST 41518 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29802 from a total of 755124 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5570 -61.35941 -8.85880 0.61293 INTE EXTERN> -30.92568 -30.43373 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.3594" Parameter: A <- "-61.3594" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9257" Parameter: B <- "-30.9257" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.4337" Parameter: C <- "-30.4337" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5570 TOTAL ENERGY = -61.3594 RDTITL> * VAN DER WAALS = -30.9257 ELECTROSTATIC = -30.4337 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5570" Parameter: CONF_N -> "8002" Comparing "5570" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5571" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755124 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758534 ATOM PAIRS WERE FOUND FOR ATOM LIST 41639 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29889 from a total of 758534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5571 -59.17848 -2.18093 0.51355 INTE EXTERN> -31.79474 -27.38374 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.1785" Parameter: A <- "-59.1785" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7947" Parameter: B <- "-31.7947" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.3837" Parameter: C <- "-27.3837" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5571 TOTAL ENERGY = -59.1785 RDTITL> * VAN DER WAALS = -31.7947 ELECTROSTATIC = -27.3837 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5571" Parameter: CONF_N -> "8002" Comparing "5571" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5572" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762132 ATOM PAIRS WERE FOUND FOR ATOM LIST 41876 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30595 from a total of 762132 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5572 -69.20027 10.02180 0.67768 INTE EXTERN> -27.63395 -41.56632 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2003" Parameter: A <- "-69.2003" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.634" Parameter: B <- "-27.634" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5663" Parameter: C <- "-41.5663" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5572 TOTAL ENERGY = -69.2003 RDTITL> * VAN DER WAALS = -27.634 ELECTROSTATIC = -41.5663 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5572" Parameter: CONF_N -> "8002" Comparing "5572" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5573" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762132 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753474 ATOM PAIRS WERE FOUND FOR ATOM LIST 41484 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30435 from a total of 753474 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5573 -64.56293 -4.63734 0.51863 INTE EXTERN> -31.95195 -32.61098 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5629" Parameter: A <- "-64.5629" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.952" Parameter: B <- "-31.952" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.611" Parameter: C <- "-32.611" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5573 TOTAL ENERGY = -64.5629 RDTITL> * VAN DER WAALS = -31.952 ELECTROSTATIC = -32.611 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5573" Parameter: CONF_N -> "8002" Comparing "5573" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5574" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753474 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758675 ATOM PAIRS WERE FOUND FOR ATOM LIST 41472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30439 from a total of 758675 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5574 -76.97840 12.41547 0.62819 INTE EXTERN> -31.20014 -45.77826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9784" Parameter: A <- "-76.9784" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2001" Parameter: B <- "-31.2001" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7783" Parameter: C <- "-45.7783" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5574 TOTAL ENERGY = -76.9784 RDTITL> * VAN DER WAALS = -31.2001 ELECTROSTATIC = -45.7783 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5574" Parameter: CONF_N -> "8002" Comparing "5574" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5575" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758675 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760015 ATOM PAIRS WERE FOUND FOR ATOM LIST 41865 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30666 from a total of 760015 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5575 -75.65983 -1.31857 0.67826 INTE EXTERN> -32.47705 -43.18278 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6598" Parameter: A <- "-75.6598" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4771" Parameter: B <- "-32.4771" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1828" Parameter: C <- "-43.1828" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5575 TOTAL ENERGY = -75.6598 RDTITL> * VAN DER WAALS = -32.4771 ELECTROSTATIC = -43.1828 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5575" Parameter: CONF_N -> "8002" Comparing "5575" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5576" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760015 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759669 ATOM PAIRS WERE FOUND FOR ATOM LIST 41728 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29785 from a total of 759669 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5576 -70.81069 -4.84915 0.50254 INTE EXTERN> -32.97389 -37.83679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8107" Parameter: A <- "-70.8107" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9739" Parameter: B <- "-32.9739" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8368" Parameter: C <- "-37.8368" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5576 TOTAL ENERGY = -70.8107 RDTITL> * VAN DER WAALS = -32.9739 ELECTROSTATIC = -37.8368 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5576" Parameter: CONF_N -> "8002" Comparing "5576" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5577" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759669 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759247 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30138 from a total of 759247 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5577 -73.63848 2.82780 0.57874 INTE EXTERN> -30.24051 -43.39797 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6385" Parameter: A <- "-73.6385" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2405" Parameter: B <- "-30.2405" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.398" Parameter: C <- "-43.398" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5577 TOTAL ENERGY = -73.6385 RDTITL> * VAN DER WAALS = -30.2405 ELECTROSTATIC = -43.398 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5577" Parameter: CONF_N -> "8002" Comparing "5577" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5578" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759247 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761507 ATOM PAIRS WERE FOUND FOR ATOM LIST 41811 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30094 from a total of 761507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5578 -71.11136 -2.52712 0.68455 INTE EXTERN> -29.04387 -42.06749 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1114" Parameter: A <- "-71.1114" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0439" Parameter: B <- "-29.0439" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0675" Parameter: C <- "-42.0675" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5578 TOTAL ENERGY = -71.1114 RDTITL> * VAN DER WAALS = -29.0439 ELECTROSTATIC = -42.0675 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5578" Parameter: CONF_N -> "8002" Comparing "5578" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5579" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760482 ATOM PAIRS WERE FOUND FOR ATOM LIST 41532 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30313 from a total of 760482 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5579 -72.47358 1.36221 0.52722 INTE EXTERN> -33.40665 -39.06692 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4736" Parameter: A <- "-72.4736" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4067" Parameter: B <- "-33.4067" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0669" Parameter: C <- "-39.0669" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5579 TOTAL ENERGY = -72.4736 RDTITL> * VAN DER WAALS = -33.4067 ELECTROSTATIC = -39.0669 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5579" Parameter: CONF_N -> "8002" Comparing "5579" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5580" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760482 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762633 ATOM PAIRS WERE FOUND FOR ATOM LIST 41732 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30900 from a total of 762633 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5580 -62.90609 -9.56749 0.61894 INTE EXTERN> -27.86407 -35.04202 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9061" Parameter: A <- "-62.9061" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8641" Parameter: B <- "-27.8641" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.042" Parameter: C <- "-35.042" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5580 TOTAL ENERGY = -62.9061 RDTITL> * VAN DER WAALS = -27.8641 ELECTROSTATIC = -35.042 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5580" Parameter: CONF_N -> "8002" Comparing "5580" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5581" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762633 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754497 ATOM PAIRS WERE FOUND FOR ATOM LIST 41473 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29913 from a total of 754497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5581 -73.12385 10.21777 0.62463 INTE EXTERN> -29.89479 -43.22906 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1239" Parameter: A <- "-73.1239" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8948" Parameter: B <- "-29.8948" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2291" Parameter: C <- "-43.2291" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5581 TOTAL ENERGY = -73.1239 RDTITL> * VAN DER WAALS = -29.8948 ELECTROSTATIC = -43.2291 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5581" Parameter: CONF_N -> "8002" Comparing "5581" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5582" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756712 ATOM PAIRS WERE FOUND FOR ATOM LIST 41623 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30435 from a total of 756712 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5582 -64.42529 -8.69857 0.53683 INTE EXTERN> -30.95434 -33.47095 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.4253" Parameter: A <- "-64.4253" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9543" Parameter: B <- "-30.9543" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.4709" Parameter: C <- "-33.4709" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5582 TOTAL ENERGY = -64.4253 RDTITL> * VAN DER WAALS = -30.9543 ELECTROSTATIC = -33.4709 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5582" Parameter: CONF_N -> "8002" Comparing "5582" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5583" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756712 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758766 ATOM PAIRS WERE FOUND FOR ATOM LIST 41752 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30389 from a total of 758766 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5583 -70.46887 6.04358 0.52840 INTE EXTERN> -31.60450 -38.86437 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4689" Parameter: A <- "-70.4689" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6045" Parameter: B <- "-31.6045" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8644" Parameter: C <- "-38.8644" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5583 TOTAL ENERGY = -70.4689 RDTITL> * VAN DER WAALS = -31.6045 ELECTROSTATIC = -38.8644 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5583" Parameter: CONF_N -> "8002" Comparing "5583" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5584" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758766 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763017 ATOM PAIRS WERE FOUND FOR ATOM LIST 41738 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30610 from a total of 763017 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5584 -65.49041 -4.97846 0.61729 INTE EXTERN> -31.03380 -34.45661 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4904" Parameter: A <- "-65.4904" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0338" Parameter: B <- "-31.0338" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4566" Parameter: C <- "-34.4566" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5584 TOTAL ENERGY = -65.4904 RDTITL> * VAN DER WAALS = -31.0338 ELECTROSTATIC = -34.4566 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5584" Parameter: CONF_N -> "8002" Comparing "5584" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5585" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763017 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767268 ATOM PAIRS WERE FOUND FOR ATOM LIST 42055 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30813 from a total of 767268 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5585 -77.47086 11.98045 0.65534 INTE EXTERN> -28.47197 -48.99890 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4709" Parameter: A <- "-77.4709" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.472" Parameter: B <- "-28.472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9989" Parameter: C <- "-48.9989" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5585 TOTAL ENERGY = -77.4709 RDTITL> * VAN DER WAALS = -28.472 ELECTROSTATIC = -48.9989 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5585" Parameter: CONF_N -> "8002" Comparing "5585" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5586" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767268 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762498 ATOM PAIRS WERE FOUND FOR ATOM LIST 41785 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30017 from a total of 762498 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5586 -65.50530 -11.96556 0.52709 INTE EXTERN> -32.40379 -33.10151 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5053" Parameter: A <- "-65.5053" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4038" Parameter: B <- "-32.4038" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1015" Parameter: C <- "-33.1015" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5586 TOTAL ENERGY = -65.5053 RDTITL> * VAN DER WAALS = -32.4038 ELECTROSTATIC = -33.1015 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5586" Parameter: CONF_N -> "8002" Comparing "5586" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5587" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762498 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760968 ATOM PAIRS WERE FOUND FOR ATOM LIST 41739 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29585 from a total of 760968 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5587 -70.82922 5.32392 0.52470 INTE EXTERN> -32.49734 -38.33188 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8292" Parameter: A <- "-70.8292" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4973" Parameter: B <- "-32.4973" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3319" Parameter: C <- "-38.3319" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5587 TOTAL ENERGY = -70.8292 RDTITL> * VAN DER WAALS = -32.4973 ELECTROSTATIC = -38.3319 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5587" Parameter: CONF_N -> "8002" Comparing "5587" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5588" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760968 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758301 ATOM PAIRS WERE FOUND FOR ATOM LIST 41826 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30395 from a total of 758301 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5588 -67.47205 -3.35717 0.55732 INTE EXTERN> -30.49279 -36.97926 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.472" Parameter: A <- "-67.472" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4928" Parameter: B <- "-30.4928" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9793" Parameter: C <- "-36.9793" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5588 TOTAL ENERGY = -67.472 RDTITL> * VAN DER WAALS = -30.4928 ELECTROSTATIC = -36.9793 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5588" Parameter: CONF_N -> "8002" Comparing "5588" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5589" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758301 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762252 ATOM PAIRS WERE FOUND FOR ATOM LIST 42049 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30912 from a total of 762252 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5589 -70.27485 2.80280 0.58643 INTE EXTERN> -29.47353 -40.80132 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2748" Parameter: A <- "-70.2748" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4735" Parameter: B <- "-29.4735" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8013" Parameter: C <- "-40.8013" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5589 TOTAL ENERGY = -70.2748 RDTITL> * VAN DER WAALS = -29.4735 ELECTROSTATIC = -40.8013 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5589" Parameter: CONF_N -> "8002" Comparing "5589" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5590" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762252 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766161 ATOM PAIRS WERE FOUND FOR ATOM LIST 42075 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30687 from a total of 766161 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5590 -70.66182 0.38697 0.58419 INTE EXTERN> -30.73061 -39.93121 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6618" Parameter: A <- "-70.6618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7306" Parameter: B <- "-30.7306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9312" Parameter: C <- "-39.9312" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5590 TOTAL ENERGY = -70.6618 RDTITL> * VAN DER WAALS = -30.7306 ELECTROSTATIC = -39.9312 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5590" Parameter: CONF_N -> "8002" Comparing "5590" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5591" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766161 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764266 ATOM PAIRS WERE FOUND FOR ATOM LIST 42052 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30317 from a total of 764266 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5591 -67.37973 -3.28209 0.54234 INTE EXTERN> -32.74617 -34.63356 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3797" Parameter: A <- "-67.3797" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7462" Parameter: B <- "-32.7462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.6336" Parameter: C <- "-34.6336" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5591 TOTAL ENERGY = -67.3797 RDTITL> * VAN DER WAALS = -32.7462 ELECTROSTATIC = -34.6336 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5591" Parameter: CONF_N -> "8002" Comparing "5591" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5592" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764266 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762069 ATOM PAIRS WERE FOUND FOR ATOM LIST 41840 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30404 from a total of 762069 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5592 -69.04722 1.66749 0.57906 INTE EXTERN> -28.19828 -40.84894 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0472" Parameter: A <- "-69.0472" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1983" Parameter: B <- "-28.1983" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8489" Parameter: C <- "-40.8489" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5592 TOTAL ENERGY = -69.0472 RDTITL> * VAN DER WAALS = -28.1983 ELECTROSTATIC = -40.8489 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5592" Parameter: CONF_N -> "8002" Comparing "5592" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5593" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762069 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759203 ATOM PAIRS WERE FOUND FOR ATOM LIST 41670 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29888 from a total of 759203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5593 -71.19460 2.14739 0.60389 INTE EXTERN> -32.76749 -38.42711 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1946" Parameter: A <- "-71.1946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7675" Parameter: B <- "-32.7675" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4271" Parameter: C <- "-38.4271" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5593 TOTAL ENERGY = -71.1946 RDTITL> * VAN DER WAALS = -32.7675 ELECTROSTATIC = -38.4271 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5593" Parameter: CONF_N -> "8002" Comparing "5593" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5594" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765636 ATOM PAIRS WERE FOUND FOR ATOM LIST 42022 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29620 from a total of 765636 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5594 -63.28453 -7.91008 0.61755 INTE EXTERN> -25.89841 -37.38612 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.2845" Parameter: A <- "-63.2845" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8984" Parameter: B <- "-25.8984" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3861" Parameter: C <- "-37.3861" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5594 TOTAL ENERGY = -63.2845 RDTITL> * VAN DER WAALS = -25.8984 ELECTROSTATIC = -37.3861 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5594" Parameter: CONF_N -> "8002" Comparing "5594" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5595" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765636 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 770469 ATOM PAIRS WERE FOUND FOR ATOM LIST 42328 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 31092 from a total of 770469 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5595 -73.97586 10.69133 0.59148 INTE EXTERN> -32.30614 -41.66972 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9759" Parameter: A <- "-73.9759" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3061" Parameter: B <- "-32.3061" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6697" Parameter: C <- "-41.6697" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5595 TOTAL ENERGY = -73.9759 RDTITL> * VAN DER WAALS = -32.3061 ELECTROSTATIC = -41.6697 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5595" Parameter: CONF_N -> "8002" Comparing "5595" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5596" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 770469 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762131 ATOM PAIRS WERE FOUND FOR ATOM LIST 41634 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30272 from a total of 762131 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5596 -71.76141 -2.21445 0.60806 INTE EXTERN> -29.91164 -41.84977 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7614" Parameter: A <- "-71.7614" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9116" Parameter: B <- "-29.9116" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8498" Parameter: C <- "-41.8498" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5596 TOTAL ENERGY = -71.7614 RDTITL> * VAN DER WAALS = -29.9116 ELECTROSTATIC = -41.8498 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5596" Parameter: CONF_N -> "8002" Comparing "5596" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5597" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762131 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766391 ATOM PAIRS WERE FOUND FOR ATOM LIST 42078 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30034 from a total of 766391 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5597 -69.89108 -1.87033 0.51845 INTE EXTERN> -32.06293 -37.82815 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8911" Parameter: A <- "-69.8911" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0629" Parameter: B <- "-32.0629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8282" Parameter: C <- "-37.8282" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5597 TOTAL ENERGY = -69.8911 RDTITL> * VAN DER WAALS = -32.0629 ELECTROSTATIC = -37.8282 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5597" Parameter: CONF_N -> "8002" Comparing "5597" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5598" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766391 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759451 ATOM PAIRS WERE FOUND FOR ATOM LIST 41699 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29844 from a total of 759451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5598 -69.51956 -0.37152 0.47252 INTE EXTERN> -35.31211 -34.20746 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5196" Parameter: A <- "-69.5196" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.3121" Parameter: B <- "-35.3121" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2075" Parameter: C <- "-34.2075" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5598 TOTAL ENERGY = -69.5196 RDTITL> * VAN DER WAALS = -35.3121 ELECTROSTATIC = -34.2075 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5598" Parameter: CONF_N -> "8002" Comparing "5598" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5599" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758507 ATOM PAIRS WERE FOUND FOR ATOM LIST 41685 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30213 from a total of 758507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5599 -71.54415 2.02459 0.57273 INTE EXTERN> -34.01344 -37.53071 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5441" Parameter: A <- "-71.5441" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0134" Parameter: B <- "-34.0134" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5307" Parameter: C <- "-37.5307" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5599 TOTAL ENERGY = -71.5441 RDTITL> * VAN DER WAALS = -34.0134 ELECTROSTATIC = -37.5307 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5599" Parameter: CONF_N -> "8002" Comparing "5599" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5600" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760548 ATOM PAIRS WERE FOUND FOR ATOM LIST 41715 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29790 from a total of 760548 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5600 -72.61243 1.06828 0.59108 INTE EXTERN> -28.66856 -43.94387 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6124" Parameter: A <- "-72.6124" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6686" Parameter: B <- "-28.6686" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9439" Parameter: C <- "-43.9439" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5600 TOTAL ENERGY = -72.6124 RDTITL> * VAN DER WAALS = -28.6686 ELECTROSTATIC = -43.9439 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5600" Parameter: CONF_N -> "8002" Comparing "5600" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5601" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760548 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760637 ATOM PAIRS WERE FOUND FOR ATOM LIST 41883 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30502 from a total of 760637 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5601 -74.50750 1.89508 0.60073 INTE EXTERN> -30.27573 -44.23178 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5075" Parameter: A <- "-74.5075" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2757" Parameter: B <- "-30.2757" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2318" Parameter: C <- "-44.2318" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5601 TOTAL ENERGY = -74.5075 RDTITL> * VAN DER WAALS = -30.2757 ELECTROSTATIC = -44.2318 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5601" Parameter: CONF_N -> "8002" Comparing "5601" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5602" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760637 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758205 ATOM PAIRS WERE FOUND FOR ATOM LIST 41728 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29513 from a total of 758205 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5602 -72.35114 -2.15636 0.55421 INTE EXTERN> -30.40288 -41.94826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3511" Parameter: A <- "-72.3511" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4029" Parameter: B <- "-30.4029" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9483" Parameter: C <- "-41.9483" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5602 TOTAL ENERGY = -72.3511 RDTITL> * VAN DER WAALS = -30.4029 ELECTROSTATIC = -41.9483 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5602" Parameter: CONF_N -> "8002" Comparing "5602" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5603" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758205 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762592 ATOM PAIRS WERE FOUND FOR ATOM LIST 41888 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30565 from a total of 762592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5603 -70.71693 -1.63421 0.56836 INTE EXTERN> -31.22731 -39.48962 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7169" Parameter: A <- "-70.7169" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2273" Parameter: B <- "-31.2273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4896" Parameter: C <- "-39.4896" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5603 TOTAL ENERGY = -70.7169 RDTITL> * VAN DER WAALS = -31.2273 ELECTROSTATIC = -39.4896 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5603" Parameter: CONF_N -> "8002" Comparing "5603" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5604" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762390 ATOM PAIRS WERE FOUND FOR ATOM LIST 42022 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29951 from a total of 762390 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5604 -77.28572 6.56879 0.53314 INTE EXTERN> -32.79773 -44.48799 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2857" Parameter: A <- "-77.2857" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7977" Parameter: B <- "-32.7977" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.488" Parameter: C <- "-44.488" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5604 TOTAL ENERGY = -77.2857 RDTITL> * VAN DER WAALS = -32.7977 ELECTROSTATIC = -44.488 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5604" Parameter: CONF_N -> "8002" Comparing "5604" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5605" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762390 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767941 ATOM PAIRS WERE FOUND FOR ATOM LIST 42203 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30231 from a total of 767941 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5605 -69.38200 -7.90373 0.51121 INTE EXTERN> -30.79780 -38.58420 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.382" Parameter: A <- "-69.382" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7978" Parameter: B <- "-30.7978" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5842" Parameter: C <- "-38.5842" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5605 TOTAL ENERGY = -69.382 RDTITL> * VAN DER WAALS = -30.7978 ELECTROSTATIC = -38.5842 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5605" Parameter: CONF_N -> "8002" Comparing "5605" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5606" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767941 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760629 ATOM PAIRS WERE FOUND FOR ATOM LIST 41915 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30102 from a total of 760629 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5606 -64.81543 -4.56657 0.57462 INTE EXTERN> -25.47532 -39.34010 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8154" Parameter: A <- "-64.8154" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4753" Parameter: B <- "-25.4753" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3401" Parameter: C <- "-39.3401" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5606 TOTAL ENERGY = -64.8154 RDTITL> * VAN DER WAALS = -25.4753 ELECTROSTATIC = -39.3401 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5606" Parameter: CONF_N -> "8002" Comparing "5606" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5607" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760629 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761185 ATOM PAIRS WERE FOUND FOR ATOM LIST 41865 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30318 from a total of 761185 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5607 -76.71620 11.90077 0.59019 INTE EXTERN> -30.58618 -46.13002 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7162" Parameter: A <- "-76.7162" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5862" Parameter: B <- "-30.5862" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.13" Parameter: C <- "-46.13" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5607 TOTAL ENERGY = -76.7162 RDTITL> * VAN DER WAALS = -30.5862 ELECTROSTATIC = -46.13 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5607" Parameter: CONF_N -> "8002" Comparing "5607" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5608" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761185 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765389 ATOM PAIRS WERE FOUND FOR ATOM LIST 42011 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29983 from a total of 765389 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5608 -66.49247 -10.22373 0.63785 INTE EXTERN> -26.92493 -39.56754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4925" Parameter: A <- "-66.4925" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9249" Parameter: B <- "-26.9249" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5675" Parameter: C <- "-39.5675" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5608 TOTAL ENERGY = -66.4925 RDTITL> * VAN DER WAALS = -26.9249 ELECTROSTATIC = -39.5675 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5608" Parameter: CONF_N -> "8002" Comparing "5608" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5609" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765389 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763413 ATOM PAIRS WERE FOUND FOR ATOM LIST 41951 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29586 from a total of 763413 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5609 -64.50651 -1.98596 0.53297 INTE EXTERN> -33.05868 -31.44784 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5065" Parameter: A <- "-64.5065" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0587" Parameter: B <- "-33.0587" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4478" Parameter: C <- "-31.4478" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5609 TOTAL ENERGY = -64.5065 RDTITL> * VAN DER WAALS = -33.0587 ELECTROSTATIC = -31.4478 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5609" Parameter: CONF_N -> "8002" Comparing "5609" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5610" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763413 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762058 ATOM PAIRS WERE FOUND FOR ATOM LIST 41768 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29429 from a total of 762058 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5610 -73.10625 8.59974 0.57380 INTE EXTERN> -32.80602 -40.30023 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1062" Parameter: A <- "-73.1062" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.806" Parameter: B <- "-32.806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3002" Parameter: C <- "-40.3002" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5610 TOTAL ENERGY = -73.1062 RDTITL> * VAN DER WAALS = -32.806 ELECTROSTATIC = -40.3002 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5610" Parameter: CONF_N -> "8002" Comparing "5610" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5611" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762058 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762915 ATOM PAIRS WERE FOUND FOR ATOM LIST 41925 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29746 from a total of 762915 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5611 -67.26753 -5.83872 0.46820 INTE EXTERN> -33.95606 -33.31147 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2675" Parameter: A <- "-67.2675" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9561" Parameter: B <- "-33.9561" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.3115" Parameter: C <- "-33.3115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5611 TOTAL ENERGY = -67.2675 RDTITL> * VAN DER WAALS = -33.9561 ELECTROSTATIC = -33.3115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5611" Parameter: CONF_N -> "8002" Comparing "5611" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5612" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762915 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769730 ATOM PAIRS WERE FOUND FOR ATOM LIST 42106 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30507 from a total of 769730 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5612 -68.08111 0.81358 0.52865 INTE EXTERN> -33.15429 -34.92681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0811" Parameter: A <- "-68.0811" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1543" Parameter: B <- "-33.1543" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9268" Parameter: C <- "-34.9268" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5612 TOTAL ENERGY = -68.0811 RDTITL> * VAN DER WAALS = -33.1543 ELECTROSTATIC = -34.9268 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5612" Parameter: CONF_N -> "8002" Comparing "5612" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5613" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769730 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766724 ATOM PAIRS WERE FOUND FOR ATOM LIST 42218 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30176 from a total of 766724 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5613 -70.47974 2.39863 0.53410 INTE EXTERN> -33.75581 -36.72393 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4797" Parameter: A <- "-70.4797" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7558" Parameter: B <- "-33.7558" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7239" Parameter: C <- "-36.7239" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5613 TOTAL ENERGY = -70.4797 RDTITL> * VAN DER WAALS = -33.7558 ELECTROSTATIC = -36.7239 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5613" Parameter: CONF_N -> "8002" Comparing "5613" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5614" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766724 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766495 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30028 from a total of 766495 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5614 -69.61357 -0.86617 0.57730 INTE EXTERN> -32.16765 -37.44591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6136" Parameter: A <- "-69.6136" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1677" Parameter: B <- "-32.1677" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4459" Parameter: C <- "-37.4459" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5614 TOTAL ENERGY = -69.6136 RDTITL> * VAN DER WAALS = -32.1677 ELECTROSTATIC = -37.4459 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5614" Parameter: CONF_N -> "8002" Comparing "5614" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5615" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766495 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765316 ATOM PAIRS WERE FOUND FOR ATOM LIST 42095 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29908 from a total of 765316 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5615 -71.63998 2.02641 0.56059 INTE EXTERN> -30.12625 -41.51373 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.64" Parameter: A <- "-71.64" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1262" Parameter: B <- "-30.1262" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5137" Parameter: C <- "-41.5137" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5615 TOTAL ENERGY = -71.64 RDTITL> * VAN DER WAALS = -30.1262 ELECTROSTATIC = -41.5137 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5615" Parameter: CONF_N -> "8002" Comparing "5615" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5616" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765316 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763142 ATOM PAIRS WERE FOUND FOR ATOM LIST 41846 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29957 from a total of 763142 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5616 -67.73273 -3.90725 0.57807 INTE EXTERN> -28.08884 -39.64389 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7327" Parameter: A <- "-67.7327" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0888" Parameter: B <- "-28.0888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6439" Parameter: C <- "-39.6439" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5616 TOTAL ENERGY = -67.7327 RDTITL> * VAN DER WAALS = -28.0888 ELECTROSTATIC = -39.6439 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5616" Parameter: CONF_N -> "8002" Comparing "5616" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5617" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763142 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765892 ATOM PAIRS WERE FOUND FOR ATOM LIST 41606 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29945 from a total of 765892 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5617 -69.29916 1.56643 0.55254 INTE EXTERN> -28.80140 -40.49776 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2992" Parameter: A <- "-69.2992" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8014" Parameter: B <- "-28.8014" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4978" Parameter: C <- "-40.4978" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5617 TOTAL ENERGY = -69.2992 RDTITL> * VAN DER WAALS = -28.8014 ELECTROSTATIC = -40.4978 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5617" Parameter: CONF_N -> "8002" Comparing "5617" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5618" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765892 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767153 ATOM PAIRS WERE FOUND FOR ATOM LIST 42058 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30358 from a total of 767153 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5618 -69.79838 0.49921 0.60401 INTE EXTERN> -31.03684 -38.76154 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7984" Parameter: A <- "-69.7984" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0368" Parameter: B <- "-31.0368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7615" Parameter: C <- "-38.7615" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5618 TOTAL ENERGY = -69.7984 RDTITL> * VAN DER WAALS = -31.0368 ELECTROSTATIC = -38.7615 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5618" Parameter: CONF_N -> "8002" Comparing "5618" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5619" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767153 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767089 ATOM PAIRS WERE FOUND FOR ATOM LIST 41951 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30291 from a total of 767089 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5619 -70.22873 0.43035 0.54986 INTE EXTERN> -29.95864 -40.27008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2287" Parameter: A <- "-70.2287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9586" Parameter: B <- "-29.9586" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2701" Parameter: C <- "-40.2701" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5619 TOTAL ENERGY = -70.2287 RDTITL> * VAN DER WAALS = -29.9586 ELECTROSTATIC = -40.2701 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5619" Parameter: CONF_N -> "8002" Comparing "5619" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5620" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767089 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766786 ATOM PAIRS WERE FOUND FOR ATOM LIST 41925 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30322 from a total of 766786 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5620 -73.39319 3.16447 0.53613 INTE EXTERN> -34.15306 -39.24013 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3932" Parameter: A <- "-73.3932" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1531" Parameter: B <- "-34.1531" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2401" Parameter: C <- "-39.2401" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5620 TOTAL ENERGY = -73.3932 RDTITL> * VAN DER WAALS = -34.1531 ELECTROSTATIC = -39.2401 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5620" Parameter: CONF_N -> "8002" Comparing "5620" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5621" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766786 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764977 ATOM PAIRS WERE FOUND FOR ATOM LIST 41799 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30465 from a total of 764977 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5621 -70.60732 -2.78587 0.50239 INTE EXTERN> -32.51530 -38.09202 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6073" Parameter: A <- "-70.6073" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5153" Parameter: B <- "-32.5153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.092" Parameter: C <- "-38.092" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5621 TOTAL ENERGY = -70.6073 RDTITL> * VAN DER WAALS = -32.5153 ELECTROSTATIC = -38.092 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5621" Parameter: CONF_N -> "8002" Comparing "5621" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5622" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764977 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763082 ATOM PAIRS WERE FOUND FOR ATOM LIST 41874 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30278 from a total of 763082 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5622 -70.21876 -0.38856 0.46976 INTE EXTERN> -32.32903 -37.88973 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2188" Parameter: A <- "-70.2188" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.329" Parameter: B <- "-32.329" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8897" Parameter: C <- "-37.8897" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5622 TOTAL ENERGY = -70.2188 RDTITL> * VAN DER WAALS = -32.329 ELECTROSTATIC = -37.8897 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5622" Parameter: CONF_N -> "8002" Comparing "5622" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5623" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763082 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760219 ATOM PAIRS WERE FOUND FOR ATOM LIST 41702 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29929 from a total of 760219 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5623 -71.10039 0.88163 0.57647 INTE EXTERN> -30.89584 -40.20455 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1004" Parameter: A <- "-71.1004" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8958" Parameter: B <- "-30.8958" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2046" Parameter: C <- "-40.2046" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5623 TOTAL ENERGY = -71.1004 RDTITL> * VAN DER WAALS = -30.8958 ELECTROSTATIC = -40.2046 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5623" Parameter: CONF_N -> "8002" Comparing "5623" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5624" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760219 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761627 ATOM PAIRS WERE FOUND FOR ATOM LIST 41880 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29513 from a total of 761627 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5624 -65.20152 -5.89887 0.60981 INTE EXTERN> -29.55706 -35.64446 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2015" Parameter: A <- "-65.2015" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5571" Parameter: B <- "-29.5571" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6445" Parameter: C <- "-35.6445" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5624 TOTAL ENERGY = -65.2015 RDTITL> * VAN DER WAALS = -29.5571 ELECTROSTATIC = -35.6445 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5624" Parameter: CONF_N -> "8002" Comparing "5624" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5625" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761627 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766316 ATOM PAIRS WERE FOUND FOR ATOM LIST 41995 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30354 from a total of 766316 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5625 -70.71205 5.51053 0.54302 INTE EXTERN> -29.59288 -41.11917 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7121" Parameter: A <- "-70.7121" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5929" Parameter: B <- "-29.5929" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1192" Parameter: C <- "-41.1192" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5625 TOTAL ENERGY = -70.7121 RDTITL> * VAN DER WAALS = -29.5929 ELECTROSTATIC = -41.1192 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5625" Parameter: CONF_N -> "8002" Comparing "5625" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5626" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766316 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762938 ATOM PAIRS WERE FOUND FOR ATOM LIST 41891 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29930 from a total of 762938 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5626 -68.15629 -2.55576 0.62151 INTE EXTERN> -26.60934 -41.54695 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1563" Parameter: A <- "-68.1563" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6093" Parameter: B <- "-26.6093" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.547" Parameter: C <- "-41.547" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5626 TOTAL ENERGY = -68.1563 RDTITL> * VAN DER WAALS = -26.6093 ELECTROSTATIC = -41.547 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5626" Parameter: CONF_N -> "8002" Comparing "5626" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5627" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762938 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763408 ATOM PAIRS WERE FOUND FOR ATOM LIST 41915 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30060 from a total of 763408 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5627 -71.37124 3.21495 0.51986 INTE EXTERN> -34.19597 -37.17528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3712" Parameter: A <- "-71.3712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.196" Parameter: B <- "-34.196" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1753" Parameter: C <- "-37.1753" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5627 TOTAL ENERGY = -71.3712 RDTITL> * VAN DER WAALS = -34.196 ELECTROSTATIC = -37.1753 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5627" Parameter: CONF_N -> "8002" Comparing "5627" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5628" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763408 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759982 ATOM PAIRS WERE FOUND FOR ATOM LIST 41708 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30111 from a total of 759982 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5628 -69.43439 -1.93685 0.53534 INTE EXTERN> -30.50947 -38.92492 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4344" Parameter: A <- "-69.4344" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5095" Parameter: B <- "-30.5095" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9249" Parameter: C <- "-38.9249" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5628 TOTAL ENERGY = -69.4344 RDTITL> * VAN DER WAALS = -30.5095 ELECTROSTATIC = -38.9249 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5628" Parameter: CONF_N -> "8002" Comparing "5628" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5629" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759982 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756555 ATOM PAIRS WERE FOUND FOR ATOM LIST 41560 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30030 from a total of 756555 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5629 -72.37735 2.94296 0.55790 INTE EXTERN> -33.51871 -38.85864 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3774" Parameter: A <- "-72.3774" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5187" Parameter: B <- "-33.5187" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8586" Parameter: C <- "-38.8586" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5629 TOTAL ENERGY = -72.3774 RDTITL> * VAN DER WAALS = -33.5187 ELECTROSTATIC = -38.8586 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5629" Parameter: CONF_N -> "8002" Comparing "5629" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5630" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756555 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763758 ATOM PAIRS WERE FOUND FOR ATOM LIST 41778 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30229 from a total of 763758 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5630 -67.46632 -4.91103 0.51285 INTE EXTERN> -34.93643 -32.52989 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4663" Parameter: A <- "-67.4663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9364" Parameter: B <- "-34.9364" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5299" Parameter: C <- "-32.5299" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5630 TOTAL ENERGY = -67.4663 RDTITL> * VAN DER WAALS = -34.9364 ELECTROSTATIC = -32.5299 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5630" Parameter: CONF_N -> "8002" Comparing "5630" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5631" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763758 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768986 ATOM PAIRS WERE FOUND FOR ATOM LIST 42097 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30193 from a total of 768986 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5631 -70.46199 2.99567 0.56456 INTE EXTERN> -30.96425 -39.49775 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.462" Parameter: A <- "-70.462" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9642" Parameter: B <- "-30.9642" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4977" Parameter: C <- "-39.4977" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5631 TOTAL ENERGY = -70.462 RDTITL> * VAN DER WAALS = -30.9642 ELECTROSTATIC = -39.4977 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5631" Parameter: CONF_N -> "8002" Comparing "5631" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5632" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768986 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760424 ATOM PAIRS WERE FOUND FOR ATOM LIST 41722 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30082 from a total of 760424 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5632 -72.17983 1.71784 0.60306 INTE EXTERN> -27.39693 -44.78290 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1798" Parameter: A <- "-72.1798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3969" Parameter: B <- "-27.3969" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7829" Parameter: C <- "-44.7829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5632 TOTAL ENERGY = -72.1798 RDTITL> * VAN DER WAALS = -27.3969 ELECTROSTATIC = -44.7829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5632" Parameter: CONF_N -> "8002" Comparing "5632" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5633" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760424 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753690 ATOM PAIRS WERE FOUND FOR ATOM LIST 41428 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29067 from a total of 753690 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5633 -61.53582 -10.64401 0.49546 INTE EXTERN> -31.49849 -30.03733 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.5358" Parameter: A <- "-61.5358" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4985" Parameter: B <- "-31.4985" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.0373" Parameter: C <- "-30.0373" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5633 TOTAL ENERGY = -61.5358 RDTITL> * VAN DER WAALS = -31.4985 ELECTROSTATIC = -30.0373 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5633" Parameter: CONF_N -> "8002" Comparing "5633" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5634" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753690 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756835 ATOM PAIRS WERE FOUND FOR ATOM LIST 41532 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28967 from a total of 756835 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5634 -66.10767 4.57185 0.45109 INTE EXTERN> -31.44379 -34.66387 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1077" Parameter: A <- "-66.1077" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4438" Parameter: B <- "-31.4438" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.6639" Parameter: C <- "-34.6639" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5634 TOTAL ENERGY = -66.1077 RDTITL> * VAN DER WAALS = -31.4438 ELECTROSTATIC = -34.6639 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5634" Parameter: CONF_N -> "8002" Comparing "5634" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5635" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756835 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756402 ATOM PAIRS WERE FOUND FOR ATOM LIST 41676 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28804 from a total of 756402 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5635 -63.50501 -2.60266 0.42927 INTE EXTERN> -33.62568 -29.87932 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.505" Parameter: A <- "-63.505" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6257" Parameter: B <- "-33.6257" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.8793" Parameter: C <- "-29.8793" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5635 TOTAL ENERGY = -63.505 RDTITL> * VAN DER WAALS = -33.6257 ELECTROSTATIC = -29.8793 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5635" Parameter: CONF_N -> "8002" Comparing "5635" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5636" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756402 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765189 ATOM PAIRS WERE FOUND FOR ATOM LIST 41946 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29765 from a total of 765189 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5636 -74.75220 11.24720 0.51114 INTE EXTERN> -34.94615 -39.80605 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7522" Parameter: A <- "-74.7522" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9461" Parameter: B <- "-34.9461" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8061" Parameter: C <- "-39.8061" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5636 TOTAL ENERGY = -74.7522 RDTITL> * VAN DER WAALS = -34.9461 ELECTROSTATIC = -39.8061 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5636" Parameter: CONF_N -> "8002" Comparing "5636" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5637" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765189 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761450 ATOM PAIRS WERE FOUND FOR ATOM LIST 41610 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29386 from a total of 761450 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5637 -72.25414 -2.49806 0.51045 INTE EXTERN> -34.56103 -37.69311 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2541" Parameter: A <- "-72.2541" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.561" Parameter: B <- "-34.561" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6931" Parameter: C <- "-37.6931" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5637 TOTAL ENERGY = -72.2541 RDTITL> * VAN DER WAALS = -34.561 ELECTROSTATIC = -37.6931 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5637" Parameter: CONF_N -> "8002" Comparing "5637" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5638" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761450 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755918 ATOM PAIRS WERE FOUND FOR ATOM LIST 41529 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29688 from a total of 755918 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5638 -65.19430 -7.05984 0.55298 INTE EXTERN> -30.06500 -35.12930 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1943" Parameter: A <- "-65.1943" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.065" Parameter: B <- "-30.065" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1293" Parameter: C <- "-35.1293" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5638 TOTAL ENERGY = -65.1943 RDTITL> * VAN DER WAALS = -30.065 ELECTROSTATIC = -35.1293 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5638" Parameter: CONF_N -> "8002" Comparing "5638" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5639" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755918 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759085 ATOM PAIRS WERE FOUND FOR ATOM LIST 41785 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29590 from a total of 759085 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5639 -67.55195 2.35765 0.58959 INTE EXTERN> -29.06788 -38.48407 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.552" Parameter: A <- "-67.552" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0679" Parameter: B <- "-29.0679" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4841" Parameter: C <- "-38.4841" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5639 TOTAL ENERGY = -67.552 RDTITL> * VAN DER WAALS = -29.0679 ELECTROSTATIC = -38.4841 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5639" Parameter: CONF_N -> "8002" Comparing "5639" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5640" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759085 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760333 ATOM PAIRS WERE FOUND FOR ATOM LIST 41785 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29620 from a total of 760333 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5640 -62.69028 -4.86167 0.60432 INTE EXTERN> -27.13895 -35.55133 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.6903" Parameter: A <- "-62.6903" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.139" Parameter: B <- "-27.139" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5513" Parameter: C <- "-35.5513" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5640 TOTAL ENERGY = -62.6903 RDTITL> * VAN DER WAALS = -27.139 ELECTROSTATIC = -35.5513 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5640" Parameter: CONF_N -> "8002" Comparing "5640" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5641" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760333 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761023 ATOM PAIRS WERE FOUND FOR ATOM LIST 41569 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28413 from a total of 761023 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5641 -66.82121 4.13093 0.43996 INTE EXTERN> -30.29897 -36.52224 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8212" Parameter: A <- "-66.8212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.299" Parameter: B <- "-30.299" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5222" Parameter: C <- "-36.5222" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5641 TOTAL ENERGY = -66.8212 RDTITL> * VAN DER WAALS = -30.299 ELECTROSTATIC = -36.5222 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5641" Parameter: CONF_N -> "8002" Comparing "5641" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5642" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761023 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759115 ATOM PAIRS WERE FOUND FOR ATOM LIST 41523 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28633 from a total of 759115 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5642 -64.37873 -2.44249 0.48897 INTE EXTERN> -31.45863 -32.92010 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3787" Parameter: A <- "-64.3787" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4586" Parameter: B <- "-31.4586" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.9201" Parameter: C <- "-32.9201" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5642 TOTAL ENERGY = -64.3787 RDTITL> * VAN DER WAALS = -31.4586 ELECTROSTATIC = -32.9201 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5642" Parameter: CONF_N -> "8002" Comparing "5642" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5643" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759115 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761603 ATOM PAIRS WERE FOUND FOR ATOM LIST 41667 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29688 from a total of 761603 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5643 -66.68623 2.30750 0.51501 INTE EXTERN> -30.36844 -36.31778 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6862" Parameter: A <- "-66.6862" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3684" Parameter: B <- "-30.3684" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3178" Parameter: C <- "-36.3178" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5643 TOTAL ENERGY = -66.6862 RDTITL> * VAN DER WAALS = -30.3684 ELECTROSTATIC = -36.3178 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5643" Parameter: CONF_N -> "8002" Comparing "5643" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5644" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761603 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759244 ATOM PAIRS WERE FOUND FOR ATOM LIST 41652 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28914 from a total of 759244 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5644 -69.05624 2.37002 0.62343 INTE EXTERN> -26.91634 -42.13990 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0562" Parameter: A <- "-69.0562" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9163" Parameter: B <- "-26.9163" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1399" Parameter: C <- "-42.1399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5644 TOTAL ENERGY = -69.0562 RDTITL> * VAN DER WAALS = -26.9163 ELECTROSTATIC = -42.1399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5644" Parameter: CONF_N -> "8002" Comparing "5644" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5645" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759244 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759988 ATOM PAIRS WERE FOUND FOR ATOM LIST 41705 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29293 from a total of 759988 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5645 -73.88507 4.82882 0.44697 INTE EXTERN> -34.42995 -39.45511 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8851" Parameter: A <- "-73.8851" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.43" Parameter: B <- "-34.43" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4551" Parameter: C <- "-39.4551" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5645 TOTAL ENERGY = -73.8851 RDTITL> * VAN DER WAALS = -34.43 ELECTROSTATIC = -39.4551 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5645" Parameter: CONF_N -> "8002" Comparing "5645" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5646" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759988 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760232 ATOM PAIRS WERE FOUND FOR ATOM LIST 41794 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29459 from a total of 760232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5646 -64.01302 -9.87205 0.56168 INTE EXTERN> -28.85138 -35.16164 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.013" Parameter: A <- "-64.013" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8514" Parameter: B <- "-28.8514" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1616" Parameter: C <- "-35.1616" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5646 TOTAL ENERGY = -64.013 RDTITL> * VAN DER WAALS = -28.8514 ELECTROSTATIC = -35.1616 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5646" Parameter: CONF_N -> "8002" Comparing "5646" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5647" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760930 ATOM PAIRS WERE FOUND FOR ATOM LIST 41748 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29159 from a total of 760930 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5647 -72.11837 8.10535 0.53030 INTE EXTERN> -33.39715 -38.72122 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1184" Parameter: A <- "-72.1184" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3971" Parameter: B <- "-33.3971" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7212" Parameter: C <- "-38.7212" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5647 TOTAL ENERGY = -72.1184 RDTITL> * VAN DER WAALS = -33.3971 ELECTROSTATIC = -38.7212 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5647" Parameter: CONF_N -> "8002" Comparing "5647" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5648" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760930 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761370 ATOM PAIRS WERE FOUND FOR ATOM LIST 41703 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29706 from a total of 761370 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5648 -70.72128 -1.39709 0.54886 INTE EXTERN> -32.52712 -38.19416 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7213" Parameter: A <- "-70.7213" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5271" Parameter: B <- "-32.5271" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1942" Parameter: C <- "-38.1942" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5648 TOTAL ENERGY = -70.7213 RDTITL> * VAN DER WAALS = -32.5271 ELECTROSTATIC = -38.1942 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5648" Parameter: CONF_N -> "8002" Comparing "5648" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5649" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761370 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 768762 ATOM PAIRS WERE FOUND FOR ATOM LIST 42052 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30381 from a total of 768762 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5649 -74.94538 4.22411 0.57520 INTE EXTERN> -30.84896 -44.09643 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9454" Parameter: A <- "-74.9454" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.849" Parameter: B <- "-30.849" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0964" Parameter: C <- "-44.0964" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5649 TOTAL ENERGY = -74.9454 RDTITL> * VAN DER WAALS = -30.849 ELECTROSTATIC = -44.0964 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5649" Parameter: CONF_N -> "8002" Comparing "5649" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5650" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 768762 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756683 ATOM PAIRS WERE FOUND FOR ATOM LIST 41481 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29648 from a total of 756683 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5650 -69.02597 -5.91941 0.64616 INTE EXTERN> -28.11110 -40.91487 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.026" Parameter: A <- "-69.026" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1111" Parameter: B <- "-28.1111" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9149" Parameter: C <- "-40.9149" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5650 TOTAL ENERGY = -69.026 RDTITL> * VAN DER WAALS = -28.1111 ELECTROSTATIC = -40.9149 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5650" Parameter: CONF_N -> "8002" Comparing "5650" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5651" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756683 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751668 ATOM PAIRS WERE FOUND FOR ATOM LIST 41327 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29268 from a total of 751668 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5651 -67.95421 -1.07176 0.53394 INTE EXTERN> -29.74302 -38.21119 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9542" Parameter: A <- "-67.9542" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.743" Parameter: B <- "-29.743" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2112" Parameter: C <- "-38.2112" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5651 TOTAL ENERGY = -67.9542 RDTITL> * VAN DER WAALS = -29.743 ELECTROSTATIC = -38.2112 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5651" Parameter: CONF_N -> "8002" Comparing "5651" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5652" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751668 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759106 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30051 from a total of 759106 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5652 -76.78702 8.83280 0.56990 INTE EXTERN> -31.71023 -45.07679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.787" Parameter: A <- "-76.787" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7102" Parameter: B <- "-31.7102" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0768" Parameter: C <- "-45.0768" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5652 TOTAL ENERGY = -76.787 RDTITL> * VAN DER WAALS = -31.7102 ELECTROSTATIC = -45.0768 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5652" Parameter: CONF_N -> "8002" Comparing "5652" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5653" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759106 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760931 ATOM PAIRS WERE FOUND FOR ATOM LIST 41869 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29743 from a total of 760931 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5653 -63.43986 -13.34716 0.62681 INTE EXTERN> -29.75617 -33.68369 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4399" Parameter: A <- "-63.4399" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7562" Parameter: B <- "-29.7562" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6837" Parameter: C <- "-33.6837" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5653 TOTAL ENERGY = -63.4399 RDTITL> * VAN DER WAALS = -29.7562 ELECTROSTATIC = -33.6837 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5653" Parameter: CONF_N -> "8002" Comparing "5653" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5654" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760931 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767500 ATOM PAIRS WERE FOUND FOR ATOM LIST 42049 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30010 from a total of 767500 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5654 -62.25491 -1.18494 0.74854 INTE EXTERN> -25.67602 -36.57889 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.2549" Parameter: A <- "-62.2549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.676" Parameter: B <- "-25.676" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5789" Parameter: C <- "-36.5789" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5654 TOTAL ENERGY = -62.2549 RDTITL> * VAN DER WAALS = -25.676 ELECTROSTATIC = -36.5789 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5654" Parameter: CONF_N -> "8002" Comparing "5654" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5655" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767500 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764464 ATOM PAIRS WERE FOUND FOR ATOM LIST 41955 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29936 from a total of 764464 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5655 -60.40155 -1.85337 0.57900 INTE EXTERN> -31.59295 -28.80860 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.4015" Parameter: A <- "-60.4015" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.593" Parameter: B <- "-31.593" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.8086" Parameter: C <- "-28.8086" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5655 TOTAL ENERGY = -60.4015 RDTITL> * VAN DER WAALS = -31.593 ELECTROSTATIC = -28.8086 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5655" Parameter: CONF_N -> "8002" Comparing "5655" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5656" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764464 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760494 ATOM PAIRS WERE FOUND FOR ATOM LIST 41788 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29991 from a total of 760494 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5656 -70.25573 9.85419 0.51087 INTE EXTERN> -35.66135 -34.59439 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2557" Parameter: A <- "-70.2557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.6613" Parameter: B <- "-35.6613" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5944" Parameter: C <- "-34.5944" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5656 TOTAL ENERGY = -70.2557 RDTITL> * VAN DER WAALS = -35.6613 ELECTROSTATIC = -34.5944 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5656" Parameter: CONF_N -> "8002" Comparing "5656" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5657" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760494 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764098 ATOM PAIRS WERE FOUND FOR ATOM LIST 41964 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30213 from a total of 764098 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5657 -68.05761 -2.19813 0.51858 INTE EXTERN> -34.31657 -33.74103 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0576" Parameter: A <- "-68.0576" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3166" Parameter: B <- "-34.3166" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.741" Parameter: C <- "-33.741" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5657 TOTAL ENERGY = -68.0576 RDTITL> * VAN DER WAALS = -34.3166 ELECTROSTATIC = -33.741 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5657" Parameter: CONF_N -> "8002" Comparing "5657" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5658" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764098 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758257 ATOM PAIRS WERE FOUND FOR ATOM LIST 41672 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30299 from a total of 758257 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5658 -70.33545 2.27785 0.56039 INTE EXTERN> -32.86685 -37.46860 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3355" Parameter: A <- "-70.3355" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8669" Parameter: B <- "-32.8669" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4686" Parameter: C <- "-37.4686" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5658 TOTAL ENERGY = -70.3355 RDTITL> * VAN DER WAALS = -32.8669 ELECTROSTATIC = -37.4686 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5658" Parameter: CONF_N -> "8002" Comparing "5658" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5659" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758257 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757974 ATOM PAIRS WERE FOUND FOR ATOM LIST 41666 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30259 from a total of 757974 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5659 -69.38891 -0.94654 0.57709 INTE EXTERN> -34.54500 -34.84391 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3889" Parameter: A <- "-69.3889" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.545" Parameter: B <- "-34.545" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8439" Parameter: C <- "-34.8439" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5659 TOTAL ENERGY = -69.3889 RDTITL> * VAN DER WAALS = -34.545 ELECTROSTATIC = -34.8439 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5659" Parameter: CONF_N -> "8002" Comparing "5659" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5660" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757974 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755122 ATOM PAIRS WERE FOUND FOR ATOM LIST 41468 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29744 from a total of 755122 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5660 -70.09537 0.70646 0.66105 INTE EXTERN> -29.81906 -40.27630 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0954" Parameter: A <- "-70.0954" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8191" Parameter: B <- "-29.8191" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2763" Parameter: C <- "-40.2763" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5660 TOTAL ENERGY = -70.0954 RDTITL> * VAN DER WAALS = -29.8191 ELECTROSTATIC = -40.2763 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5660" Parameter: CONF_N -> "8002" Comparing "5660" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5661" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755122 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755005 ATOM PAIRS WERE FOUND FOR ATOM LIST 41425 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29939 from a total of 755005 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5661 -70.07376 -0.02161 0.67144 INTE EXTERN> -31.06314 -39.01061 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0738" Parameter: A <- "-70.0738" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0631" Parameter: B <- "-31.0631" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0106" Parameter: C <- "-39.0106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5661 TOTAL ENERGY = -70.0738 RDTITL> * VAN DER WAALS = -31.0631 ELECTROSTATIC = -39.0106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5661" Parameter: CONF_N -> "8002" Comparing "5661" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5662" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755005 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759857 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30863 from a total of 759857 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5662 -72.10941 2.03565 0.55484 INTE EXTERN> -32.38785 -39.72156 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1094" Parameter: A <- "-72.1094" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3878" Parameter: B <- "-32.3878" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7216" Parameter: C <- "-39.7216" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5662 TOTAL ENERGY = -72.1094 RDTITL> * VAN DER WAALS = -32.3878 ELECTROSTATIC = -39.7216 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5662" Parameter: CONF_N -> "8002" Comparing "5662" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5663" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759857 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765133 ATOM PAIRS WERE FOUND FOR ATOM LIST 41975 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30789 from a total of 765133 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5663 -71.71354 -0.39587 0.51515 INTE EXTERN> -35.36757 -36.34597 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7135" Parameter: A <- "-71.7135" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.3676" Parameter: B <- "-35.3676" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.346" Parameter: C <- "-36.346" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5663 TOTAL ENERGY = -71.7135 RDTITL> * VAN DER WAALS = -35.3676 ELECTROSTATIC = -36.346 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5663" Parameter: CONF_N -> "8002" Comparing "5663" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5664" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765133 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762334 ATOM PAIRS WERE FOUND FOR ATOM LIST 42081 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30240 from a total of 762334 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5664 -66.90565 -4.80789 0.53653 INTE EXTERN> -32.08857 -34.81708 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9057" Parameter: A <- "-66.9057" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0886" Parameter: B <- "-32.0886" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8171" Parameter: C <- "-34.8171" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5664 TOTAL ENERGY = -66.9057 RDTITL> * VAN DER WAALS = -32.0886 ELECTROSTATIC = -34.8171 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5664" Parameter: CONF_N -> "8002" Comparing "5664" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5665" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762334 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760200 ATOM PAIRS WERE FOUND FOR ATOM LIST 41615 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30709 from a total of 760200 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5665 -74.49155 7.58590 0.63038 INTE EXTERN> -30.72501 -43.76654 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4915" Parameter: A <- "-74.4915" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.725" Parameter: B <- "-30.725" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7665" Parameter: C <- "-43.7665" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5665 TOTAL ENERGY = -74.4915 RDTITL> * VAN DER WAALS = -30.725 ELECTROSTATIC = -43.7665 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5665" Parameter: CONF_N -> "8002" Comparing "5665" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5666" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760200 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763477 ATOM PAIRS WERE FOUND FOR ATOM LIST 41952 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30666 from a total of 763477 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5666 -69.46272 -5.02883 0.65411 INTE EXTERN> -27.67709 -41.78563 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4627" Parameter: A <- "-69.4627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6771" Parameter: B <- "-27.6771" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7856" Parameter: C <- "-41.7856" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5666 TOTAL ENERGY = -69.4627 RDTITL> * VAN DER WAALS = -27.6771 ELECTROSTATIC = -41.7856 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5666" Parameter: CONF_N -> "8002" Comparing "5666" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5667" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763477 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763541 ATOM PAIRS WERE FOUND FOR ATOM LIST 41871 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30180 from a total of 763541 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5667 -70.64581 1.18310 0.67349 INTE EXTERN> -29.82459 -40.82122 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6458" Parameter: A <- "-70.6458" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8246" Parameter: B <- "-29.8246" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8212" Parameter: C <- "-40.8212" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5667 TOTAL ENERGY = -70.6458 RDTITL> * VAN DER WAALS = -29.8246 ELECTROSTATIC = -40.8212 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5667" Parameter: CONF_N -> "8002" Comparing "5667" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5668" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763541 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760546 ATOM PAIRS WERE FOUND FOR ATOM LIST 41952 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30498 from a total of 760546 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5668 -74.37613 3.73032 0.66338 INTE EXTERN> -32.30593 -42.07020 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3761" Parameter: A <- "-74.3761" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3059" Parameter: B <- "-32.3059" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0702" Parameter: C <- "-42.0702" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5668 TOTAL ENERGY = -74.3761 RDTITL> * VAN DER WAALS = -32.3059 ELECTROSTATIC = -42.0702 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5668" Parameter: CONF_N -> "8002" Comparing "5668" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5669" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760546 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757050 ATOM PAIRS WERE FOUND FOR ATOM LIST 41436 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30104 from a total of 757050 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5669 -74.19797 -0.17816 0.58783 INTE EXTERN> -31.33997 -42.85800 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.198" Parameter: A <- "-74.198" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.34" Parameter: B <- "-31.34" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.858" Parameter: C <- "-42.858" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5669 TOTAL ENERGY = -74.198 RDTITL> * VAN DER WAALS = -31.34 ELECTROSTATIC = -42.858 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5669" Parameter: CONF_N -> "8002" Comparing "5669" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5670" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757050 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762062 ATOM PAIRS WERE FOUND FOR ATOM LIST 41800 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30524 from a total of 762062 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5670 -67.31057 -6.88741 0.56883 INTE EXTERN> -30.80856 -36.50200 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3106" Parameter: A <- "-67.3106" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8086" Parameter: B <- "-30.8086" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.502" Parameter: C <- "-36.502" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5670 TOTAL ENERGY = -67.3106 RDTITL> * VAN DER WAALS = -30.8086 ELECTROSTATIC = -36.502 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5670" Parameter: CONF_N -> "8002" Comparing "5670" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5671" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762062 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764248 ATOM PAIRS WERE FOUND FOR ATOM LIST 41938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30427 from a total of 764248 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5671 -72.45951 5.14894 0.57251 INTE EXTERN> -32.53415 -39.92536 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4595" Parameter: A <- "-72.4595" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5342" Parameter: B <- "-32.5342" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9254" Parameter: C <- "-39.9254" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5671 TOTAL ENERGY = -72.4595 RDTITL> * VAN DER WAALS = -32.5342 ELECTROSTATIC = -39.9254 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5671" Parameter: CONF_N -> "8002" Comparing "5671" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5672" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764248 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756444 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30017 from a total of 756444 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5672 -68.42909 -4.03042 0.63641 INTE EXTERN> -25.69748 -42.73161 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4291" Parameter: A <- "-68.4291" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6975" Parameter: B <- "-25.6975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7316" Parameter: C <- "-42.7316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5672 TOTAL ENERGY = -68.4291 RDTITL> * VAN DER WAALS = -25.6975 ELECTROSTATIC = -42.7316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5672" Parameter: CONF_N -> "8002" Comparing "5672" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5673" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756444 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759979 ATOM PAIRS WERE FOUND FOR ATOM LIST 41608 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30171 from a total of 759979 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5673 -75.23624 6.80715 0.63092 INTE EXTERN> -29.59942 -45.63681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2362" Parameter: A <- "-75.2362" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5994" Parameter: B <- "-29.5994" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6368" Parameter: C <- "-45.6368" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5673 TOTAL ENERGY = -75.2362 RDTITL> * VAN DER WAALS = -29.5994 ELECTROSTATIC = -45.6368 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5673" Parameter: CONF_N -> "8002" Comparing "5673" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5674" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759979 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758529 ATOM PAIRS WERE FOUND FOR ATOM LIST 41739 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29875 from a total of 758529 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5674 -67.42439 -7.81185 0.72863 INTE EXTERN> -26.11595 -41.30845 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4244" Parameter: A <- "-67.4244" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1159" Parameter: B <- "-26.1159" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3084" Parameter: C <- "-41.3084" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5674 TOTAL ENERGY = -67.4244 RDTITL> * VAN DER WAALS = -26.1159 ELECTROSTATIC = -41.3084 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5674" Parameter: CONF_N -> "8002" Comparing "5674" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5675" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758529 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760969 ATOM PAIRS WERE FOUND FOR ATOM LIST 41748 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30148 from a total of 760969 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5675 -68.92982 1.50542 0.62836 INTE EXTERN> -30.38551 -38.54431 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9298" Parameter: A <- "-68.9298" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3855" Parameter: B <- "-30.3855" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5443" Parameter: C <- "-38.5443" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5675 TOTAL ENERGY = -68.9298 RDTITL> * VAN DER WAALS = -30.3855 ELECTROSTATIC = -38.5443 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5675" Parameter: CONF_N -> "8002" Comparing "5675" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5676" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760969 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756924 ATOM PAIRS WERE FOUND FOR ATOM LIST 41680 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29990 from a total of 756924 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5676 -70.32387 1.39405 0.58004 INTE EXTERN> -31.14219 -39.18168 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3239" Parameter: A <- "-70.3239" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1422" Parameter: B <- "-31.1422" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1817" Parameter: C <- "-39.1817" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5676 TOTAL ENERGY = -70.3239 RDTITL> * VAN DER WAALS = -31.1422 ELECTROSTATIC = -39.1817 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5676" Parameter: CONF_N -> "8002" Comparing "5676" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5677" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756924 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757344 ATOM PAIRS WERE FOUND FOR ATOM LIST 41418 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29727 from a total of 757344 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5677 -68.47580 -1.84807 0.63908 INTE EXTERN> -28.88492 -39.59088 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4758" Parameter: A <- "-68.4758" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8849" Parameter: B <- "-28.8849" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5909" Parameter: C <- "-39.5909" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5677 TOTAL ENERGY = -68.4758 RDTITL> * VAN DER WAALS = -28.8849 ELECTROSTATIC = -39.5909 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5677" Parameter: CONF_N -> "8002" Comparing "5677" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5678" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757344 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757419 ATOM PAIRS WERE FOUND FOR ATOM LIST 41631 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30054 from a total of 757419 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5678 -72.44098 3.96518 0.60308 INTE EXTERN> -32.85937 -39.58161 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.441" Parameter: A <- "-72.441" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8594" Parameter: B <- "-32.8594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5816" Parameter: C <- "-39.5816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5678 TOTAL ENERGY = -72.441 RDTITL> * VAN DER WAALS = -32.8594 ELECTROSTATIC = -39.5816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5678" Parameter: CONF_N -> "8002" Comparing "5678" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5679" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757419 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762999 ATOM PAIRS WERE FOUND FOR ATOM LIST 41749 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30367 from a total of 762999 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5679 -71.70710 -0.73388 0.56070 INTE EXTERN> -31.35713 -40.34997 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7071" Parameter: A <- "-71.7071" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3571" Parameter: B <- "-31.3571" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.35" Parameter: C <- "-40.35" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5679 TOTAL ENERGY = -71.7071 RDTITL> * VAN DER WAALS = -31.3571 ELECTROSTATIC = -40.35 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5679" Parameter: CONF_N -> "8002" Comparing "5679" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5680" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762999 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761130 ATOM PAIRS WERE FOUND FOR ATOM LIST 41793 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30273 from a total of 761130 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5680 -71.47352 -0.23358 0.57049 INTE EXTERN> -31.46460 -40.00892 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4735" Parameter: A <- "-71.4735" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4646" Parameter: B <- "-31.4646" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0089" Parameter: C <- "-40.0089" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5680 TOTAL ENERGY = -71.4735 RDTITL> * VAN DER WAALS = -31.4646 ELECTROSTATIC = -40.0089 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5680" Parameter: CONF_N -> "8002" Comparing "5680" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5681" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761130 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759210 ATOM PAIRS WERE FOUND FOR ATOM LIST 41636 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29716 from a total of 759210 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5681 -67.35616 -4.11736 0.45310 INTE EXTERN> -34.98723 -32.36892 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3562" Parameter: A <- "-67.3562" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9872" Parameter: B <- "-34.9872" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.3689" Parameter: C <- "-32.3689" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5681 TOTAL ENERGY = -67.3562 RDTITL> * VAN DER WAALS = -34.9872 ELECTROSTATIC = -32.3689 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5681" Parameter: CONF_N -> "8002" Comparing "5681" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5682" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759210 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760363 ATOM PAIRS WERE FOUND FOR ATOM LIST 41609 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29940 from a total of 760363 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5682 -66.23600 -1.12016 0.55923 INTE EXTERN> -29.35457 -36.88143 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.236" Parameter: A <- "-66.236" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3546" Parameter: B <- "-29.3546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8814" Parameter: C <- "-36.8814" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5682 TOTAL ENERGY = -66.236 RDTITL> * VAN DER WAALS = -29.3546 ELECTROSTATIC = -36.8814 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5682" Parameter: CONF_N -> "8002" Comparing "5682" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5683" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760363 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759531 ATOM PAIRS WERE FOUND FOR ATOM LIST 41667 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30195 from a total of 759531 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5683 -63.74351 -2.49249 0.61690 INTE EXTERN> -28.55631 -35.18720 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7435" Parameter: A <- "-63.7435" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5563" Parameter: B <- "-28.5563" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1872" Parameter: C <- "-35.1872" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5683 TOTAL ENERGY = -63.7435 RDTITL> * VAN DER WAALS = -28.5563 ELECTROSTATIC = -35.1872 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5683" Parameter: CONF_N -> "8002" Comparing "5683" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5684" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759531 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757865 ATOM PAIRS WERE FOUND FOR ATOM LIST 41331 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30071 from a total of 757865 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5684 -67.20104 3.45754 0.52527 INTE EXTERN> -29.57445 -37.62659 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.201" Parameter: A <- "-67.201" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5744" Parameter: B <- "-29.5744" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6266" Parameter: C <- "-37.6266" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5684 TOTAL ENERGY = -67.201 RDTITL> * VAN DER WAALS = -29.5744 ELECTROSTATIC = -37.6266 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5684" Parameter: CONF_N -> "8002" Comparing "5684" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5685" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757865 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755201 ATOM PAIRS WERE FOUND FOR ATOM LIST 41526 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30059 from a total of 755201 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5685 -66.69815 -0.50289 0.53877 INTE EXTERN> -30.10159 -36.59656 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6981" Parameter: A <- "-66.6981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1016" Parameter: B <- "-30.1016" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5966" Parameter: C <- "-36.5966" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5685 TOTAL ENERGY = -66.6981 RDTITL> * VAN DER WAALS = -30.1016 ELECTROSTATIC = -36.5966 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5685" Parameter: CONF_N -> "8002" Comparing "5685" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5686" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755201 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761506 ATOM PAIRS WERE FOUND FOR ATOM LIST 41818 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30167 from a total of 761506 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5686 -72.21557 5.51742 0.51213 INTE EXTERN> -34.25548 -37.96009 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2156" Parameter: A <- "-72.2156" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.2555" Parameter: B <- "-34.2555" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9601" Parameter: C <- "-37.9601" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5686 TOTAL ENERGY = -72.2156 RDTITL> * VAN DER WAALS = -34.2555 ELECTROSTATIC = -37.9601 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5686" Parameter: CONF_N -> "8002" Comparing "5686" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5687" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761506 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756099 ATOM PAIRS WERE FOUND FOR ATOM LIST 41590 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30092 from a total of 756099 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5687 -67.09292 -5.12265 0.56659 INTE EXTERN> -33.04250 -34.05042 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0929" Parameter: A <- "-67.0929" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0425" Parameter: B <- "-33.0425" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.0504" Parameter: C <- "-34.0504" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5687 TOTAL ENERGY = -67.0929 RDTITL> * VAN DER WAALS = -33.0425 ELECTROSTATIC = -34.0504 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5687" Parameter: CONF_N -> "8002" Comparing "5687" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5688" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756099 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757651 ATOM PAIRS WERE FOUND FOR ATOM LIST 41503 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29906 from a total of 757651 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5688 -68.82446 1.73154 0.52063 INTE EXTERN> -33.34508 -35.47939 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8245" Parameter: A <- "-68.8245" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3451" Parameter: B <- "-33.3451" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4794" Parameter: C <- "-35.4794" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5688 TOTAL ENERGY = -68.8245 RDTITL> * VAN DER WAALS = -33.3451 ELECTROSTATIC = -35.4794 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5688" Parameter: CONF_N -> "8002" Comparing "5688" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5689" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757651 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756373 ATOM PAIRS WERE FOUND FOR ATOM LIST 41382 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29304 from a total of 756373 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5689 -64.81101 -4.01345 0.46621 INTE EXTERN> -33.75666 -31.05435 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.811" Parameter: A <- "-64.811" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7567" Parameter: B <- "-33.7567" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.0543" Parameter: C <- "-31.0543" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5689 TOTAL ENERGY = -64.811 RDTITL> * VAN DER WAALS = -33.7567 ELECTROSTATIC = -31.0543 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5689" Parameter: CONF_N -> "8002" Comparing "5689" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5690" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756373 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752570 ATOM PAIRS WERE FOUND FOR ATOM LIST 41122 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29922 from a total of 752570 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5690 -64.65613 -0.15488 0.50018 INTE EXTERN> -31.62245 -33.03368 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6561" Parameter: A <- "-64.6561" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6225" Parameter: B <- "-31.6225" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.0337" Parameter: C <- "-33.0337" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5690 TOTAL ENERGY = -64.6561 RDTITL> * VAN DER WAALS = -31.6225 ELECTROSTATIC = -33.0337 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5690" Parameter: CONF_N -> "8002" Comparing "5690" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5691" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752570 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748829 ATOM PAIRS WERE FOUND FOR ATOM LIST 41090 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29433 from a total of 748829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5691 -74.51914 9.86301 0.52706 INTE EXTERN> -31.35250 -43.16664 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5191" Parameter: A <- "-74.5191" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3525" Parameter: B <- "-31.3525" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1666" Parameter: C <- "-43.1666" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5691 TOTAL ENERGY = -74.5191 RDTITL> * VAN DER WAALS = -31.3525 ELECTROSTATIC = -43.1666 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5691" Parameter: CONF_N -> "8002" Comparing "5691" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5692" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754151 ATOM PAIRS WERE FOUND FOR ATOM LIST 41395 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29524 from a total of 754151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5692 -70.53932 -3.97982 0.55015 INTE EXTERN> -33.44593 -37.09339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5393" Parameter: A <- "-70.5393" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4459" Parameter: B <- "-33.4459" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0934" Parameter: C <- "-37.0934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5692 TOTAL ENERGY = -70.5393 RDTITL> * VAN DER WAALS = -33.4459 ELECTROSTATIC = -37.0934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5692" Parameter: CONF_N -> "8002" Comparing "5692" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5693" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751380 ATOM PAIRS WERE FOUND FOR ATOM LIST 41237 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29215 from a total of 751380 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5693 -70.91337 0.37404 0.57371 INTE EXTERN> -29.11615 -41.79722 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9134" Parameter: A <- "-70.9134" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1161" Parameter: B <- "-29.1161" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7972" Parameter: C <- "-41.7972" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5693 TOTAL ENERGY = -70.9134 RDTITL> * VAN DER WAALS = -29.1161 ELECTROSTATIC = -41.7972 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5693" Parameter: CONF_N -> "8002" Comparing "5693" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5694" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751380 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746389 ATOM PAIRS WERE FOUND FOR ATOM LIST 40831 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28728 from a total of 746389 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5694 -72.25171 1.33834 0.55441 INTE EXTERN> -31.63664 -40.61506 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2517" Parameter: A <- "-72.2517" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6366" Parameter: B <- "-31.6366" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6151" Parameter: C <- "-40.6151" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5694 TOTAL ENERGY = -72.2517 RDTITL> * VAN DER WAALS = -31.6366 ELECTROSTATIC = -40.6151 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5694" Parameter: CONF_N -> "8002" Comparing "5694" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5695" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746389 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757269 ATOM PAIRS WERE FOUND FOR ATOM LIST 41466 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29717 from a total of 757269 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5695 -80.16076 7.90905 0.63358 INTE EXTERN> -33.00123 -47.15953 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1608" Parameter: A <- "-80.1608" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0012" Parameter: B <- "-33.0012" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1595" Parameter: C <- "-47.1595" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5695 TOTAL ENERGY = -80.1608 RDTITL> * VAN DER WAALS = -33.0012 ELECTROSTATIC = -47.1595 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5695" Parameter: CONF_N -> "8002" Comparing "5695" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5696" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757269 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764431 ATOM PAIRS WERE FOUND FOR ATOM LIST 41789 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30386 from a total of 764431 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5696 -71.24647 -8.91429 0.59133 INTE EXTERN> -29.67532 -41.57115 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2465" Parameter: A <- "-71.2465" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6753" Parameter: B <- "-29.6753" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5712" Parameter: C <- "-41.5712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5696 TOTAL ENERGY = -71.2465 RDTITL> * VAN DER WAALS = -29.6753 ELECTROSTATIC = -41.5712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5696" Parameter: CONF_N -> "8002" Comparing "5696" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5697" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764431 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760160 ATOM PAIRS WERE FOUND FOR ATOM LIST 41406 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29976 from a total of 760160 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5697 -73.23630 1.98983 0.50672 INTE EXTERN> -33.58620 -39.65010 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2363" Parameter: A <- "-73.2363" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5862" Parameter: B <- "-33.5862" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6501" Parameter: C <- "-39.6501" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5697 TOTAL ENERGY = -73.2363 RDTITL> * VAN DER WAALS = -33.5862 ELECTROSTATIC = -39.6501 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5697" Parameter: CONF_N -> "8002" Comparing "5697" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5698" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760160 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755980 ATOM PAIRS WERE FOUND FOR ATOM LIST 41217 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29402 from a total of 755980 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5698 -63.10084 -10.13546 0.45812 INTE EXTERN> -29.96517 -33.13568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1008" Parameter: A <- "-63.1008" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9652" Parameter: B <- "-29.9652" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1357" Parameter: C <- "-33.1357" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5698 TOTAL ENERGY = -63.1008 RDTITL> * VAN DER WAALS = -29.9652 ELECTROSTATIC = -33.1357 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5698" Parameter: CONF_N -> "8002" Comparing "5698" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5699" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755980 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755072 ATOM PAIRS WERE FOUND FOR ATOM LIST 41437 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29351 from a total of 755072 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5699 -64.55211 1.45127 0.66611 INTE EXTERN> -26.91193 -37.64017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5521" Parameter: A <- "-64.5521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9119" Parameter: B <- "-26.9119" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6402" Parameter: C <- "-37.6402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5699 TOTAL ENERGY = -64.5521 RDTITL> * VAN DER WAALS = -26.9119 ELECTROSTATIC = -37.6402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5699" Parameter: CONF_N -> "8002" Comparing "5699" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5700" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755072 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760252 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29539 from a total of 760252 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5700 -67.45840 2.90630 0.50138 INTE EXTERN> -32.24973 -35.20867 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4584" Parameter: A <- "-67.4584" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2497" Parameter: B <- "-32.2497" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2087" Parameter: C <- "-35.2087" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5700 TOTAL ENERGY = -67.4584 RDTITL> * VAN DER WAALS = -32.2497 ELECTROSTATIC = -35.2087 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5700" Parameter: CONF_N -> "8002" Comparing "5700" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5701" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760252 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759995 ATOM PAIRS WERE FOUND FOR ATOM LIST 41655 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29305 from a total of 759995 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5701 -70.99071 3.53230 0.58810 INTE EXTERN> -30.06330 -40.92741 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9907" Parameter: A <- "-70.9907" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0633" Parameter: B <- "-30.0633" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9274" Parameter: C <- "-40.9274" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5701 TOTAL ENERGY = -70.9907 RDTITL> * VAN DER WAALS = -30.0633 ELECTROSTATIC = -40.9274 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5701" Parameter: CONF_N -> "8002" Comparing "5701" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5702" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759995 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762474 ATOM PAIRS WERE FOUND FOR ATOM LIST 41779 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30067 from a total of 762474 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5702 -73.53403 2.54332 0.73956 INTE EXTERN> -29.38305 -44.15099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.534" Parameter: A <- "-73.534" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.383" Parameter: B <- "-29.383" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.151" Parameter: C <- "-44.151" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5702 TOTAL ENERGY = -73.534 RDTITL> * VAN DER WAALS = -29.383 ELECTROSTATIC = -44.151 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5702" Parameter: CONF_N -> "8002" Comparing "5702" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5703" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762474 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758901 ATOM PAIRS WERE FOUND FOR ATOM LIST 41557 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29527 from a total of 758901 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5703 -66.27261 -7.26142 0.61217 INTE EXTERN> -28.85165 -37.42096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2726" Parameter: A <- "-66.2726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8517" Parameter: B <- "-28.8517" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.421" Parameter: C <- "-37.421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5703 TOTAL ENERGY = -66.2726 RDTITL> * VAN DER WAALS = -28.8517 ELECTROSTATIC = -37.421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5703" Parameter: CONF_N -> "8002" Comparing "5703" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5704" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758901 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755762 ATOM PAIRS WERE FOUND FOR ATOM LIST 41513 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29632 from a total of 755762 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5704 -66.50130 0.22869 0.57418 INTE EXTERN> -30.73574 -35.76555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5013" Parameter: A <- "-66.5013" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7357" Parameter: B <- "-30.7357" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7656" Parameter: C <- "-35.7656" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5704 TOTAL ENERGY = -66.5013 RDTITL> * VAN DER WAALS = -30.7357 ELECTROSTATIC = -35.7656 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5704" Parameter: CONF_N -> "8002" Comparing "5704" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5705" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755762 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761524 ATOM PAIRS WERE FOUND FOR ATOM LIST 41613 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29553 from a total of 761524 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5705 -69.05971 2.55841 0.60068 INTE EXTERN> -30.23130 -38.82841 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0597" Parameter: A <- "-69.0597" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2313" Parameter: B <- "-30.2313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8284" Parameter: C <- "-38.8284" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5705 TOTAL ENERGY = -69.0597 RDTITL> * VAN DER WAALS = -30.2313 ELECTROSTATIC = -38.8284 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5705" Parameter: CONF_N -> "8002" Comparing "5705" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5706" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761524 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759916 ATOM PAIRS WERE FOUND FOR ATOM LIST 41649 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29464 from a total of 759916 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5706 -59.48947 -9.57024 0.44449 INTE EXTERN> -34.70773 -24.78174 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.4895" Parameter: A <- "-59.4895" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.7077" Parameter: B <- "-34.7077" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-24.7817" Parameter: C <- "-24.7817" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5706 TOTAL ENERGY = -59.4895 RDTITL> * VAN DER WAALS = -34.7077 ELECTROSTATIC = -24.7817 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5706" Parameter: CONF_N -> "8002" Comparing "5706" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5707" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759916 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760068 ATOM PAIRS WERE FOUND FOR ATOM LIST 41881 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29522 from a total of 760068 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5707 -65.09776 5.60829 0.57757 INTE EXTERN> -31.21152 -33.88624 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0978" Parameter: A <- "-65.0978" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2115" Parameter: B <- "-31.2115" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8862" Parameter: C <- "-33.8862" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5707 TOTAL ENERGY = -65.0978 RDTITL> * VAN DER WAALS = -31.2115 ELECTROSTATIC = -33.8862 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5707" Parameter: CONF_N -> "8002" Comparing "5707" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5708" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760068 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753026 ATOM PAIRS WERE FOUND FOR ATOM LIST 41296 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29169 from a total of 753026 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5708 -64.08477 -1.01298 0.66321 INTE EXTERN> -30.31520 -33.76957 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0848" Parameter: A <- "-64.0848" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3152" Parameter: B <- "-30.3152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7696" Parameter: C <- "-33.7696" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5708 TOTAL ENERGY = -64.0848 RDTITL> * VAN DER WAALS = -30.3152 ELECTROSTATIC = -33.7696 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5708" Parameter: CONF_N -> "8002" Comparing "5708" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5709" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753026 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756321 ATOM PAIRS WERE FOUND FOR ATOM LIST 41431 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29401 from a total of 756321 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5709 -69.46289 5.37811 0.62185 INTE EXTERN> -29.94178 -39.52111 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4629" Parameter: A <- "-69.4629" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9418" Parameter: B <- "-29.9418" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5211" Parameter: C <- "-39.5211" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5709 TOTAL ENERGY = -69.4629 RDTITL> * VAN DER WAALS = -29.9418 ELECTROSTATIC = -39.5211 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5709" Parameter: CONF_N -> "8002" Comparing "5709" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5710" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756321 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756747 ATOM PAIRS WERE FOUND FOR ATOM LIST 41516 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30183 from a total of 756747 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5710 -71.30245 1.83956 0.50013 INTE EXTERN> -35.63856 -35.66389 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3024" Parameter: A <- "-71.3024" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.6386" Parameter: B <- "-35.6386" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6639" Parameter: C <- "-35.6639" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5710 TOTAL ENERGY = -71.3024 RDTITL> * VAN DER WAALS = -35.6386 ELECTROSTATIC = -35.6639 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5710" Parameter: CONF_N -> "8002" Comparing "5710" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5711" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756747 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755491 ATOM PAIRS WERE FOUND FOR ATOM LIST 41694 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30550 from a total of 755491 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5711 -73.95338 2.65094 0.54743 INTE EXTERN> -35.48332 -38.47006 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9534" Parameter: A <- "-73.9534" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.4833" Parameter: B <- "-35.4833" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4701" Parameter: C <- "-38.4701" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5711 TOTAL ENERGY = -73.9534 RDTITL> * VAN DER WAALS = -35.4833 ELECTROSTATIC = -38.4701 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5711" Parameter: CONF_N -> "8002" Comparing "5711" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5712" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755491 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757487 ATOM PAIRS WERE FOUND FOR ATOM LIST 41643 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29894 from a total of 757487 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5712 -71.79375 -2.15963 0.65605 INTE EXTERN> -28.17002 -43.62373 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7937" Parameter: A <- "-71.7937" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.17" Parameter: B <- "-28.17" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6237" Parameter: C <- "-43.6237" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5712 TOTAL ENERGY = -71.7937 RDTITL> * VAN DER WAALS = -28.17 ELECTROSTATIC = -43.6237 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5712" Parameter: CONF_N -> "8002" Comparing "5712" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5713" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757487 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761994 ATOM PAIRS WERE FOUND FOR ATOM LIST 41708 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30208 from a total of 761994 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5713 -71.76648 -0.02727 0.61675 INTE EXTERN> -30.23589 -41.53058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7665" Parameter: A <- "-71.7665" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2359" Parameter: B <- "-30.2359" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5306" Parameter: C <- "-41.5306" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5713 TOTAL ENERGY = -71.7665 RDTITL> * VAN DER WAALS = -30.2359 ELECTROSTATIC = -41.5306 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5713" Parameter: CONF_N -> "8002" Comparing "5713" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5714" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761994 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758927 ATOM PAIRS WERE FOUND FOR ATOM LIST 41575 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29588 from a total of 758927 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5714 -62.19536 -9.57111 0.55366 INTE EXTERN> -31.58663 -30.60873 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.1954" Parameter: A <- "-62.1954" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5866" Parameter: B <- "-31.5866" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.6087" Parameter: C <- "-30.6087" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5714 TOTAL ENERGY = -62.1954 RDTITL> * VAN DER WAALS = -31.5866 ELECTROSTATIC = -30.6087 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5714" Parameter: CONF_N -> "8002" Comparing "5714" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5715" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758927 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761918 ATOM PAIRS WERE FOUND FOR ATOM LIST 41830 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30373 from a total of 761918 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5715 -76.59452 14.39915 0.60529 INTE EXTERN> -32.32314 -44.27137 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5945" Parameter: A <- "-76.5945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3231" Parameter: B <- "-32.3231" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2714" Parameter: C <- "-44.2714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5715 TOTAL ENERGY = -76.5945 RDTITL> * VAN DER WAALS = -32.3231 ELECTROSTATIC = -44.2714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5715" Parameter: CONF_N -> "8002" Comparing "5715" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5716" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761918 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764304 ATOM PAIRS WERE FOUND FOR ATOM LIST 41977 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30289 from a total of 764304 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5716 -69.00507 -7.58945 0.55482 INTE EXTERN> -32.70800 -36.29706 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0051" Parameter: A <- "-69.0051" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.708" Parameter: B <- "-32.708" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2971" Parameter: C <- "-36.2971" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5716 TOTAL ENERGY = -69.0051 RDTITL> * VAN DER WAALS = -32.708 ELECTROSTATIC = -36.2971 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5716" Parameter: CONF_N -> "8002" Comparing "5716" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5717" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764304 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761414 ATOM PAIRS WERE FOUND FOR ATOM LIST 41933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30059 from a total of 761414 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5717 -72.94241 3.93735 0.53817 INTE EXTERN> -34.09294 -38.84947 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9424" Parameter: A <- "-72.9424" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0929" Parameter: B <- "-34.0929" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8495" Parameter: C <- "-38.8495" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5717 TOTAL ENERGY = -72.9424 RDTITL> * VAN DER WAALS = -34.0929 ELECTROSTATIC = -38.8495 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5717" Parameter: CONF_N -> "8002" Comparing "5717" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5718" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761414 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767534 ATOM PAIRS WERE FOUND FOR ATOM LIST 42077 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30517 from a total of 767534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5718 -63.88761 -9.05480 0.59512 INTE EXTERN> -31.06352 -32.82410 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.8876" Parameter: A <- "-63.8876" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0635" Parameter: B <- "-31.0635" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.8241" Parameter: C <- "-32.8241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5718 TOTAL ENERGY = -63.8876 RDTITL> * VAN DER WAALS = -31.0635 ELECTROSTATIC = -32.8241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5718" Parameter: CONF_N -> "8002" Comparing "5718" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5719" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762782 ATOM PAIRS WERE FOUND FOR ATOM LIST 42170 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29824 from a total of 762782 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5719 -67.33405 3.44644 0.57218 INTE EXTERN> -28.98998 -38.34407 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3341" Parameter: A <- "-67.3341" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.99" Parameter: B <- "-28.99" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3441" Parameter: C <- "-38.3441" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5719 TOTAL ENERGY = -67.3341 RDTITL> * VAN DER WAALS = -28.99 ELECTROSTATIC = -38.3441 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5719" Parameter: CONF_N -> "8002" Comparing "5719" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5720" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762782 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763625 ATOM PAIRS WERE FOUND FOR ATOM LIST 42048 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29964 from a total of 763625 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5720 -65.94799 -1.38606 0.56991 INTE EXTERN> -31.09398 -34.85401 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.948" Parameter: A <- "-65.948" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.094" Parameter: B <- "-31.094" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.854" Parameter: C <- "-34.854" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5720 TOTAL ENERGY = -65.948 RDTITL> * VAN DER WAALS = -31.094 ELECTROSTATIC = -34.854 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5720" Parameter: CONF_N -> "8002" Comparing "5720" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5721" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763625 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760059 ATOM PAIRS WERE FOUND FOR ATOM LIST 41746 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29701 from a total of 760059 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5721 -63.73037 -2.21762 0.54881 INTE EXTERN> -31.85687 -31.87350 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7304" Parameter: A <- "-63.7304" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8569" Parameter: B <- "-31.8569" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.8735" Parameter: C <- "-31.8735" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5721 TOTAL ENERGY = -63.7304 RDTITL> * VAN DER WAALS = -31.8569 ELECTROSTATIC = -31.8735 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5721" Parameter: CONF_N -> "8002" Comparing "5721" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5722" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760059 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761506 ATOM PAIRS WERE FOUND FOR ATOM LIST 41838 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29937 from a total of 761506 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5722 -67.98666 4.25629 0.65315 INTE EXTERN> -27.07503 -40.91163 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9867" Parameter: A <- "-67.9867" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.075" Parameter: B <- "-27.075" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9116" Parameter: C <- "-40.9116" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5722 TOTAL ENERGY = -67.9867 RDTITL> * VAN DER WAALS = -27.075 ELECTROSTATIC = -40.9116 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5722" Parameter: CONF_N -> "8002" Comparing "5722" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5723" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761506 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760552 ATOM PAIRS WERE FOUND FOR ATOM LIST 41768 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29777 from a total of 760552 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5723 -72.77878 4.79212 0.58269 INTE EXTERN> -27.49149 -45.28730 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7788" Parameter: A <- "-72.7788" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4915" Parameter: B <- "-27.4915" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2873" Parameter: C <- "-45.2873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5723 TOTAL ENERGY = -72.7788 RDTITL> * VAN DER WAALS = -27.4915 ELECTROSTATIC = -45.2873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5723" Parameter: CONF_N -> "8002" Comparing "5723" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5724" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760552 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759681 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29312 from a total of 759681 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5724 -71.03183 -1.74695 0.65101 INTE EXTERN> -31.17132 -39.86051 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0318" Parameter: A <- "-71.0318" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1713" Parameter: B <- "-31.1713" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8605" Parameter: C <- "-39.8605" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5724 TOTAL ENERGY = -71.0318 RDTITL> * VAN DER WAALS = -31.1713 ELECTROSTATIC = -39.8605 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5724" Parameter: CONF_N -> "8002" Comparing "5724" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5725" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759681 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756549 ATOM PAIRS WERE FOUND FOR ATOM LIST 41570 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29323 from a total of 756549 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5725 -75.58443 4.55260 0.52984 INTE EXTERN> -31.42255 -44.16189 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5844" Parameter: A <- "-75.5844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4225" Parameter: B <- "-31.4225" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1619" Parameter: C <- "-44.1619" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5725 TOTAL ENERGY = -75.5844 RDTITL> * VAN DER WAALS = -31.4225 ELECTROSTATIC = -44.1619 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5725" Parameter: CONF_N -> "8002" Comparing "5725" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5726" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756549 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760210 ATOM PAIRS WERE FOUND FOR ATOM LIST 41655 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30033 from a total of 760210 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5726 -68.76194 -6.82250 0.51409 INTE EXTERN> -32.89670 -35.86524 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7619" Parameter: A <- "-68.7619" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8967" Parameter: B <- "-32.8967" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8652" Parameter: C <- "-35.8652" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5726 TOTAL ENERGY = -68.7619 RDTITL> * VAN DER WAALS = -32.8967 ELECTROSTATIC = -35.8652 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5726" Parameter: CONF_N -> "8002" Comparing "5726" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5727" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760210 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758350 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30007 from a total of 758350 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5727 -66.85173 -1.91021 0.50774 INTE EXTERN> -32.95387 -33.89786 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8517" Parameter: A <- "-66.8517" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9539" Parameter: B <- "-32.9539" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8979" Parameter: C <- "-33.8979" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5727 TOTAL ENERGY = -66.8517 RDTITL> * VAN DER WAALS = -32.9539 ELECTROSTATIC = -33.8979 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5727" Parameter: CONF_N -> "8002" Comparing "5727" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5728" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758350 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759898 ATOM PAIRS WERE FOUND FOR ATOM LIST 41599 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30004 from a total of 759898 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5728 -71.12551 4.27378 0.55496 INTE EXTERN> -30.82864 -40.29687 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1255" Parameter: A <- "-71.1255" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8286" Parameter: B <- "-30.8286" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2969" Parameter: C <- "-40.2969" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5728 TOTAL ENERGY = -71.1255 RDTITL> * VAN DER WAALS = -30.8286 ELECTROSTATIC = -40.2969 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5728" Parameter: CONF_N -> "8002" Comparing "5728" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5729" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759898 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760239 ATOM PAIRS WERE FOUND FOR ATOM LIST 41656 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30223 from a total of 760239 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5729 -71.26726 0.14175 0.46459 INTE EXTERN> -34.11902 -37.14824 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2673" Parameter: A <- "-71.2673" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.119" Parameter: B <- "-34.119" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1482" Parameter: C <- "-37.1482" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5729 TOTAL ENERGY = -71.2673 RDTITL> * VAN DER WAALS = -34.119 ELECTROSTATIC = -37.1482 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5729" Parameter: CONF_N -> "8002" Comparing "5729" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5730" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760239 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762087 ATOM PAIRS WERE FOUND FOR ATOM LIST 41729 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30233 from a total of 762087 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5730 -71.13976 -0.12750 0.63534 INTE EXTERN> -28.77883 -42.36093 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1398" Parameter: A <- "-71.1398" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7788" Parameter: B <- "-28.7788" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3609" Parameter: C <- "-42.3609" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5730 TOTAL ENERGY = -71.1398 RDTITL> * VAN DER WAALS = -28.7788 ELECTROSTATIC = -42.3609 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5730" Parameter: CONF_N -> "8002" Comparing "5730" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5731" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762087 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760830 ATOM PAIRS WERE FOUND FOR ATOM LIST 41926 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29930 from a total of 760830 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5731 -66.72458 -4.41518 0.51180 INTE EXTERN> -31.35638 -35.36820 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7246" Parameter: A <- "-66.7246" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3564" Parameter: B <- "-31.3564" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3682" Parameter: C <- "-35.3682" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5731 TOTAL ENERGY = -66.7246 RDTITL> * VAN DER WAALS = -31.3564 ELECTROSTATIC = -35.3682 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5731" Parameter: CONF_N -> "8002" Comparing "5731" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5732" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760830 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763551 ATOM PAIRS WERE FOUND FOR ATOM LIST 41685 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30029 from a total of 763551 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5732 -72.82637 6.10179 0.63900 INTE EXTERN> -31.56438 -41.26198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8264" Parameter: A <- "-72.8264" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5644" Parameter: B <- "-31.5644" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.262" Parameter: C <- "-41.262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5732 TOTAL ENERGY = -72.8264 RDTITL> * VAN DER WAALS = -31.5644 ELECTROSTATIC = -41.262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5732" Parameter: CONF_N -> "8002" Comparing "5732" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5733" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763551 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761437 ATOM PAIRS WERE FOUND FOR ATOM LIST 41662 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29522 from a total of 761437 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5733 -70.98979 -1.83658 0.55854 INTE EXTERN> -33.03683 -37.95296 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9898" Parameter: A <- "-70.9898" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0368" Parameter: B <- "-33.0368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.953" Parameter: C <- "-37.953" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5733 TOTAL ENERGY = -70.9898 RDTITL> * VAN DER WAALS = -33.0368 ELECTROSTATIC = -37.953 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5733" Parameter: CONF_N -> "8002" Comparing "5733" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5734" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761437 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757623 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29709 from a total of 757623 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5734 -71.49295 0.50317 0.57294 INTE EXTERN> -30.37727 -41.11568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.493" Parameter: A <- "-71.493" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3773" Parameter: B <- "-30.3773" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1157" Parameter: C <- "-41.1157" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5734 TOTAL ENERGY = -71.493 RDTITL> * VAN DER WAALS = -30.3773 ELECTROSTATIC = -41.1157 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5734" Parameter: CONF_N -> "8002" Comparing "5734" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5735" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757623 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760825 ATOM PAIRS WERE FOUND FOR ATOM LIST 41636 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29669 from a total of 760825 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5735 -69.96559 -1.52736 0.48995 INTE EXTERN> -33.71358 -36.25201 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9656" Parameter: A <- "-69.9656" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7136" Parameter: B <- "-33.7136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.252" Parameter: C <- "-36.252" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5735 TOTAL ENERGY = -69.9656 RDTITL> * VAN DER WAALS = -33.7136 ELECTROSTATIC = -36.252 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5735" Parameter: CONF_N -> "8002" Comparing "5735" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5736" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760825 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760541 ATOM PAIRS WERE FOUND FOR ATOM LIST 41651 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29669 from a total of 760541 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5736 -71.59500 1.62941 0.55088 INTE EXTERN> -30.40612 -41.18888 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.595" Parameter: A <- "-71.595" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4061" Parameter: B <- "-30.4061" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1889" Parameter: C <- "-41.1889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5736 TOTAL ENERGY = -71.595 RDTITL> * VAN DER WAALS = -30.4061 ELECTROSTATIC = -41.1889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5736" Parameter: CONF_N -> "8002" Comparing "5736" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5737" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760541 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763836 ATOM PAIRS WERE FOUND FOR ATOM LIST 41737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29879 from a total of 763836 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5737 -72.58744 0.99244 0.57510 INTE EXTERN> -31.15282 -41.43462 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5874" Parameter: A <- "-72.5874" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1528" Parameter: B <- "-31.1528" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4346" Parameter: C <- "-41.4346" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5737 TOTAL ENERGY = -72.5874 RDTITL> * VAN DER WAALS = -31.1528 ELECTROSTATIC = -41.4346 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5737" Parameter: CONF_N -> "8002" Comparing "5737" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5738" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763836 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758265 ATOM PAIRS WERE FOUND FOR ATOM LIST 41546 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29868 from a total of 758265 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5738 -67.64464 -4.94280 0.79773 INTE EXTERN> -23.83001 -43.81464 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6446" Parameter: A <- "-67.6446" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.83" Parameter: B <- "-23.83" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8146" Parameter: C <- "-43.8146" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5738 TOTAL ENERGY = -67.6446 RDTITL> * VAN DER WAALS = -23.83 ELECTROSTATIC = -43.8146 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5738" Parameter: CONF_N -> "8002" Comparing "5738" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5739" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758265 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758546 ATOM PAIRS WERE FOUND FOR ATOM LIST 41584 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30075 from a total of 758546 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5739 -65.47411 -2.17053 0.54464 INTE EXTERN> -32.40985 -33.06426 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4741" Parameter: A <- "-65.4741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4099" Parameter: B <- "-32.4099" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.0643" Parameter: C <- "-33.0643" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5739 TOTAL ENERGY = -65.4741 RDTITL> * VAN DER WAALS = -32.4099 ELECTROSTATIC = -33.0643 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5739" Parameter: CONF_N -> "8002" Comparing "5739" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5740" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758546 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767291 ATOM PAIRS WERE FOUND FOR ATOM LIST 42114 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30332 from a total of 767291 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5740 -61.99644 -3.47767 0.65384 INTE EXTERN> -27.82258 -34.17386 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.9964" Parameter: A <- "-61.9964" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8226" Parameter: B <- "-27.8226" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1739" Parameter: C <- "-34.1739" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5740 TOTAL ENERGY = -61.9964 RDTITL> * VAN DER WAALS = -27.8226 ELECTROSTATIC = -34.1739 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5740" Parameter: CONF_N -> "8002" Comparing "5740" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5741" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767291 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766454 ATOM PAIRS WERE FOUND FOR ATOM LIST 41954 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30141 from a total of 766454 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5741 -68.47495 6.47851 0.57747 INTE EXTERN> -30.35896 -38.11599 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.475" Parameter: A <- "-68.475" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.359" Parameter: B <- "-30.359" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.116" Parameter: C <- "-38.116" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5741 TOTAL ENERGY = -68.475 RDTITL> * VAN DER WAALS = -30.359 ELECTROSTATIC = -38.116 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5741" Parameter: CONF_N -> "8002" Comparing "5741" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5742" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766454 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762291 ATOM PAIRS WERE FOUND FOR ATOM LIST 41812 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29707 from a total of 762291 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5742 -65.35785 -3.11710 0.58360 INTE EXTERN> -31.08830 -34.26955 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3578" Parameter: A <- "-65.3578" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0883" Parameter: B <- "-31.0883" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2696" Parameter: C <- "-34.2696" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5742 TOTAL ENERGY = -65.3578 RDTITL> * VAN DER WAALS = -31.0883 ELECTROSTATIC = -34.2696 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5742" Parameter: CONF_N -> "8002" Comparing "5742" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5743" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762291 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761340 ATOM PAIRS WERE FOUND FOR ATOM LIST 41753 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29783 from a total of 761340 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5743 -56.53219 -8.82565 0.67049 INTE EXTERN> -26.47202 -30.06017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-56.5322" Parameter: A <- "-56.5322" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.472" Parameter: B <- "-26.472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.0602" Parameter: C <- "-30.0602" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5743 TOTAL ENERGY = -56.5322 RDTITL> * VAN DER WAALS = -26.472 ELECTROSTATIC = -30.0602 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5743" Parameter: CONF_N -> "8002" Comparing "5743" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5744" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761340 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755040 ATOM PAIRS WERE FOUND FOR ATOM LIST 41584 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28964 from a total of 755040 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5744 -61.17695 4.64476 0.56485 INTE EXTERN> -29.06792 -32.10903 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.177" Parameter: A <- "-61.177" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0679" Parameter: B <- "-29.0679" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.109" Parameter: C <- "-32.109" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5744 TOTAL ENERGY = -61.177 RDTITL> * VAN DER WAALS = -29.0679 ELECTROSTATIC = -32.109 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5744" Parameter: CONF_N -> "8002" Comparing "5744" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5745" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755040 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759198 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29724 from a total of 759198 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5745 -63.35740 2.18045 0.46076 INTE EXTERN> -35.42248 -27.93492 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3574" Parameter: A <- "-63.3574" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.4225" Parameter: B <- "-35.4225" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.9349" Parameter: C <- "-27.9349" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5745 TOTAL ENERGY = -63.3574 RDTITL> * VAN DER WAALS = -35.4225 ELECTROSTATIC = -27.9349 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5745" Parameter: CONF_N -> "8002" Comparing "5745" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5746" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759198 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753273 ATOM PAIRS WERE FOUND FOR ATOM LIST 41394 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29122 from a total of 753273 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5746 -58.17460 -5.18280 0.59251 INTE EXTERN> -27.49392 -30.68068 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.1746" Parameter: A <- "-58.1746" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4939" Parameter: B <- "-27.4939" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.6807" Parameter: C <- "-30.6807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5746 TOTAL ENERGY = -58.1746 RDTITL> * VAN DER WAALS = -27.4939 ELECTROSTATIC = -30.6807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5746" Parameter: CONF_N -> "8002" Comparing "5746" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5747" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753273 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758602 ATOM PAIRS WERE FOUND FOR ATOM LIST 41575 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29434 from a total of 758602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5747 -73.67801 15.50341 0.52972 INTE EXTERN> -33.40265 -40.27535 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.678" Parameter: A <- "-73.678" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4027" Parameter: B <- "-33.4027" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2754" Parameter: C <- "-40.2754" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5747 TOTAL ENERGY = -73.678 RDTITL> * VAN DER WAALS = -33.4027 ELECTROSTATIC = -40.2754 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5747" Parameter: CONF_N -> "8002" Comparing "5747" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5748" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758167 ATOM PAIRS WERE FOUND FOR ATOM LIST 41426 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28870 from a total of 758167 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5748 -64.20835 -9.46965 0.51692 INTE EXTERN> -29.09280 -35.11556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2084" Parameter: A <- "-64.2084" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0928" Parameter: B <- "-29.0928" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1156" Parameter: C <- "-35.1156" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5748 TOTAL ENERGY = -64.2084 RDTITL> * VAN DER WAALS = -29.0928 ELECTROSTATIC = -35.1156 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5748" Parameter: CONF_N -> "8002" Comparing "5748" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5749" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758167 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758883 ATOM PAIRS WERE FOUND FOR ATOM LIST 41463 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29695 from a total of 758883 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5749 -69.22677 5.01842 0.58639 INTE EXTERN> -31.23092 -37.99586 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2268" Parameter: A <- "-69.2268" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2309" Parameter: B <- "-31.2309" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9959" Parameter: C <- "-37.9959" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5749 TOTAL ENERGY = -69.2268 RDTITL> * VAN DER WAALS = -31.2309 ELECTROSTATIC = -37.9959 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5749" Parameter: CONF_N -> "8002" Comparing "5749" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5750" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758883 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759964 ATOM PAIRS WERE FOUND FOR ATOM LIST 41751 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29972 from a total of 759964 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5750 -72.15286 2.92609 0.61126 INTE EXTERN> -30.93782 -41.21504 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1529" Parameter: A <- "-72.1529" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9378" Parameter: B <- "-30.9378" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.215" Parameter: C <- "-41.215" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5750 TOTAL ENERGY = -72.1529 RDTITL> * VAN DER WAALS = -30.9378 ELECTROSTATIC = -41.215 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5750" Parameter: CONF_N -> "8002" Comparing "5750" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5751" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759964 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761388 ATOM PAIRS WERE FOUND FOR ATOM LIST 41807 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29567 from a total of 761388 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5751 -66.52500 -5.62787 0.55041 INTE EXTERN> -33.93168 -32.59332 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.525" Parameter: A <- "-66.525" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9317" Parameter: B <- "-33.9317" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5933" Parameter: C <- "-32.5933" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5751 TOTAL ENERGY = -66.525 RDTITL> * VAN DER WAALS = -33.9317 ELECTROSTATIC = -32.5933 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5751" Parameter: CONF_N -> "8002" Comparing "5751" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5752" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761388 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755324 ATOM PAIRS WERE FOUND FOR ATOM LIST 41612 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29776 from a total of 755324 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5752 -76.57554 10.05054 0.62645 INTE EXTERN> -29.64663 -46.92891 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5755" Parameter: A <- "-76.5755" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6466" Parameter: B <- "-29.6466" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9289" Parameter: C <- "-46.9289" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5752 TOTAL ENERGY = -76.5755 RDTITL> * VAN DER WAALS = -29.6466 ELECTROSTATIC = -46.9289 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5752" Parameter: CONF_N -> "8002" Comparing "5752" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5753" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755324 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762406 ATOM PAIRS WERE FOUND FOR ATOM LIST 41901 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29833 from a total of 762406 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5753 -66.81377 -9.76176 0.62227 INTE EXTERN> -29.59852 -37.21525 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8138" Parameter: A <- "-66.8138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5985" Parameter: B <- "-29.5985" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2152" Parameter: C <- "-37.2152" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5753 TOTAL ENERGY = -66.8138 RDTITL> * VAN DER WAALS = -29.5985 ELECTROSTATIC = -37.2152 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5753" Parameter: CONF_N -> "8002" Comparing "5753" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5754" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762406 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758604 ATOM PAIRS WERE FOUND FOR ATOM LIST 41709 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29324 from a total of 758604 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5754 -62.62971 -4.18406 0.66726 INTE EXTERN> -26.87445 -35.75526 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.6297" Parameter: A <- "-62.6297" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8744" Parameter: B <- "-26.8744" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7553" Parameter: C <- "-35.7553" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5754 TOTAL ENERGY = -62.6297 RDTITL> * VAN DER WAALS = -26.8744 ELECTROSTATIC = -35.7553 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5754" Parameter: CONF_N -> "8002" Comparing "5754" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5755" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758604 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755201 ATOM PAIRS WERE FOUND FOR ATOM LIST 41350 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29443 from a total of 755201 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5755 -68.44450 5.81479 0.43639 INTE EXTERN> -34.05043 -34.39407 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4445" Parameter: A <- "-68.4445" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0504" Parameter: B <- "-34.0504" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3941" Parameter: C <- "-34.3941" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5755 TOTAL ENERGY = -68.4445 RDTITL> * VAN DER WAALS = -34.0504 ELECTROSTATIC = -34.3941 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5755" Parameter: CONF_N -> "8002" Comparing "5755" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5756" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755201 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758294 ATOM PAIRS WERE FOUND FOR ATOM LIST 41632 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28834 from a total of 758294 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5756 -66.59028 -1.85422 0.60879 INTE EXTERN> -25.60803 -40.98225 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5903" Parameter: A <- "-66.5903" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.608" Parameter: B <- "-25.608" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9823" Parameter: C <- "-40.9823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5756 TOTAL ENERGY = -66.5903 RDTITL> * VAN DER WAALS = -25.608 ELECTROSTATIC = -40.9823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5756" Parameter: CONF_N -> "8002" Comparing "5756" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5757" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758294 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763602 ATOM PAIRS WERE FOUND FOR ATOM LIST 41915 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29641 from a total of 763602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5757 -65.98704 -0.60323 0.65585 INTE EXTERN> -22.74514 -43.24191 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.987" Parameter: A <- "-65.987" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.7451" Parameter: B <- "-22.7451" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2419" Parameter: C <- "-43.2419" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5757 TOTAL ENERGY = -65.987 RDTITL> * VAN DER WAALS = -22.7451 ELECTROSTATIC = -43.2419 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5757" Parameter: CONF_N -> "8002" Comparing "5757" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5758" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762611 ATOM PAIRS WERE FOUND FOR ATOM LIST 41680 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29648 from a total of 762611 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5758 -64.86726 -1.11978 0.48526 INTE EXTERN> -32.20471 -32.66255 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8673" Parameter: A <- "-64.8673" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2047" Parameter: B <- "-32.2047" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.6625" Parameter: C <- "-32.6625" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5758 TOTAL ENERGY = -64.8673 RDTITL> * VAN DER WAALS = -32.2047 ELECTROSTATIC = -32.6625 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5758" Parameter: CONF_N -> "8002" Comparing "5758" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5759" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762611 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756511 ATOM PAIRS WERE FOUND FOR ATOM LIST 41612 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29223 from a total of 756511 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5759 -64.08044 -0.78682 0.54484 INTE EXTERN> -29.76897 -34.31147 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0804" Parameter: A <- "-64.0804" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.769" Parameter: B <- "-29.769" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3115" Parameter: C <- "-34.3115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5759 TOTAL ENERGY = -64.0804 RDTITL> * VAN DER WAALS = -29.769 ELECTROSTATIC = -34.3115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5759" Parameter: CONF_N -> "8002" Comparing "5759" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5760" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756511 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759345 ATOM PAIRS WERE FOUND FOR ATOM LIST 41698 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29800 from a total of 759345 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5760 -68.28853 4.20809 0.62721 INTE EXTERN> -31.06088 -37.22765 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2885" Parameter: A <- "-68.2885" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0609" Parameter: B <- "-31.0609" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2276" Parameter: C <- "-37.2276" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5760 TOTAL ENERGY = -68.2885 RDTITL> * VAN DER WAALS = -31.0609 ELECTROSTATIC = -37.2276 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5760" Parameter: CONF_N -> "8002" Comparing "5760" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5761" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759345 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758123 ATOM PAIRS WERE FOUND FOR ATOM LIST 41657 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29192 from a total of 758123 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5761 -62.38405 -5.90448 0.66986 INTE EXTERN> -26.65856 -35.72549 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.384" Parameter: A <- "-62.384" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6586" Parameter: B <- "-26.6586" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7255" Parameter: C <- "-35.7255" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5761 TOTAL ENERGY = -62.384 RDTITL> * VAN DER WAALS = -26.6586 ELECTROSTATIC = -35.7255 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5761" Parameter: CONF_N -> "8002" Comparing "5761" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5762" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758123 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754346 ATOM PAIRS WERE FOUND FOR ATOM LIST 41399 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29555 from a total of 754346 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5762 -70.29574 7.91170 0.52259 INTE EXTERN> -34.02493 -36.27082 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2957" Parameter: A <- "-70.2957" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0249" Parameter: B <- "-34.0249" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2708" Parameter: C <- "-36.2708" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5762 TOTAL ENERGY = -70.2957 RDTITL> * VAN DER WAALS = -34.0249 ELECTROSTATIC = -36.2708 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5762" Parameter: CONF_N -> "8002" Comparing "5762" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5763" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754346 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753707 ATOM PAIRS WERE FOUND FOR ATOM LIST 41420 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29355 from a total of 753707 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5763 -68.22963 -2.06611 0.60117 INTE EXTERN> -29.25993 -38.96971 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2296" Parameter: A <- "-68.2296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2599" Parameter: B <- "-29.2599" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9697" Parameter: C <- "-38.9697" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5763 TOTAL ENERGY = -68.2296 RDTITL> * VAN DER WAALS = -29.2599 ELECTROSTATIC = -38.9697 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5763" Parameter: CONF_N -> "8002" Comparing "5763" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5764" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753707 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752784 ATOM PAIRS WERE FOUND FOR ATOM LIST 41070 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29357 from a total of 752784 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5764 -65.22834 -3.00129 0.44503 INTE EXTERN> -33.75266 -31.47568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2283" Parameter: A <- "-65.2283" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7527" Parameter: B <- "-33.7527" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.4757" Parameter: C <- "-31.4757" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5764 TOTAL ENERGY = -65.2283 RDTITL> * VAN DER WAALS = -33.7527 ELECTROSTATIC = -31.4757 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5764" Parameter: CONF_N -> "8002" Comparing "5764" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5765" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752784 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748689 ATOM PAIRS WERE FOUND FOR ATOM LIST 41091 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29616 from a total of 748689 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5765 -72.98252 7.75418 0.61814 INTE EXTERN> -31.46803 -41.51448 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9825" Parameter: A <- "-72.9825" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.468" Parameter: B <- "-31.468" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5145" Parameter: C <- "-41.5145" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5765 TOTAL ENERGY = -72.9825 RDTITL> * VAN DER WAALS = -31.468 ELECTROSTATIC = -41.5145 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5765" Parameter: CONF_N -> "8002" Comparing "5765" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5766" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748689 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745787 ATOM PAIRS WERE FOUND FOR ATOM LIST 41143 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29168 from a total of 745787 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5766 -64.11378 -8.86874 0.45755 INTE EXTERN> -35.10954 -29.00423 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1138" Parameter: A <- "-64.1138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.1095" Parameter: B <- "-35.1095" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.0042" Parameter: C <- "-29.0042" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5766 TOTAL ENERGY = -64.1138 RDTITL> * VAN DER WAALS = -35.1095 ELECTROSTATIC = -29.0042 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5766" Parameter: CONF_N -> "8002" Comparing "5766" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5767" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745787 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754501 ATOM PAIRS WERE FOUND FOR ATOM LIST 41381 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29861 from a total of 754501 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5767 -64.01184 -0.10194 0.44516 INTE EXTERN> -37.28338 -26.72846 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0118" Parameter: A <- "-64.0118" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-37.2834" Parameter: B <- "-37.2834" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-26.7285" Parameter: C <- "-26.7285" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5767 TOTAL ENERGY = -64.0118 RDTITL> * VAN DER WAALS = -37.2834 ELECTROSTATIC = -26.7285 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5767" Parameter: CONF_N -> "8002" Comparing "5767" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5768" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754501 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758859 ATOM PAIRS WERE FOUND FOR ATOM LIST 41567 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30247 from a total of 758859 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5768 -67.91359 3.90175 0.63114 INTE EXTERN> -29.59650 -38.31709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9136" Parameter: A <- "-67.9136" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5965" Parameter: B <- "-29.5965" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3171" Parameter: C <- "-38.3171" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5768 TOTAL ENERGY = -67.9136 RDTITL> * VAN DER WAALS = -29.5965 ELECTROSTATIC = -38.3171 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5768" Parameter: CONF_N -> "8002" Comparing "5768" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5769" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758859 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752461 ATOM PAIRS WERE FOUND FOR ATOM LIST 41081 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29774 from a total of 752461 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5769 -65.35309 -2.56049 0.55471 INTE EXTERN> -32.81199 -32.54111 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3531" Parameter: A <- "-65.3531" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.812" Parameter: B <- "-32.812" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5411" Parameter: C <- "-32.5411" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5769 TOTAL ENERGY = -65.3531 RDTITL> * VAN DER WAALS = -32.812 ELECTROSTATIC = -32.5411 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5769" Parameter: CONF_N -> "8002" Comparing "5769" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5770" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752461 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755541 ATOM PAIRS WERE FOUND FOR ATOM LIST 41499 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29518 from a total of 755541 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5770 -63.22809 -2.12500 0.58630 INTE EXTERN> -33.74317 -29.48492 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.2281" Parameter: A <- "-63.2281" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7432" Parameter: B <- "-33.7432" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.4849" Parameter: C <- "-29.4849" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5770 TOTAL ENERGY = -63.2281 RDTITL> * VAN DER WAALS = -33.7432 ELECTROSTATIC = -29.4849 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5770" Parameter: CONF_N -> "8002" Comparing "5770" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5771" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755541 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760523 ATOM PAIRS WERE FOUND FOR ATOM LIST 41913 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30018 from a total of 760523 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5771 -68.06114 4.83305 0.52490 INTE EXTERN> -38.00291 -30.05823 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0611" Parameter: A <- "-68.0611" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-38.0029" Parameter: B <- "-38.0029" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.0582" Parameter: C <- "-30.0582" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5771 TOTAL ENERGY = -68.0611 RDTITL> * VAN DER WAALS = -38.0029 ELECTROSTATIC = -30.0582 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5771" Parameter: CONF_N -> "8002" Comparing "5771" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5772" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760523 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758170 ATOM PAIRS WERE FOUND FOR ATOM LIST 41547 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29272 from a total of 758170 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5772 -66.81063 -1.25051 0.56365 INTE EXTERN> -33.27652 -33.53411 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8106" Parameter: A <- "-66.8106" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2765" Parameter: B <- "-33.2765" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.5341" Parameter: C <- "-33.5341" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5772 TOTAL ENERGY = -66.8106 RDTITL> * VAN DER WAALS = -33.2765 ELECTROSTATIC = -33.5341 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5772" Parameter: CONF_N -> "8002" Comparing "5772" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5773" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758170 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757738 ATOM PAIRS WERE FOUND FOR ATOM LIST 41538 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29625 from a total of 757738 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5773 -62.16581 -4.64483 0.49032 INTE EXTERN> -35.84218 -26.32363 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.1658" Parameter: A <- "-62.1658" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.8422" Parameter: B <- "-35.8422" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-26.3236" Parameter: C <- "-26.3236" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5773 TOTAL ENERGY = -62.1658 RDTITL> * VAN DER WAALS = -35.8422 ELECTROSTATIC = -26.3236 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5773" Parameter: CONF_N -> "8002" Comparing "5773" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5774" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757738 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754104 ATOM PAIRS WERE FOUND FOR ATOM LIST 41463 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29180 from a total of 754104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5774 -64.38909 2.22328 0.53470 INTE EXTERN> -29.27135 -35.11774 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3891" Parameter: A <- "-64.3891" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2713" Parameter: B <- "-29.2713" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1177" Parameter: C <- "-35.1177" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5774 TOTAL ENERGY = -64.3891 RDTITL> * VAN DER WAALS = -29.2713 ELECTROSTATIC = -35.1177 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5774" Parameter: CONF_N -> "8002" Comparing "5774" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5775" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761811 ATOM PAIRS WERE FOUND FOR ATOM LIST 41809 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30134 from a total of 761811 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5775 -72.40020 8.01111 0.50780 INTE EXTERN> -35.05969 -37.34051 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4002" Parameter: A <- "-72.4002" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.0597" Parameter: B <- "-35.0597" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3405" Parameter: C <- "-37.3405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5775 TOTAL ENERGY = -72.4002 RDTITL> * VAN DER WAALS = -35.0597 ELECTROSTATIC = -37.3405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5775" Parameter: CONF_N -> "8002" Comparing "5775" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5776" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761811 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764629 ATOM PAIRS WERE FOUND FOR ATOM LIST 41767 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29731 from a total of 764629 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5776 -69.30492 -3.09528 0.64473 INTE EXTERN> -27.52397 -41.78095 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3049" Parameter: A <- "-69.3049" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.524" Parameter: B <- "-27.524" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.781" Parameter: C <- "-41.781" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5776 TOTAL ENERGY = -69.3049 RDTITL> * VAN DER WAALS = -27.524 ELECTROSTATIC = -41.781 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5776" Parameter: CONF_N -> "8002" Comparing "5776" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5777" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764629 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752727 ATOM PAIRS WERE FOUND FOR ATOM LIST 41164 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29876 from a total of 752727 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5777 -68.94215 -0.36277 0.55700 INTE EXTERN> -34.39332 -34.54883 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9422" Parameter: A <- "-68.9422" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3933" Parameter: B <- "-34.3933" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5488" Parameter: C <- "-34.5488" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5777 TOTAL ENERGY = -68.9422 RDTITL> * VAN DER WAALS = -34.3933 ELECTROSTATIC = -34.5488 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5777" Parameter: CONF_N -> "8002" Comparing "5777" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5778" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752727 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757297 ATOM PAIRS WERE FOUND FOR ATOM LIST 41323 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29915 from a total of 757297 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5778 -70.38509 1.44294 0.60379 INTE EXTERN> -31.29554 -39.08955 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3851" Parameter: A <- "-70.3851" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2955" Parameter: B <- "-31.2955" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0896" Parameter: C <- "-39.0896" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5778 TOTAL ENERGY = -70.3851 RDTITL> * VAN DER WAALS = -31.2955 ELECTROSTATIC = -39.0896 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5778" Parameter: CONF_N -> "8002" Comparing "5778" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5779" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757297 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761232 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30200 from a total of 761232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5779 -76.25166 5.86657 0.59162 INTE EXTERN> -35.10166 -41.15000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2517" Parameter: A <- "-76.2517" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.1017" Parameter: B <- "-35.1017" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.15" Parameter: C <- "-41.15" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5779 TOTAL ENERGY = -76.2517 RDTITL> * VAN DER WAALS = -35.1017 ELECTROSTATIC = -41.15 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5779" Parameter: CONF_N -> "8002" Comparing "5779" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5780" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755314 ATOM PAIRS WERE FOUND FOR ATOM LIST 41338 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29791 from a total of 755314 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5780 -62.77986 -13.47180 0.63559 INTE EXTERN> -28.38287 -34.39698 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.7799" Parameter: A <- "-62.7799" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3829" Parameter: B <- "-28.3829" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.397" Parameter: C <- "-34.397" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5780 TOTAL ENERGY = -62.7799 RDTITL> * VAN DER WAALS = -28.3829 ELECTROSTATIC = -34.397 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5780" Parameter: CONF_N -> "8002" Comparing "5780" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5781" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755314 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759573 ATOM PAIRS WERE FOUND FOR ATOM LIST 41744 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29816 from a total of 759573 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5781 -72.14679 9.36693 0.55720 INTE EXTERN> -32.68012 -39.46666 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1468" Parameter: A <- "-72.1468" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6801" Parameter: B <- "-32.6801" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4667" Parameter: C <- "-39.4667" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5781 TOTAL ENERGY = -72.1468 RDTITL> * VAN DER WAALS = -32.6801 ELECTROSTATIC = -39.4667 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5781" Parameter: CONF_N -> "8002" Comparing "5781" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5782" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759573 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755134 ATOM PAIRS WERE FOUND FOR ATOM LIST 41396 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29510 from a total of 755134 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5782 -72.72361 0.57682 0.55009 INTE EXTERN> -33.23655 -39.48705 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7236" Parameter: A <- "-72.7236" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2366" Parameter: B <- "-33.2366" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4871" Parameter: C <- "-39.4871" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5782 TOTAL ENERGY = -72.7236 RDTITL> * VAN DER WAALS = -33.2366 ELECTROSTATIC = -39.4871 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5782" Parameter: CONF_N -> "8002" Comparing "5782" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5783" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755134 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753732 ATOM PAIRS WERE FOUND FOR ATOM LIST 41420 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29636 from a total of 753732 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5783 -66.79221 -5.93139 0.60003 INTE EXTERN> -29.84821 -36.94400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7922" Parameter: A <- "-66.7922" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8482" Parameter: B <- "-29.8482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.944" Parameter: C <- "-36.944" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5783 TOTAL ENERGY = -66.7922 RDTITL> * VAN DER WAALS = -29.8482 ELECTROSTATIC = -36.944 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5783" Parameter: CONF_N -> "8002" Comparing "5783" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5784" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753732 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41599 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29473 from a total of 758526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5784 -73.21791 6.42570 0.57858 INTE EXTERN> -31.61549 -41.60242 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2179" Parameter: A <- "-73.2179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6155" Parameter: B <- "-31.6155" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6024" Parameter: C <- "-41.6024" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5784 TOTAL ENERGY = -73.2179 RDTITL> * VAN DER WAALS = -31.6155 ELECTROSTATIC = -41.6024 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5784" Parameter: CONF_N -> "8002" Comparing "5784" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5785" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755436 ATOM PAIRS WERE FOUND FOR ATOM LIST 41486 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29768 from a total of 755436 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5785 -67.79623 -5.42169 0.63730 INTE EXTERN> -26.40897 -41.38725 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7962" Parameter: A <- "-67.7962" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.409" Parameter: B <- "-26.409" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3873" Parameter: C <- "-41.3873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5785 TOTAL ENERGY = -67.7962 RDTITL> * VAN DER WAALS = -26.409 ELECTROSTATIC = -41.3873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5785" Parameter: CONF_N -> "8002" Comparing "5785" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5786" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755436 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755974 ATOM PAIRS WERE FOUND FOR ATOM LIST 41360 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29425 from a total of 755974 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5786 -65.45072 -2.34551 0.55297 INTE EXTERN> -30.28309 -35.16763 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4507" Parameter: A <- "-65.4507" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2831" Parameter: B <- "-30.2831" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1676" Parameter: C <- "-35.1676" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5786 TOTAL ENERGY = -65.4507 RDTITL> * VAN DER WAALS = -30.2831 ELECTROSTATIC = -35.1676 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5786" Parameter: CONF_N -> "8002" Comparing "5786" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5787" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755974 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759873 ATOM PAIRS WERE FOUND FOR ATOM LIST 41796 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 759873 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5787 -69.02962 3.57890 0.49713 INTE EXTERN> -34.33638 -34.69324 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0296" Parameter: A <- "-69.0296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3364" Parameter: B <- "-34.3364" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.6932" Parameter: C <- "-34.6932" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5787 TOTAL ENERGY = -69.0296 RDTITL> * VAN DER WAALS = -34.3364 ELECTROSTATIC = -34.6932 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5787" Parameter: CONF_N -> "8002" Comparing "5787" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5788" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759873 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756358 ATOM PAIRS WERE FOUND FOR ATOM LIST 41496 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29040 from a total of 756358 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5788 -68.38557 -0.64405 0.54196 INTE EXTERN> -30.62451 -37.76106 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3856" Parameter: A <- "-68.3856" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6245" Parameter: B <- "-30.6245" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7611" Parameter: C <- "-37.7611" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5788 TOTAL ENERGY = -68.3856 RDTITL> * VAN DER WAALS = -30.6245 ELECTROSTATIC = -37.7611 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5788" Parameter: CONF_N -> "8002" Comparing "5788" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5789" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756358 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757322 ATOM PAIRS WERE FOUND FOR ATOM LIST 41504 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28989 from a total of 757322 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5789 -67.17113 -1.21444 0.48722 INTE EXTERN> -32.53850 -34.63263 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1711" Parameter: A <- "-67.1711" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5385" Parameter: B <- "-32.5385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.6326" Parameter: C <- "-34.6326" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5789 TOTAL ENERGY = -67.1711 RDTITL> * VAN DER WAALS = -32.5385 ELECTROSTATIC = -34.6326 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5789" Parameter: CONF_N -> "8002" Comparing "5789" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5790" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757322 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761645 ATOM PAIRS WERE FOUND FOR ATOM LIST 41596 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29908 from a total of 761645 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5790 -75.39467 8.22355 0.55779 INTE EXTERN> -31.60648 -43.78819 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3947" Parameter: A <- "-75.3947" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6065" Parameter: B <- "-31.6065" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7882" Parameter: C <- "-43.7882" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5790 TOTAL ENERGY = -75.3947 RDTITL> * VAN DER WAALS = -31.6065 ELECTROSTATIC = -43.7882 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5790" Parameter: CONF_N -> "8002" Comparing "5790" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5791" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761645 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753158 ATOM PAIRS WERE FOUND FOR ATOM LIST 41396 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29073 from a total of 753158 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5791 -64.56550 -10.82918 0.56459 INTE EXTERN> -31.43142 -33.13408 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5655" Parameter: A <- "-64.5655" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4314" Parameter: B <- "-31.4314" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1341" Parameter: C <- "-33.1341" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5791 TOTAL ENERGY = -64.5655 RDTITL> * VAN DER WAALS = -31.4314 ELECTROSTATIC = -33.1341 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5791" Parameter: CONF_N -> "8002" Comparing "5791" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5792" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753158 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753745 ATOM PAIRS WERE FOUND FOR ATOM LIST 41527 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29640 from a total of 753745 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5792 -71.27404 6.70854 0.57420 INTE EXTERN> -32.06777 -39.20627 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.274" Parameter: A <- "-71.274" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0678" Parameter: B <- "-32.0678" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2063" Parameter: C <- "-39.2063" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5792 TOTAL ENERGY = -71.274 RDTITL> * VAN DER WAALS = -32.0678 ELECTROSTATIC = -39.2063 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5792" Parameter: CONF_N -> "8002" Comparing "5792" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5793" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753745 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756527 ATOM PAIRS WERE FOUND FOR ATOM LIST 41460 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29514 from a total of 756527 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5793 -65.02090 -6.25314 0.60363 INTE EXTERN> -29.89420 -35.12671 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0209" Parameter: A <- "-65.0209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8942" Parameter: B <- "-29.8942" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1267" Parameter: C <- "-35.1267" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5793 TOTAL ENERGY = -65.0209 RDTITL> * VAN DER WAALS = -29.8942 ELECTROSTATIC = -35.1267 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5793" Parameter: CONF_N -> "8002" Comparing "5793" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5794" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756527 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754778 ATOM PAIRS WERE FOUND FOR ATOM LIST 41560 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29131 from a total of 754778 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5794 -62.32350 -2.69740 0.51624 INTE EXTERN> -31.14139 -31.18211 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3235" Parameter: A <- "-62.3235" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1414" Parameter: B <- "-31.1414" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.1821" Parameter: C <- "-31.1821" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5794 TOTAL ENERGY = -62.3235 RDTITL> * VAN DER WAALS = -31.1414 ELECTROSTATIC = -31.1821 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5794" Parameter: CONF_N -> "8002" Comparing "5794" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5795" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754778 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753645 ATOM PAIRS WERE FOUND FOR ATOM LIST 41550 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29563 from a total of 753645 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5795 -70.39706 8.07356 0.65034 INTE EXTERN> -31.56640 -38.83066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3971" Parameter: A <- "-70.3971" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5664" Parameter: B <- "-31.5664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8307" Parameter: C <- "-38.8307" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5795 TOTAL ENERGY = -70.3971 RDTITL> * VAN DER WAALS = -31.5664 ELECTROSTATIC = -38.8307 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5795" Parameter: CONF_N -> "8002" Comparing "5795" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5796" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753645 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750583 ATOM PAIRS WERE FOUND FOR ATOM LIST 41273 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29691 from a total of 750583 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5796 -72.35800 1.96095 0.54443 INTE EXTERN> -32.96553 -39.39247 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.358" Parameter: A <- "-72.358" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9655" Parameter: B <- "-32.9655" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3925" Parameter: C <- "-39.3925" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5796 TOTAL ENERGY = -72.358 RDTITL> * VAN DER WAALS = -32.9655 ELECTROSTATIC = -39.3925 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5796" Parameter: CONF_N -> "8002" Comparing "5796" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5797" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750583 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754080 ATOM PAIRS WERE FOUND FOR ATOM LIST 41200 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29491 from a total of 754080 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5797 -67.45769 -4.90031 0.53815 INTE EXTERN> -32.60549 -34.85220 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4577" Parameter: A <- "-67.4577" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6055" Parameter: B <- "-32.6055" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8522" Parameter: C <- "-34.8522" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5797 TOTAL ENERGY = -67.4577 RDTITL> * VAN DER WAALS = -32.6055 ELECTROSTATIC = -34.8522 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5797" Parameter: CONF_N -> "8002" Comparing "5797" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5798" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754080 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757637 ATOM PAIRS WERE FOUND FOR ATOM LIST 41424 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29713 from a total of 757637 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5798 -69.50446 2.04677 0.55316 INTE EXTERN> -31.76848 -37.73598 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5045" Parameter: A <- "-69.5045" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7685" Parameter: B <- "-31.7685" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.736" Parameter: C <- "-37.736" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5798 TOTAL ENERGY = -69.5045 RDTITL> * VAN DER WAALS = -31.7685 ELECTROSTATIC = -37.736 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5798" Parameter: CONF_N -> "8002" Comparing "5798" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5799" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757637 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752049 ATOM PAIRS WERE FOUND FOR ATOM LIST 41021 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28715 from a total of 752049 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5799 -69.43726 -0.06720 0.54776 INTE EXTERN> -31.45205 -37.98521 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4373" Parameter: A <- "-69.4373" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4521" Parameter: B <- "-31.4521" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9852" Parameter: C <- "-37.9852" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5799 TOTAL ENERGY = -69.4373 RDTITL> * VAN DER WAALS = -31.4521 ELECTROSTATIC = -37.9852 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5799" Parameter: CONF_N -> "8002" Comparing "5799" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5800" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752049 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745908 ATOM PAIRS WERE FOUND FOR ATOM LIST 40708 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28485 from a total of 745908 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5800 -65.07644 -4.36082 0.51379 INTE EXTERN> -30.51560 -34.56084 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0764" Parameter: A <- "-65.0764" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5156" Parameter: B <- "-30.5156" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5608" Parameter: C <- "-34.5608" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5800 TOTAL ENERGY = -65.0764 RDTITL> * VAN DER WAALS = -30.5156 ELECTROSTATIC = -34.5608 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5800" Parameter: CONF_N -> "8002" Comparing "5800" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5801" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745908 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751988 ATOM PAIRS WERE FOUND FOR ATOM LIST 41140 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28162 from a total of 751988 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5801 -65.77128 0.69484 0.59851 INTE EXTERN> -29.53470 -36.23658 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7713" Parameter: A <- "-65.7713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5347" Parameter: B <- "-29.5347" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2366" Parameter: C <- "-36.2366" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5801 TOTAL ENERGY = -65.7713 RDTITL> * VAN DER WAALS = -29.5347 ELECTROSTATIC = -36.2366 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5801" Parameter: CONF_N -> "8002" Comparing "5801" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5802" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751988 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751933 ATOM PAIRS WERE FOUND FOR ATOM LIST 41102 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28065 from a total of 751933 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5802 -65.12616 -0.64512 0.52129 INTE EXTERN> -29.05033 -36.07583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1262" Parameter: A <- "-65.1262" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0503" Parameter: B <- "-29.0503" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0758" Parameter: C <- "-36.0758" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5802 TOTAL ENERGY = -65.1262 RDTITL> * VAN DER WAALS = -29.0503 ELECTROSTATIC = -36.0758 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5802" Parameter: CONF_N -> "8002" Comparing "5802" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5803" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751933 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754365 ATOM PAIRS WERE FOUND FOR ATOM LIST 41319 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28373 from a total of 754365 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5803 -63.96729 -1.15887 0.63200 INTE EXTERN> -25.40468 -38.56261 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.9673" Parameter: A <- "-63.9673" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4047" Parameter: B <- "-25.4047" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5626" Parameter: C <- "-38.5626" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5803 TOTAL ENERGY = -63.9673 RDTITL> * VAN DER WAALS = -25.4047 ELECTROSTATIC = -38.5626 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5803" Parameter: CONF_N -> "8002" Comparing "5803" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5804" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754365 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751075 ATOM PAIRS WERE FOUND FOR ATOM LIST 41137 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28635 from a total of 751075 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5804 -65.47383 1.50653 0.48205 INTE EXTERN> -32.88189 -32.59193 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4738" Parameter: A <- "-65.4738" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8819" Parameter: B <- "-32.8819" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5919" Parameter: C <- "-32.5919" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5804 TOTAL ENERGY = -65.4738 RDTITL> * VAN DER WAALS = -32.8819 ELECTROSTATIC = -32.5919 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5804" Parameter: CONF_N -> "8002" Comparing "5804" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5805" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751075 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754447 ATOM PAIRS WERE FOUND FOR ATOM LIST 41430 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29411 from a total of 754447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5805 -66.92734 1.45351 0.49250 INTE EXTERN> -30.14528 -36.78205 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9273" Parameter: A <- "-66.9273" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1453" Parameter: B <- "-30.1453" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7821" Parameter: C <- "-36.7821" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5805 TOTAL ENERGY = -66.9273 RDTITL> * VAN DER WAALS = -30.1453 ELECTROSTATIC = -36.7821 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5805" Parameter: CONF_N -> "8002" Comparing "5805" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5806" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762658 ATOM PAIRS WERE FOUND FOR ATOM LIST 41770 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29746 from a total of 762658 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5806 -67.95471 1.02737 0.64823 INTE EXTERN> -27.31844 -40.63627 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9547" Parameter: A <- "-67.9547" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3184" Parameter: B <- "-27.3184" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6363" Parameter: C <- "-40.6363" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5806 TOTAL ENERGY = -67.9547 RDTITL> * VAN DER WAALS = -27.3184 ELECTROSTATIC = -40.6363 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5806" Parameter: CONF_N -> "8002" Comparing "5806" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5807" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762658 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754125 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29430 from a total of 754125 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5807 -69.33098 1.37627 0.64554 INTE EXTERN> -29.56830 -39.76269 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.331" Parameter: A <- "-69.331" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5683" Parameter: B <- "-29.5683" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7627" Parameter: C <- "-39.7627" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5807 TOTAL ENERGY = -69.331 RDTITL> * VAN DER WAALS = -29.5683 ELECTROSTATIC = -39.7627 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5807" Parameter: CONF_N -> "8002" Comparing "5807" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5808" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754125 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754690 ATOM PAIRS WERE FOUND FOR ATOM LIST 41253 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29199 from a total of 754690 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5808 -67.73111 -1.59987 0.57261 INTE EXTERN> -28.93408 -38.79703 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7311" Parameter: A <- "-67.7311" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9341" Parameter: B <- "-28.9341" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.797" Parameter: C <- "-38.797" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5808 TOTAL ENERGY = -67.7311 RDTITL> * VAN DER WAALS = -28.9341 ELECTROSTATIC = -38.797 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5808" Parameter: CONF_N -> "8002" Comparing "5808" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5809" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754690 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758503 ATOM PAIRS WERE FOUND FOR ATOM LIST 41584 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30020 from a total of 758503 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5809 -74.49756 6.76644 0.56960 INTE EXTERN> -32.69309 -41.80447 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4976" Parameter: A <- "-74.4976" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6931" Parameter: B <- "-32.6931" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8045" Parameter: C <- "-41.8045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5809 TOTAL ENERGY = -74.4976 RDTITL> * VAN DER WAALS = -32.6931 ELECTROSTATIC = -41.8045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5809" Parameter: CONF_N -> "8002" Comparing "5809" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5810" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758503 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762436 ATOM PAIRS WERE FOUND FOR ATOM LIST 41625 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29633 from a total of 762436 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5810 -70.60372 -3.89383 0.55707 INTE EXTERN> -31.05030 -39.55342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6037" Parameter: A <- "-70.6037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0503" Parameter: B <- "-31.0503" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5534" Parameter: C <- "-39.5534" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5810 TOTAL ENERGY = -70.6037 RDTITL> * VAN DER WAALS = -31.0503 ELECTROSTATIC = -39.5534 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5810" Parameter: CONF_N -> "8002" Comparing "5810" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5811" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762436 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762211 ATOM PAIRS WERE FOUND FOR ATOM LIST 41636 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29724 from a total of 762211 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5811 -71.90337 1.29964 0.55723 INTE EXTERN> -32.88138 -39.02199 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9034" Parameter: A <- "-71.9034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8814" Parameter: B <- "-32.8814" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.022" Parameter: C <- "-39.022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5811 TOTAL ENERGY = -71.9034 RDTITL> * VAN DER WAALS = -32.8814 ELECTROSTATIC = -39.022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5811" Parameter: CONF_N -> "8002" Comparing "5811" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5812" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762211 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756914 ATOM PAIRS WERE FOUND FOR ATOM LIST 41476 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29161 from a total of 756914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5812 -79.07788 7.17451 0.57177 INTE EXTERN> -33.49251 -45.58536 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0779" Parameter: A <- "-79.0779" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4925" Parameter: B <- "-33.4925" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5854" Parameter: C <- "-45.5854" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5812 TOTAL ENERGY = -79.0779 RDTITL> * VAN DER WAALS = -33.4925 ELECTROSTATIC = -45.5854 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5812" Parameter: CONF_N -> "8002" Comparing "5812" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5813" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761411 ATOM PAIRS WERE FOUND FOR ATOM LIST 41683 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29318 from a total of 761411 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5813 -71.33795 -7.73993 0.59722 INTE EXTERN> -30.75023 -40.58771 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3379" Parameter: A <- "-71.3379" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7502" Parameter: B <- "-30.7502" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5877" Parameter: C <- "-40.5877" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5813 TOTAL ENERGY = -71.3379 RDTITL> * VAN DER WAALS = -30.7502 ELECTROSTATIC = -40.5877 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5813" Parameter: CONF_N -> "8002" Comparing "5813" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5814" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761411 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758635 ATOM PAIRS WERE FOUND FOR ATOM LIST 41658 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29817 from a total of 758635 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5814 -71.30015 -0.03780 0.57612 INTE EXTERN> -33.94798 -37.35217 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3001" Parameter: A <- "-71.3001" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.948" Parameter: B <- "-33.948" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3522" Parameter: C <- "-37.3522" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5814 TOTAL ENERGY = -71.3001 RDTITL> * VAN DER WAALS = -33.948 ELECTROSTATIC = -37.3522 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5814" Parameter: CONF_N -> "8002" Comparing "5814" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5815" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758635 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760139 ATOM PAIRS WERE FOUND FOR ATOM LIST 41717 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30354 from a total of 760139 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5815 -73.99786 2.69771 0.65999 INTE EXTERN> -27.82957 -46.16829 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9979" Parameter: A <- "-73.9979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8296" Parameter: B <- "-27.8296" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1683" Parameter: C <- "-46.1683" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5815 TOTAL ENERGY = -73.9979 RDTITL> * VAN DER WAALS = -27.8296 ELECTROSTATIC = -46.1683 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5815" Parameter: CONF_N -> "8002" Comparing "5815" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5816" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760139 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761935 ATOM PAIRS WERE FOUND FOR ATOM LIST 41796 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30070 from a total of 761935 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5816 -66.83982 -7.15804 0.53159 INTE EXTERN> -34.04414 -32.79568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8398" Parameter: A <- "-66.8398" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0441" Parameter: B <- "-34.0441" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.7957" Parameter: C <- "-32.7957" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5816 TOTAL ENERGY = -66.8398 RDTITL> * VAN DER WAALS = -34.0441 ELECTROSTATIC = -32.7957 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5816" Parameter: CONF_N -> "8002" Comparing "5816" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5817" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761935 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763061 ATOM PAIRS WERE FOUND FOR ATOM LIST 41994 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30491 from a total of 763061 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5817 -67.23872 0.39890 0.57090 INTE EXTERN> -33.08675 -34.15197 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2387" Parameter: A <- "-67.2387" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0867" Parameter: B <- "-33.0867" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.152" Parameter: C <- "-34.152" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5817 TOTAL ENERGY = -67.2387 RDTITL> * VAN DER WAALS = -33.0867 ELECTROSTATIC = -34.152 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5817" Parameter: CONF_N -> "8002" Comparing "5817" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5818" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763061 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759972 ATOM PAIRS WERE FOUND FOR ATOM LIST 42029 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29993 from a total of 759972 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5818 -68.40484 1.16612 0.85001 INTE EXTERN> -24.99109 -43.41375 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4048" Parameter: A <- "-68.4048" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9911" Parameter: B <- "-24.9911" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4138" Parameter: C <- "-43.4138" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5818 TOTAL ENERGY = -68.4048 RDTITL> * VAN DER WAALS = -24.9911 ELECTROSTATIC = -43.4138 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5818" Parameter: CONF_N -> "8002" Comparing "5818" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5819" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759972 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756067 ATOM PAIRS WERE FOUND FOR ATOM LIST 41561 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29385 from a total of 756067 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5819 -60.57990 -7.82494 0.52343 INTE EXTERN> -33.92366 -26.65625 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.5799" Parameter: A <- "-60.5799" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9237" Parameter: B <- "-33.9237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-26.6562" Parameter: C <- "-26.6562" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5819 TOTAL ENERGY = -60.5799 RDTITL> * VAN DER WAALS = -33.9237 ELECTROSTATIC = -26.6562 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5819" Parameter: CONF_N -> "8002" Comparing "5819" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5820" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756067 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761750 ATOM PAIRS WERE FOUND FOR ATOM LIST 41755 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29648 from a total of 761750 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5820 -76.01333 15.43343 0.64656 INTE EXTERN> -31.35202 -44.66131 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0133" Parameter: A <- "-76.0133" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.352" Parameter: B <- "-31.352" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6613" Parameter: C <- "-44.6613" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5820 TOTAL ENERGY = -76.0133 RDTITL> * VAN DER WAALS = -31.352 ELECTROSTATIC = -44.6613 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5820" Parameter: CONF_N -> "8002" Comparing "5820" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5821" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761750 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755979 ATOM PAIRS WERE FOUND FOR ATOM LIST 41407 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29819 from a total of 755979 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5821 -74.31452 -1.69881 0.65938 INTE EXTERN> -30.17279 -44.14174 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3145" Parameter: A <- "-74.3145" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1728" Parameter: B <- "-30.1728" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1417" Parameter: C <- "-44.1417" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5821 TOTAL ENERGY = -74.3145 RDTITL> * VAN DER WAALS = -30.1728 ELECTROSTATIC = -44.1417 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5821" Parameter: CONF_N -> "8002" Comparing "5821" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5822" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755979 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756819 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30428 from a total of 756819 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5822 -67.81158 -6.50294 0.61688 INTE EXTERN> -31.31630 -36.49528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8116" Parameter: A <- "-67.8116" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3163" Parameter: B <- "-31.3163" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4953" Parameter: C <- "-36.4953" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5822 TOTAL ENERGY = -67.8116 RDTITL> * VAN DER WAALS = -31.3163 ELECTROSTATIC = -36.4953 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5822" Parameter: CONF_N -> "8002" Comparing "5822" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5823" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756819 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41896 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29356 from a total of 762601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5823 -70.15175 2.34017 0.64912 INTE EXTERN> -27.07269 -43.07906 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1517" Parameter: A <- "-70.1517" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0727" Parameter: B <- "-27.0727" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0791" Parameter: C <- "-43.0791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5823 TOTAL ENERGY = -70.1517 RDTITL> * VAN DER WAALS = -27.0727 ELECTROSTATIC = -43.0791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5823" Parameter: CONF_N -> "8002" Comparing "5823" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5824" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752582 ATOM PAIRS WERE FOUND FOR ATOM LIST 41314 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29638 from a total of 752582 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5824 -71.22468 1.07293 0.54188 INTE EXTERN> -33.77352 -37.45116 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2247" Parameter: A <- "-71.2247" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7735" Parameter: B <- "-33.7735" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4512" Parameter: C <- "-37.4512" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5824 TOTAL ENERGY = -71.2247 RDTITL> * VAN DER WAALS = -33.7735 ELECTROSTATIC = -37.4512 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5824" Parameter: CONF_N -> "8002" Comparing "5824" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5825" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752582 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755276 ATOM PAIRS WERE FOUND FOR ATOM LIST 41505 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30226 from a total of 755276 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5825 -72.91308 1.68840 0.56906 INTE EXTERN> -32.93453 -39.97855 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9131" Parameter: A <- "-72.9131" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9345" Parameter: B <- "-32.9345" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9785" Parameter: C <- "-39.9785" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5825 TOTAL ENERGY = -72.9131 RDTITL> * VAN DER WAALS = -32.9345 ELECTROSTATIC = -39.9785 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5825" Parameter: CONF_N -> "8002" Comparing "5825" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5826" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755276 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758636 ATOM PAIRS WERE FOUND FOR ATOM LIST 41577 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30200 from a total of 758636 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5826 -74.85220 1.93912 0.55212 INTE EXTERN> -34.74622 -40.10597 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8522" Parameter: A <- "-74.8522" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.7462" Parameter: B <- "-34.7462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.106" Parameter: C <- "-40.106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5826 TOTAL ENERGY = -74.8522 RDTITL> * VAN DER WAALS = -34.7462 ELECTROSTATIC = -40.106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5826" Parameter: CONF_N -> "8002" Comparing "5826" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5827" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758636 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754886 ATOM PAIRS WERE FOUND FOR ATOM LIST 41415 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29967 from a total of 754886 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5827 -70.32682 -4.52538 0.55234 INTE EXTERN> -30.29972 -40.02709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3268" Parameter: A <- "-70.3268" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2997" Parameter: B <- "-30.2997" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0271" Parameter: C <- "-40.0271" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5827 TOTAL ENERGY = -70.3268 RDTITL> * VAN DER WAALS = -30.2997 ELECTROSTATIC = -40.0271 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5827" Parameter: CONF_N -> "8002" Comparing "5827" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5828" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754886 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755437 ATOM PAIRS WERE FOUND FOR ATOM LIST 41362 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29613 from a total of 755437 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5828 -69.82069 -0.50612 0.64356 INTE EXTERN> -28.06463 -41.75606 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8207" Parameter: A <- "-69.8207" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0646" Parameter: B <- "-28.0646" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7561" Parameter: C <- "-41.7561" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5828 TOTAL ENERGY = -69.8207 RDTITL> * VAN DER WAALS = -28.0646 ELECTROSTATIC = -41.7561 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5828" Parameter: CONF_N -> "8002" Comparing "5828" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5829" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755437 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756436 ATOM PAIRS WERE FOUND FOR ATOM LIST 41577 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30538 from a total of 756436 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5829 -73.03437 3.21368 0.64496 INTE EXTERN> -28.42452 -44.60985 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0344" Parameter: A <- "-73.0344" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4245" Parameter: B <- "-28.4245" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6098" Parameter: C <- "-44.6098" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5829 TOTAL ENERGY = -73.0344 RDTITL> * VAN DER WAALS = -28.4245 ELECTROSTATIC = -44.6098 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5829" Parameter: CONF_N -> "8002" Comparing "5829" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5830" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756436 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755329 ATOM PAIRS WERE FOUND FOR ATOM LIST 41532 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30073 from a total of 755329 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5830 -73.88469 0.85032 0.64292 INTE EXTERN> -29.62315 -44.26154 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8847" Parameter: A <- "-73.8847" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6232" Parameter: B <- "-29.6232" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2615" Parameter: C <- "-44.2615" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5830 TOTAL ENERGY = -73.8847 RDTITL> * VAN DER WAALS = -29.6232 ELECTROSTATIC = -44.2615 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5830" Parameter: CONF_N -> "8002" Comparing "5830" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5831" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755329 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41666 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29920 from a total of 756958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5831 -70.69498 -3.18971 0.63567 INTE EXTERN> -31.18124 -39.51375 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.695" Parameter: A <- "-70.695" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1812" Parameter: B <- "-31.1812" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5137" Parameter: C <- "-39.5137" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5831 TOTAL ENERGY = -70.695 RDTITL> * VAN DER WAALS = -31.1812 ELECTROSTATIC = -39.5137 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5831" Parameter: CONF_N -> "8002" Comparing "5831" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5832" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761143 ATOM PAIRS WERE FOUND FOR ATOM LIST 41870 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29221 from a total of 761143 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5832 -66.93072 -3.76427 0.54322 INTE EXTERN> -33.00818 -33.92254 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9307" Parameter: A <- "-66.9307" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0082" Parameter: B <- "-33.0082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9225" Parameter: C <- "-33.9225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5832 TOTAL ENERGY = -66.9307 RDTITL> * VAN DER WAALS = -33.0082 ELECTROSTATIC = -33.9225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5832" Parameter: CONF_N -> "8002" Comparing "5832" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5833" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761143 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760695 ATOM PAIRS WERE FOUND FOR ATOM LIST 41728 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30061 from a total of 760695 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5833 -65.60321 -1.32750 0.61233 INTE EXTERN> -27.49941 -38.10381 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6032" Parameter: A <- "-65.6032" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4994" Parameter: B <- "-27.4994" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1038" Parameter: C <- "-38.1038" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5833 TOTAL ENERGY = -65.6032 RDTITL> * VAN DER WAALS = -27.4994 ELECTROSTATIC = -38.1038 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5833" Parameter: CONF_N -> "8002" Comparing "5833" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5834" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760695 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754983 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29981 from a total of 754983 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5834 -69.59542 3.99221 0.51652 INTE EXTERN> -31.49399 -38.10143 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5954" Parameter: A <- "-69.5954" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.494" Parameter: B <- "-31.494" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1014" Parameter: C <- "-38.1014" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5834 TOTAL ENERGY = -69.5954 RDTITL> * VAN DER WAALS = -31.494 ELECTROSTATIC = -38.1014 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5834" Parameter: CONF_N -> "8002" Comparing "5834" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5835" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754983 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763497 ATOM PAIRS WERE FOUND FOR ATOM LIST 41857 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29835 from a total of 763497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5835 -70.89968 1.30426 0.66152 INTE EXTERN> -29.48013 -41.41955 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8997" Parameter: A <- "-70.8997" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4801" Parameter: B <- "-29.4801" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4196" Parameter: C <- "-41.4196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5835 TOTAL ENERGY = -70.8997 RDTITL> * VAN DER WAALS = -29.4801 ELECTROSTATIC = -41.4196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5835" Parameter: CONF_N -> "8002" Comparing "5835" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5836" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752685 ATOM PAIRS WERE FOUND FOR ATOM LIST 41020 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29812 from a total of 752685 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5836 -72.13245 1.23277 0.59122 INTE EXTERN> -34.84651 -37.28594 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1325" Parameter: A <- "-72.1325" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.8465" Parameter: B <- "-34.8465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2859" Parameter: C <- "-37.2859" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5836 TOTAL ENERGY = -72.1325 RDTITL> * VAN DER WAALS = -34.8465 ELECTROSTATIC = -37.2859 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5836" Parameter: CONF_N -> "8002" Comparing "5836" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5837" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752685 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754592 ATOM PAIRS WERE FOUND FOR ATOM LIST 41535 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30050 from a total of 754592 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5837 -71.94812 -0.18434 0.56927 INTE EXTERN> -33.09175 -38.85636 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9481" Parameter: A <- "-71.9481" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0918" Parameter: B <- "-33.0918" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8564" Parameter: C <- "-38.8564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5837 TOTAL ENERGY = -71.9481 RDTITL> * VAN DER WAALS = -33.0918 ELECTROSTATIC = -38.8564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5837" Parameter: CONF_N -> "8002" Comparing "5837" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5838" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754592 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755239 ATOM PAIRS WERE FOUND FOR ATOM LIST 41502 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29950 from a total of 755239 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5838 -73.85807 1.90995 0.68612 INTE EXTERN> -27.60689 -46.25118 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8581" Parameter: A <- "-73.8581" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6069" Parameter: B <- "-27.6069" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2512" Parameter: C <- "-46.2512" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5838 TOTAL ENERGY = -73.8581 RDTITL> * VAN DER WAALS = -27.6069 ELECTROSTATIC = -46.2512 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5838" Parameter: CONF_N -> "8002" Comparing "5838" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5839" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755239 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758550 ATOM PAIRS WERE FOUND FOR ATOM LIST 41643 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30114 from a total of 758550 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5839 -65.80692 -8.05115 0.68677 INTE EXTERN> -27.03189 -38.77503 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8069" Parameter: A <- "-65.8069" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0319" Parameter: B <- "-27.0319" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.775" Parameter: C <- "-38.775" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5839 TOTAL ENERGY = -65.8069 RDTITL> * VAN DER WAALS = -27.0319 ELECTROSTATIC = -38.775 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5839" Parameter: CONF_N -> "8002" Comparing "5839" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5840" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758550 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760549 ATOM PAIRS WERE FOUND FOR ATOM LIST 41689 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30319 from a total of 760549 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5840 -68.51205 2.70512 0.58628 INTE EXTERN> -31.22354 -37.28851 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.512" Parameter: A <- "-68.512" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2235" Parameter: B <- "-31.2235" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2885" Parameter: C <- "-37.2885" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5840 TOTAL ENERGY = -68.512 RDTITL> * VAN DER WAALS = -31.2235 ELECTROSTATIC = -37.2885 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5840" Parameter: CONF_N -> "8002" Comparing "5840" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5841" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760549 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760191 ATOM PAIRS WERE FOUND FOR ATOM LIST 41767 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30725 from a total of 760191 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5841 -69.98804 1.47600 0.50870 INTE EXTERN> -35.09214 -34.89591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.988" Parameter: A <- "-69.988" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.0921" Parameter: B <- "-35.0921" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8959" Parameter: C <- "-34.8959" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5841 TOTAL ENERGY = -69.988 RDTITL> * VAN DER WAALS = -35.0921 ELECTROSTATIC = -34.8959 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5841" Parameter: CONF_N -> "8002" Comparing "5841" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5842" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760191 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756490 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29845 from a total of 756490 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5842 -62.16178 -7.82626 0.52312 INTE EXTERN> -33.23718 -28.92459 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.1618" Parameter: A <- "-62.1618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2372" Parameter: B <- "-33.2372" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.9246" Parameter: C <- "-28.9246" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5842 TOTAL ENERGY = -62.1618 RDTITL> * VAN DER WAALS = -33.2372 ELECTROSTATIC = -28.9246 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5842" Parameter: CONF_N -> "8002" Comparing "5842" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5843" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756490 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755016 ATOM PAIRS WERE FOUND FOR ATOM LIST 41371 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29741 from a total of 755016 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5843 -68.61594 6.45416 0.51261 INTE EXTERN> -34.67764 -33.93829 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6159" Parameter: A <- "-68.6159" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6776" Parameter: B <- "-34.6776" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9383" Parameter: C <- "-33.9383" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5843 TOTAL ENERGY = -68.6159 RDTITL> * VAN DER WAALS = -34.6776 ELECTROSTATIC = -33.9383 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5843" Parameter: CONF_N -> "8002" Comparing "5843" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5844" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755016 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758557 ATOM PAIRS WERE FOUND FOR ATOM LIST 41619 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30526 from a total of 758557 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5844 -67.01038 -1.60556 0.56761 INTE EXTERN> -30.07007 -36.94031 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0104" Parameter: A <- "-67.0104" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0701" Parameter: B <- "-30.0701" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9403" Parameter: C <- "-36.9403" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5844 TOTAL ENERGY = -67.0104 RDTITL> * VAN DER WAALS = -30.0701 ELECTROSTATIC = -36.9403 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5844" Parameter: CONF_N -> "8002" Comparing "5844" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5845" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758557 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756552 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30044 from a total of 756552 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5845 -68.47812 1.46774 0.52618 INTE EXTERN> -32.22201 -36.25611 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4781" Parameter: A <- "-68.4781" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.222" Parameter: B <- "-32.222" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2561" Parameter: C <- "-36.2561" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5845 TOTAL ENERGY = -68.4781 RDTITL> * VAN DER WAALS = -32.222 ELECTROSTATIC = -36.2561 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5845" Parameter: CONF_N -> "8002" Comparing "5845" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5846" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756552 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758257 ATOM PAIRS WERE FOUND FOR ATOM LIST 41790 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30411 from a total of 758257 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5846 -66.65828 -1.81984 0.61327 INTE EXTERN> -32.74099 -33.91729 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6583" Parameter: A <- "-66.6583" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.741" Parameter: B <- "-32.741" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9173" Parameter: C <- "-33.9173" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5846 TOTAL ENERGY = -66.6583 RDTITL> * VAN DER WAALS = -32.741 ELECTROSTATIC = -33.9173 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5846" Parameter: CONF_N -> "8002" Comparing "5846" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5847" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758257 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763915 ATOM PAIRS WERE FOUND FOR ATOM LIST 41988 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30692 from a total of 763915 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5847 -77.15115 10.49287 0.55343 INTE EXTERN> -33.35005 -43.80110 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1512" Parameter: A <- "-77.1512" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.35" Parameter: B <- "-33.35" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8011" Parameter: C <- "-43.8011" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5847 TOTAL ENERGY = -77.1512 RDTITL> * VAN DER WAALS = -33.35 ELECTROSTATIC = -43.8011 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5847" Parameter: CONF_N -> "8002" Comparing "5847" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5848" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763915 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756424 ATOM PAIRS WERE FOUND FOR ATOM LIST 41622 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29538 from a total of 756424 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5848 -62.34024 -14.81091 0.45501 INTE EXTERN> -34.80639 -27.53385 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3402" Parameter: A <- "-62.3402" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.8064" Parameter: B <- "-34.8064" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.5339" Parameter: C <- "-27.5339" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5848 TOTAL ENERGY = -62.3402 RDTITL> * VAN DER WAALS = -34.8064 ELECTROSTATIC = -27.5339 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5848" Parameter: CONF_N -> "8002" Comparing "5848" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5849" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756424 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750908 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29954 from a total of 750908 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5849 -69.46548 7.12524 0.54686 INTE EXTERN> -32.01923 -37.44625 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4655" Parameter: A <- "-69.4655" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0192" Parameter: B <- "-32.0192" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4462" Parameter: C <- "-37.4462" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5849 TOTAL ENERGY = -69.4655 RDTITL> * VAN DER WAALS = -32.0192 ELECTROSTATIC = -37.4462 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5849" Parameter: CONF_N -> "8002" Comparing "5849" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5850" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750908 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753990 ATOM PAIRS WERE FOUND FOR ATOM LIST 41559 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29622 from a total of 753990 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5850 -68.34592 -1.11956 0.51259 INTE EXTERN> -35.74958 -32.59634 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3459" Parameter: A <- "-68.3459" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.7496" Parameter: B <- "-35.7496" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.5963" Parameter: C <- "-32.5963" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5850 TOTAL ENERGY = -68.3459 RDTITL> * VAN DER WAALS = -35.7496 ELECTROSTATIC = -32.5963 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5850" Parameter: CONF_N -> "8002" Comparing "5850" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5851" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753990 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763296 ATOM PAIRS WERE FOUND FOR ATOM LIST 41912 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30364 from a total of 763296 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5851 -69.86842 1.52251 0.57854 INTE EXTERN> -32.23853 -37.62989 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8684" Parameter: A <- "-69.8684" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2385" Parameter: B <- "-32.2385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6299" Parameter: C <- "-37.6299" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5851 TOTAL ENERGY = -69.8684 RDTITL> * VAN DER WAALS = -32.2385 ELECTROSTATIC = -37.6299 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5851" Parameter: CONF_N -> "8002" Comparing "5851" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5852" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763296 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756048 ATOM PAIRS WERE FOUND FOR ATOM LIST 41662 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29715 from a total of 756048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5852 -67.87905 -1.98937 0.50677 INTE EXTERN> -35.08189 -32.79716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.879" Parameter: A <- "-67.879" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.0819" Parameter: B <- "-35.0819" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.7972" Parameter: C <- "-32.7972" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5852 TOTAL ENERGY = -67.879 RDTITL> * VAN DER WAALS = -35.0819 ELECTROSTATIC = -32.7972 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5852" Parameter: CONF_N -> "8002" Comparing "5852" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5853" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757828 ATOM PAIRS WERE FOUND FOR ATOM LIST 41754 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30281 from a total of 757828 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5853 -70.57591 2.69686 0.59684 INTE EXTERN> -29.91899 -40.65692 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5759" Parameter: A <- "-70.5759" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.919" Parameter: B <- "-29.919" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6569" Parameter: C <- "-40.6569" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5853 TOTAL ENERGY = -70.5759 RDTITL> * VAN DER WAALS = -29.919 ELECTROSTATIC = -40.6569 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5853" Parameter: CONF_N -> "8002" Comparing "5853" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5854" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757828 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41315 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29930 from a total of 752958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5854 -71.56063 0.98472 0.49646 INTE EXTERN> -34.05559 -37.50504 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5606" Parameter: A <- "-71.5606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0556" Parameter: B <- "-34.0556" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.505" Parameter: C <- "-37.505" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5854 TOTAL ENERGY = -71.5606 RDTITL> * VAN DER WAALS = -34.0556 ELECTROSTATIC = -37.505 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5854" Parameter: CONF_N -> "8002" Comparing "5854" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5855" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756828 ATOM PAIRS WERE FOUND FOR ATOM LIST 41540 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30212 from a total of 756828 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5855 -72.65323 1.09260 0.52995 INTE EXTERN> -35.09717 -37.55606 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6532" Parameter: A <- "-72.6532" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.0972" Parameter: B <- "-35.0972" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5561" Parameter: C <- "-37.5561" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5855 TOTAL ENERGY = -72.6532 RDTITL> * VAN DER WAALS = -35.0972 ELECTROSTATIC = -37.5561 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5855" Parameter: CONF_N -> "8002" Comparing "5855" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5856" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756828 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757561 ATOM PAIRS WERE FOUND FOR ATOM LIST 41534 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29895 from a total of 757561 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5856 -74.58582 1.93259 0.53999 INTE EXTERN> -32.53302 -42.05280 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5858" Parameter: A <- "-74.5858" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.533" Parameter: B <- "-32.533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0528" Parameter: C <- "-42.0528" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5856 TOTAL ENERGY = -74.5858 RDTITL> * VAN DER WAALS = -32.533 ELECTROSTATIC = -42.0528 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5856" Parameter: CONF_N -> "8002" Comparing "5856" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5857" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757561 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757712 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30227 from a total of 757712 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5857 -72.35216 -2.23366 0.66434 INTE EXTERN> -29.66863 -42.68352 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3522" Parameter: A <- "-72.3522" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6686" Parameter: B <- "-29.6686" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6835" Parameter: C <- "-42.6835" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5857 TOTAL ENERGY = -72.3522 RDTITL> * VAN DER WAALS = -29.6686 ELECTROSTATIC = -42.6835 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5857" Parameter: CONF_N -> "8002" Comparing "5857" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5858" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757712 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752359 ATOM PAIRS WERE FOUND FOR ATOM LIST 41354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29929 from a total of 752359 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5858 -72.25870 -0.09346 0.54737 INTE EXTERN> -31.99719 -40.26151 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2587" Parameter: A <- "-72.2587" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9972" Parameter: B <- "-31.9972" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2615" Parameter: C <- "-40.2615" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5858 TOTAL ENERGY = -72.2587 RDTITL> * VAN DER WAALS = -31.9972 ELECTROSTATIC = -40.2615 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5858" Parameter: CONF_N -> "8002" Comparing "5858" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5859" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752359 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752537 ATOM PAIRS WERE FOUND FOR ATOM LIST 41204 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28981 from a total of 752537 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5859 -69.02304 -3.23566 0.61991 INTE EXTERN> -29.28092 -39.74212 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.023" Parameter: A <- "-69.023" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2809" Parameter: B <- "-29.2809" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7421" Parameter: C <- "-39.7421" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5859 TOTAL ENERGY = -69.023 RDTITL> * VAN DER WAALS = -29.2809 ELECTROSTATIC = -39.7421 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5859" Parameter: CONF_N -> "8002" Comparing "5859" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5860" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752537 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750577 ATOM PAIRS WERE FOUND FOR ATOM LIST 41245 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29005 from a total of 750577 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5860 -73.33994 4.31690 0.50281 INTE EXTERN> -33.95882 -39.38112 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3399" Parameter: A <- "-73.3399" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9588" Parameter: B <- "-33.9588" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3811" Parameter: C <- "-39.3811" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5860 TOTAL ENERGY = -73.3399 RDTITL> * VAN DER WAALS = -33.9588 ELECTROSTATIC = -39.3811 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5860" Parameter: CONF_N -> "8002" Comparing "5860" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5861" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750577 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752742 ATOM PAIRS WERE FOUND FOR ATOM LIST 41274 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29547 from a total of 752742 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5861 -69.41893 -3.92102 0.60651 INTE EXTERN> -32.09877 -37.32016 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4189" Parameter: A <- "-69.4189" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0988" Parameter: B <- "-32.0988" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3202" Parameter: C <- "-37.3202" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5861 TOTAL ENERGY = -69.4189 RDTITL> * VAN DER WAALS = -32.0988 ELECTROSTATIC = -37.3202 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5861" Parameter: CONF_N -> "8002" Comparing "5861" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5862" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752742 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747444 ATOM PAIRS WERE FOUND FOR ATOM LIST 40921 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29287 from a total of 747444 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5862 -70.92272 1.50379 0.60392 INTE EXTERN> -29.71002 -41.21269 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9227" Parameter: A <- "-70.9227" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.71" Parameter: B <- "-29.71" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2127" Parameter: C <- "-41.2127" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5862 TOTAL ENERGY = -70.9227 RDTITL> * VAN DER WAALS = -29.71 ELECTROSTATIC = -41.2127 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5862" Parameter: CONF_N -> "8002" Comparing "5862" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5863" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747444 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753072 ATOM PAIRS WERE FOUND FOR ATOM LIST 41234 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29729 from a total of 753072 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5863 -73.97090 3.04818 0.55972 INTE EXTERN> -32.01343 -41.95747 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9709" Parameter: A <- "-73.9709" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0134" Parameter: B <- "-32.0134" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9575" Parameter: C <- "-41.9575" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5863 TOTAL ENERGY = -73.9709 RDTITL> * VAN DER WAALS = -32.0134 ELECTROSTATIC = -41.9575 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5863" Parameter: CONF_N -> "8002" Comparing "5863" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5864" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753072 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745895 ATOM PAIRS WERE FOUND FOR ATOM LIST 40902 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29906 from a total of 745895 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5864 -68.73007 -5.24083 0.53288 INTE EXTERN> -31.55694 -37.17313 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7301" Parameter: A <- "-68.7301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5569" Parameter: B <- "-31.5569" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1731" Parameter: C <- "-37.1731" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5864 TOTAL ENERGY = -68.7301 RDTITL> * VAN DER WAALS = -31.5569 ELECTROSTATIC = -37.1731 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5864" Parameter: CONF_N -> "8002" Comparing "5864" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5865" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745895 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749995 ATOM PAIRS WERE FOUND FOR ATOM LIST 41289 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30239 from a total of 749995 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5865 -66.90671 -1.82336 0.47465 INTE EXTERN> -32.80513 -34.10158 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9067" Parameter: A <- "-66.9067" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8051" Parameter: B <- "-32.8051" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1016" Parameter: C <- "-34.1016" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5865 TOTAL ENERGY = -66.9067 RDTITL> * VAN DER WAALS = -32.8051 ELECTROSTATIC = -34.1016 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5865" Parameter: CONF_N -> "8002" Comparing "5865" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5866" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749995 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753934 ATOM PAIRS WERE FOUND FOR ATOM LIST 41410 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30468 from a total of 753934 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5866 -73.74843 6.84172 0.56663 INTE EXTERN> -33.55701 -40.19142 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7484" Parameter: A <- "-73.7484" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.557" Parameter: B <- "-33.557" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1914" Parameter: C <- "-40.1914" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5866 TOTAL ENERGY = -73.7484 RDTITL> * VAN DER WAALS = -33.557 ELECTROSTATIC = -40.1914 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5866" Parameter: CONF_N -> "8002" Comparing "5866" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5867" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753934 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748473 ATOM PAIRS WERE FOUND FOR ATOM LIST 41354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30066 from a total of 748473 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5867 -72.00483 -1.74360 0.69248 INTE EXTERN> -30.21013 -41.79470 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0048" Parameter: A <- "-72.0048" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2101" Parameter: B <- "-30.2101" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7947" Parameter: C <- "-41.7947" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5867 TOTAL ENERGY = -72.0048 RDTITL> * VAN DER WAALS = -30.2101 ELECTROSTATIC = -41.7947 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5867" Parameter: CONF_N -> "8002" Comparing "5867" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5868" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748473 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751865 ATOM PAIRS WERE FOUND FOR ATOM LIST 41441 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29346 from a total of 751865 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5868 -64.24061 -7.76422 0.56001 INTE EXTERN> -30.97049 -33.27012 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2406" Parameter: A <- "-64.2406" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9705" Parameter: B <- "-30.9705" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2701" Parameter: C <- "-33.2701" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5868 TOTAL ENERGY = -64.2406 RDTITL> * VAN DER WAALS = -30.9705 ELECTROSTATIC = -33.2701 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5868" Parameter: CONF_N -> "8002" Comparing "5868" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5869" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751865 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754336 ATOM PAIRS WERE FOUND FOR ATOM LIST 41496 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30155 from a total of 754336 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5869 -76.00282 11.76221 0.53771 INTE EXTERN> -32.79648 -43.20634 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0028" Parameter: A <- "-76.0028" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7965" Parameter: B <- "-32.7965" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2063" Parameter: C <- "-43.2063" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5869 TOTAL ENERGY = -76.0028 RDTITL> * VAN DER WAALS = -32.7965 ELECTROSTATIC = -43.2063 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5869" Parameter: CONF_N -> "8002" Comparing "5869" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5870" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754336 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746176 ATOM PAIRS WERE FOUND FOR ATOM LIST 41022 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29493 from a total of 746176 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5870 -72.27959 -3.72323 0.54837 INTE EXTERN> -33.51150 -38.76809 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2796" Parameter: A <- "-72.2796" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5115" Parameter: B <- "-33.5115" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7681" Parameter: C <- "-38.7681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5870 TOTAL ENERGY = -72.2796 RDTITL> * VAN DER WAALS = -33.5115 ELECTROSTATIC = -38.7681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5870" Parameter: CONF_N -> "8002" Comparing "5870" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5871" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746176 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750061 ATOM PAIRS WERE FOUND FOR ATOM LIST 41248 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30228 from a total of 750061 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5871 -66.89183 -5.38777 0.66451 INTE EXTERN> -29.45544 -37.43639 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8918" Parameter: A <- "-66.8918" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4554" Parameter: B <- "-29.4554" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4364" Parameter: C <- "-37.4364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5871 TOTAL ENERGY = -66.8918 RDTITL> * VAN DER WAALS = -29.4554 ELECTROSTATIC = -37.4364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5871" Parameter: CONF_N -> "8002" Comparing "5871" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5872" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750061 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757831 ATOM PAIRS WERE FOUND FOR ATOM LIST 41662 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29802 from a total of 757831 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5872 -71.95795 5.06612 0.54442 INTE EXTERN> -30.55432 -41.40363 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9579" Parameter: A <- "-71.9579" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5543" Parameter: B <- "-30.5543" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4036" Parameter: C <- "-41.4036" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5872 TOTAL ENERGY = -71.9579 RDTITL> * VAN DER WAALS = -30.5543 ELECTROSTATIC = -41.4036 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5872" Parameter: CONF_N -> "8002" Comparing "5872" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5873" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757831 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753792 ATOM PAIRS WERE FOUND FOR ATOM LIST 41710 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29753 from a total of 753792 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5873 -76.77509 4.81715 0.66163 INTE EXTERN> -29.96342 -46.81167 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7751" Parameter: A <- "-76.7751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9634" Parameter: B <- "-29.9634" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8117" Parameter: C <- "-46.8117" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5873 TOTAL ENERGY = -76.7751 RDTITL> * VAN DER WAALS = -29.9634 ELECTROSTATIC = -46.8117 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5873" Parameter: CONF_N -> "8002" Comparing "5873" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5874" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753792 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750008 ATOM PAIRS WERE FOUND FOR ATOM LIST 41148 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29693 from a total of 750008 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5874 -71.22260 -5.55249 0.58839 INTE EXTERN> -31.81097 -39.41164 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2226" Parameter: A <- "-71.2226" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.811" Parameter: B <- "-31.811" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4116" Parameter: C <- "-39.4116" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5874 TOTAL ENERGY = -71.2226 RDTITL> * VAN DER WAALS = -31.811 ELECTROSTATIC = -39.4116 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5874" Parameter: CONF_N -> "8002" Comparing "5874" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5875" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750008 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754405 ATOM PAIRS WERE FOUND FOR ATOM LIST 41566 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29716 from a total of 754405 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5875 -68.24210 -2.98050 0.55047 INTE EXTERN> -33.43540 -34.80671 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2421" Parameter: A <- "-68.2421" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4354" Parameter: B <- "-33.4354" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8067" Parameter: C <- "-34.8067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5875 TOTAL ENERGY = -68.2421 RDTITL> * VAN DER WAALS = -33.4354 ELECTROSTATIC = -34.8067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5875" Parameter: CONF_N -> "8002" Comparing "5875" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5876" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754405 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753480 ATOM PAIRS WERE FOUND FOR ATOM LIST 41456 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30092 from a total of 753480 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5876 -68.86680 0.62470 0.85893 INTE EXTERN> -21.92708 -46.93972 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8668" Parameter: A <- "-68.8668" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.9271" Parameter: B <- "-21.9271" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9397" Parameter: C <- "-46.9397" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5876 TOTAL ENERGY = -68.8668 RDTITL> * VAN DER WAALS = -21.9271 ELECTROSTATIC = -46.9397 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5876" Parameter: CONF_N -> "8002" Comparing "5876" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5877" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753480 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751480 ATOM PAIRS WERE FOUND FOR ATOM LIST 41292 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29569 from a total of 751480 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5877 -72.41579 3.54899 0.53616 INTE EXTERN> -31.55864 -40.85715 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4158" Parameter: A <- "-72.4158" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5586" Parameter: B <- "-31.5586" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8571" Parameter: C <- "-40.8571" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5877 TOTAL ENERGY = -72.4158 RDTITL> * VAN DER WAALS = -31.5586 ELECTROSTATIC = -40.8571 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5877" Parameter: CONF_N -> "8002" Comparing "5877" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5878" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751480 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757245 ATOM PAIRS WERE FOUND FOR ATOM LIST 41337 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29613 from a total of 757245 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5878 -65.23078 -7.18501 0.45007 INTE EXTERN> -35.55551 -29.67527 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.2308" Parameter: A <- "-65.2308" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.5555" Parameter: B <- "-35.5555" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.6753" Parameter: C <- "-29.6753" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5878 TOTAL ENERGY = -65.2308 RDTITL> * VAN DER WAALS = -35.5555 ELECTROSTATIC = -29.6753 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5878" Parameter: CONF_N -> "8002" Comparing "5878" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5879" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757245 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751498 ATOM PAIRS WERE FOUND FOR ATOM LIST 41183 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29630 from a total of 751498 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5879 -70.16396 4.93318 0.59574 INTE EXTERN> -31.03025 -39.13371 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.164" Parameter: A <- "-70.164" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0302" Parameter: B <- "-31.0302" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1337" Parameter: C <- "-39.1337" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5879 TOTAL ENERGY = -70.164 RDTITL> * VAN DER WAALS = -31.0302 ELECTROSTATIC = -39.1337 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5879" Parameter: CONF_N -> "8002" Comparing "5879" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5880" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751498 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750988 ATOM PAIRS WERE FOUND FOR ATOM LIST 41203 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28994 from a total of 750988 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5880 -75.61195 5.44800 0.57998 INTE EXTERN> -32.24460 -43.36735 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.612" Parameter: A <- "-75.612" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2446" Parameter: B <- "-32.2446" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3674" Parameter: C <- "-43.3674" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5880 TOTAL ENERGY = -75.612 RDTITL> * VAN DER WAALS = -32.2446 ELECTROSTATIC = -43.3674 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5880" Parameter: CONF_N -> "8002" Comparing "5880" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5881" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750988 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754432 ATOM PAIRS WERE FOUND FOR ATOM LIST 41497 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29478 from a total of 754432 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5881 -71.62722 -3.98473 0.58615 INTE EXTERN> -30.90543 -40.72180 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6272" Parameter: A <- "-71.6272" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9054" Parameter: B <- "-30.9054" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7218" Parameter: C <- "-40.7218" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5881 TOTAL ENERGY = -71.6272 RDTITL> * VAN DER WAALS = -30.9054 ELECTROSTATIC = -40.7218 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5881" Parameter: CONF_N -> "8002" Comparing "5881" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5882" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754432 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760462 ATOM PAIRS WERE FOUND FOR ATOM LIST 41864 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30038 from a total of 760462 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5882 -73.66735 2.04012 0.54126 INTE EXTERN> -32.34982 -41.31753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6673" Parameter: A <- "-73.6673" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3498" Parameter: B <- "-32.3498" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3175" Parameter: C <- "-41.3175" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5882 TOTAL ENERGY = -73.6673 RDTITL> * VAN DER WAALS = -32.3498 ELECTROSTATIC = -41.3175 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5882" Parameter: CONF_N -> "8002" Comparing "5882" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5883" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760462 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758304 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30029 from a total of 758304 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5883 -67.38958 -6.27777 0.46292 INTE EXTERN> -35.22551 -32.16407 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3896" Parameter: A <- "-67.3896" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.2255" Parameter: B <- "-35.2255" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.1641" Parameter: C <- "-32.1641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5883 TOTAL ENERGY = -67.3896 RDTITL> * VAN DER WAALS = -35.2255 ELECTROSTATIC = -32.1641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5883" Parameter: CONF_N -> "8002" Comparing "5883" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5884" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758304 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758064 ATOM PAIRS WERE FOUND FOR ATOM LIST 41701 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29694 from a total of 758064 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5884 -68.91648 1.52690 0.63780 INTE EXTERN> -27.90302 -41.01346 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9165" Parameter: A <- "-68.9165" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.903" Parameter: B <- "-27.903" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0135" Parameter: C <- "-41.0135" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5884 TOTAL ENERGY = -68.9165 RDTITL> * VAN DER WAALS = -27.903 ELECTROSTATIC = -41.0135 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5884" Parameter: CONF_N -> "8002" Comparing "5884" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5885" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758064 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756801 ATOM PAIRS WERE FOUND FOR ATOM LIST 41611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30419 from a total of 756801 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5885 -72.85590 3.93942 0.61262 INTE EXTERN> -32.63175 -40.22415 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8559" Parameter: A <- "-72.8559" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6318" Parameter: B <- "-32.6318" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2241" Parameter: C <- "-40.2241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5885 TOTAL ENERGY = -72.8559 RDTITL> * VAN DER WAALS = -32.6318 ELECTROSTATIC = -40.2241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5885" Parameter: CONF_N -> "8002" Comparing "5885" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5886" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756801 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753796 ATOM PAIRS WERE FOUND FOR ATOM LIST 41530 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30216 from a total of 753796 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5886 -66.65249 -6.20341 0.57754 INTE EXTERN> -31.00912 -35.64336 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6525" Parameter: A <- "-66.6525" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0091" Parameter: B <- "-31.0091" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6434" Parameter: C <- "-35.6434" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5886 TOTAL ENERGY = -66.6525 RDTITL> * VAN DER WAALS = -31.0091 ELECTROSTATIC = -35.6434 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5886" Parameter: CONF_N -> "8002" Comparing "5886" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5887" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753796 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755308 ATOM PAIRS WERE FOUND FOR ATOM LIST 41459 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30324 from a total of 755308 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5887 -65.11900 -1.53349 0.65433 INTE EXTERN> -29.46375 -35.65525 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.119" Parameter: A <- "-65.119" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4638" Parameter: B <- "-29.4638" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6552" Parameter: C <- "-35.6552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5887 TOTAL ENERGY = -65.119 RDTITL> * VAN DER WAALS = -29.4638 ELECTROSTATIC = -35.6552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5887" Parameter: CONF_N -> "8002" Comparing "5887" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5888" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755308 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760450 ATOM PAIRS WERE FOUND FOR ATOM LIST 41896 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30101 from a total of 760450 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5888 -71.15382 6.03482 0.53297 INTE EXTERN> -33.09940 -38.05442 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1538" Parameter: A <- "-71.1538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0994" Parameter: B <- "-33.0994" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0544" Parameter: C <- "-38.0544" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5888 TOTAL ENERGY = -71.1538 RDTITL> * VAN DER WAALS = -33.0994 ELECTROSTATIC = -38.0544 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5888" Parameter: CONF_N -> "8002" Comparing "5888" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5889" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760450 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755521 ATOM PAIRS WERE FOUND FOR ATOM LIST 41517 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29863 from a total of 755521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5889 -68.66218 -2.49164 0.53501 INTE EXTERN> -32.20212 -36.46005 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6622" Parameter: A <- "-68.6622" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2021" Parameter: B <- "-32.2021" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4601" Parameter: C <- "-36.4601" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5889 TOTAL ENERGY = -68.6622 RDTITL> * VAN DER WAALS = -32.2021 ELECTROSTATIC = -36.4601 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5889" Parameter: CONF_N -> "8002" Comparing "5889" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5890" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759486 ATOM PAIRS WERE FOUND FOR ATOM LIST 41654 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29978 from a total of 759486 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5890 -72.26631 3.60414 0.55604 INTE EXTERN> -32.81422 -39.45209 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2663" Parameter: A <- "-72.2663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8142" Parameter: B <- "-32.8142" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4521" Parameter: C <- "-39.4521" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5890 TOTAL ENERGY = -72.2663 RDTITL> * VAN DER WAALS = -32.8142 ELECTROSTATIC = -39.4521 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5890" Parameter: CONF_N -> "8002" Comparing "5890" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5891" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759486 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759013 ATOM PAIRS WERE FOUND FOR ATOM LIST 41592 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30267 from a total of 759013 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5891 -79.73079 7.46448 0.60202 INTE EXTERN> -32.34323 -47.38756 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7308" Parameter: A <- "-79.7308" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3432" Parameter: B <- "-32.3432" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3876" Parameter: C <- "-47.3876" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5891 TOTAL ENERGY = -79.7308 RDTITL> * VAN DER WAALS = -32.3432 ELECTROSTATIC = -47.3876 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5891" Parameter: CONF_N -> "8002" Comparing "5891" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5892" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759013 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755829 ATOM PAIRS WERE FOUND FOR ATOM LIST 41422 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30125 from a total of 755829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5892 -73.29673 -6.43406 0.52703 INTE EXTERN> -34.37844 -38.91829 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2967" Parameter: A <- "-73.2967" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3784" Parameter: B <- "-34.3784" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9183" Parameter: C <- "-38.9183" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5892 TOTAL ENERGY = -73.2967 RDTITL> * VAN DER WAALS = -34.3784 ELECTROSTATIC = -38.9183 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5892" Parameter: CONF_N -> "8002" Comparing "5892" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5893" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754417 ATOM PAIRS WERE FOUND FOR ATOM LIST 41430 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29734 from a total of 754417 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5893 -74.53821 1.24147 0.59230 INTE EXTERN> -32.53087 -42.00734 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5382" Parameter: A <- "-74.5382" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5309" Parameter: B <- "-32.5309" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0073" Parameter: C <- "-42.0073" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5893 TOTAL ENERGY = -74.5382 RDTITL> * VAN DER WAALS = -32.5309 ELECTROSTATIC = -42.0073 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5893" Parameter: CONF_N -> "8002" Comparing "5893" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5894" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754417 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753982 ATOM PAIRS WERE FOUND FOR ATOM LIST 41475 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29284 from a total of 753982 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5894 -66.45053 -8.08767 0.51282 INTE EXTERN> -34.60029 -31.85024 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4505" Parameter: A <- "-66.4505" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6003" Parameter: B <- "-34.6003" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.8502" Parameter: C <- "-31.8502" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5894 TOTAL ENERGY = -66.4505 RDTITL> * VAN DER WAALS = -34.6003 ELECTROSTATIC = -31.8502 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5894" Parameter: CONF_N -> "8002" Comparing "5894" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5895" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753982 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753066 ATOM PAIRS WERE FOUND FOR ATOM LIST 41285 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30054 from a total of 753066 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5895 -73.47981 7.02927 0.51597 INTE EXTERN> -33.93618 -39.54363 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4798" Parameter: A <- "-73.4798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9362" Parameter: B <- "-33.9362" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5436" Parameter: C <- "-39.5436" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5895 TOTAL ENERGY = -73.4798 RDTITL> * VAN DER WAALS = -33.9362 ELECTROSTATIC = -39.5436 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5895" Parameter: CONF_N -> "8002" Comparing "5895" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5896" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753066 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756221 ATOM PAIRS WERE FOUND FOR ATOM LIST 41644 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29807 from a total of 756221 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5896 -69.25521 -4.22460 0.47460 INTE EXTERN> -34.22439 -35.03082 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2552" Parameter: A <- "-69.2552" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.2244" Parameter: B <- "-34.2244" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0308" Parameter: C <- "-35.0308" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5896 TOTAL ENERGY = -69.2552 RDTITL> * VAN DER WAALS = -34.2244 ELECTROSTATIC = -35.0308 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5896" Parameter: CONF_N -> "8002" Comparing "5896" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5897" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756221 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759017 ATOM PAIRS WERE FOUND FOR ATOM LIST 41772 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28865 from a total of 759017 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5897 -68.23777 -1.01744 0.51583 INTE EXTERN> -32.92712 -35.31066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2378" Parameter: A <- "-68.2378" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9271" Parameter: B <- "-32.9271" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3107" Parameter: C <- "-35.3107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5897 TOTAL ENERGY = -68.2378 RDTITL> * VAN DER WAALS = -32.9271 ELECTROSTATIC = -35.3107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5897" Parameter: CONF_N -> "8002" Comparing "5897" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5898" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759017 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758905 ATOM PAIRS WERE FOUND FOR ATOM LIST 41819 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29914 from a total of 758905 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5898 -70.69390 2.45613 0.59506 INTE EXTERN> -29.81463 -40.87927 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6939" Parameter: A <- "-70.6939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8146" Parameter: B <- "-29.8146" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8793" Parameter: C <- "-40.8793" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5898 TOTAL ENERGY = -70.6939 RDTITL> * VAN DER WAALS = -29.8146 ELECTROSTATIC = -40.8793 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5898" Parameter: CONF_N -> "8002" Comparing "5898" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5899" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758905 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759572 ATOM PAIRS WERE FOUND FOR ATOM LIST 41764 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29388 from a total of 759572 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5899 -73.74911 3.05521 0.49288 INTE EXTERN> -31.64536 -42.10376 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7491" Parameter: A <- "-73.7491" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6454" Parameter: B <- "-31.6454" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1038" Parameter: C <- "-42.1038" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5899 TOTAL ENERGY = -73.7491 RDTITL> * VAN DER WAALS = -31.6454 ELECTROSTATIC = -42.1038 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5899" Parameter: CONF_N -> "8002" Comparing "5899" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5900" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759572 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756913 ATOM PAIRS WERE FOUND FOR ATOM LIST 41658 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29483 from a total of 756913 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5900 -65.69899 -8.05012 0.57619 INTE EXTERN> -30.88123 -34.81776 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.699" Parameter: A <- "-65.699" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8812" Parameter: B <- "-30.8812" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8178" Parameter: C <- "-34.8178" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5900 TOTAL ENERGY = -65.699 RDTITL> * VAN DER WAALS = -30.8812 ELECTROSTATIC = -34.8178 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5900" Parameter: CONF_N -> "8002" Comparing "5900" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5901" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756913 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756896 ATOM PAIRS WERE FOUND FOR ATOM LIST 41455 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29781 from a total of 756896 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5901 -72.58760 6.88861 0.56303 INTE EXTERN> -32.76792 -39.81967 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5876" Parameter: A <- "-72.5876" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7679" Parameter: B <- "-32.7679" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8197" Parameter: C <- "-39.8197" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5901 TOTAL ENERGY = -72.5876 RDTITL> * VAN DER WAALS = -32.7679 ELECTROSTATIC = -39.8197 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5901" Parameter: CONF_N -> "8002" Comparing "5901" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5902" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756896 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754411 ATOM PAIRS WERE FOUND FOR ATOM LIST 41593 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29844 from a total of 754411 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5902 -65.01306 -7.57454 0.50950 INTE EXTERN> -33.39058 -31.62248 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0131" Parameter: A <- "-65.0131" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3906" Parameter: B <- "-33.3906" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.6225" Parameter: C <- "-31.6225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5902 TOTAL ENERGY = -65.0131 RDTITL> * VAN DER WAALS = -33.3906 ELECTROSTATIC = -31.6225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5902" Parameter: CONF_N -> "8002" Comparing "5902" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5903" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754411 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756922 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29603 from a total of 756922 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5903 -68.90905 3.89599 0.67402 INTE EXTERN> -30.75749 -38.15155 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.909" Parameter: A <- "-68.909" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7575" Parameter: B <- "-30.7575" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1516" Parameter: C <- "-38.1516" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5903 TOTAL ENERGY = -68.909 RDTITL> * VAN DER WAALS = -30.7575 ELECTROSTATIC = -38.1516 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5903" Parameter: CONF_N -> "8002" Comparing "5903" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5904" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756922 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756219 ATOM PAIRS WERE FOUND FOR ATOM LIST 41538 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28860 from a total of 756219 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5904 -69.46304 0.55399 0.56449 INTE EXTERN> -28.42778 -41.03526 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.463" Parameter: A <- "-69.463" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4278" Parameter: B <- "-28.4278" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0353" Parameter: C <- "-41.0353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5904 TOTAL ENERGY = -69.463 RDTITL> * VAN DER WAALS = -28.4278 ELECTROSTATIC = -41.0353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5904" Parameter: CONF_N -> "8002" Comparing "5904" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5905" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756219 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758289 ATOM PAIRS WERE FOUND FOR ATOM LIST 41756 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29520 from a total of 758289 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5905 -66.87063 -2.59241 0.54348 INTE EXTERN> -31.14417 -35.72645 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8706" Parameter: A <- "-66.8706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1442" Parameter: B <- "-31.1442" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7265" Parameter: C <- "-35.7265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5905 TOTAL ENERGY = -66.8706 RDTITL> * VAN DER WAALS = -31.1442 ELECTROSTATIC = -35.7265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5905" Parameter: CONF_N -> "8002" Comparing "5905" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5906" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758289 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752479 ATOM PAIRS WERE FOUND FOR ATOM LIST 41178 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29801 from a total of 752479 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5906 -66.64814 -0.22248 0.61355 INTE EXTERN> -30.03807 -36.61007 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6481" Parameter: A <- "-66.6481" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0381" Parameter: B <- "-30.0381" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6101" Parameter: C <- "-36.6101" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5906 TOTAL ENERGY = -66.6481 RDTITL> * VAN DER WAALS = -30.0381 ELECTROSTATIC = -36.6101 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5906" Parameter: CONF_N -> "8002" Comparing "5906" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5907" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752479 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748183 ATOM PAIRS WERE FOUND FOR ATOM LIST 40857 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29012 from a total of 748183 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5907 -68.88126 2.23312 0.53556 INTE EXTERN> -31.79231 -37.08895 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8813" Parameter: A <- "-68.8813" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7923" Parameter: B <- "-31.7923" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0889" Parameter: C <- "-37.0889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5907 TOTAL ENERGY = -68.8813 RDTITL> * VAN DER WAALS = -31.7923 ELECTROSTATIC = -37.0889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5907" Parameter: CONF_N -> "8002" Comparing "5907" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5908" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748183 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752121 ATOM PAIRS WERE FOUND FOR ATOM LIST 41250 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28813 from a total of 752121 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5908 -71.39743 2.51617 0.59178 INTE EXTERN> -30.05514 -41.34229 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3974" Parameter: A <- "-71.3974" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0551" Parameter: B <- "-30.0551" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3423" Parameter: C <- "-41.3423" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5908 TOTAL ENERGY = -71.3974 RDTITL> * VAN DER WAALS = -30.0551 ELECTROSTATIC = -41.3423 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5908" Parameter: CONF_N -> "8002" Comparing "5908" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5909" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752121 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758780 ATOM PAIRS WERE FOUND FOR ATOM LIST 41677 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29447 from a total of 758780 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5909 -67.18452 -4.21291 0.54897 INTE EXTERN> -33.57866 -33.60587 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1845" Parameter: A <- "-67.1845" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5787" Parameter: B <- "-33.5787" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6059" Parameter: C <- "-33.6059" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5909 TOTAL ENERGY = -67.1845 RDTITL> * VAN DER WAALS = -33.5787 ELECTROSTATIC = -33.6059 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5909" Parameter: CONF_N -> "8002" Comparing "5909" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5910" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758780 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753766 ATOM PAIRS WERE FOUND FOR ATOM LIST 41610 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28996 from a total of 753766 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5910 -67.94321 0.75869 0.59810 INTE EXTERN> -28.87789 -39.06532 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9432" Parameter: A <- "-67.9432" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8779" Parameter: B <- "-28.8779" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0653" Parameter: C <- "-39.0653" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5910 TOTAL ENERGY = -67.9432 RDTITL> * VAN DER WAALS = -28.8779 ELECTROSTATIC = -39.0653 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5910" Parameter: CONF_N -> "8002" Comparing "5910" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5911" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753766 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755119 ATOM PAIRS WERE FOUND FOR ATOM LIST 41589 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29392 from a total of 755119 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5911 -70.01986 2.07665 0.55679 INTE EXTERN> -31.41774 -38.60212 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0199" Parameter: A <- "-70.0199" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4177" Parameter: B <- "-31.4177" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6021" Parameter: C <- "-38.6021" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5911 TOTAL ENERGY = -70.0199 RDTITL> * VAN DER WAALS = -31.4177 ELECTROSTATIC = -38.6021 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5911" Parameter: CONF_N -> "8002" Comparing "5911" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5912" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755119 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757145 ATOM PAIRS WERE FOUND FOR ATOM LIST 41469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28896 from a total of 757145 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5912 -67.20770 -2.81216 0.54709 INTE EXTERN> -29.90210 -37.30560 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2077" Parameter: A <- "-67.2077" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9021" Parameter: B <- "-29.9021" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3056" Parameter: C <- "-37.3056" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5912 TOTAL ENERGY = -67.2077 RDTITL> * VAN DER WAALS = -29.9021 ELECTROSTATIC = -37.3056 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5912" Parameter: CONF_N -> "8002" Comparing "5912" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5913" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757145 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754403 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29238 from a total of 754403 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5913 -72.80991 5.60221 0.54587 INTE EXTERN> -32.45068 -40.35924 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8099" Parameter: A <- "-72.8099" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4507" Parameter: B <- "-32.4507" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3592" Parameter: C <- "-40.3592" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5913 TOTAL ENERGY = -72.8099 RDTITL> * VAN DER WAALS = -32.4507 ELECTROSTATIC = -40.3592 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5913" Parameter: CONF_N -> "8002" Comparing "5913" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5914" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754403 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754836 ATOM PAIRS WERE FOUND FOR ATOM LIST 41481 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29087 from a total of 754836 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5914 -69.57212 -3.23779 0.50474 INTE EXTERN> -35.40151 -34.17061 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5721" Parameter: A <- "-69.5721" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.4015" Parameter: B <- "-35.4015" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1706" Parameter: C <- "-34.1706" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5914 TOTAL ENERGY = -69.5721 RDTITL> * VAN DER WAALS = -35.4015 ELECTROSTATIC = -34.1706 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5914" Parameter: CONF_N -> "8002" Comparing "5914" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5915" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754836 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758682 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29520 from a total of 758682 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5915 -71.56149 1.98937 0.60350 INTE EXTERN> -28.67395 -42.88754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5615" Parameter: A <- "-71.5615" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6739" Parameter: B <- "-28.6739" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8875" Parameter: C <- "-42.8875" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5915 TOTAL ENERGY = -71.5615 RDTITL> * VAN DER WAALS = -28.6739 ELECTROSTATIC = -42.8875 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5915" Parameter: CONF_N -> "8002" Comparing "5915" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5916" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758682 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757744 ATOM PAIRS WERE FOUND FOR ATOM LIST 41618 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29581 from a total of 757744 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5916 -68.84216 -2.71933 0.55891 INTE EXTERN> -31.89310 -36.94905 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8422" Parameter: A <- "-68.8422" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8931" Parameter: B <- "-31.8931" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9491" Parameter: C <- "-36.9491" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5916 TOTAL ENERGY = -68.8422 RDTITL> * VAN DER WAALS = -31.8931 ELECTROSTATIC = -36.9491 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5916" Parameter: CONF_N -> "8002" Comparing "5916" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5917" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757744 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757717 ATOM PAIRS WERE FOUND FOR ATOM LIST 41675 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29434 from a total of 757717 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5917 -66.48675 -2.35541 0.64198 INTE EXTERN> -31.99810 -34.48865 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4868" Parameter: A <- "-66.4868" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9981" Parameter: B <- "-31.9981" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4886" Parameter: C <- "-34.4886" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5917 TOTAL ENERGY = -66.4868 RDTITL> * VAN DER WAALS = -31.9981 ELECTROSTATIC = -34.4886 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5917" Parameter: CONF_N -> "8002" Comparing "5917" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5918" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757717 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756829 ATOM PAIRS WERE FOUND FOR ATOM LIST 41532 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29669 from a total of 756829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5918 -63.48949 -2.99726 0.52221 INTE EXTERN> -29.80478 -33.68472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4895" Parameter: A <- "-63.4895" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8048" Parameter: B <- "-29.8048" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6847" Parameter: C <- "-33.6847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5918 TOTAL ENERGY = -63.4895 RDTITL> * VAN DER WAALS = -29.8048 ELECTROSTATIC = -33.6847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5918" Parameter: CONF_N -> "8002" Comparing "5918" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5919" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757590 ATOM PAIRS WERE FOUND FOR ATOM LIST 41557 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29977 from a total of 757590 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5919 -68.90072 5.41123 0.56234 INTE EXTERN> -29.63146 -39.26926 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9007" Parameter: A <- "-68.9007" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6315" Parameter: B <- "-29.6315" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2693" Parameter: C <- "-39.2693" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5919 TOTAL ENERGY = -68.9007 RDTITL> * VAN DER WAALS = -29.6315 ELECTROSTATIC = -39.2693 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5919" Parameter: CONF_N -> "8002" Comparing "5919" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5920" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757590 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753749 ATOM PAIRS WERE FOUND FOR ATOM LIST 41323 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29275 from a total of 753749 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5920 -73.54869 4.64796 0.57098 INTE EXTERN> -32.01376 -41.53493 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5487" Parameter: A <- "-73.5487" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0138" Parameter: B <- "-32.0138" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5349" Parameter: C <- "-41.5349" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5920 TOTAL ENERGY = -73.5487 RDTITL> * VAN DER WAALS = -32.0138 ELECTROSTATIC = -41.5349 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5920" Parameter: CONF_N -> "8002" Comparing "5920" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5921" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753749 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753141 ATOM PAIRS WERE FOUND FOR ATOM LIST 41425 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29688 from a total of 753141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5921 -71.86852 -1.68016 0.54404 INTE EXTERN> -32.53682 -39.33170 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8685" Parameter: A <- "-71.8685" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5368" Parameter: B <- "-32.5368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3317" Parameter: C <- "-39.3317" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5921 TOTAL ENERGY = -71.8685 RDTITL> * VAN DER WAALS = -32.5368 ELECTROSTATIC = -39.3317 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5921" Parameter: CONF_N -> "8002" Comparing "5921" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5922" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755333 ATOM PAIRS WERE FOUND FOR ATOM LIST 41544 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29669 from a total of 755333 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5922 -72.45296 0.58444 0.54006 INTE EXTERN> -33.50264 -38.95032 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.453" Parameter: A <- "-72.453" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5026" Parameter: B <- "-33.5026" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9503" Parameter: C <- "-38.9503" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5922 TOTAL ENERGY = -72.453 RDTITL> * VAN DER WAALS = -33.5026 ELECTROSTATIC = -38.9503 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5922" Parameter: CONF_N -> "8002" Comparing "5922" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5923" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755333 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758904 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29257 from a total of 758904 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5923 -75.19772 2.74476 0.63867 INTE EXTERN> -29.24442 -45.95331 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1977" Parameter: A <- "-75.1977" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2444" Parameter: B <- "-29.2444" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9533" Parameter: C <- "-45.9533" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5923 TOTAL ENERGY = -75.1977 RDTITL> * VAN DER WAALS = -29.2444 ELECTROSTATIC = -45.9533 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5923" Parameter: CONF_N -> "8002" Comparing "5923" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5924" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758904 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758062 ATOM PAIRS WERE FOUND FOR ATOM LIST 41557 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29243 from a total of 758062 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5924 -71.19851 -3.99921 0.58624 INTE EXTERN> -31.46323 -39.73528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1985" Parameter: A <- "-71.1985" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4632" Parameter: B <- "-31.4632" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7353" Parameter: C <- "-39.7353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5924 TOTAL ENERGY = -71.1985 RDTITL> * VAN DER WAALS = -31.4632 ELECTROSTATIC = -39.7353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5924" Parameter: CONF_N -> "8002" Comparing "5924" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5925" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758062 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752999 ATOM PAIRS WERE FOUND FOR ATOM LIST 41503 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28894 from a total of 752999 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5925 -68.77602 -2.42249 0.49443 INTE EXTERN> -33.61658 -35.15944 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.776" Parameter: A <- "-68.776" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6166" Parameter: B <- "-33.6166" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1594" Parameter: C <- "-35.1594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5925 TOTAL ENERGY = -68.776 RDTITL> * VAN DER WAALS = -33.6166 ELECTROSTATIC = -35.1594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5925" Parameter: CONF_N -> "8002" Comparing "5925" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5926" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752999 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756861 ATOM PAIRS WERE FOUND FOR ATOM LIST 41592 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29560 from a total of 756861 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5926 -70.97800 2.20198 0.64247 INTE EXTERN> -30.23409 -40.74391 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.978" Parameter: A <- "-70.978" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2341" Parameter: B <- "-30.2341" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7439" Parameter: C <- "-40.7439" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5926 TOTAL ENERGY = -70.978 RDTITL> * VAN DER WAALS = -30.2341 ELECTROSTATIC = -40.7439 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5926" Parameter: CONF_N -> "8002" Comparing "5926" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5927" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756861 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752397 ATOM PAIRS WERE FOUND FOR ATOM LIST 41427 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28893 from a total of 752397 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5927 -67.32788 -3.65011 0.51351 INTE EXTERN> -33.53428 -33.79361 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3279" Parameter: A <- "-67.3279" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5343" Parameter: B <- "-33.5343" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7936" Parameter: C <- "-33.7936" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5927 TOTAL ENERGY = -67.3279 RDTITL> * VAN DER WAALS = -33.5343 ELECTROSTATIC = -33.7936 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5927" Parameter: CONF_N -> "8002" Comparing "5927" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5928" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752397 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747265 ATOM PAIRS WERE FOUND FOR ATOM LIST 41337 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29135 from a total of 747265 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5928 -69.12267 1.79479 0.56873 INTE EXTERN> -33.14553 -35.97714 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1227" Parameter: A <- "-69.1227" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1455" Parameter: B <- "-33.1455" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9771" Parameter: C <- "-35.9771" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5928 TOTAL ENERGY = -69.1227 RDTITL> * VAN DER WAALS = -33.1455 ELECTROSTATIC = -35.9771 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5928" Parameter: CONF_N -> "8002" Comparing "5928" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5929" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747265 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748101 ATOM PAIRS WERE FOUND FOR ATOM LIST 41115 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29636 from a total of 748101 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5929 -67.09624 -2.02642 0.57918 INTE EXTERN> -31.11701 -35.97923 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0962" Parameter: A <- "-67.0962" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.117" Parameter: B <- "-31.117" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9792" Parameter: C <- "-35.9792" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5929 TOTAL ENERGY = -67.0962 RDTITL> * VAN DER WAALS = -31.117 ELECTROSTATIC = -35.9792 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5929" Parameter: CONF_N -> "8002" Comparing "5929" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5930" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748101 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753105 ATOM PAIRS WERE FOUND FOR ATOM LIST 41405 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29722 from a total of 753105 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5930 -64.15146 -2.94478 0.47362 INTE EXTERN> -34.51572 -29.63574 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1515" Parameter: A <- "-64.1515" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.5157" Parameter: B <- "-34.5157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.6357" Parameter: C <- "-29.6357" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5930 TOTAL ENERGY = -64.1515 RDTITL> * VAN DER WAALS = -34.5157 ELECTROSTATIC = -29.6357 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5930" Parameter: CONF_N -> "8002" Comparing "5930" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5931" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753105 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755465 ATOM PAIRS WERE FOUND FOR ATOM LIST 41603 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30023 from a total of 755465 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5931 -69.56570 5.41424 0.56858 INTE EXTERN> -30.77619 -38.78951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5657" Parameter: A <- "-69.5657" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7762" Parameter: B <- "-30.7762" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7895" Parameter: C <- "-38.7895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5931 TOTAL ENERGY = -69.5657 RDTITL> * VAN DER WAALS = -30.7762 ELECTROSTATIC = -38.7895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5931" Parameter: CONF_N -> "8002" Comparing "5931" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5932" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755465 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755451 ATOM PAIRS WERE FOUND FOR ATOM LIST 41509 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30326 from a total of 755451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5932 -72.73968 3.17398 0.57826 INTE EXTERN> -33.37219 -39.36750 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7397" Parameter: A <- "-72.7397" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3722" Parameter: B <- "-33.3722" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3675" Parameter: C <- "-39.3675" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5932 TOTAL ENERGY = -72.7397 RDTITL> * VAN DER WAALS = -33.3722 ELECTROSTATIC = -39.3675 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5932" Parameter: CONF_N -> "8002" Comparing "5932" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5933" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753672 ATOM PAIRS WERE FOUND FOR ATOM LIST 41463 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29841 from a total of 753672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5933 -68.74504 -3.99464 0.66850 INTE EXTERN> -28.20035 -40.54469 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.745" Parameter: A <- "-68.745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2004" Parameter: B <- "-28.2004" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5447" Parameter: C <- "-40.5447" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5933 TOTAL ENERGY = -68.745 RDTITL> * VAN DER WAALS = -28.2004 ELECTROSTATIC = -40.5447 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5933" Parameter: CONF_N -> "8002" Comparing "5933" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5934" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758925 ATOM PAIRS WERE FOUND FOR ATOM LIST 41654 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29851 from a total of 758925 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5934 -72.73179 3.98675 0.54689 INTE EXTERN> -33.96805 -38.76374 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7318" Parameter: A <- "-72.7318" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.968" Parameter: B <- "-33.968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7637" Parameter: C <- "-38.7637" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5934 TOTAL ENERGY = -72.7318 RDTITL> * VAN DER WAALS = -33.968 ELECTROSTATIC = -38.7637 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5934" Parameter: CONF_N -> "8002" Comparing "5934" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5935" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758925 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756465 ATOM PAIRS WERE FOUND FOR ATOM LIST 41392 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30051 from a total of 756465 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5935 -75.72420 2.99241 0.62119 INTE EXTERN> -31.94183 -43.78237 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7242" Parameter: A <- "-75.7242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9418" Parameter: B <- "-31.9418" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7824" Parameter: C <- "-43.7824" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5935 TOTAL ENERGY = -75.7242 RDTITL> * VAN DER WAALS = -31.9418 ELECTROSTATIC = -43.7824 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5935" Parameter: CONF_N -> "8002" Comparing "5935" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5936" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756465 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752935 ATOM PAIRS WERE FOUND FOR ATOM LIST 41326 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29628 from a total of 752935 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5936 -62.42666 -13.29754 0.56387 INTE EXTERN> -31.88947 -30.53719 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.4267" Parameter: A <- "-62.4267" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8895" Parameter: B <- "-31.8895" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.5372" Parameter: C <- "-30.5372" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5936 TOTAL ENERGY = -62.4267 RDTITL> * VAN DER WAALS = -31.8895 ELECTROSTATIC = -30.5372 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5936" Parameter: CONF_N -> "8002" Comparing "5936" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5937" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752935 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756195 ATOM PAIRS WERE FOUND FOR ATOM LIST 41760 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29440 from a total of 756195 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5937 -72.87261 10.44595 0.61442 INTE EXTERN> -31.12601 -41.74659 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8726" Parameter: A <- "-72.8726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.126" Parameter: B <- "-31.126" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7466" Parameter: C <- "-41.7466" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5937 TOTAL ENERGY = -72.8726 RDTITL> * VAN DER WAALS = -31.126 ELECTROSTATIC = -41.7466 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5937" Parameter: CONF_N -> "8002" Comparing "5937" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5938" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756195 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 767048 ATOM PAIRS WERE FOUND FOR ATOM LIST 42051 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29389 from a total of 767048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5938 -67.23245 -5.64016 0.57165 INTE EXTERN> -30.24111 -36.99134 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2324" Parameter: A <- "-67.2324" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2411" Parameter: B <- "-30.2411" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9913" Parameter: C <- "-36.9913" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5938 TOTAL ENERGY = -67.2324 RDTITL> * VAN DER WAALS = -30.2411 ELECTROSTATIC = -36.9913 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5938" Parameter: CONF_N -> "8002" Comparing "5938" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5939" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 767048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758588 ATOM PAIRS WERE FOUND FOR ATOM LIST 41673 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29767 from a total of 758588 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5939 -67.98706 0.75461 0.55016 INTE EXTERN> -32.54563 -35.44143 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9871" Parameter: A <- "-67.9871" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5456" Parameter: B <- "-32.5456" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4414" Parameter: C <- "-35.4414" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5939 TOTAL ENERGY = -67.9871 RDTITL> * VAN DER WAALS = -32.5456 ELECTROSTATIC = -35.4414 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5939" Parameter: CONF_N -> "8002" Comparing "5939" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5940" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758588 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754290 ATOM PAIRS WERE FOUND FOR ATOM LIST 41450 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29981 from a total of 754290 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5940 -69.90203 1.91497 0.52301 INTE EXTERN> -33.21191 -36.69012 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.902" Parameter: A <- "-69.902" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2119" Parameter: B <- "-33.2119" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6901" Parameter: C <- "-36.6901" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5940 TOTAL ENERGY = -69.902 RDTITL> * VAN DER WAALS = -33.2119 ELECTROSTATIC = -36.6901 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5940" Parameter: CONF_N -> "8002" Comparing "5940" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5941" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754290 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753155 ATOM PAIRS WERE FOUND FOR ATOM LIST 41423 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29807 from a total of 753155 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5941 -75.92517 6.02314 0.55812 INTE EXTERN> -34.56648 -41.35869 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9252" Parameter: A <- "-75.9252" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.5665" Parameter: B <- "-34.5665" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3587" Parameter: C <- "-41.3587" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5941 TOTAL ENERGY = -75.9252 RDTITL> * VAN DER WAALS = -34.5665 ELECTROSTATIC = -41.3587 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5941" Parameter: CONF_N -> "8002" Comparing "5941" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5942" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753155 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751298 ATOM PAIRS WERE FOUND FOR ATOM LIST 41251 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29888 from a total of 751298 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5942 -70.79230 -5.13287 0.63357 INTE EXTERN> -29.48081 -41.31149 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7923" Parameter: A <- "-70.7923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4808" Parameter: B <- "-29.4808" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3115" Parameter: C <- "-41.3115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5942 TOTAL ENERGY = -70.7923 RDTITL> * VAN DER WAALS = -29.4808 ELECTROSTATIC = -41.3115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5942" Parameter: CONF_N -> "8002" Comparing "5942" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5943" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751298 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750590 ATOM PAIRS WERE FOUND FOR ATOM LIST 41215 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29613 from a total of 750590 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5943 -62.22293 -8.56937 0.61670 INTE EXTERN> -28.93877 -33.28416 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.2229" Parameter: A <- "-62.2229" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9388" Parameter: B <- "-28.9388" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2842" Parameter: C <- "-33.2842" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5943 TOTAL ENERGY = -62.2229 RDTITL> * VAN DER WAALS = -28.9388 ELECTROSTATIC = -33.2842 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5943" Parameter: CONF_N -> "8002" Comparing "5943" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5944" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750590 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759011 ATOM PAIRS WERE FOUND FOR ATOM LIST 41834 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30151 from a total of 759011 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5944 -74.31490 12.09197 0.52238 INTE EXTERN> -35.70235 -38.61255 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3149" Parameter: A <- "-74.3149" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.7024" Parameter: B <- "-35.7024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6125" Parameter: C <- "-38.6125" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5944 TOTAL ENERGY = -74.3149 RDTITL> * VAN DER WAALS = -35.7024 ELECTROSTATIC = -38.6125 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5944" Parameter: CONF_N -> "8002" Comparing "5944" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5945" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759011 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750921 ATOM PAIRS WERE FOUND FOR ATOM LIST 41349 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28820 from a total of 750921 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5945 -58.37560 -15.93930 0.58523 INTE EXTERN> -28.44678 -29.92882 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.3756" Parameter: A <- "-58.3756" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4468" Parameter: B <- "-28.4468" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.9288" Parameter: C <- "-29.9288" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5945 TOTAL ENERGY = -58.3756 RDTITL> * VAN DER WAALS = -28.4468 ELECTROSTATIC = -29.9288 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5945" Parameter: CONF_N -> "8002" Comparing "5945" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5946" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750921 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752617 ATOM PAIRS WERE FOUND FOR ATOM LIST 41332 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29194 from a total of 752617 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5946 -72.54007 14.16447 0.55360 INTE EXTERN> -30.43353 -42.10654 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5401" Parameter: A <- "-72.5401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4335" Parameter: B <- "-30.4335" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1065" Parameter: C <- "-42.1065" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5946 TOTAL ENERGY = -72.5401 RDTITL> * VAN DER WAALS = -30.4335 ELECTROSTATIC = -42.1065 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5946" Parameter: CONF_N -> "8002" Comparing "5946" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5947" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752617 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751285 ATOM PAIRS WERE FOUND FOR ATOM LIST 41385 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29616 from a total of 751285 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5947 -66.91319 -5.62688 0.47085 INTE EXTERN> -35.23303 -31.68016 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9132" Parameter: A <- "-66.9132" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.233" Parameter: B <- "-35.233" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.6802" Parameter: C <- "-31.6802" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5947 TOTAL ENERGY = -66.9132 RDTITL> * VAN DER WAALS = -35.233 ELECTROSTATIC = -31.6802 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5947" Parameter: CONF_N -> "8002" Comparing "5947" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5948" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751285 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756717 ATOM PAIRS WERE FOUND FOR ATOM LIST 41602 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29557 from a total of 756717 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5948 -71.23910 4.32592 0.57111 INTE EXTERN> -31.91517 -39.32393 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2391" Parameter: A <- "-71.2391" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9152" Parameter: B <- "-31.9152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3239" Parameter: C <- "-39.3239" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5948 TOTAL ENERGY = -71.2391 RDTITL> * VAN DER WAALS = -31.9152 ELECTROSTATIC = -39.3239 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5948" Parameter: CONF_N -> "8002" Comparing "5948" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5949" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756717 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754348 ATOM PAIRS WERE FOUND FOR ATOM LIST 41289 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29486 from a total of 754348 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5949 -74.68157 3.44247 0.54667 INTE EXTERN> -34.96999 -39.71158 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6816" Parameter: A <- "-74.6816" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.97" Parameter: B <- "-34.97" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7116" Parameter: C <- "-39.7116" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5949 TOTAL ENERGY = -74.6816 RDTITL> * VAN DER WAALS = -34.97 ELECTROSTATIC = -39.7116 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5949" Parameter: CONF_N -> "8002" Comparing "5949" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5950" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754348 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749044 ATOM PAIRS WERE FOUND FOR ATOM LIST 41213 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29382 from a total of 749044 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5950 -71.55747 -3.12410 0.56791 INTE EXTERN> -31.08501 -40.47246 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5575" Parameter: A <- "-71.5575" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.085" Parameter: B <- "-31.085" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4725" Parameter: C <- "-40.4725" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5950 TOTAL ENERGY = -71.5575 RDTITL> * VAN DER WAALS = -31.085 ELECTROSTATIC = -40.4725 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5950" Parameter: CONF_N -> "8002" Comparing "5950" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5951" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749044 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753823 ATOM PAIRS WERE FOUND FOR ATOM LIST 41591 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29939 from a total of 753823 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5951 -72.59274 1.03527 0.51923 INTE EXTERN> -36.04769 -36.54504 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5927" Parameter: A <- "-72.5927" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.0477" Parameter: B <- "-36.0477" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.545" Parameter: C <- "-36.545" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5951 TOTAL ENERGY = -72.5927 RDTITL> * VAN DER WAALS = -36.0477 ELECTROSTATIC = -36.545 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5951" Parameter: CONF_N -> "8002" Comparing "5951" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5952" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753823 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763021 ATOM PAIRS WERE FOUND FOR ATOM LIST 41935 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30026 from a total of 763021 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5952 -69.87413 -2.71860 0.64770 INTE EXTERN> -28.79208 -41.08205 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8741" Parameter: A <- "-69.8741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7921" Parameter: B <- "-28.7921" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0821" Parameter: C <- "-41.0821" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5952 TOTAL ENERGY = -69.8741 RDTITL> * VAN DER WAALS = -28.7921 ELECTROSTATIC = -41.0821 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5952" Parameter: CONF_N -> "8002" Comparing "5952" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5953" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763021 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754970 ATOM PAIRS WERE FOUND FOR ATOM LIST 41551 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29743 from a total of 754970 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5953 -68.71665 -1.15748 0.56498 INTE EXTERN> -29.93017 -38.78649 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7167" Parameter: A <- "-68.7167" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9302" Parameter: B <- "-29.9302" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.7865" Parameter: C <- "-38.7865" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5953 TOTAL ENERGY = -68.7167 RDTITL> * VAN DER WAALS = -29.9302 ELECTROSTATIC = -38.7865 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5953" Parameter: CONF_N -> "8002" Comparing "5953" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5954" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754970 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763416 ATOM PAIRS WERE FOUND FOR ATOM LIST 41665 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30164 from a total of 763416 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5954 -70.79231 2.07566 0.77329 INTE EXTERN> -28.08111 -42.71121 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7923" Parameter: A <- "-70.7923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0811" Parameter: B <- "-28.0811" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7112" Parameter: C <- "-42.7112" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5954 TOTAL ENERGY = -70.7923 RDTITL> * VAN DER WAALS = -28.0811 ELECTROSTATIC = -42.7112 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5954" Parameter: CONF_N -> "8002" Comparing "5954" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5955" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763416 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761745 ATOM PAIRS WERE FOUND FOR ATOM LIST 41631 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 761745 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5955 -66.42958 -4.36273 0.59070 INTE EXTERN> -29.68607 -36.74352 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4296" Parameter: A <- "-66.4296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6861" Parameter: B <- "-29.6861" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7435" Parameter: C <- "-36.7435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5955 TOTAL ENERGY = -66.4296 RDTITL> * VAN DER WAALS = -29.6861 ELECTROSTATIC = -36.7435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5955" Parameter: CONF_N -> "8002" Comparing "5955" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5956" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761745 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757692 ATOM PAIRS WERE FOUND FOR ATOM LIST 41369 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29044 from a total of 757692 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5956 -68.48834 2.05876 0.52201 INTE EXTERN> -32.41163 -36.07671 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4883" Parameter: A <- "-68.4883" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4116" Parameter: B <- "-32.4116" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0767" Parameter: C <- "-36.0767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5956 TOTAL ENERGY = -68.4883 RDTITL> * VAN DER WAALS = -32.4116 ELECTROSTATIC = -36.0767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5956" Parameter: CONF_N -> "8002" Comparing "5956" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5957" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757692 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756675 ATOM PAIRS WERE FOUND FOR ATOM LIST 41583 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30190 from a total of 756675 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5957 -69.07368 0.58534 0.49164 INTE EXTERN> -34.12333 -34.95035 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0737" Parameter: A <- "-69.0737" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1233" Parameter: B <- "-34.1233" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9504" Parameter: C <- "-34.9504" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5957 TOTAL ENERGY = -69.0737 RDTITL> * VAN DER WAALS = -34.1233 ELECTROSTATIC = -34.9504 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5957" Parameter: CONF_N -> "8002" Comparing "5957" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5958" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756675 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758305 ATOM PAIRS WERE FOUND FOR ATOM LIST 41406 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29646 from a total of 758305 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5958 -68.25581 -0.81787 0.64042 INTE EXTERN> -30.74960 -37.50621 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2558" Parameter: A <- "-68.2558" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7496" Parameter: B <- "-30.7496" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5062" Parameter: C <- "-37.5062" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5958 TOTAL ENERGY = -68.2558 RDTITL> * VAN DER WAALS = -30.7496 ELECTROSTATIC = -37.5062 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5958" Parameter: CONF_N -> "8002" Comparing "5958" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5959" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758305 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755776 ATOM PAIRS WERE FOUND FOR ATOM LIST 41207 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29484 from a total of 755776 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5959 -66.69209 -1.56371 0.60143 INTE EXTERN> -27.08127 -39.61082 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6921" Parameter: A <- "-66.6921" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0813" Parameter: B <- "-27.0813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6108" Parameter: C <- "-39.6108" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5959 TOTAL ENERGY = -66.6921 RDTITL> * VAN DER WAALS = -27.0813 ELECTROSTATIC = -39.6108 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5959" Parameter: CONF_N -> "8002" Comparing "5959" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5960" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755776 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757803 ATOM PAIRS WERE FOUND FOR ATOM LIST 41490 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29494 from a total of 757803 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5960 -71.77659 5.08450 0.58247 INTE EXTERN> -30.13195 -41.64465 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7766" Parameter: A <- "-71.7766" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1319" Parameter: B <- "-30.1319" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6446" Parameter: C <- "-41.6446" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5960 TOTAL ENERGY = -71.7766 RDTITL> * VAN DER WAALS = -30.1319 ELECTROSTATIC = -41.6446 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5960" Parameter: CONF_N -> "8002" Comparing "5960" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5961" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757803 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761214 ATOM PAIRS WERE FOUND FOR ATOM LIST 41724 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 761214 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5961 -71.03628 -0.74031 0.56830 INTE EXTERN> -31.48855 -39.54773 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0363" Parameter: A <- "-71.0363" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4885" Parameter: B <- "-31.4885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5477" Parameter: C <- "-39.5477" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5961 TOTAL ENERGY = -71.0363 RDTITL> * VAN DER WAALS = -31.4885 ELECTROSTATIC = -39.5477 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5961" Parameter: CONF_N -> "8002" Comparing "5961" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5962" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761214 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758845 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30132 from a total of 758845 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5962 -70.06844 -0.96785 0.65007 INTE EXTERN> -29.84162 -40.22682 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0684" Parameter: A <- "-70.0684" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8416" Parameter: B <- "-29.8416" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2268" Parameter: C <- "-40.2268" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5962 TOTAL ENERGY = -70.0684 RDTITL> * VAN DER WAALS = -29.8416 ELECTROSTATIC = -40.2268 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5962" Parameter: CONF_N -> "8002" Comparing "5962" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5963" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758845 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755920 ATOM PAIRS WERE FOUND FOR ATOM LIST 41327 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29643 from a total of 755920 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5963 -73.30529 3.23685 0.50618 INTE EXTERN> -32.90322 -40.40206 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3053" Parameter: A <- "-73.3053" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9032" Parameter: B <- "-32.9032" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4021" Parameter: C <- "-40.4021" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5963 TOTAL ENERGY = -73.3053 RDTITL> * VAN DER WAALS = -32.9032 ELECTROSTATIC = -40.4021 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5963" Parameter: CONF_N -> "8002" Comparing "5963" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5964" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755920 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757464 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29594 from a total of 757464 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5964 -71.59513 -1.71016 0.69792 INTE EXTERN> -28.04432 -43.55081 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5951" Parameter: A <- "-71.5951" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0443" Parameter: B <- "-28.0443" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5508" Parameter: C <- "-43.5508" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5964 TOTAL ENERGY = -71.5951 RDTITL> * VAN DER WAALS = -28.0443 ELECTROSTATIC = -43.5508 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5964" Parameter: CONF_N -> "8002" Comparing "5964" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5965" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757464 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759372 ATOM PAIRS WERE FOUND FOR ATOM LIST 41711 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29915 from a total of 759372 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5965 -71.84465 0.24952 0.56839 INTE EXTERN> -34.92962 -36.91503 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8446" Parameter: A <- "-71.8446" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9296" Parameter: B <- "-34.9296" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.915" Parameter: C <- "-36.915" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5965 TOTAL ENERGY = -71.8446 RDTITL> * VAN DER WAALS = -34.9296 ELECTROSTATIC = -36.915 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5965" Parameter: CONF_N -> "8002" Comparing "5965" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5966" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759372 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758283 ATOM PAIRS WERE FOUND FOR ATOM LIST 41589 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29896 from a total of 758283 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5966 -74.91788 3.07323 0.51062 INTE EXTERN> -33.43399 -41.48389 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9179" Parameter: A <- "-74.9179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.434" Parameter: B <- "-33.434" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4839" Parameter: C <- "-41.4839" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5966 TOTAL ENERGY = -74.9179 RDTITL> * VAN DER WAALS = -33.434 ELECTROSTATIC = -41.4839 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5966" Parameter: CONF_N -> "8002" Comparing "5966" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5967" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758283 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756721 ATOM PAIRS WERE FOUND FOR ATOM LIST 41471 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29364 from a total of 756721 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5967 -74.09664 -0.82124 0.55795 INTE EXTERN> -32.84434 -41.25230 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0966" Parameter: A <- "-74.0966" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8443" Parameter: B <- "-32.8443" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2523" Parameter: C <- "-41.2523" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5967 TOTAL ENERGY = -74.0966 RDTITL> * VAN DER WAALS = -32.8443 ELECTROSTATIC = -41.2523 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5967" Parameter: CONF_N -> "8002" Comparing "5967" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5968" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756721 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760217 ATOM PAIRS WERE FOUND FOR ATOM LIST 41775 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30017 from a total of 760217 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5968 -74.06663 -0.03001 0.57774 INTE EXTERN> -31.84057 -42.22607 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0666" Parameter: A <- "-74.0666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8406" Parameter: B <- "-31.8406" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2261" Parameter: C <- "-42.2261" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5968 TOTAL ENERGY = -74.0666 RDTITL> * VAN DER WAALS = -31.8406 ELECTROSTATIC = -42.2261 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5968" Parameter: CONF_N -> "8002" Comparing "5968" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5969" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760217 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759664 ATOM PAIRS WERE FOUND FOR ATOM LIST 41551 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29900 from a total of 759664 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5969 -69.77169 -4.29494 0.52706 INTE EXTERN> -32.16456 -37.60713 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7717" Parameter: A <- "-69.7717" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1646" Parameter: B <- "-32.1646" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6071" Parameter: C <- "-37.6071" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5969 TOTAL ENERGY = -69.7717 RDTITL> * VAN DER WAALS = -32.1646 ELECTROSTATIC = -37.6071 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5969" Parameter: CONF_N -> "8002" Comparing "5969" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5970" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759664 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756839 ATOM PAIRS WERE FOUND FOR ATOM LIST 41287 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29665 from a total of 756839 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5970 -73.84365 4.07196 0.55365 INTE EXTERN> -30.33608 -43.50757 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8436" Parameter: A <- "-73.8436" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3361" Parameter: B <- "-30.3361" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5076" Parameter: C <- "-43.5076" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5970 TOTAL ENERGY = -73.8436 RDTITL> * VAN DER WAALS = -30.3361 ELECTROSTATIC = -43.5076 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5970" Parameter: CONF_N -> "8002" Comparing "5970" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5971" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756839 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756893 ATOM PAIRS WERE FOUND FOR ATOM LIST 41421 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30182 from a total of 756893 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5971 -75.06941 1.22576 0.58028 INTE EXTERN> -34.05407 -41.01534 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0694" Parameter: A <- "-75.0694" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0541" Parameter: B <- "-34.0541" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0153" Parameter: C <- "-41.0153" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5971 TOTAL ENERGY = -75.0694 RDTITL> * VAN DER WAALS = -34.0541 ELECTROSTATIC = -41.0153 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5971" Parameter: CONF_N -> "8002" Comparing "5971" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5972" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756893 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762178 ATOM PAIRS WERE FOUND FOR ATOM LIST 41722 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29863 from a total of 762178 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5972 -69.85723 -5.21218 0.56311 INTE EXTERN> -33.94174 -35.91549 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8572" Parameter: A <- "-69.8572" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9417" Parameter: B <- "-33.9417" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9155" Parameter: C <- "-35.9155" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5972 TOTAL ENERGY = -69.8572 RDTITL> * VAN DER WAALS = -33.9417 ELECTROSTATIC = -35.9155 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5972" Parameter: CONF_N -> "8002" Comparing "5972" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5973" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762178 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760011 ATOM PAIRS WERE FOUND FOR ATOM LIST 41666 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30046 from a total of 760011 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5973 -74.38240 4.52517 0.58275 INTE EXTERN> -31.86331 -42.51909 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3824" Parameter: A <- "-74.3824" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8633" Parameter: B <- "-31.8633" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5191" Parameter: C <- "-42.5191" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5973 TOTAL ENERGY = -74.3824 RDTITL> * VAN DER WAALS = -31.8633 ELECTROSTATIC = -42.5191 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5973" Parameter: CONF_N -> "8002" Comparing "5973" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5974" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760011 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763624 ATOM PAIRS WERE FOUND FOR ATOM LIST 41893 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30396 from a total of 763624 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5974 -77.02301 2.64061 0.56933 INTE EXTERN> -33.70045 -43.32256 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.023" Parameter: A <- "-77.023" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7004" Parameter: B <- "-33.7004" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3226" Parameter: C <- "-43.3226" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5974 TOTAL ENERGY = -77.023 RDTITL> * VAN DER WAALS = -33.7004 ELECTROSTATIC = -43.3226 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5974" Parameter: CONF_N -> "8002" Comparing "5974" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5975" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763624 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764531 ATOM PAIRS WERE FOUND FOR ATOM LIST 41986 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30167 from a total of 764531 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5975 -64.00246 -13.02056 0.47585 INTE EXTERN> -35.63429 -28.36817 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0025" Parameter: A <- "-64.0025" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.6343" Parameter: B <- "-35.6343" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-28.3682" Parameter: C <- "-28.3682" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5975 TOTAL ENERGY = -64.0025 RDTITL> * VAN DER WAALS = -35.6343 ELECTROSTATIC = -28.3682 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5975" Parameter: CONF_N -> "8002" Comparing "5975" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5976" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764531 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758612 ATOM PAIRS WERE FOUND FOR ATOM LIST 41557 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30393 from a total of 758612 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5976 -72.60795 8.60549 0.50821 INTE EXTERN> -34.37423 -38.23372 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6079" Parameter: A <- "-72.6079" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3742" Parameter: B <- "-34.3742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2337" Parameter: C <- "-38.2337" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5976 TOTAL ENERGY = -72.6079 RDTITL> * VAN DER WAALS = -34.3742 ELECTROSTATIC = -38.2337 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5976" Parameter: CONF_N -> "8002" Comparing "5976" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5977" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758612 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756934 ATOM PAIRS WERE FOUND FOR ATOM LIST 41500 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29959 from a total of 756934 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5977 -64.64695 -7.96100 0.69250 INTE EXTERN> -28.96718 -35.67976 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6469" Parameter: A <- "-64.6469" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9672" Parameter: B <- "-28.9672" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6798" Parameter: C <- "-35.6798" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5977 TOTAL ENERGY = -64.6469 RDTITL> * VAN DER WAALS = -28.9672 ELECTROSTATIC = -35.6798 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5977" Parameter: CONF_N -> "8002" Comparing "5977" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5978" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756934 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757691 ATOM PAIRS WERE FOUND FOR ATOM LIST 41607 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30494 from a total of 757691 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5978 -71.01024 6.36329 0.56763 INTE EXTERN> -31.37980 -39.63044 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0102" Parameter: A <- "-71.0102" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3798" Parameter: B <- "-31.3798" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6304" Parameter: C <- "-39.6304" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5978 TOTAL ENERGY = -71.0102 RDTITL> * VAN DER WAALS = -31.3798 ELECTROSTATIC = -39.6304 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5978" Parameter: CONF_N -> "8002" Comparing "5978" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5979" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757691 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41475 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30016 from a total of 754118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5979 -68.38183 -2.62841 0.58085 INTE EXTERN> -33.70224 -34.67959 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3818" Parameter: A <- "-68.3818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7022" Parameter: B <- "-33.7022" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.6796" Parameter: C <- "-34.6796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5979 TOTAL ENERGY = -68.3818 RDTITL> * VAN DER WAALS = -33.7022 ELECTROSTATIC = -34.6796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5979" Parameter: CONF_N -> "8002" Comparing "5979" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5980" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752446 ATOM PAIRS WERE FOUND FOR ATOM LIST 41331 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29637 from a total of 752446 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5980 -65.92506 -2.45677 0.56306 INTE EXTERN> -31.52018 -34.40488 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9251" Parameter: A <- "-65.9251" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5202" Parameter: B <- "-31.5202" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4049" Parameter: C <- "-34.4049" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5980 TOTAL ENERGY = -65.9251 RDTITL> * VAN DER WAALS = -31.5202 ELECTROSTATIC = -34.4049 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5980" Parameter: CONF_N -> "8002" Comparing "5980" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5981" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752446 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755596 ATOM PAIRS WERE FOUND FOR ATOM LIST 41503 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29621 from a total of 755596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5981 -67.53116 1.60610 0.55298 INTE EXTERN> -32.60511 -34.92605 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5312" Parameter: A <- "-67.5312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6051" Parameter: B <- "-32.6051" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9261" Parameter: C <- "-34.9261" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5981 TOTAL ENERGY = -67.5312 RDTITL> * VAN DER WAALS = -32.6051 ELECTROSTATIC = -34.9261 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5981" Parameter: CONF_N -> "8002" Comparing "5981" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5982" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754671 ATOM PAIRS WERE FOUND FOR ATOM LIST 41413 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29817 from a total of 754671 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5982 -71.87500 4.34384 0.55809 INTE EXTERN> -35.39869 -36.47631 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.875" Parameter: A <- "-71.875" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.3987" Parameter: B <- "-35.3987" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4763" Parameter: C <- "-36.4763" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5982 TOTAL ENERGY = -71.875 RDTITL> * VAN DER WAALS = -35.3987 ELECTROSTATIC = -36.4763 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5982" Parameter: CONF_N -> "8002" Comparing "5982" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5983" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754671 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754572 ATOM PAIRS WERE FOUND FOR ATOM LIST 41390 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30450 from a total of 754572 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5983 -70.01710 -1.85790 0.65109 INTE EXTERN> -31.61031 -38.40679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0171" Parameter: A <- "-70.0171" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6103" Parameter: B <- "-31.6103" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4068" Parameter: C <- "-38.4068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5983 TOTAL ENERGY = -70.0171 RDTITL> * VAN DER WAALS = -31.6103 ELECTROSTATIC = -38.4068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5983" Parameter: CONF_N -> "8002" Comparing "5983" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5984" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754572 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757620 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29708 from a total of 757620 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5984 -67.77574 -2.24135 0.58630 INTE EXTERN> -31.97123 -35.80452 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7757" Parameter: A <- "-67.7757" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9712" Parameter: B <- "-31.9712" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8045" Parameter: C <- "-35.8045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5984 TOTAL ENERGY = -67.7757 RDTITL> * VAN DER WAALS = -31.9712 ELECTROSTATIC = -35.8045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5984" Parameter: CONF_N -> "8002" Comparing "5984" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5985" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757620 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754175 ATOM PAIRS WERE FOUND FOR ATOM LIST 41252 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29321 from a total of 754175 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5985 -65.93732 -1.83842 0.52555 INTE EXTERN> -32.07446 -33.86286 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9373" Parameter: A <- "-65.9373" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0745" Parameter: B <- "-32.0745" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8629" Parameter: C <- "-33.8629" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5985 TOTAL ENERGY = -65.9373 RDTITL> * VAN DER WAALS = -32.0745 ELECTROSTATIC = -33.8629 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5985" Parameter: CONF_N -> "8002" Comparing "5985" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5986" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754175 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748036 ATOM PAIRS WERE FOUND FOR ATOM LIST 40982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29313 from a total of 748036 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5986 -68.57342 2.63609 0.54240 INTE EXTERN> -31.72966 -36.84376 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5734" Parameter: A <- "-68.5734" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7297" Parameter: B <- "-31.7297" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8438" Parameter: C <- "-36.8438" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5986 TOTAL ENERGY = -68.5734 RDTITL> * VAN DER WAALS = -31.7297 ELECTROSTATIC = -36.8438 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5986" Parameter: CONF_N -> "8002" Comparing "5986" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5987" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748036 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752916 ATOM PAIRS WERE FOUND FOR ATOM LIST 41304 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29982 from a total of 752916 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5987 -71.55101 2.97760 0.51848 INTE EXTERN> -34.43879 -37.11222 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.551" Parameter: A <- "-71.551" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.4388" Parameter: B <- "-34.4388" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1122" Parameter: C <- "-37.1122" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5987 TOTAL ENERGY = -71.551 RDTITL> * VAN DER WAALS = -34.4388 ELECTROSTATIC = -37.1122 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5987" Parameter: CONF_N -> "8002" Comparing "5987" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5988" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752916 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756521 ATOM PAIRS WERE FOUND FOR ATOM LIST 41599 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29329 from a total of 756521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5988 -66.13326 -5.41775 0.53259 INTE EXTERN> -33.75093 -32.38233 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1333" Parameter: A <- "-66.1333" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7509" Parameter: B <- "-33.7509" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.3823" Parameter: C <- "-32.3823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5988 TOTAL ENERGY = -66.1333 RDTITL> * VAN DER WAALS = -33.7509 ELECTROSTATIC = -32.3823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5988" Parameter: CONF_N -> "8002" Comparing "5988" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5989" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758084 ATOM PAIRS WERE FOUND FOR ATOM LIST 41836 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30036 from a total of 758084 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5989 -68.74670 2.61344 0.61891 INTE EXTERN> -32.63190 -36.11480 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7467" Parameter: A <- "-68.7467" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6319" Parameter: B <- "-32.6319" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1148" Parameter: C <- "-36.1148" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5989 TOTAL ENERGY = -68.7467 RDTITL> * VAN DER WAALS = -32.6319 ELECTROSTATIC = -36.1148 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5989" Parameter: CONF_N -> "8002" Comparing "5989" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5990" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758084 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756384 ATOM PAIRS WERE FOUND FOR ATOM LIST 41474 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29946 from a total of 756384 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5990 -65.01486 -3.73184 0.46549 INTE EXTERN> -32.92442 -32.09044 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0149" Parameter: A <- "-65.0149" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9244" Parameter: B <- "-32.9244" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.0904" Parameter: C <- "-32.0904" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5990 TOTAL ENERGY = -65.0149 RDTITL> * VAN DER WAALS = -32.9244 ELECTROSTATIC = -32.0904 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5990" Parameter: CONF_N -> "8002" Comparing "5990" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5991" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756384 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753080 ATOM PAIRS WERE FOUND FOR ATOM LIST 41293 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29736 from a total of 753080 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5991 -73.72485 8.70999 0.53837 INTE EXTERN> -31.81855 -41.90630 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7249" Parameter: A <- "-73.7249" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8185" Parameter: B <- "-31.8185" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9063" Parameter: C <- "-41.9063" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5991 TOTAL ENERGY = -73.7249 RDTITL> * VAN DER WAALS = -31.8185 ELECTROSTATIC = -41.9063 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5991" Parameter: CONF_N -> "8002" Comparing "5991" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5992" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753080 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754907 ATOM PAIRS WERE FOUND FOR ATOM LIST 41345 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30322 from a total of 754907 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5992 -74.60247 0.87762 0.60376 INTE EXTERN> -30.02180 -44.58067 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6025" Parameter: A <- "-74.6025" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0218" Parameter: B <- "-30.0218" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5807" Parameter: C <- "-44.5807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5992 TOTAL ENERGY = -74.6025 RDTITL> * VAN DER WAALS = -30.0218 ELECTROSTATIC = -44.5807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5992" Parameter: CONF_N -> "8002" Comparing "5992" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5993" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754907 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747968 ATOM PAIRS WERE FOUND FOR ATOM LIST 41078 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29917 from a total of 747968 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5993 -72.81404 -1.78843 0.58634 INTE EXTERN> -29.15650 -43.65754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.814" Parameter: A <- "-72.814" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1565" Parameter: B <- "-29.1565" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6575" Parameter: C <- "-43.6575" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5993 TOTAL ENERGY = -72.814 RDTITL> * VAN DER WAALS = -29.1565 ELECTROSTATIC = -43.6575 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5993" Parameter: CONF_N -> "8002" Comparing "5993" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5994" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747968 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746754 ATOM PAIRS WERE FOUND FOR ATOM LIST 41085 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29777 from a total of 746754 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5994 -70.63102 -2.18301 0.51529 INTE EXTERN> -31.35712 -39.27390 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.631" Parameter: A <- "-70.631" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3571" Parameter: B <- "-31.3571" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2739" Parameter: C <- "-39.2739" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5994 TOTAL ENERGY = -70.631 RDTITL> * VAN DER WAALS = -31.3571 ELECTROSTATIC = -39.2739 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5994" Parameter: CONF_N -> "8002" Comparing "5994" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5995" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746754 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755279 ATOM PAIRS WERE FOUND FOR ATOM LIST 41354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29677 from a total of 755279 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5995 -68.80111 -1.82991 0.52046 INTE EXTERN> -31.79955 -37.00156 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8011" Parameter: A <- "-68.8011" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7995" Parameter: B <- "-31.7995" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0016" Parameter: C <- "-37.0016" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5995 TOTAL ENERGY = -68.8011 RDTITL> * VAN DER WAALS = -31.7995 ELECTROSTATIC = -37.0016 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5995" Parameter: CONF_N -> "8002" Comparing "5995" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5996" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755279 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745822 ATOM PAIRS WERE FOUND FOR ATOM LIST 41138 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30021 from a total of 745822 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5996 -67.67590 -1.12522 0.49362 INTE EXTERN> -28.84593 -38.82997 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6759" Parameter: A <- "-67.6759" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8459" Parameter: B <- "-28.8459" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.83" Parameter: C <- "-38.83" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5996 TOTAL ENERGY = -67.6759 RDTITL> * VAN DER WAALS = -28.8459 ELECTROSTATIC = -38.83 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5996" Parameter: CONF_N -> "8002" Comparing "5996" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5997" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745822 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41036 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29848 from a total of 747526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5997 -64.18279 -3.49311 0.49604 INTE EXTERN> -29.34351 -34.83928 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1828" Parameter: A <- "-64.1828" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3435" Parameter: B <- "-29.3435" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8393" Parameter: C <- "-34.8393" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5997 TOTAL ENERGY = -64.1828 RDTITL> * VAN DER WAALS = -29.3435 ELECTROSTATIC = -34.8393 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5997" Parameter: CONF_N -> "8002" Comparing "5997" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5998" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756729 ATOM PAIRS WERE FOUND FOR ATOM LIST 41443 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30806 from a total of 756729 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5998 -66.89785 2.71506 0.48925 INTE EXTERN> -32.93907 -33.95879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8979" Parameter: A <- "-66.8979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9391" Parameter: B <- "-32.9391" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9588" Parameter: C <- "-33.9588" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5998 TOTAL ENERGY = -66.8979 RDTITL> * VAN DER WAALS = -32.9391 ELECTROSTATIC = -33.9588 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5998" Parameter: CONF_N -> "8002" Comparing "5998" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "5999" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756729 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752490 ATOM PAIRS WERE FOUND FOR ATOM LIST 41488 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29708 from a total of 752490 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 5999 -66.30447 -0.59338 0.51285 INTE EXTERN> -31.68561 -34.61886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3045" Parameter: A <- "-66.3045" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6856" Parameter: B <- "-31.6856" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.6189" Parameter: C <- "-34.6189" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 5999 TOTAL ENERGY = -66.3045 RDTITL> * VAN DER WAALS = -31.6856 ELECTROSTATIC = -34.6189 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "5999" Parameter: CONF_N -> "8002" Comparing "5999" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6000" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752490 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746111 ATOM PAIRS WERE FOUND FOR ATOM LIST 41109 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29188 from a total of 746111 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6000 -71.10432 4.79985 0.58958 INTE EXTERN> -29.80877 -41.29555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1043" Parameter: A <- "-71.1043" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8088" Parameter: B <- "-29.8088" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2956" Parameter: C <- "-41.2956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6000 TOTAL ENERGY = -71.1043 RDTITL> * VAN DER WAALS = -29.8088 ELECTROSTATIC = -41.2956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6000" Parameter: CONF_N -> "8002" Comparing "6000" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6001" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746111 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752775 ATOM PAIRS WERE FOUND FOR ATOM LIST 41526 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30249 from a total of 752775 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6001 -67.95714 -3.14719 0.56275 INTE EXTERN> -31.35896 -36.59817 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9571" Parameter: A <- "-67.9571" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.359" Parameter: B <- "-31.359" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5982" Parameter: C <- "-36.5982" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6001 TOTAL ENERGY = -67.9571 RDTITL> * VAN DER WAALS = -31.359 ELECTROSTATIC = -36.5982 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6001" Parameter: CONF_N -> "8002" Comparing "6001" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6002" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752775 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752522 ATOM PAIRS WERE FOUND FOR ATOM LIST 41282 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29622 from a total of 752522 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6002 -66.91041 -1.04673 0.58783 INTE EXTERN> -31.37524 -35.53517 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9104" Parameter: A <- "-66.9104" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3752" Parameter: B <- "-31.3752" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5352" Parameter: C <- "-35.5352" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6002 TOTAL ENERGY = -66.9104 RDTITL> * VAN DER WAALS = -31.3752 ELECTROSTATIC = -35.5352 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6002" Parameter: CONF_N -> "8002" Comparing "6002" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6003" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752522 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752836 ATOM PAIRS WERE FOUND FOR ATOM LIST 41352 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30145 from a total of 752836 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6003 -69.13708 2.22667 0.53765 INTE EXTERN> -32.11048 -37.02660 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1371" Parameter: A <- "-69.1371" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1105" Parameter: B <- "-32.1105" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0266" Parameter: C <- "-37.0266" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6003 TOTAL ENERGY = -69.1371 RDTITL> * VAN DER WAALS = -32.1105 ELECTROSTATIC = -37.0266 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6003" Parameter: CONF_N -> "8002" Comparing "6003" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6004" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752836 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757071 ATOM PAIRS WERE FOUND FOR ATOM LIST 41587 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30517 from a total of 757071 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6004 -74.25126 5.11419 0.57460 INTE EXTERN> -32.51268 -41.73859 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2513" Parameter: A <- "-74.2513" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5127" Parameter: B <- "-32.5127" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7386" Parameter: C <- "-41.7386" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6004 TOTAL ENERGY = -74.2513 RDTITL> * VAN DER WAALS = -32.5127 ELECTROSTATIC = -41.7386 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6004" Parameter: CONF_N -> "8002" Comparing "6004" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6005" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757071 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753420 ATOM PAIRS WERE FOUND FOR ATOM LIST 41333 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29614 from a total of 753420 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6005 -73.37207 -0.87920 0.50643 INTE EXTERN> -34.31471 -39.05736 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3721" Parameter: A <- "-73.3721" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.3147" Parameter: B <- "-34.3147" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0574" Parameter: C <- "-39.0574" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6005 TOTAL ENERGY = -73.3721 RDTITL> * VAN DER WAALS = -34.3147 ELECTROSTATIC = -39.0574 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6005" Parameter: CONF_N -> "8002" Comparing "6005" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6006" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753420 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756216 ATOM PAIRS WERE FOUND FOR ATOM LIST 41629 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29434 from a total of 756216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6006 -70.03054 -3.34153 0.47706 INTE EXTERN> -33.68681 -36.34373 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0305" Parameter: A <- "-70.0305" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6868" Parameter: B <- "-33.6868" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3437" Parameter: C <- "-36.3437" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6006 TOTAL ENERGY = -70.0305 RDTITL> * VAN DER WAALS = -33.6868 ELECTROSTATIC = -36.3437 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6006" Parameter: CONF_N -> "8002" Comparing "6006" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6007" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751029 ATOM PAIRS WERE FOUND FOR ATOM LIST 41316 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29946 from a total of 751029 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6007 -70.01965 -0.01089 0.47816 INTE EXTERN> -32.80292 -37.21673 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0196" Parameter: A <- "-70.0196" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8029" Parameter: B <- "-32.8029" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2167" Parameter: C <- "-37.2167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6007 TOTAL ENERGY = -70.0196 RDTITL> * VAN DER WAALS = -32.8029 ELECTROSTATIC = -37.2167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6007" Parameter: CONF_N -> "8002" Comparing "6007" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6008" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751029 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759441 ATOM PAIRS WERE FOUND FOR ATOM LIST 41779 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30236 from a total of 759441 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6008 -67.37412 -2.64552 0.55386 INTE EXTERN> -32.38598 -34.98814 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3741" Parameter: A <- "-67.3741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.386" Parameter: B <- "-32.386" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9881" Parameter: C <- "-34.9881" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6008 TOTAL ENERGY = -67.3741 RDTITL> * VAN DER WAALS = -32.386 ELECTROSTATIC = -34.9881 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6008" Parameter: CONF_N -> "8002" Comparing "6008" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6009" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759441 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746098 ATOM PAIRS WERE FOUND FOR ATOM LIST 41144 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29445 from a total of 746098 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6009 -70.39839 3.02427 0.54635 INTE EXTERN> -32.02082 -38.37758 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3984" Parameter: A <- "-70.3984" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0208" Parameter: B <- "-32.0208" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.3776" Parameter: C <- "-38.3776" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6009 TOTAL ENERGY = -70.3984 RDTITL> * VAN DER WAALS = -32.0208 ELECTROSTATIC = -38.3776 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6009" Parameter: CONF_N -> "8002" Comparing "6009" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6010" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746098 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749945 ATOM PAIRS WERE FOUND FOR ATOM LIST 41223 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29537 from a total of 749945 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6010 -69.89894 -0.49945 0.45352 INTE EXTERN> -34.41734 -35.48160 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8989" Parameter: A <- "-69.8989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.4173" Parameter: B <- "-34.4173" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4816" Parameter: C <- "-35.4816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6010 TOTAL ENERGY = -69.8989 RDTITL> * VAN DER WAALS = -34.4173 ELECTROSTATIC = -35.4816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6010" Parameter: CONF_N -> "8002" Comparing "6010" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6011" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749945 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750903 ATOM PAIRS WERE FOUND FOR ATOM LIST 41105 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29523 from a total of 750903 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6011 -74.80687 4.90793 0.62935 INTE EXTERN> -30.64876 -44.15811 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8069" Parameter: A <- "-74.8069" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6488" Parameter: B <- "-30.6488" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1581" Parameter: C <- "-44.1581" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6011 TOTAL ENERGY = -74.8069 RDTITL> * VAN DER WAALS = -30.6488 ELECTROSTATIC = -44.1581 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6011" Parameter: CONF_N -> "8002" Comparing "6011" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6012" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750903 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748757 ATOM PAIRS WERE FOUND FOR ATOM LIST 41087 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29830 from a total of 748757 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6012 -66.66355 -8.14333 0.49652 INTE EXTERN> -33.49924 -33.16431 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6635" Parameter: A <- "-66.6635" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4992" Parameter: B <- "-33.4992" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1643" Parameter: C <- "-33.1643" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6012 TOTAL ENERGY = -66.6635 RDTITL> * VAN DER WAALS = -33.4992 ELECTROSTATIC = -33.1643 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6012" Parameter: CONF_N -> "8002" Comparing "6012" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6013" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748757 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749993 ATOM PAIRS WERE FOUND FOR ATOM LIST 41301 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29325 from a total of 749993 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6013 -72.55476 5.89122 0.55180 INTE EXTERN> -32.14448 -40.41028 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5548" Parameter: A <- "-72.5548" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1445" Parameter: B <- "-32.1445" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4103" Parameter: C <- "-40.4103" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6013 TOTAL ENERGY = -72.5548 RDTITL> * VAN DER WAALS = -32.1445 ELECTROSTATIC = -40.4103 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6013" Parameter: CONF_N -> "8002" Comparing "6013" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6014" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749993 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746566 ATOM PAIRS WERE FOUND FOR ATOM LIST 41048 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28875 from a total of 746566 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6014 -72.57116 0.01639 0.54851 INTE EXTERN> -32.99918 -39.57197 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5712" Parameter: A <- "-72.5712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9992" Parameter: B <- "-32.9992" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.572" Parameter: C <- "-39.572" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6014 TOTAL ENERGY = -72.5712 RDTITL> * VAN DER WAALS = -32.9992 ELECTROSTATIC = -39.572 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6014" Parameter: CONF_N -> "8002" Comparing "6014" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6015" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746566 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749702 ATOM PAIRS WERE FOUND FOR ATOM LIST 41136 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28821 from a total of 749702 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6015 -71.99580 -0.57536 0.49973 INTE EXTERN> -32.28057 -39.71523 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9958" Parameter: A <- "-71.9958" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2806" Parameter: B <- "-32.2806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7152" Parameter: C <- "-39.7152" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6015 TOTAL ENERGY = -71.9958 RDTITL> * VAN DER WAALS = -32.2806 ELECTROSTATIC = -39.7152 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6015" Parameter: CONF_N -> "8002" Comparing "6015" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6016" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749702 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753998 ATOM PAIRS WERE FOUND FOR ATOM LIST 41500 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29867 from a total of 753998 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6016 -71.09114 -0.90465 0.60639 INTE EXTERN> -29.90623 -41.18492 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0911" Parameter: A <- "-71.0911" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9062" Parameter: B <- "-29.9062" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1849" Parameter: C <- "-41.1849" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6016 TOTAL ENERGY = -71.0911 RDTITL> * VAN DER WAALS = -29.9062 ELECTROSTATIC = -41.1849 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6016" Parameter: CONF_N -> "8002" Comparing "6016" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6017" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753998 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756127 ATOM PAIRS WERE FOUND FOR ATOM LIST 41795 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29713 from a total of 756127 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6017 -70.05556 -1.03559 0.62570 INTE EXTERN> -27.84326 -42.21229 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0556" Parameter: A <- "-70.0556" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8433" Parameter: B <- "-27.8433" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2123" Parameter: C <- "-42.2123" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6017 TOTAL ENERGY = -70.0556 RDTITL> * VAN DER WAALS = -27.8433 ELECTROSTATIC = -42.2123 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6017" Parameter: CONF_N -> "8002" Comparing "6017" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6018" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756127 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754635 ATOM PAIRS WERE FOUND FOR ATOM LIST 41642 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29337 from a total of 754635 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6018 -66.76468 -3.29088 0.53960 INTE EXTERN> -31.39231 -35.37237 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7647" Parameter: A <- "-66.7647" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3923" Parameter: B <- "-31.3923" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3724" Parameter: C <- "-35.3724" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6018 TOTAL ENERGY = -66.7647 RDTITL> * VAN DER WAALS = -31.3923 ELECTROSTATIC = -35.3724 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6018" Parameter: CONF_N -> "8002" Comparing "6018" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6019" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754635 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751760 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30044 from a total of 751760 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6019 -67.17544 0.41076 0.51633 INTE EXTERN> -31.69743 -35.47802 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1754" Parameter: A <- "-67.1754" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6974" Parameter: B <- "-31.6974" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.478" Parameter: C <- "-35.478" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6019 TOTAL ENERGY = -67.1754 RDTITL> * VAN DER WAALS = -31.6974 ELECTROSTATIC = -35.478 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6019" Parameter: CONF_N -> "8002" Comparing "6019" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6020" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751760 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752197 ATOM PAIRS WERE FOUND FOR ATOM LIST 41105 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29489 from a total of 752197 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6020 -74.48723 7.31179 0.46703 INTE EXTERN> -32.98844 -41.49879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4872" Parameter: A <- "-74.4872" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9884" Parameter: B <- "-32.9884" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4988" Parameter: C <- "-41.4988" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6020 TOTAL ENERGY = -74.4872 RDTITL> * VAN DER WAALS = -32.9884 ELECTROSTATIC = -41.4988 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6020" Parameter: CONF_N -> "8002" Comparing "6020" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6021" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752197 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751504 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29812 from a total of 751504 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6021 -72.32284 -2.16439 0.57425 INTE EXTERN> -30.05411 -42.26873 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3228" Parameter: A <- "-72.3228" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0541" Parameter: B <- "-30.0541" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2687" Parameter: C <- "-42.2687" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6021 TOTAL ENERGY = -72.3228 RDTITL> * VAN DER WAALS = -30.0541 ELECTROSTATIC = -42.2687 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6021" Parameter: CONF_N -> "8002" Comparing "6021" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6022" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751504 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748393 ATOM PAIRS WERE FOUND FOR ATOM LIST 41058 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29201 from a total of 748393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6022 -67.40068 -4.92216 0.42190 INTE EXTERN> -32.46590 -34.93478 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4007" Parameter: A <- "-67.4007" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4659" Parameter: B <- "-32.4659" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9348" Parameter: C <- "-34.9348" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6022 TOTAL ENERGY = -67.4007 RDTITL> * VAN DER WAALS = -32.4659 ELECTROSTATIC = -34.9348 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6022" Parameter: CONF_N -> "8002" Comparing "6022" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6023" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748766 ATOM PAIRS WERE FOUND FOR ATOM LIST 41025 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29250 from a total of 748766 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6023 -73.33490 5.93422 0.49166 INTE EXTERN> -33.00978 -40.32511 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3349" Parameter: A <- "-73.3349" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0098" Parameter: B <- "-33.0098" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3251" Parameter: C <- "-40.3251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6023 TOTAL ENERGY = -73.3349 RDTITL> * VAN DER WAALS = -33.0098 ELECTROSTATIC = -40.3251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6023" Parameter: CONF_N -> "8002" Comparing "6023" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6024" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748766 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745653 ATOM PAIRS WERE FOUND FOR ATOM LIST 41386 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29483 from a total of 745653 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6024 -67.71215 -5.62274 0.56346 INTE EXTERN> -29.66515 -38.04700 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7122" Parameter: A <- "-67.7122" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6652" Parameter: B <- "-29.6652" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.047" Parameter: C <- "-38.047" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6024 TOTAL ENERGY = -67.7122 RDTITL> * VAN DER WAALS = -29.6652 ELECTROSTATIC = -38.047 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6024" Parameter: CONF_N -> "8002" Comparing "6024" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6025" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745653 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748349 ATOM PAIRS WERE FOUND FOR ATOM LIST 41078 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29862 from a total of 748349 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6025 -69.05384 1.34169 0.53635 INTE EXTERN> -31.33841 -37.71543 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0538" Parameter: A <- "-69.0538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3384" Parameter: B <- "-31.3384" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7154" Parameter: C <- "-37.7154" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6025 TOTAL ENERGY = -69.0538 RDTITL> * VAN DER WAALS = -31.3384 ELECTROSTATIC = -37.7154 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6025" Parameter: CONF_N -> "8002" Comparing "6025" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6026" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748349 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753838 ATOM PAIRS WERE FOUND FOR ATOM LIST 41395 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29734 from a total of 753838 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6026 -71.87664 2.82280 0.52709 INTE EXTERN> -32.59262 -39.28402 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8766" Parameter: A <- "-71.8766" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5926" Parameter: B <- "-32.5926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.284" Parameter: C <- "-39.284" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6026 TOTAL ENERGY = -71.8766 RDTITL> * VAN DER WAALS = -32.5926 ELECTROSTATIC = -39.284 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6026" Parameter: CONF_N -> "8002" Comparing "6026" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6027" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753838 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754472 ATOM PAIRS WERE FOUND FOR ATOM LIST 41342 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30173 from a total of 754472 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6027 -68.88596 -2.99068 0.47247 INTE EXTERN> -33.07104 -35.81492 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.886" Parameter: A <- "-68.886" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.071" Parameter: B <- "-33.071" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.8149" Parameter: C <- "-35.8149" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6027 TOTAL ENERGY = -68.886 RDTITL> * VAN DER WAALS = -33.071 ELECTROSTATIC = -35.8149 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6027" Parameter: CONF_N -> "8002" Comparing "6027" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6028" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754472 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746634 ATOM PAIRS WERE FOUND FOR ATOM LIST 40905 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29494 from a total of 746634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6028 -71.90739 3.02143 0.45788 INTE EXTERN> -33.94711 -37.96028 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9074" Parameter: A <- "-71.9074" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9471" Parameter: B <- "-33.9471" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9603" Parameter: C <- "-37.9603" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6028 TOTAL ENERGY = -71.9074 RDTITL> * VAN DER WAALS = -33.9471 ELECTROSTATIC = -37.9603 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6028" Parameter: CONF_N -> "8002" Comparing "6028" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6029" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751651 ATOM PAIRS WERE FOUND FOR ATOM LIST 41442 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29261 from a total of 751651 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6029 -67.82545 -4.08194 0.52799 INTE EXTERN> -30.47257 -37.35288 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8254" Parameter: A <- "-67.8254" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4726" Parameter: B <- "-30.4726" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3529" Parameter: C <- "-37.3529" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6029 TOTAL ENERGY = -67.8254 RDTITL> * VAN DER WAALS = -30.4726 ELECTROSTATIC = -37.3529 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6029" Parameter: CONF_N -> "8002" Comparing "6029" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6030" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751651 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750614 ATOM PAIRS WERE FOUND FOR ATOM LIST 41353 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30054 from a total of 750614 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6030 -72.02400 4.19855 0.51075 INTE EXTERN> -30.16458 -41.85942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.024" Parameter: A <- "-72.024" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1646" Parameter: B <- "-30.1646" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8594" Parameter: C <- "-41.8594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6030 TOTAL ENERGY = -72.024 RDTITL> * VAN DER WAALS = -30.1646 ELECTROSTATIC = -41.8594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6030" Parameter: CONF_N -> "8002" Comparing "6030" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6031" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750614 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749830 ATOM PAIRS WERE FOUND FOR ATOM LIST 41295 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29474 from a total of 749830 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6031 -69.31292 -2.71108 0.47659 INTE EXTERN> -33.04844 -36.26447 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3129" Parameter: A <- "-69.3129" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0484" Parameter: B <- "-33.0484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2645" Parameter: C <- "-36.2645" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6031 TOTAL ENERGY = -69.3129 RDTITL> * VAN DER WAALS = -33.0484 ELECTROSTATIC = -36.2645 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6031" Parameter: CONF_N -> "8002" Comparing "6031" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6032" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749830 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748529 ATOM PAIRS WERE FOUND FOR ATOM LIST 41173 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29895 from a total of 748529 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6032 -70.25219 0.93928 0.52338 INTE EXTERN> -33.99716 -36.25503 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2522" Parameter: A <- "-70.2522" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9972" Parameter: B <- "-33.9972" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.255" Parameter: C <- "-36.255" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6032 TOTAL ENERGY = -70.2522 RDTITL> * VAN DER WAALS = -33.9972 ELECTROSTATIC = -36.255 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6032" Parameter: CONF_N -> "8002" Comparing "6032" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6033" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748529 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751711 ATOM PAIRS WERE FOUND FOR ATOM LIST 41225 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30425 from a total of 751711 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6033 -68.64537 -1.60682 0.52696 INTE EXTERN> -31.08696 -37.55841 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6454" Parameter: A <- "-68.6454" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.087" Parameter: B <- "-31.087" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5584" Parameter: C <- "-37.5584" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6033 TOTAL ENERGY = -68.6454 RDTITL> * VAN DER WAALS = -31.087 ELECTROSTATIC = -37.5584 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6033" Parameter: CONF_N -> "8002" Comparing "6033" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6034" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751711 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747090 ATOM PAIRS WERE FOUND FOR ATOM LIST 41215 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29241 from a total of 747090 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6034 -70.70070 2.05533 0.53402 INTE EXTERN> -29.30050 -41.40020 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7007" Parameter: A <- "-70.7007" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3005" Parameter: B <- "-29.3005" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4002" Parameter: C <- "-41.4002" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6034 TOTAL ENERGY = -70.7007 RDTITL> * VAN DER WAALS = -29.3005 ELECTROSTATIC = -41.4002 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6034" Parameter: CONF_N -> "8002" Comparing "6034" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6035" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747090 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753138 ATOM PAIRS WERE FOUND FOR ATOM LIST 41389 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29571 from a total of 753138 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6035 -69.63656 -1.06414 0.60602 INTE EXTERN> -30.48882 -39.14774 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6366" Parameter: A <- "-69.6366" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4888" Parameter: B <- "-30.4888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1477" Parameter: C <- "-39.1477" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6035 TOTAL ENERGY = -69.6366 RDTITL> * VAN DER WAALS = -30.4888 ELECTROSTATIC = -39.1477 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6035" Parameter: CONF_N -> "8002" Comparing "6035" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6036" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753138 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748493 ATOM PAIRS WERE FOUND FOR ATOM LIST 41158 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29610 from a total of 748493 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6036 -71.16683 1.53027 0.57692 INTE EXTERN> -31.45013 -39.71670 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1668" Parameter: A <- "-71.1668" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4501" Parameter: B <- "-31.4501" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7167" Parameter: C <- "-39.7167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6036 TOTAL ENERGY = -71.1668 RDTITL> * VAN DER WAALS = -31.4501 ELECTROSTATIC = -39.7167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6036" Parameter: CONF_N -> "8002" Comparing "6036" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6037" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748493 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752131 ATOM PAIRS WERE FOUND FOR ATOM LIST 41200 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29096 from a total of 752131 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6037 -70.43092 -0.73590 0.60293 INTE EXTERN> -29.39673 -41.03420 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4309" Parameter: A <- "-70.4309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3967" Parameter: B <- "-29.3967" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0342" Parameter: C <- "-41.0342" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6037 TOTAL ENERGY = -70.4309 RDTITL> * VAN DER WAALS = -29.3967 ELECTROSTATIC = -41.0342 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6037" Parameter: CONF_N -> "8002" Comparing "6037" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6038" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752131 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755236 ATOM PAIRS WERE FOUND FOR ATOM LIST 41266 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29866 from a total of 755236 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6038 -68.04496 -2.38597 0.45809 INTE EXTERN> -32.91557 -35.12939 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.045" Parameter: A <- "-68.045" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9156" Parameter: B <- "-32.9156" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.1294" Parameter: C <- "-35.1294" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6038 TOTAL ENERGY = -68.045 RDTITL> * VAN DER WAALS = -32.9156 ELECTROSTATIC = -35.1294 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6038" Parameter: CONF_N -> "8002" Comparing "6038" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6039" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755236 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758891 ATOM PAIRS WERE FOUND FOR ATOM LIST 41632 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30350 from a total of 758891 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6039 -66.59809 -1.44687 0.49619 INTE EXTERN> -32.58242 -34.01567 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5981" Parameter: A <- "-66.5981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5824" Parameter: B <- "-32.5824" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.0157" Parameter: C <- "-34.0157" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6039 TOTAL ENERGY = -66.5981 RDTITL> * VAN DER WAALS = -32.5824 ELECTROSTATIC = -34.0157 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6039" Parameter: CONF_N -> "8002" Comparing "6039" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6040" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758891 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753180 ATOM PAIRS WERE FOUND FOR ATOM LIST 41469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29468 from a total of 753180 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6040 -65.04719 -1.55090 0.59026 INTE EXTERN> -30.81518 -34.23201 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0472" Parameter: A <- "-65.0472" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8152" Parameter: B <- "-30.8152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.232" Parameter: C <- "-34.232" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6040 TOTAL ENERGY = -65.0472 RDTITL> * VAN DER WAALS = -30.8152 ELECTROSTATIC = -34.232 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6040" Parameter: CONF_N -> "8002" Comparing "6040" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6041" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753180 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750873 ATOM PAIRS WERE FOUND FOR ATOM LIST 41372 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29734 from a total of 750873 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6041 -65.43529 0.38810 0.45266 INTE EXTERN> -32.08170 -33.35359 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4353" Parameter: A <- "-65.4353" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0817" Parameter: B <- "-32.0817" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.3536" Parameter: C <- "-33.3536" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6041 TOTAL ENERGY = -65.4353 RDTITL> * VAN DER WAALS = -32.0817 ELECTROSTATIC = -33.3536 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6041" Parameter: CONF_N -> "8002" Comparing "6041" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6042" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750873 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751149 ATOM PAIRS WERE FOUND FOR ATOM LIST 41239 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29951 from a total of 751149 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6042 -69.42191 3.98662 0.49760 INTE EXTERN> -33.26245 -36.15947 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4219" Parameter: A <- "-69.4219" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2624" Parameter: B <- "-33.2624" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1595" Parameter: C <- "-36.1595" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6042 TOTAL ENERGY = -69.4219 RDTITL> * VAN DER WAALS = -33.2624 ELECTROSTATIC = -36.1595 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6042" Parameter: CONF_N -> "8002" Comparing "6042" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6043" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751149 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755330 ATOM PAIRS WERE FOUND FOR ATOM LIST 41450 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29942 from a total of 755330 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6043 -68.45644 -0.96548 0.60894 INTE EXTERN> -29.23961 -39.21682 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4564" Parameter: A <- "-68.4564" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2396" Parameter: B <- "-29.2396" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2168" Parameter: C <- "-39.2168" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6043 TOTAL ENERGY = -68.4564 RDTITL> * VAN DER WAALS = -29.2396 ELECTROSTATIC = -39.2168 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6043" Parameter: CONF_N -> "8002" Comparing "6043" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6044" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755330 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751733 ATOM PAIRS WERE FOUND FOR ATOM LIST 41362 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29735 from a total of 751733 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6044 -68.13368 -0.32276 0.50665 INTE EXTERN> -31.69315 -36.44053 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1337" Parameter: A <- "-68.1337" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6931" Parameter: B <- "-31.6931" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4405" Parameter: C <- "-36.4405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6044 TOTAL ENERGY = -68.1337 RDTITL> * VAN DER WAALS = -31.6931 ELECTROSTATIC = -36.4405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6044" Parameter: CONF_N -> "8002" Comparing "6044" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6045" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751733 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753386 ATOM PAIRS WERE FOUND FOR ATOM LIST 41346 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29593 from a total of 753386 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6045 -68.21924 0.08556 0.52950 INTE EXTERN> -31.68126 -36.53798 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2192" Parameter: A <- "-68.2192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6813" Parameter: B <- "-31.6813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.538" Parameter: C <- "-36.538" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6045 TOTAL ENERGY = -68.2192 RDTITL> * VAN DER WAALS = -31.6813 ELECTROSTATIC = -36.538 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6045" Parameter: CONF_N -> "8002" Comparing "6045" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6046" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753386 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753478 ATOM PAIRS WERE FOUND FOR ATOM LIST 41316 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29493 from a total of 753478 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6046 -70.22866 2.00942 0.55439 INTE EXTERN> -32.94101 -37.28765 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2287" Parameter: A <- "-70.2287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.941" Parameter: B <- "-32.941" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2876" Parameter: C <- "-37.2876" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6046 TOTAL ENERGY = -70.2287 RDTITL> * VAN DER WAALS = -32.941 ELECTROSTATIC = -37.2876 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6046" Parameter: CONF_N -> "8002" Comparing "6046" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6047" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753478 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750444 ATOM PAIRS WERE FOUND FOR ATOM LIST 41126 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29450 from a total of 750444 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6047 -75.71315 5.48449 0.53591 INTE EXTERN> -32.51202 -43.20113 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7132" Parameter: A <- "-75.7132" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.512" Parameter: B <- "-32.512" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2011" Parameter: C <- "-43.2011" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6047 TOTAL ENERGY = -75.7132 RDTITL> * VAN DER WAALS = -32.512 ELECTROSTATIC = -43.2011 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6047" Parameter: CONF_N -> "8002" Comparing "6047" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6048" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750444 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756734 ATOM PAIRS WERE FOUND FOR ATOM LIST 41448 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29835 from a total of 756734 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6048 -75.75127 0.03812 0.66276 INTE EXTERN> -28.54184 -47.20943 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7513" Parameter: A <- "-75.7513" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5418" Parameter: B <- "-28.5418" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2094" Parameter: C <- "-47.2094" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6048 TOTAL ENERGY = -75.7513 RDTITL> * VAN DER WAALS = -28.5418 ELECTROSTATIC = -47.2094 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6048" Parameter: CONF_N -> "8002" Comparing "6048" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6049" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756734 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751523 ATOM PAIRS WERE FOUND FOR ATOM LIST 41169 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29428 from a total of 751523 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6049 -70.24495 -5.50632 0.53085 INTE EXTERN> -30.99822 -39.24674 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.245" Parameter: A <- "-70.245" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9982" Parameter: B <- "-30.9982" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2467" Parameter: C <- "-39.2467" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6049 TOTAL ENERGY = -70.245 RDTITL> * VAN DER WAALS = -30.9982 ELECTROSTATIC = -39.2467 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6049" Parameter: CONF_N -> "8002" Comparing "6049" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6050" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751523 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754855 ATOM PAIRS WERE FOUND FOR ATOM LIST 41367 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29612 from a total of 754855 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6050 -71.39664 1.15169 0.52744 INTE EXTERN> -32.34765 -39.04899 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3966" Parameter: A <- "-71.3966" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3477" Parameter: B <- "-32.3477" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.049" Parameter: C <- "-39.049" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6050 TOTAL ENERGY = -71.3966 RDTITL> * VAN DER WAALS = -32.3477 ELECTROSTATIC = -39.049 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6050" Parameter: CONF_N -> "8002" Comparing "6050" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6051" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754855 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754647 ATOM PAIRS WERE FOUND FOR ATOM LIST 41307 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29492 from a total of 754647 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6051 -69.76883 -1.62781 0.48529 INTE EXTERN> -32.97241 -36.79641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7688" Parameter: A <- "-69.7688" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9724" Parameter: B <- "-32.9724" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7964" Parameter: C <- "-36.7964" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6051 TOTAL ENERGY = -69.7688 RDTITL> * VAN DER WAALS = -32.9724 ELECTROSTATIC = -36.7964 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6051" Parameter: CONF_N -> "8002" Comparing "6051" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6052" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754647 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747654 ATOM PAIRS WERE FOUND FOR ATOM LIST 41237 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29649 from a total of 747654 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6052 -71.82033 2.05150 0.56808 INTE EXTERN> -32.94733 -38.87300 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8203" Parameter: A <- "-71.8203" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9473" Parameter: B <- "-32.9473" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.873" Parameter: C <- "-38.873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6052 TOTAL ENERGY = -71.8203 RDTITL> * VAN DER WAALS = -32.9473 ELECTROSTATIC = -38.873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6052" Parameter: CONF_N -> "8002" Comparing "6052" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6053" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747654 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41131 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30221 from a total of 752110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6053 -72.31737 0.49705 0.55250 INTE EXTERN> -30.06102 -42.25635 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3174" Parameter: A <- "-72.3174" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.061" Parameter: B <- "-30.061" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2564" Parameter: C <- "-42.2564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6053 TOTAL ENERGY = -72.3174 RDTITL> * VAN DER WAALS = -30.061 ELECTROSTATIC = -42.2564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6053" Parameter: CONF_N -> "8002" Comparing "6053" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6054" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747544 ATOM PAIRS WERE FOUND FOR ATOM LIST 41128 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30031 from a total of 747544 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6054 -72.60872 0.29135 0.49861 INTE EXTERN> -33.25004 -39.35868 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6087" Parameter: A <- "-72.6087" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.25" Parameter: B <- "-33.25" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3587" Parameter: C <- "-39.3587" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6054 TOTAL ENERGY = -72.6087 RDTITL> * VAN DER WAALS = -33.25 ELECTROSTATIC = -39.3587 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6054" Parameter: CONF_N -> "8002" Comparing "6054" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6055" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747544 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752491 ATOM PAIRS WERE FOUND FOR ATOM LIST 41312 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30377 from a total of 752491 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6055 -71.87454 -0.73418 0.53855 INTE EXTERN> -32.60989 -39.26465 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8745" Parameter: A <- "-71.8745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6099" Parameter: B <- "-32.6099" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2647" Parameter: C <- "-39.2647" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6055 TOTAL ENERGY = -71.8745 RDTITL> * VAN DER WAALS = -32.6099 ELECTROSTATIC = -39.2647 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6055" Parameter: CONF_N -> "8002" Comparing "6055" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6056" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752491 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752650 ATOM PAIRS WERE FOUND FOR ATOM LIST 41648 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30485 from a total of 752650 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6056 -74.92972 3.05518 0.52668 INTE EXTERN> -34.16904 -40.76068 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9297" Parameter: A <- "-74.9297" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.169" Parameter: B <- "-34.169" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7607" Parameter: C <- "-40.7607" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6056 TOTAL ENERGY = -74.9297 RDTITL> * VAN DER WAALS = -34.169 ELECTROSTATIC = -40.7607 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6056" Parameter: CONF_N -> "8002" Comparing "6056" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6057" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752650 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755396 ATOM PAIRS WERE FOUND FOR ATOM LIST 41566 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30124 from a total of 755396 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6057 -71.49031 -3.43941 0.49942 INTE EXTERN> -35.35936 -36.13095 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4903" Parameter: A <- "-71.4903" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.3594" Parameter: B <- "-35.3594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.131" Parameter: C <- "-36.131" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6057 TOTAL ENERGY = -71.4903 RDTITL> * VAN DER WAALS = -35.3594 ELECTROSTATIC = -36.131 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6057" Parameter: CONF_N -> "8002" Comparing "6057" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6058" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755396 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751491 ATOM PAIRS WERE FOUND FOR ATOM LIST 41330 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30165 from a total of 751491 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6058 -72.56065 1.07034 0.45038 INTE EXTERN> -33.89312 -38.66753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5607" Parameter: A <- "-72.5607" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8931" Parameter: B <- "-33.8931" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6675" Parameter: C <- "-38.6675" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6058 TOTAL ENERGY = -72.5607 RDTITL> * VAN DER WAALS = -33.8931 ELECTROSTATIC = -38.6675 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6058" Parameter: CONF_N -> "8002" Comparing "6058" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6059" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751491 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753965 ATOM PAIRS WERE FOUND FOR ATOM LIST 41330 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29794 from a total of 753965 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6059 -68.66444 -3.89621 0.46280 INTE EXTERN> -34.90725 -33.75720 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6644" Parameter: A <- "-68.6644" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9072" Parameter: B <- "-34.9072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.7572" Parameter: C <- "-33.7572" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6059 TOTAL ENERGY = -68.6644 RDTITL> * VAN DER WAALS = -34.9072 ELECTROSTATIC = -33.7572 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6059" Parameter: CONF_N -> "8002" Comparing "6059" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6060" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753965 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755014 ATOM PAIRS WERE FOUND FOR ATOM LIST 41549 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30167 from a total of 755014 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6060 -71.73483 3.07038 0.63650 INTE EXTERN> -29.90614 -41.82868 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7348" Parameter: A <- "-71.7348" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9061" Parameter: B <- "-29.9061" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8287" Parameter: C <- "-41.8287" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6060 TOTAL ENERGY = -71.7348 RDTITL> * VAN DER WAALS = -29.9061 ELECTROSTATIC = -41.8287 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6060" Parameter: CONF_N -> "8002" Comparing "6060" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6061" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755014 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756956 ATOM PAIRS WERE FOUND FOR ATOM LIST 41689 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30273 from a total of 756956 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6061 -76.43968 4.70485 0.55953 INTE EXTERN> -31.61039 -44.82928 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4397" Parameter: A <- "-76.4397" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6104" Parameter: B <- "-31.6104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8293" Parameter: C <- "-44.8293" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6061 TOTAL ENERGY = -76.4397 RDTITL> * VAN DER WAALS = -31.6104 ELECTROSTATIC = -44.8293 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6061" Parameter: CONF_N -> "8002" Comparing "6061" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6062" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756956 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753915 ATOM PAIRS WERE FOUND FOR ATOM LIST 41324 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30016 from a total of 753915 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6062 -69.53158 -6.90809 0.56156 INTE EXTERN> -31.24086 -38.29073 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5316" Parameter: A <- "-69.5316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2409" Parameter: B <- "-31.2409" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2907" Parameter: C <- "-38.2907" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6062 TOTAL ENERGY = -69.5316 RDTITL> * VAN DER WAALS = -31.2409 ELECTROSTATIC = -38.2907 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6062" Parameter: CONF_N -> "8002" Comparing "6062" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6063" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753915 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752514 ATOM PAIRS WERE FOUND FOR ATOM LIST 41274 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29533 from a total of 752514 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6063 -69.14102 -0.39057 0.69323 INTE EXTERN> -26.04547 -43.09555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.141" Parameter: A <- "-69.141" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0455" Parameter: B <- "-26.0455" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0956" Parameter: C <- "-43.0956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6063 TOTAL ENERGY = -69.141 RDTITL> * VAN DER WAALS = -26.0455 ELECTROSTATIC = -43.0956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6063" Parameter: CONF_N -> "8002" Comparing "6063" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6064" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752514 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746306 ATOM PAIRS WERE FOUND FOR ATOM LIST 41201 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30182 from a total of 746306 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6064 -68.58466 -0.55636 0.58005 INTE EXTERN> -29.73482 -38.84984 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5847" Parameter: A <- "-68.5847" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7348" Parameter: B <- "-29.7348" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8498" Parameter: C <- "-38.8498" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6064 TOTAL ENERGY = -68.5847 RDTITL> * VAN DER WAALS = -29.7348 ELECTROSTATIC = -38.8498 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6064" Parameter: CONF_N -> "8002" Comparing "6064" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6065" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746306 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748815 ATOM PAIRS WERE FOUND FOR ATOM LIST 41254 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29820 from a total of 748815 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6065 -68.73147 0.14681 0.49402 INTE EXTERN> -31.93337 -36.79810 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7315" Parameter: A <- "-68.7315" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9334" Parameter: B <- "-31.9334" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7981" Parameter: C <- "-36.7981" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6065 TOTAL ENERGY = -68.7315 RDTITL> * VAN DER WAALS = -31.9334 ELECTROSTATIC = -36.7981 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6065" Parameter: CONF_N -> "8002" Comparing "6065" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6066" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748815 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751280 ATOM PAIRS WERE FOUND FOR ATOM LIST 41212 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30213 from a total of 751280 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6066 -72.32959 3.59812 0.60169 INTE EXTERN> -30.79184 -41.53775 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3296" Parameter: A <- "-72.3296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7918" Parameter: B <- "-30.7918" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5377" Parameter: C <- "-41.5377" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6066 TOTAL ENERGY = -72.3296 RDTITL> * VAN DER WAALS = -30.7918 ELECTROSTATIC = -41.5377 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6066" Parameter: CONF_N -> "8002" Comparing "6066" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6067" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751280 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749390 ATOM PAIRS WERE FOUND FOR ATOM LIST 41201 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29782 from a total of 749390 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6067 -71.48894 -0.84065 0.50807 INTE EXTERN> -31.32136 -40.16758 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4889" Parameter: A <- "-71.4889" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3214" Parameter: B <- "-31.3214" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1676" Parameter: C <- "-40.1676" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6067 TOTAL ENERGY = -71.4889 RDTITL> * VAN DER WAALS = -31.3214 ELECTROSTATIC = -40.1676 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6067" Parameter: CONF_N -> "8002" Comparing "6067" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6068" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749390 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747845 ATOM PAIRS WERE FOUND FOR ATOM LIST 41194 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30321 from a total of 747845 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6068 -68.89835 -2.59059 0.55189 INTE EXTERN> -30.88640 -38.01195 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8983" Parameter: A <- "-68.8983" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8864" Parameter: B <- "-30.8864" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.012" Parameter: C <- "-38.012" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6068 TOTAL ENERGY = -68.8983 RDTITL> * VAN DER WAALS = -30.8864 ELECTROSTATIC = -38.012 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6068" Parameter: CONF_N -> "8002" Comparing "6068" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6069" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747845 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746295 ATOM PAIRS WERE FOUND FOR ATOM LIST 40991 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30692 from a total of 746295 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6069 -70.27569 1.37735 0.50731 INTE EXTERN> -32.66427 -37.61143 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2757" Parameter: A <- "-70.2757" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6643" Parameter: B <- "-32.6643" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6114" Parameter: C <- "-37.6114" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6069 TOTAL ENERGY = -70.2757 RDTITL> * VAN DER WAALS = -32.6643 ELECTROSTATIC = -37.6114 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6069" Parameter: CONF_N -> "8002" Comparing "6069" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6070" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746295 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752140 ATOM PAIRS WERE FOUND FOR ATOM LIST 41261 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30043 from a total of 752140 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6070 -66.17650 -4.09919 0.50048 INTE EXTERN> -31.35720 -34.81930 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1765" Parameter: A <- "-66.1765" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3572" Parameter: B <- "-31.3572" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8193" Parameter: C <- "-34.8193" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6070 TOTAL ENERGY = -66.1765 RDTITL> * VAN DER WAALS = -31.3572 ELECTROSTATIC = -34.8193 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6070" Parameter: CONF_N -> "8002" Comparing "6070" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6071" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752140 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748269 ATOM PAIRS WERE FOUND FOR ATOM LIST 41222 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29479 from a total of 748269 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6071 -63.01137 -3.16513 0.59930 INTE EXTERN> -28.91301 -34.09836 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.0114" Parameter: A <- "-63.0114" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.913" Parameter: B <- "-28.913" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.0984" Parameter: C <- "-34.0984" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6071 TOTAL ENERGY = -63.0114 RDTITL> * VAN DER WAALS = -28.913 ELECTROSTATIC = -34.0984 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6071" Parameter: CONF_N -> "8002" Comparing "6071" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6072" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748269 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748830 ATOM PAIRS WERE FOUND FOR ATOM LIST 41113 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30113 from a total of 748830 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6072 -68.53003 5.51866 0.55239 INTE EXTERN> -31.01153 -37.51849 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.53" Parameter: A <- "-68.53" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0115" Parameter: B <- "-31.0115" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5185" Parameter: C <- "-37.5185" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6072 TOTAL ENERGY = -68.53 RDTITL> * VAN DER WAALS = -31.0115 ELECTROSTATIC = -37.5185 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6072" Parameter: CONF_N -> "8002" Comparing "6072" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6073" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748830 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744016 ATOM PAIRS WERE FOUND FOR ATOM LIST 41050 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29559 from a total of 744016 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6073 -64.26142 -4.26860 0.61468 INTE EXTERN> -26.92780 -37.33362 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2614" Parameter: A <- "-64.2614" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9278" Parameter: B <- "-26.9278" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3336" Parameter: C <- "-37.3336" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6073 TOTAL ENERGY = -64.2614 RDTITL> * VAN DER WAALS = -26.9278 ELECTROSTATIC = -37.3336 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6073" Parameter: CONF_N -> "8002" Comparing "6073" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6074" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744016 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753485 ATOM PAIRS WERE FOUND FOR ATOM LIST 41199 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30171 from a total of 753485 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6074 -67.57069 3.30927 0.56298 INTE EXTERN> -31.54890 -36.02178 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.5707" Parameter: A <- "-67.5707" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5489" Parameter: B <- "-31.5489" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0218" Parameter: C <- "-36.0218" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6074 TOTAL ENERGY = -67.5707 RDTITL> * VAN DER WAALS = -31.5489 ELECTROSTATIC = -36.0218 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6074" Parameter: CONF_N -> "8002" Comparing "6074" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6075" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753485 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750969 ATOM PAIRS WERE FOUND FOR ATOM LIST 41204 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29911 from a total of 750969 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6075 -69.17374 1.60305 0.53606 INTE EXTERN> -31.54710 -37.62664 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1737" Parameter: A <- "-69.1737" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5471" Parameter: B <- "-31.5471" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.6266" Parameter: C <- "-37.6266" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6075 TOTAL ENERGY = -69.1737 RDTITL> * VAN DER WAALS = -31.5471 ELECTROSTATIC = -37.6266 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6075" Parameter: CONF_N -> "8002" Comparing "6075" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6076" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750969 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755282 ATOM PAIRS WERE FOUND FOR ATOM LIST 41408 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30192 from a total of 755282 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6076 -64.77122 -4.40252 0.66530 INTE EXTERN> -24.95550 -39.81572 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7712" Parameter: A <- "-64.7712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9555" Parameter: B <- "-24.9555" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8157" Parameter: C <- "-39.8157" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6076 TOTAL ENERGY = -64.7712 RDTITL> * VAN DER WAALS = -24.9555 ELECTROSTATIC = -39.8157 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6076" Parameter: CONF_N -> "8002" Comparing "6076" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6077" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755282 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752874 ATOM PAIRS WERE FOUND FOR ATOM LIST 41345 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29669 from a total of 752874 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6077 -71.98258 7.21136 0.60212 INTE EXTERN> -26.80119 -45.18139 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9826" Parameter: A <- "-71.9826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8012" Parameter: B <- "-26.8012" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1814" Parameter: C <- "-45.1814" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6077 TOTAL ENERGY = -71.9826 RDTITL> * VAN DER WAALS = -26.8012 ELECTROSTATIC = -45.1814 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6077" Parameter: CONF_N -> "8002" Comparing "6077" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6078" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752874 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751018 ATOM PAIRS WERE FOUND FOR ATOM LIST 41183 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29442 from a total of 751018 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6078 -69.62224 -2.36034 0.59655 INTE EXTERN> -30.74305 -38.87919 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6222" Parameter: A <- "-69.6222" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.743" Parameter: B <- "-30.743" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8792" Parameter: C <- "-38.8792" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6078 TOTAL ENERGY = -69.6222 RDTITL> * VAN DER WAALS = -30.743 ELECTROSTATIC = -38.8792 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6078" Parameter: CONF_N -> "8002" Comparing "6078" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6079" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751018 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748892 ATOM PAIRS WERE FOUND FOR ATOM LIST 41222 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29938 from a total of 748892 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6079 -69.53945 -0.08279 0.53254 INTE EXTERN> -33.63413 -35.90532 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5394" Parameter: A <- "-69.5394" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6341" Parameter: B <- "-33.6341" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9053" Parameter: C <- "-35.9053" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6079 TOTAL ENERGY = -69.5394 RDTITL> * VAN DER WAALS = -33.6341 ELECTROSTATIC = -35.9053 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6079" Parameter: CONF_N -> "8002" Comparing "6079" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6080" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748892 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754356 ATOM PAIRS WERE FOUND FOR ATOM LIST 41265 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29517 from a total of 754356 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6080 -68.62503 -0.91442 0.48680 INTE EXTERN> -32.18700 -36.43803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.625" Parameter: A <- "-68.625" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.187" Parameter: B <- "-32.187" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.438" Parameter: C <- "-36.438" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6080 TOTAL ENERGY = -68.625 RDTITL> * VAN DER WAALS = -32.187 ELECTROSTATIC = -36.438 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6080" Parameter: CONF_N -> "8002" Comparing "6080" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6081" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754356 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751320 ATOM PAIRS WERE FOUND FOR ATOM LIST 41159 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29549 from a total of 751320 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6081 -62.05093 -6.57410 0.48389 INTE EXTERN> -30.86735 -31.18357 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.0509" Parameter: A <- "-62.0509" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8674" Parameter: B <- "-30.8674" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.1836" Parameter: C <- "-31.1836" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6081 TOTAL ENERGY = -62.0509 RDTITL> * VAN DER WAALS = -30.8674 ELECTROSTATIC = -31.1836 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6081" Parameter: CONF_N -> "8002" Comparing "6081" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6082" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751320 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752650 ATOM PAIRS WERE FOUND FOR ATOM LIST 41366 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29969 from a total of 752650 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6082 -69.05353 7.00261 0.60575 INTE EXTERN> -28.82010 -40.23343 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0535" Parameter: A <- "-69.0535" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8201" Parameter: B <- "-28.8201" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2334" Parameter: C <- "-40.2334" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6082 TOTAL ENERGY = -69.0535 RDTITL> * VAN DER WAALS = -28.8201 ELECTROSTATIC = -40.2334 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6082" Parameter: CONF_N -> "8002" Comparing "6082" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6083" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752650 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748781 ATOM PAIRS WERE FOUND FOR ATOM LIST 41069 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29886 from a total of 748781 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6083 -69.04234 -0.01119 0.56496 INTE EXTERN> -27.43052 -41.61182 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0423" Parameter: A <- "-69.0423" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4305" Parameter: B <- "-27.4305" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6118" Parameter: C <- "-41.6118" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6083 TOTAL ENERGY = -69.0423 RDTITL> * VAN DER WAALS = -27.4305 ELECTROSTATIC = -41.6118 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6083" Parameter: CONF_N -> "8002" Comparing "6083" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6084" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748781 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751986 ATOM PAIRS WERE FOUND FOR ATOM LIST 41328 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30106 from a total of 751986 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6084 -71.40773 2.36539 0.53370 INTE EXTERN> -31.99667 -39.41107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4077" Parameter: A <- "-71.4077" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9967" Parameter: B <- "-31.9967" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4111" Parameter: C <- "-39.4111" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6084 TOTAL ENERGY = -71.4077 RDTITL> * VAN DER WAALS = -31.9967 ELECTROSTATIC = -39.4111 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6084" Parameter: CONF_N -> "8002" Comparing "6084" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6085" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751986 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752634 ATOM PAIRS WERE FOUND FOR ATOM LIST 41285 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30263 from a total of 752634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6085 -71.53278 0.12505 0.53079 INTE EXTERN> -31.18397 -40.34881 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5328" Parameter: A <- "-71.5328" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.184" Parameter: B <- "-31.184" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3488" Parameter: C <- "-40.3488" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6085 TOTAL ENERGY = -71.5328 RDTITL> * VAN DER WAALS = -31.184 ELECTROSTATIC = -40.3488 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6085" Parameter: CONF_N -> "8002" Comparing "6085" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6086" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755223 ATOM PAIRS WERE FOUND FOR ATOM LIST 41256 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30017 from a total of 755223 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6086 -71.47427 -0.05852 0.46798 INTE EXTERN> -34.25995 -37.21431 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4743" Parameter: A <- "-71.4743" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.26" Parameter: B <- "-34.26" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2143" Parameter: C <- "-37.2143" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6086 TOTAL ENERGY = -71.4743 RDTITL> * VAN DER WAALS = -34.26 ELECTROSTATIC = -37.2143 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6086" Parameter: CONF_N -> "8002" Comparing "6086" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6087" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755223 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753728 ATOM PAIRS WERE FOUND FOR ATOM LIST 41217 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30130 from a total of 753728 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6087 -72.03168 0.55741 0.47217 INTE EXTERN> -32.18921 -39.84247 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0317" Parameter: A <- "-72.0317" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1892" Parameter: B <- "-32.1892" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8425" Parameter: C <- "-39.8425" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6087 TOTAL ENERGY = -72.0317 RDTITL> * VAN DER WAALS = -32.1892 ELECTROSTATIC = -39.8425 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6087" Parameter: CONF_N -> "8002" Comparing "6087" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6088" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753728 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41385 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29609 from a total of 753526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6088 -71.14244 -0.88924 0.56245 INTE EXTERN> -30.26543 -40.87700 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1424" Parameter: A <- "-71.1424" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2654" Parameter: B <- "-30.2654" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.877" Parameter: C <- "-40.877" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6088 TOTAL ENERGY = -71.1424 RDTITL> * VAN DER WAALS = -30.2654 ELECTROSTATIC = -40.877 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6088" Parameter: CONF_N -> "8002" Comparing "6088" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6089" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753034 ATOM PAIRS WERE FOUND FOR ATOM LIST 41284 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30026 from a total of 753034 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6089 -69.48506 -1.65737 0.59728 INTE EXTERN> -31.07644 -38.40862 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4851" Parameter: A <- "-69.4851" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0764" Parameter: B <- "-31.0764" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4086" Parameter: C <- "-38.4086" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6089 TOTAL ENERGY = -69.4851 RDTITL> * VAN DER WAALS = -31.0764 ELECTROSTATIC = -38.4086 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6089" Parameter: CONF_N -> "8002" Comparing "6089" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6090" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753034 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749092 ATOM PAIRS WERE FOUND FOR ATOM LIST 41132 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29957 from a total of 749092 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6090 -71.37231 1.88725 0.51549 INTE EXTERN> -32.53818 -38.83413 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3723" Parameter: A <- "-71.3723" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5382" Parameter: B <- "-32.5382" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8341" Parameter: C <- "-38.8341" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6090 TOTAL ENERGY = -71.3723 RDTITL> * VAN DER WAALS = -32.5382 ELECTROSTATIC = -38.8341 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6090" Parameter: CONF_N -> "8002" Comparing "6090" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6091" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749092 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751432 ATOM PAIRS WERE FOUND FOR ATOM LIST 41285 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30209 from a total of 751432 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6091 -71.85072 0.47841 0.53953 INTE EXTERN> -32.78088 -39.06983 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8507" Parameter: A <- "-71.8507" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7809" Parameter: B <- "-32.7809" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0698" Parameter: C <- "-39.0698" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6091 TOTAL ENERGY = -71.8507 RDTITL> * VAN DER WAALS = -32.7809 ELECTROSTATIC = -39.0698 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6091" Parameter: CONF_N -> "8002" Comparing "6091" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6092" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751432 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757393 ATOM PAIRS WERE FOUND FOR ATOM LIST 41503 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30177 from a total of 757393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6092 -71.88933 0.03861 0.58592 INTE EXTERN> -33.11928 -38.77005 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8893" Parameter: A <- "-71.8893" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1193" Parameter: B <- "-33.1193" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.77" Parameter: C <- "-38.77" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6092 TOTAL ENERGY = -71.8893 RDTITL> * VAN DER WAALS = -33.1193 ELECTROSTATIC = -38.77 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6092" Parameter: CONF_N -> "8002" Comparing "6092" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6093" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749811 ATOM PAIRS WERE FOUND FOR ATOM LIST 41272 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30044 from a total of 749811 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6093 -72.24124 0.35191 0.53045 INTE EXTERN> -32.14140 -40.09984 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2412" Parameter: A <- "-72.2412" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1414" Parameter: B <- "-32.1414" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0998" Parameter: C <- "-40.0998" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6093 TOTAL ENERGY = -72.2412 RDTITL> * VAN DER WAALS = -32.1414 ELECTROSTATIC = -40.0998 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6093" Parameter: CONF_N -> "8002" Comparing "6093" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6094" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749811 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753739 ATOM PAIRS WERE FOUND FOR ATOM LIST 41505 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29596 from a total of 753739 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6094 -70.71190 -1.52934 0.53013 INTE EXTERN> -32.10476 -38.60714 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7119" Parameter: A <- "-70.7119" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1048" Parameter: B <- "-32.1048" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6071" Parameter: C <- "-38.6071" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6094 TOTAL ENERGY = -70.7119 RDTITL> * VAN DER WAALS = -32.1048 ELECTROSTATIC = -38.6071 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6094" Parameter: CONF_N -> "8002" Comparing "6094" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6095" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753739 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752454 ATOM PAIRS WERE FOUND FOR ATOM LIST 41300 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29766 from a total of 752454 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6095 -77.41333 6.70143 0.59361 INTE EXTERN> -30.58256 -46.83077 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4133" Parameter: A <- "-77.4133" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5826" Parameter: B <- "-30.5826" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8308" Parameter: C <- "-46.8308" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6095 TOTAL ENERGY = -77.4133 RDTITL> * VAN DER WAALS = -30.5826 ELECTROSTATIC = -46.8308 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6095" Parameter: CONF_N -> "8002" Comparing "6095" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6096" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752454 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757571 ATOM PAIRS WERE FOUND FOR ATOM LIST 41636 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30144 from a total of 757571 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6096 -76.59193 -0.82141 0.57731 INTE EXTERN> -32.19413 -44.39780 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5919" Parameter: A <- "-76.5919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1941" Parameter: B <- "-32.1941" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3978" Parameter: C <- "-44.3978" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6096 TOTAL ENERGY = -76.5919 RDTITL> * VAN DER WAALS = -32.1941 ELECTROSTATIC = -44.3978 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6096" Parameter: CONF_N -> "8002" Comparing "6096" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6097" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757571 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758203 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29889 from a total of 758203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6097 -71.05593 -5.53600 0.55295 INTE EXTERN> -28.44553 -42.61039 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0559" Parameter: A <- "-71.0559" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4455" Parameter: B <- "-28.4455" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6104" Parameter: C <- "-42.6104" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6097 TOTAL ENERGY = -71.0559 RDTITL> * VAN DER WAALS = -28.4455 ELECTROSTATIC = -42.6104 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6097" Parameter: CONF_N -> "8002" Comparing "6097" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6098" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755099 ATOM PAIRS WERE FOUND FOR ATOM LIST 41389 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30191 from a total of 755099 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6098 -69.75180 -1.30413 0.49274 INTE EXTERN> -32.38523 -37.36657 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7518" Parameter: A <- "-69.7518" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3852" Parameter: B <- "-32.3852" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3666" Parameter: C <- "-37.3666" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6098 TOTAL ENERGY = -69.7518 RDTITL> * VAN DER WAALS = -32.3852 ELECTROSTATIC = -37.3666 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6098" Parameter: CONF_N -> "8002" Comparing "6098" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6099" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755099 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754337 ATOM PAIRS WERE FOUND FOR ATOM LIST 41307 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29404 from a total of 754337 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6099 -70.55198 0.80019 0.57258 INTE EXTERN> -27.58983 -42.96216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.552" Parameter: A <- "-70.552" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5898" Parameter: B <- "-27.5898" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9622" Parameter: C <- "-42.9622" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6099 TOTAL ENERGY = -70.552 RDTITL> * VAN DER WAALS = -27.5898 ELECTROSTATIC = -42.9622 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6099" Parameter: CONF_N -> "8002" Comparing "6099" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6100" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754337 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761075 ATOM PAIRS WERE FOUND FOR ATOM LIST 41752 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29804 from a total of 761075 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6100 -71.88061 1.32863 0.57768 INTE EXTERN> -30.66810 -41.21251 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8806" Parameter: A <- "-71.8806" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6681" Parameter: B <- "-30.6681" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2125" Parameter: C <- "-41.2125" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6100 TOTAL ENERGY = -71.8806 RDTITL> * VAN DER WAALS = -30.6681 ELECTROSTATIC = -41.2125 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6100" Parameter: CONF_N -> "8002" Comparing "6100" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6101" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761075 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762276 ATOM PAIRS WERE FOUND FOR ATOM LIST 41635 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30214 from a total of 762276 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6101 -73.54150 1.66089 0.55548 INTE EXTERN> -30.62825 -42.91325 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5415" Parameter: A <- "-73.5415" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6282" Parameter: B <- "-30.6282" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9133" Parameter: C <- "-42.9133" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6101 TOTAL ENERGY = -73.5415 RDTITL> * VAN DER WAALS = -30.6282 ELECTROSTATIC = -42.9133 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6101" Parameter: CONF_N -> "8002" Comparing "6101" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6102" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762276 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755032 ATOM PAIRS WERE FOUND FOR ATOM LIST 41375 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28749 from a total of 755032 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6102 -61.63923 -11.90228 0.48613 INTE EXTERN> -28.86675 -32.77248 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.6392" Parameter: A <- "-61.6392" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8667" Parameter: B <- "-28.8667" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.7725" Parameter: C <- "-32.7725" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6102 TOTAL ENERGY = -61.6392 RDTITL> * VAN DER WAALS = -28.8667 ELECTROSTATIC = -32.7725 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6102" Parameter: CONF_N -> "8002" Comparing "6102" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6103" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755032 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757391 ATOM PAIRS WERE FOUND FOR ATOM LIST 41528 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29103 from a total of 757391 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6103 -65.14014 3.50091 0.55637 INTE EXTERN> -27.37644 -37.76370 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1401" Parameter: A <- "-65.1401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3764" Parameter: B <- "-27.3764" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7637" Parameter: C <- "-37.7637" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6103 TOTAL ENERGY = -65.1401 RDTITL> * VAN DER WAALS = -27.3764 ELECTROSTATIC = -37.7637 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6103" Parameter: CONF_N -> "8002" Comparing "6103" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6104" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757391 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750618 ATOM PAIRS WERE FOUND FOR ATOM LIST 41069 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28680 from a total of 750618 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6104 -66.28159 1.14145 0.59006 INTE EXTERN> -27.83254 -38.44905 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2816" Parameter: A <- "-66.2816" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8325" Parameter: B <- "-27.8325" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4491" Parameter: C <- "-38.4491" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6104 TOTAL ENERGY = -66.2816 RDTITL> * VAN DER WAALS = -27.8325 ELECTROSTATIC = -38.4491 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6104" Parameter: CONF_N -> "8002" Comparing "6104" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6105" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750618 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754375 ATOM PAIRS WERE FOUND FOR ATOM LIST 41474 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29765 from a total of 754375 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6105 -60.34767 -5.93392 0.52611 INTE EXTERN> -30.05522 -30.29245 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.3477" Parameter: A <- "-60.3477" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0552" Parameter: B <- "-30.0552" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.2925" Parameter: C <- "-30.2925" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6105 TOTAL ENERGY = -60.3477 RDTITL> * VAN DER WAALS = -30.0552 ELECTROSTATIC = -30.2925 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6105" Parameter: CONF_N -> "8002" Comparing "6105" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6106" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754375 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755429 ATOM PAIRS WERE FOUND FOR ATOM LIST 41579 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29674 from a total of 755429 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6106 -69.09862 8.75095 0.56633 INTE EXTERN> -28.67477 -40.42385 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0986" Parameter: A <- "-69.0986" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6748" Parameter: B <- "-28.6748" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4238" Parameter: C <- "-40.4238" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6106 TOTAL ENERGY = -69.0986 RDTITL> * VAN DER WAALS = -28.6748 ELECTROSTATIC = -40.4238 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6106" Parameter: CONF_N -> "8002" Comparing "6106" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6107" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755429 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753509 ATOM PAIRS WERE FOUND FOR ATOM LIST 41401 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29483 from a total of 753509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6107 -72.00621 2.90759 0.66299 INTE EXTERN> -25.94020 -46.06601 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0062" Parameter: A <- "-72.0062" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9402" Parameter: B <- "-25.9402" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.066" Parameter: C <- "-46.066" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6107 TOTAL ENERGY = -72.0062 RDTITL> * VAN DER WAALS = -25.9402 ELECTROSTATIC = -46.066 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6107" Parameter: CONF_N -> "8002" Comparing "6107" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6108" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761520 ATOM PAIRS WERE FOUND FOR ATOM LIST 41717 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30248 from a total of 761520 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6108 -70.28350 -1.72270 0.53382 INTE EXTERN> -31.18411 -39.09940 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2835" Parameter: A <- "-70.2835" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1841" Parameter: B <- "-31.1841" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0994" Parameter: C <- "-39.0994" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6108 TOTAL ENERGY = -70.2835 RDTITL> * VAN DER WAALS = -31.1841 ELECTROSTATIC = -39.0994 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6108" Parameter: CONF_N -> "8002" Comparing "6108" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6109" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761520 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760147 ATOM PAIRS WERE FOUND FOR ATOM LIST 41685 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29288 from a total of 760147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6109 -64.98931 -5.29419 0.50331 INTE EXTERN> -28.98334 -36.00598 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9893" Parameter: A <- "-64.9893" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9833" Parameter: B <- "-28.9833" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.006" Parameter: C <- "-36.006" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6109 TOTAL ENERGY = -64.9893 RDTITL> * VAN DER WAALS = -28.9833 ELECTROSTATIC = -36.006 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6109" Parameter: CONF_N -> "8002" Comparing "6109" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6110" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754999 ATOM PAIRS WERE FOUND FOR ATOM LIST 41399 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29518 from a total of 754999 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6110 -69.15430 4.16499 0.55618 INTE EXTERN> -29.26665 -39.88765 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1543" Parameter: A <- "-69.1543" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2666" Parameter: B <- "-29.2666" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8877" Parameter: C <- "-39.8877" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6110 TOTAL ENERGY = -69.1543 RDTITL> * VAN DER WAALS = -29.2666 ELECTROSTATIC = -39.8877 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6110" Parameter: CONF_N -> "8002" Comparing "6110" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6111" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754999 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759155 ATOM PAIRS WERE FOUND FOR ATOM LIST 41483 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29334 from a total of 759155 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6111 -65.72035 -3.43395 0.51372 INTE EXTERN> -29.20338 -36.51697 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7203" Parameter: A <- "-65.7203" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2034" Parameter: B <- "-29.2034" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.517" Parameter: C <- "-36.517" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6111 TOTAL ENERGY = -65.7203 RDTITL> * VAN DER WAALS = -29.2034 ELECTROSTATIC = -36.517 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6111" Parameter: CONF_N -> "8002" Comparing "6111" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6112" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759155 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757505 ATOM PAIRS WERE FOUND FOR ATOM LIST 41497 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29406 from a total of 757505 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6112 -65.61272 -0.10762 0.55745 INTE EXTERN> -29.32360 -36.28912 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6127" Parameter: A <- "-65.6127" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3236" Parameter: B <- "-29.3236" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2891" Parameter: C <- "-36.2891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6112 TOTAL ENERGY = -65.6127 RDTITL> * VAN DER WAALS = -29.3236 ELECTROSTATIC = -36.2891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6112" Parameter: CONF_N -> "8002" Comparing "6112" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6113" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757505 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757300 ATOM PAIRS WERE FOUND FOR ATOM LIST 41500 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29762 from a total of 757300 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6113 -70.49595 4.88323 0.49269 INTE EXTERN> -31.50888 -38.98708 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.496" Parameter: A <- "-70.496" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5089" Parameter: B <- "-31.5089" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9871" Parameter: C <- "-38.9871" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6113 TOTAL ENERGY = -70.496 RDTITL> * VAN DER WAALS = -31.5089 ELECTROSTATIC = -38.9871 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6113" Parameter: CONF_N -> "8002" Comparing "6113" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6114" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757300 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756423 ATOM PAIRS WERE FOUND FOR ATOM LIST 41457 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29593 from a total of 756423 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6114 -66.73888 -3.75707 0.51715 INTE EXTERN> -30.54627 -36.19261 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7389" Parameter: A <- "-66.7389" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5463" Parameter: B <- "-30.5463" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1926" Parameter: C <- "-36.1926" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6114 TOTAL ENERGY = -66.7389 RDTITL> * VAN DER WAALS = -30.5463 ELECTROSTATIC = -36.1926 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6114" Parameter: CONF_N -> "8002" Comparing "6114" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6115" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756423 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756010 ATOM PAIRS WERE FOUND FOR ATOM LIST 41491 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29183 from a total of 756010 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6115 -60.43873 -6.30015 0.47177 INTE EXTERN> -27.73900 -32.69973 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.4387" Parameter: A <- "-60.4387" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.739" Parameter: B <- "-27.739" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.6997" Parameter: C <- "-32.6997" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6115 TOTAL ENERGY = -60.4387 RDTITL> * VAN DER WAALS = -27.739 ELECTROSTATIC = -32.6997 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6115" Parameter: CONF_N -> "8002" Comparing "6115" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6116" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756010 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756081 ATOM PAIRS WERE FOUND FOR ATOM LIST 41642 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29540 from a total of 756081 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6116 -63.43918 3.00046 0.55269 INTE EXTERN> -26.83144 -36.60775 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4392" Parameter: A <- "-63.4392" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8314" Parameter: B <- "-26.8314" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6077" Parameter: C <- "-36.6077" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6116 TOTAL ENERGY = -63.4392 RDTITL> * VAN DER WAALS = -26.8314 ELECTROSTATIC = -36.6077 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6116" Parameter: CONF_N -> "8002" Comparing "6116" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6117" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756081 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753551 ATOM PAIRS WERE FOUND FOR ATOM LIST 41489 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29440 from a total of 753551 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6117 -65.35651 1.91733 0.49119 INTE EXTERN> -33.21193 -32.14458 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3565" Parameter: A <- "-65.3565" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2119" Parameter: B <- "-33.2119" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.1446" Parameter: C <- "-32.1446" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6117 TOTAL ENERGY = -65.3565 RDTITL> * VAN DER WAALS = -33.2119 ELECTROSTATIC = -32.1446 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6117" Parameter: CONF_N -> "8002" Comparing "6117" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6118" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753551 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759099 ATOM PAIRS WERE FOUND FOR ATOM LIST 41590 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29310 from a total of 759099 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6118 -62.26442 -3.09209 0.52299 INTE EXTERN> -26.96919 -35.29523 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.2644" Parameter: A <- "-62.2644" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9692" Parameter: B <- "-26.9692" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2952" Parameter: C <- "-35.2952" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6118 TOTAL ENERGY = -62.2644 RDTITL> * VAN DER WAALS = -26.9692 ELECTROSTATIC = -35.2952 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6118" Parameter: CONF_N -> "8002" Comparing "6118" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6119" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759099 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760153 ATOM PAIRS WERE FOUND FOR ATOM LIST 41741 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29827 from a total of 760153 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6119 -67.42419 5.15977 0.52654 INTE EXTERN> -28.56538 -38.85881 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4242" Parameter: A <- "-67.4242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5654" Parameter: B <- "-28.5654" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8588" Parameter: C <- "-38.8588" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6119 TOTAL ENERGY = -67.4242 RDTITL> * VAN DER WAALS = -28.5654 ELECTROSTATIC = -38.8588 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6119" Parameter: CONF_N -> "8002" Comparing "6119" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6120" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760153 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753302 ATOM PAIRS WERE FOUND FOR ATOM LIST 41439 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30139 from a total of 753302 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6120 -64.08625 -3.33793 0.51188 INTE EXTERN> -29.33534 -34.75091 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.0863" Parameter: A <- "-64.0863" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3353" Parameter: B <- "-29.3353" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7509" Parameter: C <- "-34.7509" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6120 TOTAL ENERGY = -64.0863 RDTITL> * VAN DER WAALS = -29.3353 ELECTROSTATIC = -34.7509 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6120" Parameter: CONF_N -> "8002" Comparing "6120" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6121" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753302 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751942 ATOM PAIRS WERE FOUND FOR ATOM LIST 41475 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29834 from a total of 751942 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6121 -72.86108 8.77482 0.54126 INTE EXTERN> -31.95080 -40.91027 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8611" Parameter: A <- "-72.8611" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9508" Parameter: B <- "-31.9508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9103" Parameter: C <- "-40.9103" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6121 TOTAL ENERGY = -72.8611 RDTITL> * VAN DER WAALS = -31.9508 ELECTROSTATIC = -40.9103 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6121" Parameter: CONF_N -> "8002" Comparing "6121" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6122" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751942 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752337 ATOM PAIRS WERE FOUND FOR ATOM LIST 41425 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30052 from a total of 752337 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6122 -65.07287 -7.78821 0.51643 INTE EXTERN> -30.15660 -34.91627 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0729" Parameter: A <- "-65.0729" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1566" Parameter: B <- "-30.1566" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9163" Parameter: C <- "-34.9163" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6122 TOTAL ENERGY = -65.0729 RDTITL> * VAN DER WAALS = -30.1566 ELECTROSTATIC = -34.9163 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6122" Parameter: CONF_N -> "8002" Comparing "6122" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6123" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752337 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745386 ATOM PAIRS WERE FOUND FOR ATOM LIST 41126 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29475 from a total of 745386 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6123 -68.32372 3.25086 0.46739 INTE EXTERN> -30.93038 -37.39335 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3237" Parameter: A <- "-68.3237" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9304" Parameter: B <- "-30.9304" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3933" Parameter: C <- "-37.3933" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6123 TOTAL ENERGY = -68.3237 RDTITL> * VAN DER WAALS = -30.9304 ELECTROSTATIC = -37.3933 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6123" Parameter: CONF_N -> "8002" Comparing "6123" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6124" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745386 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749789 ATOM PAIRS WERE FOUND FOR ATOM LIST 41327 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29316 from a total of 749789 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6124 -62.08081 -6.24291 0.58386 INTE EXTERN> -27.52062 -34.56019 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.0808" Parameter: A <- "-62.0808" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5206" Parameter: B <- "-27.5206" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5602" Parameter: C <- "-34.5602" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6124 TOTAL ENERGY = -62.0808 RDTITL> * VAN DER WAALS = -27.5206 ELECTROSTATIC = -34.5602 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6124" Parameter: CONF_N -> "8002" Comparing "6124" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6125" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749789 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752356 ATOM PAIRS WERE FOUND FOR ATOM LIST 41408 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29716 from a total of 752356 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6125 -72.14301 10.06220 0.56961 INTE EXTERN> -30.35887 -41.78414 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.143" Parameter: A <- "-72.143" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3589" Parameter: B <- "-30.3589" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7841" Parameter: C <- "-41.7841" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6125 TOTAL ENERGY = -72.143 RDTITL> * VAN DER WAALS = -30.3589 ELECTROSTATIC = -41.7841 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6125" Parameter: CONF_N -> "8002" Comparing "6125" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6126" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752356 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754229 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29960 from a total of 754229 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6126 -67.88384 -4.25917 0.48432 INTE EXTERN> -33.74819 -34.13565 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8838" Parameter: A <- "-67.8838" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7482" Parameter: B <- "-33.7482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1356" Parameter: C <- "-34.1356" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6126 TOTAL ENERGY = -67.8838 RDTITL> * VAN DER WAALS = -33.7482 ELECTROSTATIC = -34.1356 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6126" Parameter: CONF_N -> "8002" Comparing "6126" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6127" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754229 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754836 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30052 from a total of 754836 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6127 -66.45236 -1.43148 0.52754 INTE EXTERN> -29.26864 -37.18372 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4524" Parameter: A <- "-66.4524" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2686" Parameter: B <- "-29.2686" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1837" Parameter: C <- "-37.1837" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6127 TOTAL ENERGY = -66.4524 RDTITL> * VAN DER WAALS = -29.2686 ELECTROSTATIC = -37.1837 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6127" Parameter: CONF_N -> "8002" Comparing "6127" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6128" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754836 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756764 ATOM PAIRS WERE FOUND FOR ATOM LIST 41511 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29991 from a total of 756764 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6128 -70.92056 4.46819 0.70776 INTE EXTERN> -25.60410 -45.31646 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9206" Parameter: A <- "-70.9206" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6041" Parameter: B <- "-25.6041" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3165" Parameter: C <- "-45.3165" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6128 TOTAL ENERGY = -70.9206 RDTITL> * VAN DER WAALS = -25.6041 ELECTROSTATIC = -45.3165 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6128" Parameter: CONF_N -> "8002" Comparing "6128" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6129" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756764 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754428 ATOM PAIRS WERE FOUND FOR ATOM LIST 41370 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29701 from a total of 754428 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6129 -68.41253 -2.50803 0.51687 INTE EXTERN> -28.76607 -39.64646 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4125" Parameter: A <- "-68.4125" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7661" Parameter: B <- "-28.7661" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6465" Parameter: C <- "-39.6465" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6129 TOTAL ENERGY = -68.4125 RDTITL> * VAN DER WAALS = -28.7661 ELECTROSTATIC = -39.6465 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6129" Parameter: CONF_N -> "8002" Comparing "6129" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6130" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754428 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753851 ATOM PAIRS WERE FOUND FOR ATOM LIST 41379 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30297 from a total of 753851 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6130 -63.39440 -5.01813 0.53499 INTE EXTERN> -26.92226 -36.47214 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3944" Parameter: A <- "-63.3944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9223" Parameter: B <- "-26.9223" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4721" Parameter: C <- "-36.4721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6130 TOTAL ENERGY = -63.3944 RDTITL> * VAN DER WAALS = -26.9223 ELECTROSTATIC = -36.4721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6130" Parameter: CONF_N -> "8002" Comparing "6130" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6131" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753851 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751226 ATOM PAIRS WERE FOUND FOR ATOM LIST 41346 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29669 from a total of 751226 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6131 -68.56087 5.16647 0.53936 INTE EXTERN> -29.30591 -39.25495 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5609" Parameter: A <- "-68.5609" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3059" Parameter: B <- "-29.3059" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.255" Parameter: C <- "-39.255" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6131 TOTAL ENERGY = -68.5609 RDTITL> * VAN DER WAALS = -29.3059 ELECTROSTATIC = -39.255 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6131" Parameter: CONF_N -> "8002" Comparing "6131" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6132" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751226 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757803 ATOM PAIRS WERE FOUND FOR ATOM LIST 41573 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29912 from a total of 757803 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6132 -67.19439 -1.36647 0.43049 INTE EXTERN> -32.41884 -34.77555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1944" Parameter: A <- "-67.1944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4188" Parameter: B <- "-32.4188" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7756" Parameter: C <- "-34.7756" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6132 TOTAL ENERGY = -67.1944 RDTITL> * VAN DER WAALS = -32.4188 ELECTROSTATIC = -34.7756 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6132" Parameter: CONF_N -> "8002" Comparing "6132" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6133" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757803 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755351 ATOM PAIRS WERE FOUND FOR ATOM LIST 41605 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30006 from a total of 755351 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6133 -70.59254 3.39815 0.65816 INTE EXTERN> -27.34320 -43.24934 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5925" Parameter: A <- "-70.5925" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3432" Parameter: B <- "-27.3432" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2493" Parameter: C <- "-43.2493" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6133 TOTAL ENERGY = -70.5925 RDTITL> * VAN DER WAALS = -27.3432 ELECTROSTATIC = -43.2493 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6133" Parameter: CONF_N -> "8002" Comparing "6133" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6134" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755351 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752663 ATOM PAIRS WERE FOUND FOR ATOM LIST 41259 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28965 from a total of 752663 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6134 -62.94624 -7.64631 0.58814 INTE EXTERN> -29.59527 -33.35096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9462" Parameter: A <- "-62.9462" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5953" Parameter: B <- "-29.5953" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.351" Parameter: C <- "-33.351" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6134 TOTAL ENERGY = -62.9462 RDTITL> * VAN DER WAALS = -29.5953 ELECTROSTATIC = -33.351 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6134" Parameter: CONF_N -> "8002" Comparing "6134" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6135" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752663 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755451 ATOM PAIRS WERE FOUND FOR ATOM LIST 41603 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30482 from a total of 755451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6135 -68.01736 5.07112 0.54427 INTE EXTERN> -30.74512 -37.27225 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0174" Parameter: A <- "-68.0174" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7451" Parameter: B <- "-30.7451" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.2722" Parameter: C <- "-37.2722" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6135 TOTAL ENERGY = -68.0174 RDTITL> * VAN DER WAALS = -30.7451 ELECTROSTATIC = -37.2722 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6135" Parameter: CONF_N -> "8002" Comparing "6135" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6136" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753596 ATOM PAIRS WERE FOUND FOR ATOM LIST 41353 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30271 from a total of 753596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6136 -77.10699 9.08963 0.59676 INTE EXTERN> -28.92990 -48.17709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.107" Parameter: A <- "-77.107" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9299" Parameter: B <- "-28.9299" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1771" Parameter: C <- "-48.1771" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6136 TOTAL ENERGY = -77.107 RDTITL> * VAN DER WAALS = -28.9299 ELECTROSTATIC = -48.1771 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6136" Parameter: CONF_N -> "8002" Comparing "6136" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6137" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752513 ATOM PAIRS WERE FOUND FOR ATOM LIST 41282 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29734 from a total of 752513 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6137 -68.97064 -8.13635 0.57351 INTE EXTERN> -28.79009 -40.18054 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9706" Parameter: A <- "-68.9706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7901" Parameter: B <- "-28.7901" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1805" Parameter: C <- "-40.1805" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6137 TOTAL ENERGY = -68.9706 RDTITL> * VAN DER WAALS = -28.7901 ELECTROSTATIC = -40.1805 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6137" Parameter: CONF_N -> "8002" Comparing "6137" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6138" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752513 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755738 ATOM PAIRS WERE FOUND FOR ATOM LIST 41504 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30382 from a total of 755738 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6138 -78.64059 9.66995 0.66670 INTE EXTERN> -28.82843 -49.81215 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6406" Parameter: A <- "-78.6406" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8284" Parameter: B <- "-28.8284" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8122" Parameter: C <- "-49.8122" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6138 TOTAL ENERGY = -78.6406 RDTITL> * VAN DER WAALS = -28.8284 ELECTROSTATIC = -49.8122 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6138" Parameter: CONF_N -> "8002" Comparing "6138" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6139" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755738 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753880 ATOM PAIRS WERE FOUND FOR ATOM LIST 41538 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29733 from a total of 753880 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6139 -71.05019 -7.59040 0.52970 INTE EXTERN> -31.88840 -39.16179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0502" Parameter: A <- "-71.0502" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8884" Parameter: B <- "-31.8884" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1618" Parameter: C <- "-39.1618" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6139 TOTAL ENERGY = -71.0502 RDTITL> * VAN DER WAALS = -31.8884 ELECTROSTATIC = -39.1618 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6139" Parameter: CONF_N -> "8002" Comparing "6139" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6140" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753880 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748638 ATOM PAIRS WERE FOUND FOR ATOM LIST 41159 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30252 from a total of 748638 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6140 -69.88984 -1.16035 0.57779 INTE EXTERN> -30.78882 -39.10102 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8898" Parameter: A <- "-69.8898" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7888" Parameter: B <- "-30.7888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.101" Parameter: C <- "-39.101" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6140 TOTAL ENERGY = -69.8898 RDTITL> * VAN DER WAALS = -30.7888 ELECTROSTATIC = -39.101 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6140" Parameter: CONF_N -> "8002" Comparing "6140" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6141" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748638 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746336 ATOM PAIRS WERE FOUND FOR ATOM LIST 41089 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29632 from a total of 746336 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6141 -71.67786 1.78802 0.50161 INTE EXTERN> -33.24396 -38.43390 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6779" Parameter: A <- "-71.6779" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.244" Parameter: B <- "-33.244" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4339" Parameter: C <- "-38.4339" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6141 TOTAL ENERGY = -71.6779 RDTITL> * VAN DER WAALS = -33.244 ELECTROSTATIC = -38.4339 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6141" Parameter: CONF_N -> "8002" Comparing "6141" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6142" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746336 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747721 ATOM PAIRS WERE FOUND FOR ATOM LIST 41180 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30031 from a total of 747721 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6142 -75.89072 4.21286 0.65093 INTE EXTERN> -30.25275 -45.63796 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8907" Parameter: A <- "-75.8907" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2528" Parameter: B <- "-30.2528" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.638" Parameter: C <- "-45.638" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6142 TOTAL ENERGY = -75.8907 RDTITL> * VAN DER WAALS = -30.2528 ELECTROSTATIC = -45.638 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6142" Parameter: CONF_N -> "8002" Comparing "6142" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6143" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747721 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753658 ATOM PAIRS WERE FOUND FOR ATOM LIST 41284 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29676 from a total of 753658 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6143 -70.79447 -5.09625 0.63016 INTE EXTERN> -29.19567 -41.59880 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7945" Parameter: A <- "-70.7945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1957" Parameter: B <- "-29.1957" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5988" Parameter: C <- "-41.5988" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6143 TOTAL ENERGY = -70.7945 RDTITL> * VAN DER WAALS = -29.1957 ELECTROSTATIC = -41.5988 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6143" Parameter: CONF_N -> "8002" Comparing "6143" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6144" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753658 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751603 ATOM PAIRS WERE FOUND FOR ATOM LIST 41205 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30420 from a total of 751603 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6144 -79.20862 8.41415 0.56381 INTE EXTERN> -30.97743 -48.23120 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2086" Parameter: A <- "-79.2086" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9774" Parameter: B <- "-30.9774" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2312" Parameter: C <- "-48.2312" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6144 TOTAL ENERGY = -79.2086 RDTITL> * VAN DER WAALS = -30.9774 ELECTROSTATIC = -48.2312 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6144" Parameter: CONF_N -> "8002" Comparing "6144" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6145" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751603 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751378 ATOM PAIRS WERE FOUND FOR ATOM LIST 41361 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29740 from a total of 751378 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6145 -70.82726 -8.38136 0.55435 INTE EXTERN> -30.08243 -40.74483 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8273" Parameter: A <- "-70.8273" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0824" Parameter: B <- "-30.0824" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7448" Parameter: C <- "-40.7448" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6145 TOTAL ENERGY = -70.8273 RDTITL> * VAN DER WAALS = -30.0824 ELECTROSTATIC = -40.7448 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6145" Parameter: CONF_N -> "8002" Comparing "6145" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6146" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751378 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757402 ATOM PAIRS WERE FOUND FOR ATOM LIST 41449 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30449 from a total of 757402 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6146 -72.89661 2.06935 0.59060 INTE EXTERN> -30.78478 -42.11182 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8966" Parameter: A <- "-72.8966" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7848" Parameter: B <- "-30.7848" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1118" Parameter: C <- "-42.1118" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6146 TOTAL ENERGY = -72.8966 RDTITL> * VAN DER WAALS = -30.7848 ELECTROSTATIC = -42.1118 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6146" Parameter: CONF_N -> "8002" Comparing "6146" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6147" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757402 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748252 ATOM PAIRS WERE FOUND FOR ATOM LIST 41159 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29904 from a total of 748252 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6147 -71.35835 -1.53826 0.61005 INTE EXTERN> -29.32194 -42.03641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3584" Parameter: A <- "-71.3584" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3219" Parameter: B <- "-29.3219" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0364" Parameter: C <- "-42.0364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6147 TOTAL ENERGY = -71.3584 RDTITL> * VAN DER WAALS = -29.3219 ELECTROSTATIC = -42.0364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6147" Parameter: CONF_N -> "8002" Comparing "6147" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6148" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748252 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752233 ATOM PAIRS WERE FOUND FOR ATOM LIST 41334 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30134 from a total of 752233 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6148 -69.73852 -1.61983 0.82884 INTE EXTERN> -21.72396 -48.01455 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7385" Parameter: A <- "-69.7385" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.724" Parameter: B <- "-21.724" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0146" Parameter: C <- "-48.0146" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6148 TOTAL ENERGY = -69.7385 RDTITL> * VAN DER WAALS = -21.724 ELECTROSTATIC = -48.0146 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6148" Parameter: CONF_N -> "8002" Comparing "6148" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6149" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752233 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748637 ATOM PAIRS WERE FOUND FOR ATOM LIST 41141 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30415 from a total of 748637 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6149 -71.04566 1.30714 0.52687 INTE EXTERN> -32.78068 -38.26497 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0457" Parameter: A <- "-71.0457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7807" Parameter: B <- "-32.7807" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.265" Parameter: C <- "-38.265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6149 TOTAL ENERGY = -71.0457 RDTITL> * VAN DER WAALS = -32.7807 ELECTROSTATIC = -38.265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6149" Parameter: CONF_N -> "8002" Comparing "6149" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6150" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748637 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748335 ATOM PAIRS WERE FOUND FOR ATOM LIST 40867 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29929 from a total of 748335 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6150 -74.62704 3.58138 0.61514 INTE EXTERN> -30.41298 -44.21407 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.627" Parameter: A <- "-74.627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.413" Parameter: B <- "-30.413" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2141" Parameter: C <- "-44.2141" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6150 TOTAL ENERGY = -74.627 RDTITL> * VAN DER WAALS = -30.413 ELECTROSTATIC = -44.2141 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6150" Parameter: CONF_N -> "8002" Comparing "6150" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6151" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748335 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748507 ATOM PAIRS WERE FOUND FOR ATOM LIST 41160 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29946 from a total of 748507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6151 -65.95811 -8.66893 0.55426 INTE EXTERN> -30.69000 -35.26811 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9581" Parameter: A <- "-65.9581" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.69" Parameter: B <- "-30.69" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2681" Parameter: C <- "-35.2681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6151 TOTAL ENERGY = -65.9581 RDTITL> * VAN DER WAALS = -30.69 ELECTROSTATIC = -35.2681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6151" Parameter: CONF_N -> "8002" Comparing "6151" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6152" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749228 ATOM PAIRS WERE FOUND FOR ATOM LIST 41077 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29595 from a total of 749228 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6152 -66.93705 0.97894 0.58105 INTE EXTERN> -28.25343 -38.68362 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.937" Parameter: A <- "-66.937" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2534" Parameter: B <- "-28.2534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6836" Parameter: C <- "-38.6836" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6152 TOTAL ENERGY = -66.937 RDTITL> * VAN DER WAALS = -28.2534 ELECTROSTATIC = -38.6836 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6152" Parameter: CONF_N -> "8002" Comparing "6152" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6153" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749228 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754063 ATOM PAIRS WERE FOUND FOR ATOM LIST 41488 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29899 from a total of 754063 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6153 -67.75105 0.81400 0.50791 INTE EXTERN> -32.37005 -35.38100 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.751" Parameter: A <- "-67.751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.37" Parameter: B <- "-32.37" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.381" Parameter: C <- "-35.381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6153 TOTAL ENERGY = -67.751 RDTITL> * VAN DER WAALS = -32.37 ELECTROSTATIC = -35.381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6153" Parameter: CONF_N -> "8002" Comparing "6153" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6154" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754063 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753172 ATOM PAIRS WERE FOUND FOR ATOM LIST 41344 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29932 from a total of 753172 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6154 -76.81132 9.06027 0.49930 INTE EXTERN> -34.54221 -42.26911 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8113" Parameter: A <- "-76.8113" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.5422" Parameter: B <- "-34.5422" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2691" Parameter: C <- "-42.2691" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6154 TOTAL ENERGY = -76.8113 RDTITL> * VAN DER WAALS = -34.5422 ELECTROSTATIC = -42.2691 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6154" Parameter: CONF_N -> "8002" Comparing "6154" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6155" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753172 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755205 ATOM PAIRS WERE FOUND FOR ATOM LIST 41542 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30361 from a total of 755205 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6155 -69.84800 -6.96331 0.51705 INTE EXTERN> -32.99499 -36.85301 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.848" Parameter: A <- "-69.848" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.995" Parameter: B <- "-32.995" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.853" Parameter: C <- "-36.853" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6155 TOTAL ENERGY = -69.848 RDTITL> * VAN DER WAALS = -32.995 ELECTROSTATIC = -36.853 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6155" Parameter: CONF_N -> "8002" Comparing "6155" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6156" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755205 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747969 ATOM PAIRS WERE FOUND FOR ATOM LIST 41089 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29255 from a total of 747969 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6156 -65.71947 -4.12853 0.53445 INTE EXTERN> -30.33457 -35.38491 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7195" Parameter: A <- "-65.7195" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3346" Parameter: B <- "-30.3346" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.3849" Parameter: C <- "-35.3849" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6156 TOTAL ENERGY = -65.7195 RDTITL> * VAN DER WAALS = -30.3346 ELECTROSTATIC = -35.3849 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6156" Parameter: CONF_N -> "8002" Comparing "6156" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6157" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747969 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750733 ATOM PAIRS WERE FOUND FOR ATOM LIST 41030 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29480 from a total of 750733 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6157 -71.72452 6.00505 0.71291 INTE EXTERN> -27.22604 -44.49848 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7245" Parameter: A <- "-71.7245" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.226" Parameter: B <- "-27.226" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4985" Parameter: C <- "-44.4985" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6157 TOTAL ENERGY = -71.7245 RDTITL> * VAN DER WAALS = -27.226 ELECTROSTATIC = -44.4985 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6157" Parameter: CONF_N -> "8002" Comparing "6157" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6158" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750733 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752164 ATOM PAIRS WERE FOUND FOR ATOM LIST 41385 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30145 from a total of 752164 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6158 -74.19574 2.47122 0.54927 INTE EXTERN> -33.60337 -40.59236 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1957" Parameter: A <- "-74.1957" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6034" Parameter: B <- "-33.6034" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5924" Parameter: C <- "-40.5924" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6158 TOTAL ENERGY = -74.1957 RDTITL> * VAN DER WAALS = -33.6034 ELECTROSTATIC = -40.5924 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6158" Parameter: CONF_N -> "8002" Comparing "6158" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6159" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752164 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752129 ATOM PAIRS WERE FOUND FOR ATOM LIST 41388 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29485 from a total of 752129 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6159 -71.61840 -2.57734 0.51519 INTE EXTERN> -34.02390 -37.59450 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6184" Parameter: A <- "-71.6184" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0239" Parameter: B <- "-34.0239" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5945" Parameter: C <- "-37.5945" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6159 TOTAL ENERGY = -71.6184 RDTITL> * VAN DER WAALS = -34.0239 ELECTROSTATIC = -37.5945 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6159" Parameter: CONF_N -> "8002" Comparing "6159" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6160" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752129 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751917 ATOM PAIRS WERE FOUND FOR ATOM LIST 41154 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29204 from a total of 751917 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6160 -67.91904 -3.69936 0.50113 INTE EXTERN> -34.08453 -33.83451 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.919" Parameter: A <- "-67.919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0845" Parameter: B <- "-34.0845" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8345" Parameter: C <- "-33.8345" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6160 TOTAL ENERGY = -67.919 RDTITL> * VAN DER WAALS = -34.0845 ELECTROSTATIC = -33.8345 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6160" Parameter: CONF_N -> "8002" Comparing "6160" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6161" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751917 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747231 ATOM PAIRS WERE FOUND FOR ATOM LIST 40823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29929 from a total of 747231 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6161 -72.73386 4.81482 0.61116 INTE EXTERN> -28.29219 -44.44167 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7339" Parameter: A <- "-72.7339" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2922" Parameter: B <- "-28.2922" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4417" Parameter: C <- "-44.4417" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6161 TOTAL ENERGY = -72.7339 RDTITL> * VAN DER WAALS = -28.2922 ELECTROSTATIC = -44.4417 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6161" Parameter: CONF_N -> "8002" Comparing "6161" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6162" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747231 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746587 ATOM PAIRS WERE FOUND FOR ATOM LIST 40988 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29698 from a total of 746587 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6162 -74.38374 1.64988 0.54457 INTE EXTERN> -33.90394 -40.47980 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3837" Parameter: A <- "-74.3837" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9039" Parameter: B <- "-33.9039" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4798" Parameter: C <- "-40.4798" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6162 TOTAL ENERGY = -74.3837 RDTITL> * VAN DER WAALS = -33.9039 ELECTROSTATIC = -40.4798 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6162" Parameter: CONF_N -> "8002" Comparing "6162" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6163" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746587 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752880 ATOM PAIRS WERE FOUND FOR ATOM LIST 41319 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29698 from a total of 752880 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6163 -70.47450 -3.90924 0.63560 INTE EXTERN> -28.64170 -41.83280 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4745" Parameter: A <- "-70.4745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6417" Parameter: B <- "-28.6417" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8328" Parameter: C <- "-41.8328" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6163 TOTAL ENERGY = -70.4745 RDTITL> * VAN DER WAALS = -28.6417 ELECTROSTATIC = -41.8328 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6163" Parameter: CONF_N -> "8002" Comparing "6163" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6164" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752880 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 742872 ATOM PAIRS WERE FOUND FOR ATOM LIST 40828 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29059 from a total of 742872 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6164 -69.86936 -0.60514 0.54926 INTE EXTERN> -30.94012 -38.92924 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8694" Parameter: A <- "-69.8694" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9401" Parameter: B <- "-30.9401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9292" Parameter: C <- "-38.9292" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6164 TOTAL ENERGY = -69.8694 RDTITL> * VAN DER WAALS = -30.9401 ELECTROSTATIC = -38.9292 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6164" Parameter: CONF_N -> "8002" Comparing "6164" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6165" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 742872 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 743082 ATOM PAIRS WERE FOUND FOR ATOM LIST 40871 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29253 from a total of 743082 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6165 -68.44626 -1.42310 0.62356 INTE EXTERN> -27.59824 -40.84801 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4463" Parameter: A <- "-68.4463" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5982" Parameter: B <- "-27.5982" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.848" Parameter: C <- "-40.848" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6165 TOTAL ENERGY = -68.4463 RDTITL> * VAN DER WAALS = -27.5982 ELECTROSTATIC = -40.848 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6165" Parameter: CONF_N -> "8002" Comparing "6165" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6166" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 743082 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 739229 ATOM PAIRS WERE FOUND FOR ATOM LIST 40528 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29041 from a total of 739229 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6166 -60.17914 -8.26712 0.46421 INTE EXTERN> -32.32388 -27.85526 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.1791" Parameter: A <- "-60.1791" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3239" Parameter: B <- "-32.3239" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.8553" Parameter: C <- "-27.8553" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6166 TOTAL ENERGY = -60.1791 RDTITL> * VAN DER WAALS = -32.3239 ELECTROSTATIC = -27.8553 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6166" Parameter: CONF_N -> "8002" Comparing "6166" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6167" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 739229 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746415 ATOM PAIRS WERE FOUND FOR ATOM LIST 40891 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28860 from a total of 746415 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6167 -60.17524 -0.00390 0.51974 INTE EXTERN> -32.55671 -27.61853 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.1752" Parameter: A <- "-60.1752" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5567" Parameter: B <- "-32.5567" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-27.6185" Parameter: C <- "-27.6185" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6167 TOTAL ENERGY = -60.1752 RDTITL> * VAN DER WAALS = -32.5567 ELECTROSTATIC = -27.6185 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6167" Parameter: CONF_N -> "8002" Comparing "6167" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6168" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746415 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754446 ATOM PAIRS WERE FOUND FOR ATOM LIST 41265 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30640 from a total of 754446 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6168 -65.69878 5.52354 0.64429 INTE EXTERN> -25.51233 -40.18644 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6988" Parameter: A <- "-65.6988" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5123" Parameter: B <- "-25.5123" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1864" Parameter: C <- "-40.1864" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6168 TOTAL ENERGY = -65.6988 RDTITL> * VAN DER WAALS = -25.5123 ELECTROSTATIC = -40.1864 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6168" Parameter: CONF_N -> "8002" Comparing "6168" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6169" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754446 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758090 ATOM PAIRS WERE FOUND FOR ATOM LIST 41581 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30162 from a total of 758090 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6169 -77.16019 11.46142 0.67126 INTE EXTERN> -30.04372 -47.11647 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1602" Parameter: A <- "-77.1602" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0437" Parameter: B <- "-30.0437" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1165" Parameter: C <- "-47.1165" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6169 TOTAL ENERGY = -77.1602 RDTITL> * VAN DER WAALS = -30.0437 ELECTROSTATIC = -47.1165 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6169" Parameter: CONF_N -> "8002" Comparing "6169" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6170" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758090 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753696 ATOM PAIRS WERE FOUND FOR ATOM LIST 41402 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29212 from a total of 753696 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6170 -75.35737 -1.80282 0.50520 INTE EXTERN> -32.83368 -42.52370 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3574" Parameter: A <- "-75.3574" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8337" Parameter: B <- "-32.8337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5237" Parameter: C <- "-42.5237" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6170 TOTAL ENERGY = -75.3574 RDTITL> * VAN DER WAALS = -32.8337 ELECTROSTATIC = -42.5237 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6170" Parameter: CONF_N -> "8002" Comparing "6170" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6171" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753696 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758374 ATOM PAIRS WERE FOUND FOR ATOM LIST 41531 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29903 from a total of 758374 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6171 -74.57385 -0.78353 0.72152 INTE EXTERN> -26.97015 -47.60369 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5738" Parameter: A <- "-74.5738" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9702" Parameter: B <- "-26.9702" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6037" Parameter: C <- "-47.6037" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6171 TOTAL ENERGY = -74.5738 RDTITL> * VAN DER WAALS = -26.9702 ELECTROSTATIC = -47.6037 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6171" Parameter: CONF_N -> "8002" Comparing "6171" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6172" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758374 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752078 ATOM PAIRS WERE FOUND FOR ATOM LIST 41460 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29205 from a total of 752078 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6172 -74.01374 -0.56011 0.49463 INTE EXTERN> -34.25364 -39.76010 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0137" Parameter: A <- "-74.0137" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.2536" Parameter: B <- "-34.2536" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7601" Parameter: C <- "-39.7601" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6172 TOTAL ENERGY = -74.0137 RDTITL> * VAN DER WAALS = -34.2536 ELECTROSTATIC = -39.7601 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6172" Parameter: CONF_N -> "8002" Comparing "6172" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6173" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752078 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750841 ATOM PAIRS WERE FOUND FOR ATOM LIST 41303 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29485 from a total of 750841 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6173 -70.41476 -3.59898 0.57388 INTE EXTERN> -30.28152 -40.13324 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4148" Parameter: A <- "-70.4148" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2815" Parameter: B <- "-30.2815" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1332" Parameter: C <- "-40.1332" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6173 TOTAL ENERGY = -70.4148 RDTITL> * VAN DER WAALS = -30.2815 ELECTROSTATIC = -40.1332 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6173" Parameter: CONF_N -> "8002" Comparing "6173" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6174" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750841 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757627 ATOM PAIRS WERE FOUND FOR ATOM LIST 41730 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29740 from a total of 757627 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6174 -71.61738 1.20262 0.58359 INTE EXTERN> -31.25424 -40.36315 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6174" Parameter: A <- "-71.6174" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2542" Parameter: B <- "-31.2542" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3631" Parameter: C <- "-40.3631" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6174 TOTAL ENERGY = -71.6174 RDTITL> * VAN DER WAALS = -31.2542 ELECTROSTATIC = -40.3631 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6174" Parameter: CONF_N -> "8002" Comparing "6174" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6175" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757627 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752244 ATOM PAIRS WERE FOUND FOR ATOM LIST 41359 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29353 from a total of 752244 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6175 -72.84189 1.22451 0.53690 INTE EXTERN> -31.47753 -41.36435 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8419" Parameter: A <- "-72.8419" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4775" Parameter: B <- "-31.4775" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3644" Parameter: C <- "-41.3644" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6175 TOTAL ENERGY = -72.8419 RDTITL> * VAN DER WAALS = -31.4775 ELECTROSTATIC = -41.3644 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6175" Parameter: CONF_N -> "8002" Comparing "6175" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6176" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752244 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749946 ATOM PAIRS WERE FOUND FOR ATOM LIST 41237 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29489 from a total of 749946 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6176 -76.37709 3.53520 0.60158 INTE EXTERN> -29.01390 -47.36320 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3771" Parameter: A <- "-76.3771" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0139" Parameter: B <- "-29.0139" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3632" Parameter: C <- "-47.3632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6176 TOTAL ENERGY = -76.3771 RDTITL> * VAN DER WAALS = -29.0139 ELECTROSTATIC = -47.3632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6176" Parameter: CONF_N -> "8002" Comparing "6176" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6177" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749946 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749898 ATOM PAIRS WERE FOUND FOR ATOM LIST 41374 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29831 from a total of 749898 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6177 -71.91020 -4.46689 0.61879 INTE EXTERN> -31.26739 -40.64281 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9102" Parameter: A <- "-71.9102" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2674" Parameter: B <- "-31.2674" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6428" Parameter: C <- "-40.6428" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6177 TOTAL ENERGY = -71.9102 RDTITL> * VAN DER WAALS = -31.2674 ELECTROSTATIC = -40.6428 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6177" Parameter: CONF_N -> "8002" Comparing "6177" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6178" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749898 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753339 ATOM PAIRS WERE FOUND FOR ATOM LIST 41591 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30522 from a total of 753339 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6178 -70.72689 -1.18331 0.49200 INTE EXTERN> -34.57072 -36.15617 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7269" Parameter: A <- "-70.7269" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.5707" Parameter: B <- "-34.5707" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1562" Parameter: C <- "-36.1562" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6178 TOTAL ENERGY = -70.7269 RDTITL> * VAN DER WAALS = -34.5707 ELECTROSTATIC = -36.1562 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6178" Parameter: CONF_N -> "8002" Comparing "6178" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6179" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753339 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753291 ATOM PAIRS WERE FOUND FOR ATOM LIST 41386 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29991 from a total of 753291 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6179 -70.44756 -0.27933 0.54719 INTE EXTERN> -32.16587 -38.28169 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4476" Parameter: A <- "-70.4476" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1659" Parameter: B <- "-32.1659" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2817" Parameter: C <- "-38.2817" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6179 TOTAL ENERGY = -70.4476 RDTITL> * VAN DER WAALS = -32.1659 ELECTROSTATIC = -38.2817 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6179" Parameter: CONF_N -> "8002" Comparing "6179" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6180" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753291 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757623 ATOM PAIRS WERE FOUND FOR ATOM LIST 41618 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30098 from a total of 757623 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6180 -73.65914 3.21158 0.53286 INTE EXTERN> -33.90487 -39.75427 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6591" Parameter: A <- "-73.6591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9049" Parameter: B <- "-33.9049" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7543" Parameter: C <- "-39.7543" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6180 TOTAL ENERGY = -73.6591 RDTITL> * VAN DER WAALS = -33.9049 ELECTROSTATIC = -39.7543 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6180" Parameter: CONF_N -> "8002" Comparing "6180" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6181" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757623 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754872 ATOM PAIRS WERE FOUND FOR ATOM LIST 41449 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30077 from a total of 754872 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6181 -69.46183 -4.19731 0.78348 INTE EXTERN> -23.58233 -45.87950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4618" Parameter: A <- "-69.4618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.5823" Parameter: B <- "-23.5823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8795" Parameter: C <- "-45.8795" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6181 TOTAL ENERGY = -69.4618 RDTITL> * VAN DER WAALS = -23.5823 ELECTROSTATIC = -45.8795 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6181" Parameter: CONF_N -> "8002" Comparing "6181" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6182" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754872 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754593 ATOM PAIRS WERE FOUND FOR ATOM LIST 41489 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30127 from a total of 754593 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6182 -70.98124 1.51941 0.67359 INTE EXTERN> -26.17111 -44.81013 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9812" Parameter: A <- "-70.9812" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1711" Parameter: B <- "-26.1711" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8101" Parameter: C <- "-44.8101" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6182 TOTAL ENERGY = -70.9812 RDTITL> * VAN DER WAALS = -26.1711 ELECTROSTATIC = -44.8101 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6182" Parameter: CONF_N -> "8002" Comparing "6182" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6183" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754593 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752951 ATOM PAIRS WERE FOUND FOR ATOM LIST 41196 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29788 from a total of 752951 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6183 -74.89985 3.91861 0.64063 INTE EXTERN> -28.18009 -46.71976 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8998" Parameter: A <- "-74.8998" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1801" Parameter: B <- "-28.1801" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7198" Parameter: C <- "-46.7198" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6183 TOTAL ENERGY = -74.8998 RDTITL> * VAN DER WAALS = -28.1801 ELECTROSTATIC = -46.7198 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6183" Parameter: CONF_N -> "8002" Comparing "6183" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6184" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752951 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754479 ATOM PAIRS WERE FOUND FOR ATOM LIST 41545 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30300 from a total of 754479 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6184 -75.47476 0.57492 0.57770 INTE EXTERN> -31.18875 -44.28602 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4748" Parameter: A <- "-75.4748" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1887" Parameter: B <- "-31.1887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.286" Parameter: C <- "-44.286" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6184 TOTAL ENERGY = -75.4748 RDTITL> * VAN DER WAALS = -31.1887 ELECTROSTATIC = -44.286 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6184" Parameter: CONF_N -> "8002" Comparing "6184" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6185" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754479 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751805 ATOM PAIRS WERE FOUND FOR ATOM LIST 41469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30791 from a total of 751805 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6185 -74.46735 -1.00742 0.64042 INTE EXTERN> -28.11621 -46.35113 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4673" Parameter: A <- "-74.4673" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1162" Parameter: B <- "-28.1162" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3511" Parameter: C <- "-46.3511" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6185 TOTAL ENERGY = -74.4673 RDTITL> * VAN DER WAALS = -28.1162 ELECTROSTATIC = -46.3511 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6185" Parameter: CONF_N -> "8002" Comparing "6185" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6186" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751805 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750233 ATOM PAIRS WERE FOUND FOR ATOM LIST 41238 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30509 from a total of 750233 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6186 -64.43722 -10.03013 0.48128 INTE EXTERN> -32.61805 -31.81916 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.4372" Parameter: A <- "-64.4372" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6181" Parameter: B <- "-32.6181" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.8192" Parameter: C <- "-31.8192" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6186 TOTAL ENERGY = -64.4372 RDTITL> * VAN DER WAALS = -32.6181 ELECTROSTATIC = -31.8192 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6186" Parameter: CONF_N -> "8002" Comparing "6186" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6187" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750233 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754833 ATOM PAIRS WERE FOUND FOR ATOM LIST 41542 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30763 from a total of 754833 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6187 -70.72193 6.28471 0.63315 INTE EXTERN> -26.75838 -43.96354 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7219" Parameter: A <- "-70.7219" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7584" Parameter: B <- "-26.7584" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9635" Parameter: C <- "-43.9635" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6187 TOTAL ENERGY = -70.7219 RDTITL> * VAN DER WAALS = -26.7584 ELECTROSTATIC = -43.9635 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6187" Parameter: CONF_N -> "8002" Comparing "6187" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6188" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754833 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749328 ATOM PAIRS WERE FOUND FOR ATOM LIST 41356 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29747 from a total of 749328 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6188 -72.61393 1.89200 0.60866 INTE EXTERN> -28.58188 -44.03205 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6139" Parameter: A <- "-72.6139" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5819" Parameter: B <- "-28.5819" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.032" Parameter: C <- "-44.032" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6188 TOTAL ENERGY = -72.6139 RDTITL> * VAN DER WAALS = -28.5819 ELECTROSTATIC = -44.032 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6188" Parameter: CONF_N -> "8002" Comparing "6188" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6189" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749328 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752333 ATOM PAIRS WERE FOUND FOR ATOM LIST 41319 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29240 from a total of 752333 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6189 -69.14157 -3.47236 0.46374 INTE EXTERN> -34.84524 -34.29633 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1416" Parameter: A <- "-69.1416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.8452" Parameter: B <- "-34.8452" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.2963" Parameter: C <- "-34.2963" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6189 TOTAL ENERGY = -69.1416 RDTITL> * VAN DER WAALS = -34.8452 ELECTROSTATIC = -34.2963 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6189" Parameter: CONF_N -> "8002" Comparing "6189" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6190" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752333 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749774 ATOM PAIRS WERE FOUND FOR ATOM LIST 41170 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29527 from a total of 749774 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6190 -73.63463 4.49306 0.47339 INTE EXTERN> -34.17907 -39.45556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6346" Parameter: A <- "-73.6346" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1791" Parameter: B <- "-34.1791" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4556" Parameter: C <- "-39.4556" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6190 TOTAL ENERGY = -73.6346 RDTITL> * VAN DER WAALS = -34.1791 ELECTROSTATIC = -39.4556 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6190" Parameter: CONF_N -> "8002" Comparing "6190" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6191" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749774 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761204 ATOM PAIRS WERE FOUND FOR ATOM LIST 41764 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30366 from a total of 761204 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6191 -74.26046 0.62583 0.58947 INTE EXTERN> -33.93866 -40.32181 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2605" Parameter: A <- "-74.2605" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9387" Parameter: B <- "-33.9387" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3218" Parameter: C <- "-40.3218" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6191 TOTAL ENERGY = -74.2605 RDTITL> * VAN DER WAALS = -33.9387 ELECTROSTATIC = -40.3218 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6191" Parameter: CONF_N -> "8002" Comparing "6191" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6192" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761204 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758089 ATOM PAIRS WERE FOUND FOR ATOM LIST 41851 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30288 from a total of 758089 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6192 -70.49493 -3.76554 0.51717 INTE EXTERN> -32.28529 -38.20964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4949" Parameter: A <- "-70.4949" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2853" Parameter: B <- "-32.2853" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2096" Parameter: C <- "-38.2096" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6192 TOTAL ENERGY = -70.4949 RDTITL> * VAN DER WAALS = -32.2853 ELECTROSTATIC = -38.2096 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6192" Parameter: CONF_N -> "8002" Comparing "6192" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6193" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758089 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760417 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30320 from a total of 760417 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6193 -69.00175 -1.49317 0.57703 INTE EXTERN> -32.57333 -36.42842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0018" Parameter: A <- "-69.0018" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5733" Parameter: B <- "-32.5733" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4284" Parameter: C <- "-36.4284" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6193 TOTAL ENERGY = -69.0018 RDTITL> * VAN DER WAALS = -32.5733 ELECTROSTATIC = -36.4284 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6193" Parameter: CONF_N -> "8002" Comparing "6193" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6194" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760417 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758624 ATOM PAIRS WERE FOUND FOR ATOM LIST 41573 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29902 from a total of 758624 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6194 -74.00984 5.00809 0.61039 INTE EXTERN> -29.15403 -44.85581 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0098" Parameter: A <- "-74.0098" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.154" Parameter: B <- "-29.154" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8558" Parameter: C <- "-44.8558" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6194 TOTAL ENERGY = -74.0098 RDTITL> * VAN DER WAALS = -29.154 ELECTROSTATIC = -44.8558 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6194" Parameter: CONF_N -> "8002" Comparing "6194" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6195" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758624 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756262 ATOM PAIRS WERE FOUND FOR ATOM LIST 41854 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29985 from a total of 756262 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6195 -70.36513 -3.64471 0.53330 INTE EXTERN> -31.54512 -38.82001 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3651" Parameter: A <- "-70.3651" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5451" Parameter: B <- "-31.5451" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.82" Parameter: C <- "-38.82" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6195 TOTAL ENERGY = -70.3651 RDTITL> * VAN DER WAALS = -31.5451 ELECTROSTATIC = -38.82 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6195" Parameter: CONF_N -> "8002" Comparing "6195" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6196" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756262 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752937 ATOM PAIRS WERE FOUND FOR ATOM LIST 41463 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29529 from a total of 752937 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6196 -66.13953 -4.22560 0.54488 INTE EXTERN> -32.59565 -33.54388 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1395" Parameter: A <- "-66.1395" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5956" Parameter: B <- "-32.5956" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.5439" Parameter: C <- "-33.5439" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6196 TOTAL ENERGY = -66.1395 RDTITL> * VAN DER WAALS = -32.5956 ELECTROSTATIC = -33.5439 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6196" Parameter: CONF_N -> "8002" Comparing "6196" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6197" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752937 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751963 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30151 from a total of 751963 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6197 -75.47938 9.33985 0.60702 INTE EXTERN> -30.23003 -45.24935 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4794" Parameter: A <- "-75.4794" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.23" Parameter: B <- "-30.23" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2493" Parameter: C <- "-45.2493" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6197 TOTAL ENERGY = -75.4794 RDTITL> * VAN DER WAALS = -30.23 ELECTROSTATIC = -45.2493 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6197" Parameter: CONF_N -> "8002" Comparing "6197" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6198" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751963 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758808 ATOM PAIRS WERE FOUND FOR ATOM LIST 41657 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30063 from a total of 758808 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6198 -69.44878 -6.03060 0.49821 INTE EXTERN> -31.67125 -37.77753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4488" Parameter: A <- "-69.4488" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6713" Parameter: B <- "-31.6713" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7775" Parameter: C <- "-37.7775" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6198 TOTAL ENERGY = -69.4488 RDTITL> * VAN DER WAALS = -31.6713 ELECTROSTATIC = -37.7775 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6198" Parameter: CONF_N -> "8002" Comparing "6198" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6199" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758808 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754826 ATOM PAIRS WERE FOUND FOR ATOM LIST 41348 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29954 from a total of 754826 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6199 -78.04645 8.59768 0.55524 INTE EXTERN> -34.29300 -43.75346 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0465" Parameter: A <- "-78.0465" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.293" Parameter: B <- "-34.293" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7535" Parameter: C <- "-43.7535" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6199 TOTAL ENERGY = -78.0465 RDTITL> * VAN DER WAALS = -34.293 ELECTROSTATIC = -43.7535 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6199" Parameter: CONF_N -> "8002" Comparing "6199" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6200" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754826 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757201 ATOM PAIRS WERE FOUND FOR ATOM LIST 41702 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30654 from a total of 757201 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6200 -68.27583 -9.77062 0.71786 INTE EXTERN> -26.12084 -42.15499 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2758" Parameter: A <- "-68.2758" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1208" Parameter: B <- "-26.1208" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.155" Parameter: C <- "-42.155" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6200 TOTAL ENERGY = -68.2758 RDTITL> * VAN DER WAALS = -26.1208 ELECTROSTATIC = -42.155 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6200" Parameter: CONF_N -> "8002" Comparing "6200" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6201" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757201 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755320 ATOM PAIRS WERE FOUND FOR ATOM LIST 41523 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30274 from a total of 755320 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6201 -72.26644 3.99061 0.58358 INTE EXTERN> -32.37306 -39.89338 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2664" Parameter: A <- "-72.2664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3731" Parameter: B <- "-32.3731" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8934" Parameter: C <- "-39.8934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6201 TOTAL ENERGY = -72.2664 RDTITL> * VAN DER WAALS = -32.3731 ELECTROSTATIC = -39.8934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6201" Parameter: CONF_N -> "8002" Comparing "6201" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6202" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755320 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756674 ATOM PAIRS WERE FOUND FOR ATOM LIST 41612 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29974 from a total of 756674 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6202 -69.43893 -2.82751 0.57279 INTE EXTERN> -28.36156 -41.07736 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4389" Parameter: A <- "-69.4389" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3616" Parameter: B <- "-28.3616" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0774" Parameter: C <- "-41.0774" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6202 TOTAL ENERGY = -69.4389 RDTITL> * VAN DER WAALS = -28.3616 ELECTROSTATIC = -41.0774 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6202" Parameter: CONF_N -> "8002" Comparing "6202" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6203" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756674 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760483 ATOM PAIRS WERE FOUND FOR ATOM LIST 41848 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30640 from a total of 760483 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6203 -74.40669 4.96776 0.60276 INTE EXTERN> -32.26953 -42.13716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4067" Parameter: A <- "-74.4067" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2695" Parameter: B <- "-32.2695" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1372" Parameter: C <- "-42.1372" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6203 TOTAL ENERGY = -74.4067 RDTITL> * VAN DER WAALS = -32.2695 ELECTROSTATIC = -42.1372 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6203" Parameter: CONF_N -> "8002" Comparing "6203" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6204" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760483 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757186 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29367 from a total of 757186 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6204 -68.71652 -5.69017 0.53294 INTE EXTERN> -31.34795 -37.36857 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7165" Parameter: A <- "-68.7165" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.348" Parameter: B <- "-31.348" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3686" Parameter: C <- "-37.3686" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6204 TOTAL ENERGY = -68.7165 RDTITL> * VAN DER WAALS = -31.348 ELECTROSTATIC = -37.3686 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6204" Parameter: CONF_N -> "8002" Comparing "6204" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6205" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757186 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758723 ATOM PAIRS WERE FOUND FOR ATOM LIST 41666 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30171 from a total of 758723 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6205 -70.69713 1.98061 0.69573 INTE EXTERN> -31.79486 -38.90227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6971" Parameter: A <- "-70.6971" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7949" Parameter: B <- "-31.7949" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9023" Parameter: C <- "-38.9023" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6205 TOTAL ENERGY = -70.6971 RDTITL> * VAN DER WAALS = -31.7949 ELECTROSTATIC = -38.9023 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6205" Parameter: CONF_N -> "8002" Comparing "6205" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6206" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758723 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750761 ATOM PAIRS WERE FOUND FOR ATOM LIST 41244 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29434 from a total of 750761 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6206 -72.68572 1.98858 0.58712 INTE EXTERN> -29.52659 -43.15913 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6857" Parameter: A <- "-72.6857" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5266" Parameter: B <- "-29.5266" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1591" Parameter: C <- "-43.1591" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6206 TOTAL ENERGY = -72.6857 RDTITL> * VAN DER WAALS = -29.5266 ELECTROSTATIC = -43.1591 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6206" Parameter: CONF_N -> "8002" Comparing "6206" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6207" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750761 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753725 ATOM PAIRS WERE FOUND FOR ATOM LIST 41378 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30109 from a total of 753725 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6207 -74.66438 1.97867 0.67707 INTE EXTERN> -29.15652 -45.50786 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6644" Parameter: A <- "-74.6644" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1565" Parameter: B <- "-29.1565" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5079" Parameter: C <- "-45.5079" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6207 TOTAL ENERGY = -74.6644 RDTITL> * VAN DER WAALS = -29.1565 ELECTROSTATIC = -45.5079 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6207" Parameter: CONF_N -> "8002" Comparing "6207" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6208" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753725 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751545 ATOM PAIRS WERE FOUND FOR ATOM LIST 41341 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29660 from a total of 751545 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6208 -65.92470 -8.73968 0.56016 INTE EXTERN> -28.72889 -37.19581 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9247" Parameter: A <- "-65.9247" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7289" Parameter: B <- "-28.7289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1958" Parameter: C <- "-37.1958" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6208 TOTAL ENERGY = -65.9247 RDTITL> * VAN DER WAALS = -28.7289 ELECTROSTATIC = -37.1958 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6208" Parameter: CONF_N -> "8002" Comparing "6208" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6209" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751545 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747921 ATOM PAIRS WERE FOUND FOR ATOM LIST 41166 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30202 from a total of 747921 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6209 -71.25019 5.32549 0.51821 INTE EXTERN> -31.15893 -40.09126 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2502" Parameter: A <- "-71.2502" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1589" Parameter: B <- "-31.1589" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0913" Parameter: C <- "-40.0913" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6209 TOTAL ENERGY = -71.2502 RDTITL> * VAN DER WAALS = -31.1589 ELECTROSTATIC = -40.0913 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6209" Parameter: CONF_N -> "8002" Comparing "6209" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6210" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747921 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750470 ATOM PAIRS WERE FOUND FOR ATOM LIST 41228 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29750 from a total of 750470 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6210 -71.90151 0.65132 0.61425 INTE EXTERN> -29.23665 -42.66486 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9015" Parameter: A <- "-71.9015" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2367" Parameter: B <- "-29.2367" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6649" Parameter: C <- "-42.6649" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6210 TOTAL ENERGY = -71.9015 RDTITL> * VAN DER WAALS = -29.2367 ELECTROSTATIC = -42.6649 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6210" Parameter: CONF_N -> "8002" Comparing "6210" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6211" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750470 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754126 ATOM PAIRS WERE FOUND FOR ATOM LIST 41472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30038 from a total of 754126 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6211 -77.14272 5.24120 0.53022 INTE EXTERN> -34.21741 -42.92530 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1427" Parameter: A <- "-77.1427" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.2174" Parameter: B <- "-34.2174" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9253" Parameter: C <- "-42.9253" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6211 TOTAL ENERGY = -77.1427 RDTITL> * VAN DER WAALS = -34.2174 ELECTROSTATIC = -42.9253 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6211" Parameter: CONF_N -> "8002" Comparing "6211" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6212" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754126 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750544 ATOM PAIRS WERE FOUND FOR ATOM LIST 41277 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29702 from a total of 750544 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6212 -74.16109 -2.98163 0.63344 INTE EXTERN> -27.34218 -46.81891 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1611" Parameter: A <- "-74.1611" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3422" Parameter: B <- "-27.3422" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8189" Parameter: C <- "-46.8189" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6212 TOTAL ENERGY = -74.1611 RDTITL> * VAN DER WAALS = -27.3422 ELECTROSTATIC = -46.8189 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6212" Parameter: CONF_N -> "8002" Comparing "6212" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6213" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750544 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750553 ATOM PAIRS WERE FOUND FOR ATOM LIST 41478 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29948 from a total of 750553 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6213 -73.04270 -1.11839 0.63362 INTE EXTERN> -28.94510 -44.09760 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0427" Parameter: A <- "-73.0427" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9451" Parameter: B <- "-28.9451" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0976" Parameter: C <- "-44.0976" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6213 TOTAL ENERGY = -73.0427 RDTITL> * VAN DER WAALS = -28.9451 ELECTROSTATIC = -44.0976 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6213" Parameter: CONF_N -> "8002" Comparing "6213" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6214" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750553 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749786 ATOM PAIRS WERE FOUND FOR ATOM LIST 41324 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29659 from a total of 749786 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6214 -74.47138 1.42868 0.64187 INTE EXTERN> -28.47793 -45.99345 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4714" Parameter: A <- "-74.4714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4779" Parameter: B <- "-28.4779" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9934" Parameter: C <- "-45.9934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6214 TOTAL ENERGY = -74.4714 RDTITL> * VAN DER WAALS = -28.4779 ELECTROSTATIC = -45.9934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6214" Parameter: CONF_N -> "8002" Comparing "6214" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6215" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749786 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754587 ATOM PAIRS WERE FOUND FOR ATOM LIST 41482 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29937 from a total of 754587 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6215 -73.00953 -1.46185 0.50528 INTE EXTERN> -32.94258 -40.06695 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0095" Parameter: A <- "-73.0095" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9426" Parameter: B <- "-32.9426" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.067" Parameter: C <- "-40.067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6215 TOTAL ENERGY = -73.0095 RDTITL> * VAN DER WAALS = -32.9426 ELECTROSTATIC = -40.067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6215" Parameter: CONF_N -> "8002" Comparing "6215" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6216" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754587 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 743918 ATOM PAIRS WERE FOUND FOR ATOM LIST 41097 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29853 from a total of 743918 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6216 -68.34618 -4.66335 0.63800 INTE EXTERN> -28.81821 -39.52797 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3462" Parameter: A <- "-68.3462" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8182" Parameter: B <- "-28.8182" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.528" Parameter: C <- "-39.528" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6216 TOTAL ENERGY = -68.3462 RDTITL> * VAN DER WAALS = -28.8182 ELECTROSTATIC = -39.528 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6216" Parameter: CONF_N -> "8002" Comparing "6216" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6217" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 743918 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748455 ATOM PAIRS WERE FOUND FOR ATOM LIST 41219 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29982 from a total of 748455 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6217 -73.69824 5.35206 0.57534 INTE EXTERN> -31.90109 -41.79715 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6982" Parameter: A <- "-73.6982" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9011" Parameter: B <- "-31.9011" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7972" Parameter: C <- "-41.7972" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6217 TOTAL ENERGY = -73.6982 RDTITL> * VAN DER WAALS = -31.9011 ELECTROSTATIC = -41.7972 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6217" Parameter: CONF_N -> "8002" Comparing "6217" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6218" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748455 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754910 ATOM PAIRS WERE FOUND FOR ATOM LIST 41409 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30769 from a total of 754910 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6218 -72.98197 -0.71627 0.62701 INTE EXTERN> -31.55492 -41.42706 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.982" Parameter: A <- "-72.982" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5549" Parameter: B <- "-31.5549" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4271" Parameter: C <- "-41.4271" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6218 TOTAL ENERGY = -72.982 RDTITL> * VAN DER WAALS = -31.5549 ELECTROSTATIC = -41.4271 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6218" Parameter: CONF_N -> "8002" Comparing "6218" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6219" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754910 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752987 ATOM PAIRS WERE FOUND FOR ATOM LIST 41407 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29999 from a total of 752987 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6219 -81.26868 8.28671 0.55809 INTE EXTERN> -33.18922 -48.07946 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.2687" Parameter: A <- "-81.2687" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1892" Parameter: B <- "-33.1892" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0795" Parameter: C <- "-48.0795" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6219 TOTAL ENERGY = -81.2687 RDTITL> * VAN DER WAALS = -33.1892 ELECTROSTATIC = -48.0795 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6219" Parameter: CONF_N -> "8002" Comparing "6219" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6220" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752987 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751847 ATOM PAIRS WERE FOUND FOR ATOM LIST 41302 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29680 from a total of 751847 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6220 -71.11814 -10.15054 0.59056 INTE EXTERN> -28.71858 -42.39956 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1181" Parameter: A <- "-71.1181" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7186" Parameter: B <- "-28.7186" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3996" Parameter: C <- "-42.3996" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6220 TOTAL ENERGY = -71.1181 RDTITL> * VAN DER WAALS = -28.7186 ELECTROSTATIC = -42.3996 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6220" Parameter: CONF_N -> "8002" Comparing "6220" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6221" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751847 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756365 ATOM PAIRS WERE FOUND FOR ATOM LIST 41510 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29881 from a total of 756365 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6221 -66.30159 -4.81655 0.54681 INTE EXTERN> -32.15478 -34.14681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3016" Parameter: A <- "-66.3016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1548" Parameter: B <- "-32.1548" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1468" Parameter: C <- "-34.1468" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6221 TOTAL ENERGY = -66.3016 RDTITL> * VAN DER WAALS = -32.1548 ELECTROSTATIC = -34.1468 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6221" Parameter: CONF_N -> "8002" Comparing "6221" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6222" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756365 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756706 ATOM PAIRS WERE FOUND FOR ATOM LIST 41576 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29728 from a total of 756706 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6222 -70.18455 3.88296 0.50988 INTE EXTERN> -33.89035 -36.29420 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1845" Parameter: A <- "-70.1845" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8904" Parameter: B <- "-33.8904" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2942" Parameter: C <- "-36.2942" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6222 TOTAL ENERGY = -70.1845 RDTITL> * VAN DER WAALS = -33.8904 ELECTROSTATIC = -36.2942 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6222" Parameter: CONF_N -> "8002" Comparing "6222" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6223" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756706 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755676 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30061 from a total of 755676 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6223 -69.66593 -0.51862 0.53779 INTE EXTERN> -35.68382 -33.98211 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6659" Parameter: A <- "-69.6659" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.6838" Parameter: B <- "-35.6838" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9821" Parameter: C <- "-33.9821" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6223 TOTAL ENERGY = -69.6659 RDTITL> * VAN DER WAALS = -35.6838 ELECTROSTATIC = -33.9821 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6223" Parameter: CONF_N -> "8002" Comparing "6223" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6224" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755676 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757509 ATOM PAIRS WERE FOUND FOR ATOM LIST 41358 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29465 from a total of 757509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6224 -71.11093 1.44500 0.67540 INTE EXTERN> -25.27367 -45.83726 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1109" Parameter: A <- "-71.1109" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2737" Parameter: B <- "-25.2737" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8373" Parameter: C <- "-45.8373" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6224 TOTAL ENERGY = -71.1109 RDTITL> * VAN DER WAALS = -25.2737 ELECTROSTATIC = -45.8373 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6224" Parameter: CONF_N -> "8002" Comparing "6224" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6225" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758550 ATOM PAIRS WERE FOUND FOR ATOM LIST 41711 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29959 from a total of 758550 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6225 -66.91280 -4.19814 0.49064 INTE EXTERN> -36.96370 -29.94910 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9128" Parameter: A <- "-66.9128" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.9637" Parameter: B <- "-36.9637" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-29.9491" Parameter: C <- "-29.9491" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6225 TOTAL ENERGY = -66.9128 RDTITL> * VAN DER WAALS = -36.9637 ELECTROSTATIC = -29.9491 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6225" Parameter: CONF_N -> "8002" Comparing "6225" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6226" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758550 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750728 ATOM PAIRS WERE FOUND FOR ATOM LIST 41368 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29723 from a total of 750728 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6226 -75.85207 8.93928 0.57465 INTE EXTERN> -31.15243 -44.69964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8521" Parameter: A <- "-75.8521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1524" Parameter: B <- "-31.1524" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6996" Parameter: C <- "-44.6996" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6226 TOTAL ENERGY = -75.8521 RDTITL> * VAN DER WAALS = -31.1524 ELECTROSTATIC = -44.6996 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6226" Parameter: CONF_N -> "8002" Comparing "6226" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6227" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750728 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748212 ATOM PAIRS WERE FOUND FOR ATOM LIST 40955 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29679 from a total of 748212 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6227 -73.36050 -2.49157 0.49846 INTE EXTERN> -34.67164 -38.68885 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3605" Parameter: A <- "-73.3605" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.6716" Parameter: B <- "-34.6716" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6889" Parameter: C <- "-38.6889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6227 TOTAL ENERGY = -73.3605 RDTITL> * VAN DER WAALS = -34.6716 ELECTROSTATIC = -38.6889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6227" Parameter: CONF_N -> "8002" Comparing "6227" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6228" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748212 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748856 ATOM PAIRS WERE FOUND FOR ATOM LIST 41084 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29328 from a total of 748856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6228 -64.89094 -8.46956 0.53441 INTE EXTERN> -31.65070 -33.24024 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8909" Parameter: A <- "-64.8909" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6507" Parameter: B <- "-31.6507" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2402" Parameter: C <- "-33.2402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6228 TOTAL ENERGY = -64.8909 RDTITL> * VAN DER WAALS = -31.6507 ELECTROSTATIC = -33.2402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6228" Parameter: CONF_N -> "8002" Comparing "6228" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6229" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752135 ATOM PAIRS WERE FOUND FOR ATOM LIST 41267 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30173 from a total of 752135 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6229 -68.45971 3.56877 0.62029 INTE EXTERN> -31.03303 -37.42668 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4597" Parameter: A <- "-68.4597" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.033" Parameter: B <- "-31.033" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4267" Parameter: C <- "-37.4267" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6229 TOTAL ENERGY = -68.4597 RDTITL> * VAN DER WAALS = -31.033 ELECTROSTATIC = -37.4267 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6229" Parameter: CONF_N -> "8002" Comparing "6229" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6230" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752135 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749606 ATOM PAIRS WERE FOUND FOR ATOM LIST 40794 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29443 from a total of 749606 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6230 -69.85614 1.39643 0.43987 INTE EXTERN> -34.22398 -35.63216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8561" Parameter: A <- "-69.8561" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.224" Parameter: B <- "-34.224" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.6322" Parameter: C <- "-35.6322" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6230 TOTAL ENERGY = -69.8561 RDTITL> * VAN DER WAALS = -34.224 ELECTROSTATIC = -35.6322 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6230" Parameter: CONF_N -> "8002" Comparing "6230" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6231" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749606 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753478 ATOM PAIRS WERE FOUND FOR ATOM LIST 41335 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29510 from a total of 753478 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6231 -70.85176 0.99563 0.59951 INTE EXTERN> -30.82432 -40.02744 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8518" Parameter: A <- "-70.8518" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8243" Parameter: B <- "-30.8243" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0274" Parameter: C <- "-40.0274" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6231 TOTAL ENERGY = -70.8518 RDTITL> * VAN DER WAALS = -30.8243 ELECTROSTATIC = -40.0274 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6231" Parameter: CONF_N -> "8002" Comparing "6231" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6232" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753478 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749550 ATOM PAIRS WERE FOUND FOR ATOM LIST 41321 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29062 from a total of 749550 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6232 -62.03588 -8.81588 0.71465 INTE EXTERN> -24.44837 -37.58752 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.0359" Parameter: A <- "-62.0359" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4484" Parameter: B <- "-24.4484" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5875" Parameter: C <- "-37.5875" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6232 TOTAL ENERGY = -62.0359 RDTITL> * VAN DER WAALS = -24.4484 ELECTROSTATIC = -37.5875 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6232" Parameter: CONF_N -> "8002" Comparing "6232" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6233" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749550 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744886 ATOM PAIRS WERE FOUND FOR ATOM LIST 40858 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29368 from a total of 744886 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6233 -75.72869 13.69280 0.64612 INTE EXTERN> -28.94850 -46.78019 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7287" Parameter: A <- "-75.7287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9485" Parameter: B <- "-28.9485" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7802" Parameter: C <- "-46.7802" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6233 TOTAL ENERGY = -75.7287 RDTITL> * VAN DER WAALS = -28.9485 ELECTROSTATIC = -46.7802 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6233" Parameter: CONF_N -> "8002" Comparing "6233" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6234" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744886 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754072 ATOM PAIRS WERE FOUND FOR ATOM LIST 41174 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29563 from a total of 754072 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6234 -63.78100 -11.94768 0.55587 INTE EXTERN> -28.17204 -35.60897 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.781" Parameter: A <- "-63.781" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.172" Parameter: B <- "-28.172" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.609" Parameter: C <- "-35.609" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6234 TOTAL ENERGY = -63.781 RDTITL> * VAN DER WAALS = -28.172 ELECTROSTATIC = -35.609 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6234" Parameter: CONF_N -> "8002" Comparing "6234" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6235" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754072 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755046 ATOM PAIRS WERE FOUND FOR ATOM LIST 41457 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29411 from a total of 755046 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6235 -57.41642 -6.36459 0.46658 INTE EXTERN> -31.47196 -25.94446 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-57.4164" Parameter: A <- "-57.4164" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.472" Parameter: B <- "-31.472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-25.9445" Parameter: C <- "-25.9445" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6235 TOTAL ENERGY = -57.4164 RDTITL> * VAN DER WAALS = -31.472 ELECTROSTATIC = -25.9445 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6235" Parameter: CONF_N -> "8002" Comparing "6235" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6236" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755046 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748257 ATOM PAIRS WERE FOUND FOR ATOM LIST 41086 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29440 from a total of 748257 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6236 -64.25675 6.84033 0.55856 INTE EXTERN> -31.56929 -32.68746 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2568" Parameter: A <- "-64.2568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5693" Parameter: B <- "-31.5693" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.6875" Parameter: C <- "-32.6875" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6236 TOTAL ENERGY = -64.2568 RDTITL> * VAN DER WAALS = -31.5693 ELECTROSTATIC = -32.6875 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6236" Parameter: CONF_N -> "8002" Comparing "6236" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6237" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748257 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753304 ATOM PAIRS WERE FOUND FOR ATOM LIST 41282 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28913 from a total of 753304 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6237 -71.73601 7.47926 0.50333 INTE EXTERN> -32.35488 -39.38113 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.736" Parameter: A <- "-71.736" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3549" Parameter: B <- "-32.3549" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3811" Parameter: C <- "-39.3811" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6237 TOTAL ENERGY = -71.736 RDTITL> * VAN DER WAALS = -32.3549 ELECTROSTATIC = -39.3811 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6237" Parameter: CONF_N -> "8002" Comparing "6237" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6238" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753304 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756274 ATOM PAIRS WERE FOUND FOR ATOM LIST 41743 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29855 from a total of 756274 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6238 -70.94350 -0.79251 0.57133 INTE EXTERN> -31.50590 -39.43760 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9435" Parameter: A <- "-70.9435" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5059" Parameter: B <- "-31.5059" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4376" Parameter: C <- "-39.4376" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6238 TOTAL ENERGY = -70.9435 RDTITL> * VAN DER WAALS = -31.5059 ELECTROSTATIC = -39.4376 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6238" Parameter: CONF_N -> "8002" Comparing "6238" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6239" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756274 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758196 ATOM PAIRS WERE FOUND FOR ATOM LIST 41672 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29180 from a total of 758196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6239 -59.73560 -11.20790 0.56071 INTE EXTERN> -29.57020 -30.16540 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.7356" Parameter: A <- "-59.7356" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5702" Parameter: B <- "-29.5702" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.1654" Parameter: C <- "-30.1654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6239 TOTAL ENERGY = -59.7356 RDTITL> * VAN DER WAALS = -29.5702 ELECTROSTATIC = -30.1654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6239" Parameter: CONF_N -> "8002" Comparing "6239" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6240" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755333 ATOM PAIRS WERE FOUND FOR ATOM LIST 41533 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29540 from a total of 755333 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6240 -67.30710 7.57150 0.57266 INTE EXTERN> -32.42437 -34.88272 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3071" Parameter: A <- "-67.3071" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4244" Parameter: B <- "-32.4244" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8827" Parameter: C <- "-34.8827" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6240 TOTAL ENERGY = -67.3071 RDTITL> * VAN DER WAALS = -32.4244 ELECTROSTATIC = -34.8827 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6240" Parameter: CONF_N -> "8002" Comparing "6240" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6241" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755333 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 741594 ATOM PAIRS WERE FOUND FOR ATOM LIST 40878 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28693 from a total of 741594 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6241 -67.68749 0.38039 0.56207 INTE EXTERN> -29.83523 -37.85226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6875" Parameter: A <- "-67.6875" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8352" Parameter: B <- "-29.8352" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8523" Parameter: C <- "-37.8523" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6241 TOTAL ENERGY = -67.6875 RDTITL> * VAN DER WAALS = -29.8352 ELECTROSTATIC = -37.8523 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6241" Parameter: CONF_N -> "8002" Comparing "6241" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6242" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 741594 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753738 ATOM PAIRS WERE FOUND FOR ATOM LIST 41473 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30211 from a total of 753738 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6242 -66.92087 -0.76662 0.61029 INTE EXTERN> -33.05309 -33.86777 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9209" Parameter: A <- "-66.9209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0531" Parameter: B <- "-33.0531" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8678" Parameter: C <- "-33.8678" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6242 TOTAL ENERGY = -66.9209 RDTITL> * VAN DER WAALS = -33.0531 ELECTROSTATIC = -33.8678 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6242" Parameter: CONF_N -> "8002" Comparing "6242" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6243" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753738 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29935 from a total of 752110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6243 -70.53012 3.60925 0.63310 INTE EXTERN> -25.45054 -45.07958 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5301" Parameter: A <- "-70.5301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4505" Parameter: B <- "-25.4505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0796" Parameter: C <- "-45.0796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6243 TOTAL ENERGY = -70.5301 RDTITL> * VAN DER WAALS = -25.4505 ELECTROSTATIC = -45.0796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6243" Parameter: CONF_N -> "8002" Comparing "6243" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6244" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751164 ATOM PAIRS WERE FOUND FOR ATOM LIST 41407 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29273 from a total of 751164 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6244 -67.85843 -2.67169 0.55666 INTE EXTERN> -30.83026 -37.02818 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8584" Parameter: A <- "-67.8584" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8303" Parameter: B <- "-30.8303" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.0282" Parameter: C <- "-37.0282" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6244 TOTAL ENERGY = -67.8584 RDTITL> * VAN DER WAALS = -30.8303 ELECTROSTATIC = -37.0282 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6244" Parameter: CONF_N -> "8002" Comparing "6244" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6245" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751164 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747005 ATOM PAIRS WERE FOUND FOR ATOM LIST 41093 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29752 from a total of 747005 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6245 -71.52398 3.66554 0.48295 INTE EXTERN> -33.58049 -37.94348 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.524" Parameter: A <- "-71.524" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5805" Parameter: B <- "-33.5805" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9435" Parameter: C <- "-37.9435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6245 TOTAL ENERGY = -71.524 RDTITL> * VAN DER WAALS = -33.5805 ELECTROSTATIC = -37.9435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6245" Parameter: CONF_N -> "8002" Comparing "6245" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6246" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747005 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750990 ATOM PAIRS WERE FOUND FOR ATOM LIST 40979 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30069 from a total of 750990 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6246 -69.36932 -2.15466 0.70049 INTE EXTERN> -26.12005 -43.24926 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3693" Parameter: A <- "-69.3693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1201" Parameter: B <- "-26.1201" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2493" Parameter: C <- "-43.2493" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6246 TOTAL ENERGY = -69.3693 RDTITL> * VAN DER WAALS = -26.1201 ELECTROSTATIC = -43.2493 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6246" Parameter: CONF_N -> "8002" Comparing "6246" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6247" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750990 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753247 ATOM PAIRS WERE FOUND FOR ATOM LIST 41377 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30107 from a total of 753247 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6247 -69.67946 0.31014 0.57471 INTE EXTERN> -28.06757 -41.61189 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6795" Parameter: A <- "-69.6795" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0676" Parameter: B <- "-28.0676" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6119" Parameter: C <- "-41.6119" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6247 TOTAL ENERGY = -69.6795 RDTITL> * VAN DER WAALS = -28.0676 ELECTROSTATIC = -41.6119 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6247" Parameter: CONF_N -> "8002" Comparing "6247" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6248" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753247 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41277 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29943 from a total of 753110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6248 -71.38046 1.70100 0.55987 INTE EXTERN> -30.50939 -40.87107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3805" Parameter: A <- "-71.3805" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5094" Parameter: B <- "-30.5094" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8711" Parameter: C <- "-40.8711" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6248 TOTAL ENERGY = -71.3805 RDTITL> * VAN DER WAALS = -30.5094 ELECTROSTATIC = -40.8711 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6248" Parameter: CONF_N -> "8002" Comparing "6248" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6249" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745003 ATOM PAIRS WERE FOUND FOR ATOM LIST 40840 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29429 from a total of 745003 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6249 -69.48614 -1.89432 0.51176 INTE EXTERN> -32.18597 -37.30017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4861" Parameter: A <- "-69.4861" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.186" Parameter: B <- "-32.186" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.3002" Parameter: C <- "-37.3002" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6249 TOTAL ENERGY = -69.4861 RDTITL> * VAN DER WAALS = -32.186 ELECTROSTATIC = -37.3002 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6249" Parameter: CONF_N -> "8002" Comparing "6249" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6250" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745003 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748578 ATOM PAIRS WERE FOUND FOR ATOM LIST 41202 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29491 from a total of 748578 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6250 -69.19783 -0.28832 0.49604 INTE EXTERN> -32.24213 -36.95570 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1978" Parameter: A <- "-69.1978" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2421" Parameter: B <- "-32.2421" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9557" Parameter: C <- "-36.9557" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6250 TOTAL ENERGY = -69.1978 RDTITL> * VAN DER WAALS = -32.2421 ELECTROSTATIC = -36.9557 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6250" Parameter: CONF_N -> "8002" Comparing "6250" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6251" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748578 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751040 ATOM PAIRS WERE FOUND FOR ATOM LIST 41335 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 31036 from a total of 751040 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6251 -71.03811 1.84028 0.55710 INTE EXTERN> -31.61513 -39.42298 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0381" Parameter: A <- "-71.0381" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6151" Parameter: B <- "-31.6151" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.423" Parameter: C <- "-39.423" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6251 TOTAL ENERGY = -71.0381 RDTITL> * VAN DER WAALS = -31.6151 ELECTROSTATIC = -39.423 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6251" Parameter: CONF_N -> "8002" Comparing "6251" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6252" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751040 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748387 ATOM PAIRS WERE FOUND FOR ATOM LIST 41131 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29813 from a total of 748387 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6252 -63.93270 -7.10541 0.58562 INTE EXTERN> -30.09243 -33.84026 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.9327" Parameter: A <- "-63.9327" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0924" Parameter: B <- "-30.0924" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.8403" Parameter: C <- "-33.8403" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6252 TOTAL ENERGY = -63.9327 RDTITL> * VAN DER WAALS = -30.0924 ELECTROSTATIC = -33.8403 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6252" Parameter: CONF_N -> "8002" Comparing "6252" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6253" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748387 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750892 ATOM PAIRS WERE FOUND FOR ATOM LIST 41233 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29702 from a total of 750892 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6253 -73.83081 9.89811 0.52691 INTE EXTERN> -32.46752 -41.36329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8308" Parameter: A <- "-73.8308" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4675" Parameter: B <- "-32.4675" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3633" Parameter: C <- "-41.3633" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6253 TOTAL ENERGY = -73.8308 RDTITL> * VAN DER WAALS = -32.4675 ELECTROSTATIC = -41.3633 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6253" Parameter: CONF_N -> "8002" Comparing "6253" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6254" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750892 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753520 ATOM PAIRS WERE FOUND FOR ATOM LIST 41298 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29905 from a total of 753520 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6254 -72.15674 -1.67407 0.54263 INTE EXTERN> -33.88180 -38.27493 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1567" Parameter: A <- "-72.1567" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8818" Parameter: B <- "-33.8818" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2749" Parameter: C <- "-38.2749" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6254 TOTAL ENERGY = -72.1567 RDTITL> * VAN DER WAALS = -33.8818 ELECTROSTATIC = -38.2749 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6254" Parameter: CONF_N -> "8002" Comparing "6254" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6255" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753520 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745879 ATOM PAIRS WERE FOUND FOR ATOM LIST 40770 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29770 from a total of 745879 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6255 -67.80850 -4.34823 0.51476 INTE EXTERN> -31.00506 -36.80344 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8085" Parameter: A <- "-67.8085" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0051" Parameter: B <- "-31.0051" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8034" Parameter: C <- "-36.8034" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6255 TOTAL ENERGY = -67.8085 RDTITL> * VAN DER WAALS = -31.0051 ELECTROSTATIC = -36.8034 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6255" Parameter: CONF_N -> "8002" Comparing "6255" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6256" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745879 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747509 ATOM PAIRS WERE FOUND FOR ATOM LIST 40939 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29373 from a total of 747509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6256 -73.25848 5.44998 0.64891 INTE EXTERN> -26.73071 -46.52777 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2585" Parameter: A <- "-73.2585" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7307" Parameter: B <- "-26.7307" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5278" Parameter: C <- "-46.5278" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6256 TOTAL ENERGY = -73.2585 RDTITL> * VAN DER WAALS = -26.7307 ELECTROSTATIC = -46.5278 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6256" Parameter: CONF_N -> "8002" Comparing "6256" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6257" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744441 ATOM PAIRS WERE FOUND FOR ATOM LIST 40968 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29466 from a total of 744441 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6257 -64.57047 -8.68801 0.51085 INTE EXTERN> -29.71017 -34.86029 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5705" Parameter: A <- "-64.5705" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7102" Parameter: B <- "-29.7102" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.8603" Parameter: C <- "-34.8603" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6257 TOTAL ENERGY = -64.5705 RDTITL> * VAN DER WAALS = -29.7102 ELECTROSTATIC = -34.8603 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6257" Parameter: CONF_N -> "8002" Comparing "6257" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6258" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744441 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746850 ATOM PAIRS WERE FOUND FOR ATOM LIST 41237 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29729 from a total of 746850 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6258 -69.49941 4.92894 0.52302 INTE EXTERN> -32.86061 -36.63879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4994" Parameter: A <- "-69.4994" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8606" Parameter: B <- "-32.8606" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6388" Parameter: C <- "-36.6388" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6258 TOTAL ENERGY = -69.4994 RDTITL> * VAN DER WAALS = -32.8606 ELECTROSTATIC = -36.6388 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6258" Parameter: CONF_N -> "8002" Comparing "6258" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6259" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746850 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751704 ATOM PAIRS WERE FOUND FOR ATOM LIST 41028 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30417 from a total of 751704 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6259 -68.88553 -0.61387 0.51165 INTE EXTERN> -33.33211 -35.55343 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8855" Parameter: A <- "-68.8855" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3321" Parameter: B <- "-33.3321" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5534" Parameter: C <- "-35.5534" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6259 TOTAL ENERGY = -68.8855 RDTITL> * VAN DER WAALS = -33.3321 ELECTROSTATIC = -35.5534 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6259" Parameter: CONF_N -> "8002" Comparing "6259" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6260" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751704 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749926 ATOM PAIRS WERE FOUND FOR ATOM LIST 41402 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29719 from a total of 749926 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6260 -72.62641 3.74088 0.55711 INTE EXTERN> -32.64012 -39.98630 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6264" Parameter: A <- "-72.6264" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6401" Parameter: B <- "-32.6401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9863" Parameter: C <- "-39.9863" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6260 TOTAL ENERGY = -72.6264 RDTITL> * VAN DER WAALS = -32.6401 ELECTROSTATIC = -39.9863 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6260" Parameter: CONF_N -> "8002" Comparing "6260" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6261" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749926 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745378 ATOM PAIRS WERE FOUND FOR ATOM LIST 40809 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29765 from a total of 745378 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6261 -72.40932 -0.21709 0.57853 INTE EXTERN> -32.63749 -39.77183 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4093" Parameter: A <- "-72.4093" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6375" Parameter: B <- "-32.6375" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7718" Parameter: C <- "-39.7718" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6261 TOTAL ENERGY = -72.4093 RDTITL> * VAN DER WAALS = -32.6375 ELECTROSTATIC = -39.7718 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6261" Parameter: CONF_N -> "8002" Comparing "6261" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6262" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745378 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 743490 ATOM PAIRS WERE FOUND FOR ATOM LIST 40861 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30617 from a total of 743490 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6262 -65.90292 -6.50640 0.57534 INTE EXTERN> -29.10838 -36.79455 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.9029" Parameter: A <- "-65.9029" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1084" Parameter: B <- "-29.1084" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7945" Parameter: C <- "-36.7945" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6262 TOTAL ENERGY = -65.9029 RDTITL> * VAN DER WAALS = -29.1084 ELECTROSTATIC = -36.7945 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6262" Parameter: CONF_N -> "8002" Comparing "6262" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6263" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 743490 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747107 ATOM PAIRS WERE FOUND FOR ATOM LIST 41124 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29825 from a total of 747107 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6263 -75.58589 9.68296 0.66445 INTE EXTERN> -28.31040 -47.27549 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5859" Parameter: A <- "-75.5859" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3104" Parameter: B <- "-28.3104" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2755" Parameter: C <- "-47.2755" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6263 TOTAL ENERGY = -75.5859 RDTITL> * VAN DER WAALS = -28.3104 ELECTROSTATIC = -47.2755 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6263" Parameter: CONF_N -> "8002" Comparing "6263" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6264" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747107 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746612 ATOM PAIRS WERE FOUND FOR ATOM LIST 41252 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29875 from a total of 746612 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6264 -66.32746 -9.25843 0.53188 INTE EXTERN> -33.06686 -33.26061 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3275" Parameter: A <- "-66.3275" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0669" Parameter: B <- "-33.0669" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2606" Parameter: C <- "-33.2606" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6264 TOTAL ENERGY = -66.3275 RDTITL> * VAN DER WAALS = -33.0669 ELECTROSTATIC = -33.2606 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6264" Parameter: CONF_N -> "8002" Comparing "6264" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6265" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746612 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747474 ATOM PAIRS WERE FOUND FOR ATOM LIST 41261 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30448 from a total of 747474 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6265 -76.71998 10.39252 0.70520 INTE EXTERN> -27.27520 -49.44479 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.72" Parameter: A <- "-76.72" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2752" Parameter: B <- "-27.2752" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4448" Parameter: C <- "-49.4448" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6265 TOTAL ENERGY = -76.72 RDTITL> * VAN DER WAALS = -27.2752 ELECTROSTATIC = -49.4448 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6265" Parameter: CONF_N -> "8002" Comparing "6265" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6266" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747474 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748575 ATOM PAIRS WERE FOUND FOR ATOM LIST 40892 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30276 from a total of 748575 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6266 -71.39117 -5.32881 0.56047 INTE EXTERN> -32.43192 -38.95926 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3912" Parameter: A <- "-71.3912" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4319" Parameter: B <- "-32.4319" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9593" Parameter: C <- "-38.9593" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6266 TOTAL ENERGY = -71.3912 RDTITL> * VAN DER WAALS = -32.4319 ELECTROSTATIC = -38.9593 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6266" Parameter: CONF_N -> "8002" Comparing "6266" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6267" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748575 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748757 ATOM PAIRS WERE FOUND FOR ATOM LIST 41054 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29941 from a total of 748757 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6267 -70.19150 -1.19967 0.48892 INTE EXTERN> -35.17924 -35.01226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1915" Parameter: A <- "-70.1915" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.1792" Parameter: B <- "-35.1792" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0123" Parameter: C <- "-35.0123" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6267 TOTAL ENERGY = -70.1915 RDTITL> * VAN DER WAALS = -35.1792 ELECTROSTATIC = -35.0123 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6267" Parameter: CONF_N -> "8002" Comparing "6267" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6268" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748757 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751471 ATOM PAIRS WERE FOUND FOR ATOM LIST 41190 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29559 from a total of 751471 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6268 -76.36927 6.17777 0.55262 INTE EXTERN> -35.13104 -41.23824 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3693" Parameter: A <- "-76.3693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.131" Parameter: B <- "-35.131" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2382" Parameter: C <- "-41.2382" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6268 TOTAL ENERGY = -76.3693 RDTITL> * VAN DER WAALS = -35.131 ELECTROSTATIC = -41.2382 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6268" Parameter: CONF_N -> "8002" Comparing "6268" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6269" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751471 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752652 ATOM PAIRS WERE FOUND FOR ATOM LIST 41801 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29924 from a total of 752652 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6269 -71.22549 -5.14378 0.49989 INTE EXTERN> -34.72760 -36.49790 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2255" Parameter: A <- "-71.2255" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.7276" Parameter: B <- "-34.7276" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4979" Parameter: C <- "-36.4979" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6269 TOTAL ENERGY = -71.2255 RDTITL> * VAN DER WAALS = -34.7276 ELECTROSTATIC = -36.4979 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6269" Parameter: CONF_N -> "8002" Comparing "6269" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6270" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752652 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753432 ATOM PAIRS WERE FOUND FOR ATOM LIST 41439 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29527 from a total of 753432 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6270 -77.99904 6.77355 0.59841 INTE EXTERN> -31.54914 -46.44990 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.999" Parameter: A <- "-77.999" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5491" Parameter: B <- "-31.5491" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4499" Parameter: C <- "-46.4499" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6270 TOTAL ENERGY = -77.999 RDTITL> * VAN DER WAALS = -31.5491 ELECTROSTATIC = -46.4499 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6270" Parameter: CONF_N -> "8002" Comparing "6270" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6271" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753432 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747968 ATOM PAIRS WERE FOUND FOR ATOM LIST 40950 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29542 from a total of 747968 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6271 -68.36086 -9.63819 0.60971 INTE EXTERN> -30.48045 -37.88041 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3609" Parameter: A <- "-68.3609" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4804" Parameter: B <- "-30.4804" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8804" Parameter: C <- "-37.8804" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6271 TOTAL ENERGY = -68.3609 RDTITL> * VAN DER WAALS = -30.4804 ELECTROSTATIC = -37.8804 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6271" Parameter: CONF_N -> "8002" Comparing "6271" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6272" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747968 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757630 ATOM PAIRS WERE FOUND FOR ATOM LIST 41565 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29661 from a total of 757630 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6272 -71.34682 2.98596 0.60282 INTE EXTERN> -32.32632 -39.02050 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3468" Parameter: A <- "-71.3468" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3263" Parameter: B <- "-32.3263" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0205" Parameter: C <- "-39.0205" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6272 TOTAL ENERGY = -71.3468 RDTITL> * VAN DER WAALS = -32.3263 ELECTROSTATIC = -39.0205 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6272" Parameter: CONF_N -> "8002" Comparing "6272" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6273" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757630 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756637 ATOM PAIRS WERE FOUND FOR ATOM LIST 41445 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30366 from a total of 756637 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6273 -75.69131 4.34449 0.59930 INTE EXTERN> -32.77514 -42.91617 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6913" Parameter: A <- "-75.6913" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7751" Parameter: B <- "-32.7751" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9162" Parameter: C <- "-42.9162" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6273 TOTAL ENERGY = -75.6913 RDTITL> * VAN DER WAALS = -32.7751 ELECTROSTATIC = -42.9162 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6273" Parameter: CONF_N -> "8002" Comparing "6273" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6274" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756637 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751521 ATOM PAIRS WERE FOUND FOR ATOM LIST 41371 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30011 from a total of 751521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6274 -66.07695 -9.61436 0.52605 INTE EXTERN> -32.41348 -33.66347 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0769" Parameter: A <- "-66.0769" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4135" Parameter: B <- "-32.4135" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.6635" Parameter: C <- "-33.6635" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6274 TOTAL ENERGY = -66.0769 RDTITL> * VAN DER WAALS = -32.4135 ELECTROSTATIC = -33.6635 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6274" Parameter: CONF_N -> "8002" Comparing "6274" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6275" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749565 ATOM PAIRS WERE FOUND FOR ATOM LIST 41183 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30103 from a total of 749565 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6275 -74.95743 8.88048 0.59801 INTE EXTERN> -30.77489 -44.18254 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9574" Parameter: A <- "-74.9574" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7749" Parameter: B <- "-30.7749" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1825" Parameter: C <- "-44.1825" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6275 TOTAL ENERGY = -74.9574 RDTITL> * VAN DER WAALS = -30.7749 ELECTROSTATIC = -44.1825 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6275" Parameter: CONF_N -> "8002" Comparing "6275" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6276" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749565 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745844 ATOM PAIRS WERE FOUND FOR ATOM LIST 41073 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29672 from a total of 745844 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6276 -65.57970 -9.37773 0.57534 INTE EXTERN> -31.09672 -34.48298 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5797" Parameter: A <- "-65.5797" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0967" Parameter: B <- "-31.0967" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.483" Parameter: C <- "-34.483" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6276 TOTAL ENERGY = -65.5797 RDTITL> * VAN DER WAALS = -31.0967 ELECTROSTATIC = -34.483 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6276" Parameter: CONF_N -> "8002" Comparing "6276" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6277" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745844 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748661 ATOM PAIRS WERE FOUND FOR ATOM LIST 41252 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30182 from a total of 748661 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6277 -76.83484 11.25514 0.79351 INTE EXTERN> -30.25526 -46.57958 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8348" Parameter: A <- "-76.8348" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2553" Parameter: B <- "-30.2553" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5796" Parameter: C <- "-46.5796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6277 TOTAL ENERGY = -76.8348 RDTITL> * VAN DER WAALS = -30.2553 ELECTROSTATIC = -46.5796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6277" Parameter: CONF_N -> "8002" Comparing "6277" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6278" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748661 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749330 ATOM PAIRS WERE FOUND FOR ATOM LIST 41372 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29733 from a total of 749330 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6278 -73.63250 -3.20234 0.62278 INTE EXTERN> -30.83498 -42.79752 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6325" Parameter: A <- "-73.6325" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.835" Parameter: B <- "-30.835" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7975" Parameter: C <- "-42.7975" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6278 TOTAL ENERGY = -73.6325 RDTITL> * VAN DER WAALS = -30.835 ELECTROSTATIC = -42.7975 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6278" Parameter: CONF_N -> "8002" Comparing "6278" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6279" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749330 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754534 ATOM PAIRS WERE FOUND FOR ATOM LIST 41798 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29904 from a total of 754534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6279 -65.85215 -7.78036 0.58338 INTE EXTERN> -29.76257 -36.08958 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8521" Parameter: A <- "-65.8521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7626" Parameter: B <- "-29.7626" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0896" Parameter: C <- "-36.0896" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6279 TOTAL ENERGY = -65.8521 RDTITL> * VAN DER WAALS = -29.7626 ELECTROSTATIC = -36.0896 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6279" Parameter: CONF_N -> "8002" Comparing "6279" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6280" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754520 ATOM PAIRS WERE FOUND FOR ATOM LIST 41762 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29854 from a total of 754520 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6280 -71.81346 5.96132 0.60133 INTE EXTERN> -28.58705 -43.22641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8135" Parameter: A <- "-71.8135" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.587" Parameter: B <- "-28.587" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2264" Parameter: C <- "-43.2264" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6280 TOTAL ENERGY = -71.8135 RDTITL> * VAN DER WAALS = -28.587 ELECTROSTATIC = -43.2264 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6280" Parameter: CONF_N -> "8002" Comparing "6280" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6281" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754520 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751742 ATOM PAIRS WERE FOUND FOR ATOM LIST 41290 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29978 from a total of 751742 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6281 -76.54552 4.73206 0.58116 INTE EXTERN> -33.97710 -42.56842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5455" Parameter: A <- "-76.5455" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.9771" Parameter: B <- "-33.9771" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5684" Parameter: C <- "-42.5684" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6281 TOTAL ENERGY = -76.5455 RDTITL> * VAN DER WAALS = -33.9771 ELECTROSTATIC = -42.5684 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6281" Parameter: CONF_N -> "8002" Comparing "6281" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6282" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751742 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759914 ATOM PAIRS WERE FOUND FOR ATOM LIST 41848 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30231 from a total of 759914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6282 -74.75146 -1.79406 0.59347 INTE EXTERN> -31.45464 -43.29683 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7515" Parameter: A <- "-74.7515" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4546" Parameter: B <- "-31.4546" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2968" Parameter: C <- "-43.2968" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6282 TOTAL ENERGY = -74.7515 RDTITL> * VAN DER WAALS = -31.4546 ELECTROSTATIC = -43.2968 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6282" Parameter: CONF_N -> "8002" Comparing "6282" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6283" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760111 ATOM PAIRS WERE FOUND FOR ATOM LIST 41609 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30070 from a total of 760111 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6283 -67.17852 -7.57294 0.60818 INTE EXTERN> -30.87888 -36.29964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1785" Parameter: A <- "-67.1785" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8789" Parameter: B <- "-30.8789" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2996" Parameter: C <- "-36.2996" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6283 TOTAL ENERGY = -67.1785 RDTITL> * VAN DER WAALS = -30.8789 ELECTROSTATIC = -36.2996 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6283" Parameter: CONF_N -> "8002" Comparing "6283" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6284" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760111 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759665 ATOM PAIRS WERE FOUND FOR ATOM LIST 41907 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29810 from a total of 759665 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6284 -71.12470 3.94617 0.62821 INTE EXTERN> -30.83284 -40.29185 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1247" Parameter: A <- "-71.1247" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8328" Parameter: B <- "-30.8328" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2919" Parameter: C <- "-40.2919" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6284 TOTAL ENERGY = -71.1247 RDTITL> * VAN DER WAALS = -30.8328 ELECTROSTATIC = -40.2919 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6284" Parameter: CONF_N -> "8002" Comparing "6284" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6285" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759665 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756450 ATOM PAIRS WERE FOUND FOR ATOM LIST 41632 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29956 from a total of 756450 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6285 -70.72640 -0.39830 0.59234 INTE EXTERN> -31.71329 -39.01311 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7264" Parameter: A <- "-70.7264" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7133" Parameter: B <- "-31.7133" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0131" Parameter: C <- "-39.0131" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6285 TOTAL ENERGY = -70.7264 RDTITL> * VAN DER WAALS = -31.7133 ELECTROSTATIC = -39.0131 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6285" Parameter: CONF_N -> "8002" Comparing "6285" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6286" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756450 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754369 ATOM PAIRS WERE FOUND FOR ATOM LIST 41454 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29930 from a total of 754369 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6286 -71.67144 0.94504 0.60075 INTE EXTERN> -30.64815 -41.02329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6714" Parameter: A <- "-71.6714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6481" Parameter: B <- "-30.6481" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0233" Parameter: C <- "-41.0233" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6286 TOTAL ENERGY = -71.6714 RDTITL> * VAN DER WAALS = -30.6481 ELECTROSTATIC = -41.0233 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6286" Parameter: CONF_N -> "8002" Comparing "6286" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6287" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754369 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762533 ATOM PAIRS WERE FOUND FOR ATOM LIST 41894 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30401 from a total of 762533 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6287 -73.92956 2.25812 0.61559 INTE EXTERN> -33.14435 -40.78522 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9296" Parameter: A <- "-73.9296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1443" Parameter: B <- "-33.1443" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7852" Parameter: C <- "-40.7852" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6287 TOTAL ENERGY = -73.9296 RDTITL> * VAN DER WAALS = -33.1443 ELECTROSTATIC = -40.7852 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6287" Parameter: CONF_N -> "8002" Comparing "6287" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6288" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762533 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754347 ATOM PAIRS WERE FOUND FOR ATOM LIST 41335 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29138 from a total of 754347 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6288 -66.50349 -7.42607 0.52979 INTE EXTERN> -33.85470 -32.64879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5035" Parameter: A <- "-66.5035" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8547" Parameter: B <- "-33.8547" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.6488" Parameter: C <- "-32.6488" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6288 TOTAL ENERGY = -66.5035 RDTITL> * VAN DER WAALS = -33.8547 ELECTROSTATIC = -32.6488 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6288" Parameter: CONF_N -> "8002" Comparing "6288" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6289" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754347 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751896 ATOM PAIRS WERE FOUND FOR ATOM LIST 41311 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29887 from a total of 751896 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6289 -67.60403 1.10054 0.52660 INTE EXTERN> -33.16653 -34.43750 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.604" Parameter: A <- "-67.604" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1665" Parameter: B <- "-33.1665" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4375" Parameter: C <- "-34.4375" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6289 TOTAL ENERGY = -67.604 RDTITL> * VAN DER WAALS = -33.1665 ELECTROSTATIC = -34.4375 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6289" Parameter: CONF_N -> "8002" Comparing "6289" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6290" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751896 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758258 ATOM PAIRS WERE FOUND FOR ATOM LIST 41727 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30352 from a total of 758258 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6290 -74.05976 6.45572 0.52777 INTE EXTERN> -36.15517 -37.90459 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0598" Parameter: A <- "-74.0598" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-36.1552" Parameter: B <- "-36.1552" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9046" Parameter: C <- "-37.9046" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6290 TOTAL ENERGY = -74.0598 RDTITL> * VAN DER WAALS = -36.1552 ELECTROSTATIC = -37.9046 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6290" Parameter: CONF_N -> "8002" Comparing "6290" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6291" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758258 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754583 ATOM PAIRS WERE FOUND FOR ATOM LIST 41623 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30447 from a total of 754583 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6291 -71.03073 -3.02902 0.56635 INTE EXTERN> -31.91914 -39.11159 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0307" Parameter: A <- "-71.0307" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9191" Parameter: B <- "-31.9191" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.1116" Parameter: C <- "-39.1116" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6291 TOTAL ENERGY = -71.0307 RDTITL> * VAN DER WAALS = -31.9191 ELECTROSTATIC = -39.1116 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6291" Parameter: CONF_N -> "8002" Comparing "6291" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6292" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754583 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754298 ATOM PAIRS WERE FOUND FOR ATOM LIST 41567 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29845 from a total of 754298 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6292 -71.81236 0.78163 0.57121 INTE EXTERN> -30.09256 -41.71980 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8124" Parameter: A <- "-71.8124" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0926" Parameter: B <- "-30.0926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7198" Parameter: C <- "-41.7198" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6292 TOTAL ENERGY = -71.8124 RDTITL> * VAN DER WAALS = -30.0926 ELECTROSTATIC = -41.7198 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6292" Parameter: CONF_N -> "8002" Comparing "6292" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6293" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754298 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761705 ATOM PAIRS WERE FOUND FOR ATOM LIST 41675 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30141 from a total of 761705 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6293 -71.89882 0.08645 0.59135 INTE EXTERN> -31.66907 -40.22975 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8988" Parameter: A <- "-71.8988" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6691" Parameter: B <- "-31.6691" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2297" Parameter: C <- "-40.2297" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6293 TOTAL ENERGY = -71.8988 RDTITL> * VAN DER WAALS = -31.6691 ELECTROSTATIC = -40.2297 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6293" Parameter: CONF_N -> "8002" Comparing "6293" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6294" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761705 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752097 ATOM PAIRS WERE FOUND FOR ATOM LIST 41334 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29794 from a total of 752097 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6294 -72.54291 0.64410 0.57934 INTE EXTERN> -30.56273 -41.98018 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5429" Parameter: A <- "-72.5429" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5627" Parameter: B <- "-30.5627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9802" Parameter: C <- "-41.9802" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6294 TOTAL ENERGY = -72.5429 RDTITL> * VAN DER WAALS = -30.5627 ELECTROSTATIC = -41.9802 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6294" Parameter: CONF_N -> "8002" Comparing "6294" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6295" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752097 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751225 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29677 from a total of 751225 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6295 -75.69674 3.15383 0.55565 INTE EXTERN> -33.35885 -42.33789 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6967" Parameter: A <- "-75.6967" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3589" Parameter: B <- "-33.3589" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3379" Parameter: C <- "-42.3379" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6295 TOTAL ENERGY = -75.6967 RDTITL> * VAN DER WAALS = -33.3589 ELECTROSTATIC = -42.3379 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6295" Parameter: CONF_N -> "8002" Comparing "6295" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6296" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751225 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747807 ATOM PAIRS WERE FOUND FOR ATOM LIST 41191 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29294 from a total of 747807 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6296 -72.89570 -2.80105 0.71019 INTE EXTERN> -25.92719 -46.96851 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8957" Parameter: A <- "-72.8957" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9272" Parameter: B <- "-25.9272" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9685" Parameter: C <- "-46.9685" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6296 TOTAL ENERGY = -72.8957 RDTITL> * VAN DER WAALS = -25.9272 ELECTROSTATIC = -46.9685 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6296" Parameter: CONF_N -> "8002" Comparing "6296" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6297" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747807 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747835 ATOM PAIRS WERE FOUND FOR ATOM LIST 40982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28934 from a total of 747835 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6297 -71.55355 -1.34215 0.56228 INTE EXTERN> -30.75782 -40.79573 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5535" Parameter: A <- "-71.5535" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7578" Parameter: B <- "-30.7578" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7957" Parameter: C <- "-40.7957" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6297 TOTAL ENERGY = -71.5535 RDTITL> * VAN DER WAALS = -30.7578 ELECTROSTATIC = -40.7957 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6297" Parameter: CONF_N -> "8002" Comparing "6297" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6298" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747835 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757037 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30108 from a total of 757037 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6298 -76.10985 4.55630 0.62029 INTE EXTERN> -32.20249 -43.90735 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1098" Parameter: A <- "-76.1098" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2025" Parameter: B <- "-32.2025" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9074" Parameter: C <- "-43.9074" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6298 TOTAL ENERGY = -76.1098 RDTITL> * VAN DER WAALS = -32.2025 ELECTROSTATIC = -43.9074 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6298" Parameter: CONF_N -> "8002" Comparing "6298" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6299" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757037 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760414 ATOM PAIRS WERE FOUND FOR ATOM LIST 41942 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30287 from a total of 760414 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6299 -71.83900 -4.27084 0.56544 INTE EXTERN> -31.24954 -40.58946 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.839" Parameter: A <- "-71.839" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2495" Parameter: B <- "-31.2495" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5895" Parameter: C <- "-40.5895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6299 TOTAL ENERGY = -71.839 RDTITL> * VAN DER WAALS = -31.2495 ELECTROSTATIC = -40.5895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6299" Parameter: CONF_N -> "8002" Comparing "6299" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6300" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760414 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756281 ATOM PAIRS WERE FOUND FOR ATOM LIST 41542 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29198 from a total of 756281 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6300 -69.38992 -2.44909 0.46799 INTE EXTERN> -31.58876 -37.80116 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3899" Parameter: A <- "-69.3899" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5888" Parameter: B <- "-31.5888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8012" Parameter: C <- "-37.8012" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6300 TOTAL ENERGY = -69.3899 RDTITL> * VAN DER WAALS = -31.5888 ELECTROSTATIC = -37.8012 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6300" Parameter: CONF_N -> "8002" Comparing "6300" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6301" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756281 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748719 ATOM PAIRS WERE FOUND FOR ATOM LIST 41215 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29109 from a total of 748719 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6301 -70.00830 0.61838 0.51216 INTE EXTERN> -32.13791 -37.87038 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0083" Parameter: A <- "-70.0083" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1379" Parameter: B <- "-32.1379" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8704" Parameter: C <- "-37.8704" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6301 TOTAL ENERGY = -70.0083 RDTITL> * VAN DER WAALS = -32.1379 ELECTROSTATIC = -37.8704 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6301" Parameter: CONF_N -> "8002" Comparing "6301" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6302" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748719 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749523 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28847 from a total of 749523 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6302 -62.41066 -7.59764 0.52617 INTE EXTERN> -30.25376 -32.15690 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.4107" Parameter: A <- "-62.4107" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2538" Parameter: B <- "-30.2538" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.1569" Parameter: C <- "-32.1569" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6302 TOTAL ENERGY = -62.4107 RDTITL> * VAN DER WAALS = -30.2538 ELECTROSTATIC = -32.1569 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6302" Parameter: CONF_N -> "8002" Comparing "6302" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6303" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749523 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757282 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29350 from a total of 757282 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6303 -65.67992 3.26927 0.58886 INTE EXTERN> -29.72227 -35.95765 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6799" Parameter: A <- "-65.6799" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7223" Parameter: B <- "-29.7223" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9577" Parameter: C <- "-35.9577" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6303 TOTAL ENERGY = -65.6799 RDTITL> * VAN DER WAALS = -29.7223 ELECTROSTATIC = -35.9577 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6303" Parameter: CONF_N -> "8002" Comparing "6303" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6304" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757282 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750191 ATOM PAIRS WERE FOUND FOR ATOM LIST 41357 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29228 from a total of 750191 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6304 -68.00427 2.32434 0.59770 INTE EXTERN> -30.48414 -37.52013 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0043" Parameter: A <- "-68.0043" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4841" Parameter: B <- "-30.4841" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5201" Parameter: C <- "-37.5201" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6304 TOTAL ENERGY = -68.0043 RDTITL> * VAN DER WAALS = -30.4841 ELECTROSTATIC = -37.5201 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6304" Parameter: CONF_N -> "8002" Comparing "6304" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6305" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750191 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758902 ATOM PAIRS WERE FOUND FOR ATOM LIST 41778 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29304 from a total of 758902 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6305 -67.23728 -0.76699 0.60432 INTE EXTERN> -30.85973 -36.37755 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2373" Parameter: A <- "-67.2373" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8597" Parameter: B <- "-30.8597" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.3776" Parameter: C <- "-36.3776" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6305 TOTAL ENERGY = -67.2373 RDTITL> * VAN DER WAALS = -30.8597 ELECTROSTATIC = -36.3776 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6305" Parameter: CONF_N -> "8002" Comparing "6305" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6306" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758902 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759039 ATOM PAIRS WERE FOUND FOR ATOM LIST 41733 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29530 from a total of 759039 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6306 -64.35886 -2.87842 0.62520 INTE EXTERN> -30.38876 -33.97010 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3589" Parameter: A <- "-64.3589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3888" Parameter: B <- "-30.3888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.9701" Parameter: C <- "-33.9701" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6306 TOTAL ENERGY = -64.3589 RDTITL> * VAN DER WAALS = -30.3888 ELECTROSTATIC = -33.9701 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6306" Parameter: CONF_N -> "8002" Comparing "6306" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6307" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759039 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760849 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29675 from a total of 760849 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6307 -64.75926 0.40040 0.62005 INTE EXTERN> -30.36710 -34.39216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.7593" Parameter: A <- "-64.7593" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3671" Parameter: B <- "-30.3671" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3922" Parameter: C <- "-34.3922" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6307 TOTAL ENERGY = -64.7593 RDTITL> * VAN DER WAALS = -30.3671 ELECTROSTATIC = -34.3922 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6307" Parameter: CONF_N -> "8002" Comparing "6307" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6308" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760849 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755735 ATOM PAIRS WERE FOUND FOR ATOM LIST 41705 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29488 from a total of 755735 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6308 -67.93452 3.17526 0.67926 INTE EXTERN> -28.52441 -39.41011 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9345" Parameter: A <- "-67.9345" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5244" Parameter: B <- "-28.5244" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4101" Parameter: C <- "-39.4101" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6308 TOTAL ENERGY = -67.9345 RDTITL> * VAN DER WAALS = -28.5244 ELECTROSTATIC = -39.4101 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6308" Parameter: CONF_N -> "8002" Comparing "6308" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6309" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755735 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756186 ATOM PAIRS WERE FOUND FOR ATOM LIST 41550 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29438 from a total of 756186 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6309 -67.24382 -0.69070 0.58253 INTE EXTERN> -28.58096 -38.66286 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2438" Parameter: A <- "-67.2438" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.581" Parameter: B <- "-28.581" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6629" Parameter: C <- "-38.6629" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6309 TOTAL ENERGY = -67.2438 RDTITL> * VAN DER WAALS = -28.581 ELECTROSTATIC = -38.6629 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6309" Parameter: CONF_N -> "8002" Comparing "6309" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6310" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756186 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757796 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29348 from a total of 757796 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6310 -69.26828 2.02446 0.50032 INTE EXTERN> -33.31911 -35.94917 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2683" Parameter: A <- "-69.2683" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3191" Parameter: B <- "-33.3191" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9492" Parameter: C <- "-35.9492" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6310 TOTAL ENERGY = -69.2683 RDTITL> * VAN DER WAALS = -33.3191 ELECTROSTATIC = -35.9492 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6310" Parameter: CONF_N -> "8002" Comparing "6310" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6311" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757796 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750615 ATOM PAIRS WERE FOUND FOR ATOM LIST 41326 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28815 from a total of 750615 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6311 -71.07842 1.81014 0.63048 INTE EXTERN> -29.87336 -41.20506 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0784" Parameter: A <- "-71.0784" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8734" Parameter: B <- "-29.8734" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2051" Parameter: C <- "-41.2051" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6311 TOTAL ENERGY = -71.0784 RDTITL> * VAN DER WAALS = -29.8734 ELECTROSTATIC = -41.2051 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6311" Parameter: CONF_N -> "8002" Comparing "6311" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6312" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750615 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755141 ATOM PAIRS WERE FOUND FOR ATOM LIST 41519 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29480 from a total of 755141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6312 -77.28580 6.20737 0.78351 INTE EXTERN> -27.64647 -49.63933 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2858" Parameter: A <- "-77.2858" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6465" Parameter: B <- "-27.6465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6393" Parameter: C <- "-49.6393" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6312 TOTAL ENERGY = -77.2858 RDTITL> * VAN DER WAALS = -27.6465 ELECTROSTATIC = -49.6393 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6312" Parameter: CONF_N -> "8002" Comparing "6312" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6313" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757997 ATOM PAIRS WERE FOUND FOR ATOM LIST 41850 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29700 from a total of 757997 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6313 -69.51163 -7.77416 0.71178 INTE EXTERN> -29.05908 -40.45255 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5116" Parameter: A <- "-69.5116" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0591" Parameter: B <- "-29.0591" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4526" Parameter: C <- "-40.4526" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6313 TOTAL ENERGY = -69.5116 RDTITL> * VAN DER WAALS = -29.0591 ELECTROSTATIC = -40.4526 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6313" Parameter: CONF_N -> "8002" Comparing "6313" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6314" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757997 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756067 ATOM PAIRS WERE FOUND FOR ATOM LIST 41801 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29706 from a total of 756067 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6314 -76.20336 6.69173 0.75621 INTE EXTERN> -29.57011 -46.63326 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2034" Parameter: A <- "-76.2034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5701" Parameter: B <- "-29.5701" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6333" Parameter: C <- "-46.6333" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6314 TOTAL ENERGY = -76.2034 RDTITL> * VAN DER WAALS = -29.5701 ELECTROSTATIC = -46.6333 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6314" Parameter: CONF_N -> "8002" Comparing "6314" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6315" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756067 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751603 ATOM PAIRS WERE FOUND FOR ATOM LIST 41465 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29352 from a total of 751603 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6315 -65.81324 -10.39012 0.60334 INTE EXTERN> -33.35009 -32.46316 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8132" Parameter: A <- "-65.8132" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3501" Parameter: B <- "-33.3501" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.4632" Parameter: C <- "-32.4632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6315 TOTAL ENERGY = -65.8132 RDTITL> * VAN DER WAALS = -33.3501 ELECTROSTATIC = -32.4632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6315" Parameter: CONF_N -> "8002" Comparing "6315" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6316" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751603 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757933 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29168 from a total of 757933 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6316 -71.34265 5.52941 0.61310 INTE EXTERN> -32.67802 -38.66463 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3427" Parameter: A <- "-71.3427" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.678" Parameter: B <- "-32.678" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6646" Parameter: C <- "-38.6646" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6316 TOTAL ENERGY = -71.3427 RDTITL> * VAN DER WAALS = -32.678 ELECTROSTATIC = -38.6646 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6316" Parameter: CONF_N -> "8002" Comparing "6316" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6317" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757933 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752437 ATOM PAIRS WERE FOUND FOR ATOM LIST 41613 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28583 from a total of 752437 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6317 -67.19233 -4.15033 0.52059 INTE EXTERN> -31.61507 -35.57726 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1923" Parameter: A <- "-67.1923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6151" Parameter: B <- "-31.6151" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5773" Parameter: C <- "-35.5773" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6317 TOTAL ENERGY = -67.1923 RDTITL> * VAN DER WAALS = -31.6151 ELECTROSTATIC = -35.5773 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6317" Parameter: CONF_N -> "8002" Comparing "6317" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6318" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752437 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751769 ATOM PAIRS WERE FOUND FOR ATOM LIST 41387 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29257 from a total of 751769 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6318 -72.32231 5.12998 0.61549 INTE EXTERN> -33.52733 -38.79498 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3223" Parameter: A <- "-72.3223" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5273" Parameter: B <- "-33.5273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.795" Parameter: C <- "-38.795" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6318 TOTAL ENERGY = -72.3223 RDTITL> * VAN DER WAALS = -33.5273 ELECTROSTATIC = -38.795 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6318" Parameter: CONF_N -> "8002" Comparing "6318" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6319" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751769 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747238 ATOM PAIRS WERE FOUND FOR ATOM LIST 41244 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28929 from a total of 747238 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6319 -65.18237 -7.13994 0.61273 INTE EXTERN> -31.05083 -34.13154 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1824" Parameter: A <- "-65.1824" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0508" Parameter: B <- "-31.0508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1315" Parameter: C <- "-34.1315" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6319 TOTAL ENERGY = -65.1824 RDTITL> * VAN DER WAALS = -31.0508 ELECTROSTATIC = -34.1315 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6319" Parameter: CONF_N -> "8002" Comparing "6319" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6320" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747238 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750022 ATOM PAIRS WERE FOUND FOR ATOM LIST 41382 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29088 from a total of 750022 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6320 -75.29300 10.11063 0.57263 INTE EXTERN> -34.07644 -41.21656 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.293" Parameter: A <- "-75.293" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.0764" Parameter: B <- "-34.0764" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2166" Parameter: C <- "-41.2166" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6320 TOTAL ENERGY = -75.293 RDTITL> * VAN DER WAALS = -34.0764 ELECTROSTATIC = -41.2166 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6320" Parameter: CONF_N -> "8002" Comparing "6320" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6321" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750022 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749285 ATOM PAIRS WERE FOUND FOR ATOM LIST 41174 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29112 from a total of 749285 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6321 -66.52633 -8.76667 0.70413 INTE EXTERN> -28.51432 -38.01201 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5263" Parameter: A <- "-66.5263" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5143" Parameter: B <- "-28.5143" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.012" Parameter: C <- "-38.012" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6321 TOTAL ENERGY = -66.5263 RDTITL> * VAN DER WAALS = -28.5143 ELECTROSTATIC = -38.012 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6321" Parameter: CONF_N -> "8002" Comparing "6321" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6322" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749285 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749759 ATOM PAIRS WERE FOUND FOR ATOM LIST 41383 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29326 from a total of 749759 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6322 -62.58432 -3.94201 0.56111 INTE EXTERN> -31.80031 -30.78401 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.5843" Parameter: A <- "-62.5843" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8003" Parameter: B <- "-31.8003" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.784" Parameter: C <- "-30.784" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6322 TOTAL ENERGY = -62.5843 RDTITL> * VAN DER WAALS = -31.8003 ELECTROSTATIC = -30.784 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6322" Parameter: CONF_N -> "8002" Comparing "6322" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6323" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749759 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752003 ATOM PAIRS WERE FOUND FOR ATOM LIST 41481 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29691 from a total of 752003 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6323 -65.37976 2.79543 0.52625 INTE EXTERN> -34.95626 -30.42349 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3798" Parameter: A <- "-65.3798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9563" Parameter: B <- "-34.9563" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.4235" Parameter: C <- "-30.4235" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6323 TOTAL ENERGY = -65.3798 RDTITL> * VAN DER WAALS = -34.9563 ELECTROSTATIC = -30.4235 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6323" Parameter: CONF_N -> "8002" Comparing "6323" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6324" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752003 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753043 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29679 from a total of 753043 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6324 -69.61940 4.23964 0.57272 INTE EXTERN> -31.01565 -38.60375 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6194" Parameter: A <- "-69.6194" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0157" Parameter: B <- "-31.0157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.6037" Parameter: C <- "-38.6037" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6324 TOTAL ENERGY = -69.6194 RDTITL> * VAN DER WAALS = -31.0157 ELECTROSTATIC = -38.6037 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6324" Parameter: CONF_N -> "8002" Comparing "6324" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6325" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753043 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759458 ATOM PAIRS WERE FOUND FOR ATOM LIST 41769 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30040 from a total of 759458 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6325 -69.39389 -0.22551 0.74458 INTE EXTERN> -27.05067 -42.34322 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3939" Parameter: A <- "-69.3939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0507" Parameter: B <- "-27.0507" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3432" Parameter: C <- "-42.3432" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6325 TOTAL ENERGY = -69.3939 RDTITL> * VAN DER WAALS = -27.0507 ELECTROSTATIC = -42.3432 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6325" Parameter: CONF_N -> "8002" Comparing "6325" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6326" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759458 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757588 ATOM PAIRS WERE FOUND FOR ATOM LIST 41672 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29455 from a total of 757588 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6326 -71.40089 2.00700 0.63129 INTE EXTERN> -30.48469 -40.91620 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4009" Parameter: A <- "-71.4009" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4847" Parameter: B <- "-30.4847" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9162" Parameter: C <- "-40.9162" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6326 TOTAL ENERGY = -71.4009 RDTITL> * VAN DER WAALS = -30.4847 ELECTROSTATIC = -40.9162 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6326" Parameter: CONF_N -> "8002" Comparing "6326" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6327" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757588 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749750 ATOM PAIRS WERE FOUND FOR ATOM LIST 41412 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29586 from a total of 749750 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6327 -73.75375 2.35285 0.55217 INTE EXTERN> -32.74432 -41.00943 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7537" Parameter: A <- "-73.7537" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7443" Parameter: B <- "-32.7443" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0094" Parameter: C <- "-41.0094" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6327 TOTAL ENERGY = -73.7537 RDTITL> * VAN DER WAALS = -32.7443 ELECTROSTATIC = -41.0094 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6327" Parameter: CONF_N -> "8002" Comparing "6327" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6328" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749750 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754151 ATOM PAIRS WERE FOUND FOR ATOM LIST 41568 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29697 from a total of 754151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6328 -75.33825 1.58450 0.57442 INTE EXTERN> -32.91530 -42.42295 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3382" Parameter: A <- "-75.3382" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9153" Parameter: B <- "-32.9153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4229" Parameter: C <- "-42.4229" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6328 TOTAL ENERGY = -75.3382 RDTITL> * VAN DER WAALS = -32.9153 ELECTROSTATIC = -42.4229 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6328" Parameter: CONF_N -> "8002" Comparing "6328" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6329" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758380 ATOM PAIRS WERE FOUND FOR ATOM LIST 41814 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30178 from a total of 758380 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6329 -72.72601 -2.61224 0.61128 INTE EXTERN> -32.60045 -40.12556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.726" Parameter: A <- "-72.726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6004" Parameter: B <- "-32.6004" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1256" Parameter: C <- "-40.1256" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6329 TOTAL ENERGY = -72.726 RDTITL> * VAN DER WAALS = -32.6004 ELECTROSTATIC = -40.1256 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6329" Parameter: CONF_N -> "8002" Comparing "6329" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6330" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758380 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749856 ATOM PAIRS WERE FOUND FOR ATOM LIST 41351 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29602 from a total of 749856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6330 -70.23582 -2.49019 0.65328 INTE EXTERN> -30.18324 -40.05258 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2358" Parameter: A <- "-70.2358" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1832" Parameter: B <- "-30.1832" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0526" Parameter: C <- "-40.0526" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6330 TOTAL ENERGY = -70.2358 RDTITL> * VAN DER WAALS = -30.1832 ELECTROSTATIC = -40.0526 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6330" Parameter: CONF_N -> "8002" Comparing "6330" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6331" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750785 ATOM PAIRS WERE FOUND FOR ATOM LIST 41386 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29533 from a total of 750785 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6331 -80.71367 10.47785 0.68174 INTE EXTERN> -30.00251 -50.71116 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7137" Parameter: A <- "-80.7137" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0025" Parameter: B <- "-30.0025" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7112" Parameter: C <- "-50.7112" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6331 TOTAL ENERGY = -80.7137 RDTITL> * VAN DER WAALS = -30.0025 ELECTROSTATIC = -50.7112 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6331" Parameter: CONF_N -> "8002" Comparing "6331" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6332" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750785 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762962 ATOM PAIRS WERE FOUND FOR ATOM LIST 41896 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30100 from a total of 762962 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6332 -75.07422 -5.63945 0.73864 INTE EXTERN> -30.53369 -44.54053 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0742" Parameter: A <- "-75.0742" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5337" Parameter: B <- "-30.5337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5405" Parameter: C <- "-44.5405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6332 TOTAL ENERGY = -75.0742 RDTITL> * VAN DER WAALS = -30.5337 ELECTROSTATIC = -44.5405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6332" Parameter: CONF_N -> "8002" Comparing "6332" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6333" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762962 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758279 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29818 from a total of 758279 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6333 -74.23646 -0.83776 0.64683 INTE EXTERN> -31.43226 -42.80419 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2365" Parameter: A <- "-74.2365" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4323" Parameter: B <- "-31.4323" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8042" Parameter: C <- "-42.8042" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6333 TOTAL ENERGY = -74.2365 RDTITL> * VAN DER WAALS = -31.4323 ELECTROSTATIC = -42.8042 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6333" Parameter: CONF_N -> "8002" Comparing "6333" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6334" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758279 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755883 ATOM PAIRS WERE FOUND FOR ATOM LIST 41613 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29435 from a total of 755883 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6334 -73.29820 -0.93826 0.63072 INTE EXTERN> -31.32805 -41.97015 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2982" Parameter: A <- "-73.2982" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.328" Parameter: B <- "-31.328" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9702" Parameter: C <- "-41.9702" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6334 TOTAL ENERGY = -73.2982 RDTITL> * VAN DER WAALS = -31.328 ELECTROSTATIC = -41.9702 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6334" Parameter: CONF_N -> "8002" Comparing "6334" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6335" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755883 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760559 ATOM PAIRS WERE FOUND FOR ATOM LIST 41661 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29632 from a total of 760559 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6335 -69.43072 -3.86748 0.79635 INTE EXTERN> -24.08384 -45.34688 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4307" Parameter: A <- "-69.4307" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0838" Parameter: B <- "-24.0838" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3469" Parameter: C <- "-45.3469" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6335 TOTAL ENERGY = -69.4307 RDTITL> * VAN DER WAALS = -24.0838 ELECTROSTATIC = -45.3469 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6335" Parameter: CONF_N -> "8002" Comparing "6335" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6336" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760559 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751341 ATOM PAIRS WERE FOUND FOR ATOM LIST 41399 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29998 from a total of 751341 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6336 -72.57859 3.14787 0.79689 INTE EXTERN> -25.96812 -46.61048 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5786" Parameter: A <- "-72.5786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9681" Parameter: B <- "-25.9681" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6105" Parameter: C <- "-46.6105" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6336 TOTAL ENERGY = -72.5786 RDTITL> * VAN DER WAALS = -25.9681 ELECTROSTATIC = -46.6105 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6336" Parameter: CONF_N -> "8002" Comparing "6336" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6337" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751341 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750832 ATOM PAIRS WERE FOUND FOR ATOM LIST 41231 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29758 from a total of 750832 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6337 -76.83051 4.25192 0.74284 INTE EXTERN> -26.47264 -50.35787 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8305" Parameter: A <- "-76.8305" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4726" Parameter: B <- "-26.4726" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3579" Parameter: C <- "-50.3579" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6337 TOTAL ENERGY = -76.8305 RDTITL> * VAN DER WAALS = -26.4726 ELECTROSTATIC = -50.3579 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6337" Parameter: CONF_N -> "8002" Comparing "6337" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6338" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750832 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750756 ATOM PAIRS WERE FOUND FOR ATOM LIST 41251 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29469 from a total of 750756 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6338 -77.69305 0.86254 0.64573 INTE EXTERN> -30.47063 -47.22242 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.693" Parameter: A <- "-77.693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4706" Parameter: B <- "-30.4706" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2224" Parameter: C <- "-47.2224" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6338 TOTAL ENERGY = -77.693 RDTITL> * VAN DER WAALS = -30.4706 ELECTROSTATIC = -47.2224 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6338" Parameter: CONF_N -> "8002" Comparing "6338" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6339" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750756 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754286 ATOM PAIRS WERE FOUND FOR ATOM LIST 41403 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29022 from a total of 754286 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6339 -77.53499 -0.15806 0.64424 INTE EXTERN> -30.36098 -47.17401 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.535" Parameter: A <- "-77.535" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.361" Parameter: B <- "-30.361" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.174" Parameter: C <- "-47.174" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6339 TOTAL ENERGY = -77.535 RDTITL> * VAN DER WAALS = -30.361 ELECTROSTATIC = -47.174 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6339" Parameter: CONF_N -> "8002" Comparing "6339" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6340" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754286 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754216 ATOM PAIRS WERE FOUND FOR ATOM LIST 41662 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29076 from a total of 754216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6340 -75.34307 -2.19192 0.65433 INTE EXTERN> -31.17553 -44.16754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3431" Parameter: A <- "-75.3431" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1755" Parameter: B <- "-31.1755" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1675" Parameter: C <- "-44.1675" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6340 TOTAL ENERGY = -75.3431 RDTITL> * VAN DER WAALS = -31.1755 ELECTROSTATIC = -44.1675 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6340" Parameter: CONF_N -> "8002" Comparing "6340" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6341" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757518 ATOM PAIRS WERE FOUND FOR ATOM LIST 41921 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29579 from a total of 757518 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6341 -75.46431 0.12124 0.70532 INTE EXTERN> -25.69643 -49.76788 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4643" Parameter: A <- "-75.4643" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6964" Parameter: B <- "-25.6964" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7679" Parameter: C <- "-49.7679" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6341 TOTAL ENERGY = -75.4643 RDTITL> * VAN DER WAALS = -25.6964 ELECTROSTATIC = -49.7679 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6341" Parameter: CONF_N -> "8002" Comparing "6341" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6342" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757518 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752834 ATOM PAIRS WERE FOUND FOR ATOM LIST 41505 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29410 from a total of 752834 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6342 -73.05074 -2.41357 0.55572 INTE EXTERN> -33.73376 -39.31698 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0507" Parameter: A <- "-73.0507" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7338" Parameter: B <- "-33.7338" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.317" Parameter: C <- "-39.317" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6342 TOTAL ENERGY = -73.0507 RDTITL> * VAN DER WAALS = -33.7338 ELECTROSTATIC = -39.317 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6342" Parameter: CONF_N -> "8002" Comparing "6342" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6343" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752834 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749407 ATOM PAIRS WERE FOUND FOR ATOM LIST 41333 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29305 from a total of 749407 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6343 -74.67798 1.62725 0.59593 INTE EXTERN> -30.16720 -44.51078 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.678" Parameter: A <- "-74.678" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1672" Parameter: B <- "-30.1672" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5108" Parameter: C <- "-44.5108" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6343 TOTAL ENERGY = -74.678 RDTITL> * VAN DER WAALS = -30.1672 ELECTROSTATIC = -44.5108 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6343" Parameter: CONF_N -> "8002" Comparing "6343" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6344" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749407 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755559 ATOM PAIRS WERE FOUND FOR ATOM LIST 41720 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29287 from a total of 755559 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6344 -80.78906 6.11107 0.66905 INTE EXTERN> -27.98394 -52.80512 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7891" Parameter: A <- "-80.7891" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9839" Parameter: B <- "-27.9839" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8051" Parameter: C <- "-52.8051" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6344 TOTAL ENERGY = -80.7891 RDTITL> * VAN DER WAALS = -27.9839 ELECTROSTATIC = -52.8051 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6344" Parameter: CONF_N -> "8002" Comparing "6344" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6345" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755559 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754544 ATOM PAIRS WERE FOUND FOR ATOM LIST 41485 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29214 from a total of 754544 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6345 -77.66423 -3.12482 0.62928 INTE EXTERN> -31.01581 -46.64842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6642" Parameter: A <- "-77.6642" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0158" Parameter: B <- "-31.0158" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6484" Parameter: C <- "-46.6484" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6345 TOTAL ENERGY = -77.6642 RDTITL> * VAN DER WAALS = -31.0158 ELECTROSTATIC = -46.6484 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6345" Parameter: CONF_N -> "8002" Comparing "6345" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6346" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754544 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755228 ATOM PAIRS WERE FOUND FOR ATOM LIST 41571 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29225 from a total of 755228 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6346 -69.37722 -8.28701 0.58501 INTE EXTERN> -32.58200 -36.79522 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3772" Parameter: A <- "-69.3772" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.582" Parameter: B <- "-32.582" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7952" Parameter: C <- "-36.7952" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6346 TOTAL ENERGY = -69.3772 RDTITL> * VAN DER WAALS = -32.582 ELECTROSTATIC = -36.7952 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6346" Parameter: CONF_N -> "8002" Comparing "6346" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6347" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755228 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754575 ATOM PAIRS WERE FOUND FOR ATOM LIST 41537 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28664 from a total of 754575 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6347 -78.71423 9.33701 0.69299 INTE EXTERN> -26.88322 -51.83100 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7142" Parameter: A <- "-78.7142" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8832" Parameter: B <- "-26.8832" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.831" Parameter: C <- "-51.831" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6347 TOTAL ENERGY = -78.7142 RDTITL> * VAN DER WAALS = -26.8832 ELECTROSTATIC = -51.831 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6347" Parameter: CONF_N -> "8002" Comparing "6347" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6348" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754575 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747331 ATOM PAIRS WERE FOUND FOR ATOM LIST 41218 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28688 from a total of 747331 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6348 -81.98876 3.27453 0.72703 INTE EXTERN> -28.78780 -53.20096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9888" Parameter: A <- "-81.9888" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7878" Parameter: B <- "-28.7878" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.201" Parameter: C <- "-53.201" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6348 TOTAL ENERGY = -81.9888 RDTITL> * VAN DER WAALS = -28.7878 ELECTROSTATIC = -53.201 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6348" Parameter: CONF_N -> "8002" Comparing "6348" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6349" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747331 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751524 ATOM PAIRS WERE FOUND FOR ATOM LIST 41401 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28611 from a total of 751524 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6349 -81.49347 -0.49529 0.60135 INTE EXTERN> -32.30913 -49.18434 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4935" Parameter: A <- "-81.4935" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3091" Parameter: B <- "-32.3091" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1843" Parameter: C <- "-49.1843" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6349 TOTAL ENERGY = -81.4935 RDTITL> * VAN DER WAALS = -32.3091 ELECTROSTATIC = -49.1843 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6349" Parameter: CONF_N -> "8002" Comparing "6349" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6350" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751524 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752148 ATOM PAIRS WERE FOUND FOR ATOM LIST 41393 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29092 from a total of 752148 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6350 -77.25138 -4.24209 0.62057 INTE EXTERN> -31.16699 -46.08439 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2514" Parameter: A <- "-77.2514" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.167" Parameter: B <- "-31.167" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0844" Parameter: C <- "-46.0844" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6350 TOTAL ENERGY = -77.2514 RDTITL> * VAN DER WAALS = -31.167 ELECTROSTATIC = -46.0844 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6350" Parameter: CONF_N -> "8002" Comparing "6350" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6351" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752148 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41397 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29708 from a total of 750118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6351 -73.59335 -3.65803 0.65894 INTE EXTERN> -28.83760 -44.75575 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5933" Parameter: A <- "-73.5933" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8376" Parameter: B <- "-28.8376" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7557" Parameter: C <- "-44.7557" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6351 TOTAL ENERGY = -73.5933 RDTITL> * VAN DER WAALS = -28.8376 ELECTROSTATIC = -44.7557 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6351" Parameter: CONF_N -> "8002" Comparing "6351" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6352" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751227 ATOM PAIRS WERE FOUND FOR ATOM LIST 41500 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29037 from a total of 751227 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6352 -75.98140 2.38805 0.76736 INTE EXTERN> -27.43487 -48.54653 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9814" Parameter: A <- "-75.9814" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4349" Parameter: B <- "-27.4349" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5465" Parameter: C <- "-48.5465" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6352 TOTAL ENERGY = -75.9814 RDTITL> * VAN DER WAALS = -27.4349 ELECTROSTATIC = -48.5465 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6352" Parameter: CONF_N -> "8002" Comparing "6352" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6353" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751227 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755819 ATOM PAIRS WERE FOUND FOR ATOM LIST 41501 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29488 from a total of 755819 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6353 -82.78708 6.80568 0.67906 INTE EXTERN> -29.47716 -53.30992 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7871" Parameter: A <- "-82.7871" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4772" Parameter: B <- "-29.4772" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3099" Parameter: C <- "-53.3099" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6353 TOTAL ENERGY = -82.7871 RDTITL> * VAN DER WAALS = -29.4772 ELECTROSTATIC = -53.3099 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6353" Parameter: CONF_N -> "8002" Comparing "6353" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6354" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755819 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756655 ATOM PAIRS WERE FOUND FOR ATOM LIST 41529 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29086 from a total of 756655 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6354 -77.00005 -5.78703 0.62697 INTE EXTERN> -30.89686 -46.10319 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77" Parameter: A <- "-77" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8969" Parameter: B <- "-30.8969" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1032" Parameter: C <- "-46.1032" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6354 TOTAL ENERGY = -77 RDTITL> * VAN DER WAALS = -30.8969 ELECTROSTATIC = -46.1032 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6354" Parameter: CONF_N -> "8002" Comparing "6354" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6355" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756655 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756350 ATOM PAIRS WERE FOUND FOR ATOM LIST 41588 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29528 from a total of 756350 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6355 -76.90005 -0.10000 0.66191 INTE EXTERN> -31.44652 -45.45353 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9" Parameter: A <- "-76.9" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4465" Parameter: B <- "-31.4465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4535" Parameter: C <- "-45.4535" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6355 TOTAL ENERGY = -76.9 RDTITL> * VAN DER WAALS = -31.4465 ELECTROSTATIC = -45.4535 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6355" Parameter: CONF_N -> "8002" Comparing "6355" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6356" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756350 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750417 ATOM PAIRS WERE FOUND FOR ATOM LIST 41419 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29664 from a total of 750417 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6356 -78.58280 1.68276 0.74730 INTE EXTERN> -28.30937 -50.27343 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5828" Parameter: A <- "-78.5828" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3094" Parameter: B <- "-28.3094" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2734" Parameter: C <- "-50.2734" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6356 TOTAL ENERGY = -78.5828 RDTITL> * VAN DER WAALS = -28.3094 ELECTROSTATIC = -50.2734 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6356" Parameter: CONF_N -> "8002" Comparing "6356" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6357" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750417 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753244 ATOM PAIRS WERE FOUND FOR ATOM LIST 41476 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29367 from a total of 753244 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6357 -73.64809 -4.93471 0.65013 INTE EXTERN> -30.92714 -42.72095 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6481" Parameter: A <- "-73.6481" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9271" Parameter: B <- "-30.9271" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.721" Parameter: C <- "-42.721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6357 TOTAL ENERGY = -73.6481 RDTITL> * VAN DER WAALS = -30.9271 ELECTROSTATIC = -42.721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6357" Parameter: CONF_N -> "8002" Comparing "6357" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6358" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753244 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752705 ATOM PAIRS WERE FOUND FOR ATOM LIST 41547 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29327 from a total of 752705 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6358 -79.76394 6.11585 0.67569 INTE EXTERN> -30.90304 -48.86091 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7639" Parameter: A <- "-79.7639" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.903" Parameter: B <- "-30.903" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8609" Parameter: C <- "-48.8609" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6358 TOTAL ENERGY = -79.7639 RDTITL> * VAN DER WAALS = -30.903 ELECTROSTATIC = -48.8609 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6358" Parameter: CONF_N -> "8002" Comparing "6358" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6359" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752705 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752277 ATOM PAIRS WERE FOUND FOR ATOM LIST 41451 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29573 from a total of 752277 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6359 -75.47011 -4.29383 0.66136 INTE EXTERN> -29.29629 -46.17381 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4701" Parameter: A <- "-75.4701" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2963" Parameter: B <- "-29.2963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1738" Parameter: C <- "-46.1738" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6359 TOTAL ENERGY = -75.4701 RDTITL> * VAN DER WAALS = -29.2963 ELECTROSTATIC = -46.1738 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6359" Parameter: CONF_N -> "8002" Comparing "6359" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6360" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752277 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757996 ATOM PAIRS WERE FOUND FOR ATOM LIST 41623 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29912 from a total of 757996 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6360 -81.14493 5.67482 0.80902 INTE EXTERN> -26.53743 -54.60750 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1449" Parameter: A <- "-81.1449" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5374" Parameter: B <- "-26.5374" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.6075" Parameter: C <- "-54.6075" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6360 TOTAL ENERGY = -81.1449 RDTITL> * VAN DER WAALS = -26.5374 ELECTROSTATIC = -54.6075 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6360" Parameter: CONF_N -> "8002" Comparing "6360" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6361" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757996 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755397 ATOM PAIRS WERE FOUND FOR ATOM LIST 41611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29730 from a total of 755397 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6361 -77.02139 -4.12353 0.67317 INTE EXTERN> -28.64778 -48.37362 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0214" Parameter: A <- "-77.0214" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6478" Parameter: B <- "-28.6478" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3736" Parameter: C <- "-48.3736" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6361 TOTAL ENERGY = -77.0214 RDTITL> * VAN DER WAALS = -28.6478 ELECTROSTATIC = -48.3736 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6361" Parameter: CONF_N -> "8002" Comparing "6361" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6362" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755397 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750772 ATOM PAIRS WERE FOUND FOR ATOM LIST 41306 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29949 from a total of 750772 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6362 -74.16128 -2.86012 0.58252 INTE EXTERN> -32.68366 -41.47762 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1613" Parameter: A <- "-74.1613" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6837" Parameter: B <- "-32.6837" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4776" Parameter: C <- "-41.4776" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6362 TOTAL ENERGY = -74.1613 RDTITL> * VAN DER WAALS = -32.6837 ELECTROSTATIC = -41.4776 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6362" Parameter: CONF_N -> "8002" Comparing "6362" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6363" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750772 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751221 ATOM PAIRS WERE FOUND FOR ATOM LIST 41655 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29404 from a total of 751221 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6363 -74.23393 0.07265 0.59661 INTE EXTERN> -32.63452 -41.59941 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2339" Parameter: A <- "-74.2339" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6345" Parameter: B <- "-32.6345" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5994" Parameter: C <- "-41.5994" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6363 TOTAL ENERGY = -74.2339 RDTITL> * VAN DER WAALS = -32.6345 ELECTROSTATIC = -41.5994 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6363" Parameter: CONF_N -> "8002" Comparing "6363" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6364" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751221 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749172 ATOM PAIRS WERE FOUND FOR ATOM LIST 41215 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29411 from a total of 749172 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6364 -72.07056 -2.16337 0.65647 INTE EXTERN> -30.48596 -41.58460 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0706" Parameter: A <- "-72.0706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.486" Parameter: B <- "-30.486" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5846" Parameter: C <- "-41.5846" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6364 TOTAL ENERGY = -72.0706 RDTITL> * VAN DER WAALS = -30.486 ELECTROSTATIC = -41.5846 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6364" Parameter: CONF_N -> "8002" Comparing "6364" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6365" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749172 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753431 ATOM PAIRS WERE FOUND FOR ATOM LIST 41494 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29218 from a total of 753431 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6365 -70.50064 -1.56992 0.65821 INTE EXTERN> -29.76239 -40.73825 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5006" Parameter: A <- "-70.5006" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7624" Parameter: B <- "-29.7624" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7382" Parameter: C <- "-40.7382" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6365 TOTAL ENERGY = -70.5006 RDTITL> * VAN DER WAALS = -29.7624 ELECTROSTATIC = -40.7382 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6365" Parameter: CONF_N -> "8002" Comparing "6365" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6366" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753431 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756203 ATOM PAIRS WERE FOUND FOR ATOM LIST 41663 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29675 from a total of 756203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6366 -80.48585 9.98520 0.67669 INTE EXTERN> -32.50425 -47.98160 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4858" Parameter: A <- "-80.4858" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5042" Parameter: B <- "-32.5042" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9816" Parameter: C <- "-47.9816" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6366 TOTAL ENERGY = -80.4858 RDTITL> * VAN DER WAALS = -32.5042 ELECTROSTATIC = -47.9816 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6366" Parameter: CONF_N -> "8002" Comparing "6366" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6367" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757339 ATOM PAIRS WERE FOUND FOR ATOM LIST 41992 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29870 from a total of 757339 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6367 -78.32420 -2.16164 0.73053 INTE EXTERN> -30.26087 -48.06333 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3242" Parameter: A <- "-78.3242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2609" Parameter: B <- "-30.2609" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0633" Parameter: C <- "-48.0633" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6367 TOTAL ENERGY = -78.3242 RDTITL> * VAN DER WAALS = -30.2609 ELECTROSTATIC = -48.0633 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6367" Parameter: CONF_N -> "8002" Comparing "6367" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6368" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757339 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762386 ATOM PAIRS WERE FOUND FOR ATOM LIST 41929 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30406 from a total of 762386 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6368 -75.99618 -2.32802 0.78109 INTE EXTERN> -27.84313 -48.15305 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9962" Parameter: A <- "-75.9962" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8431" Parameter: B <- "-27.8431" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1531" Parameter: C <- "-48.1531" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6368 TOTAL ENERGY = -75.9962 RDTITL> * VAN DER WAALS = -27.8431 ELECTROSTATIC = -48.1531 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6368" Parameter: CONF_N -> "8002" Comparing "6368" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6369" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762386 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755753 ATOM PAIRS WERE FOUND FOR ATOM LIST 41708 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29413 from a total of 755753 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6369 -77.73078 1.73460 0.68275 INTE EXTERN> -29.45427 -48.27651 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7308" Parameter: A <- "-77.7308" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4543" Parameter: B <- "-29.4543" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2765" Parameter: C <- "-48.2765" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6369 TOTAL ENERGY = -77.7308 RDTITL> * VAN DER WAALS = -29.4543 ELECTROSTATIC = -48.2765 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6369" Parameter: CONF_N -> "8002" Comparing "6369" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6370" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755753 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752052 ATOM PAIRS WERE FOUND FOR ATOM LIST 41399 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30205 from a total of 752052 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6370 -74.46697 -3.26381 0.68413 INTE EXTERN> -28.05738 -46.40959 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.467" Parameter: A <- "-74.467" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0574" Parameter: B <- "-28.0574" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4096" Parameter: C <- "-46.4096" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6370 TOTAL ENERGY = -74.467 RDTITL> * VAN DER WAALS = -28.0574 ELECTROSTATIC = -46.4096 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6370" Parameter: CONF_N -> "8002" Comparing "6370" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6371" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752052 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755804 ATOM PAIRS WERE FOUND FOR ATOM LIST 41765 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30089 from a total of 755804 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6371 -75.75746 1.29049 0.77568 INTE EXTERN> -25.89395 -49.86351 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7575" Parameter: A <- "-75.7575" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.894" Parameter: B <- "-25.894" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8635" Parameter: C <- "-49.8635" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6371 TOTAL ENERGY = -75.7575 RDTITL> * VAN DER WAALS = -25.894 ELECTROSTATIC = -49.8635 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6371" Parameter: CONF_N -> "8002" Comparing "6371" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6372" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755804 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755978 ATOM PAIRS WERE FOUND FOR ATOM LIST 41472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29594 from a total of 755978 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6372 -81.78111 6.02365 0.66033 INTE EXTERN> -28.87418 -52.90693 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.7811" Parameter: A <- "-81.7811" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8742" Parameter: B <- "-28.8742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9069" Parameter: C <- "-52.9069" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6372 TOTAL ENERGY = -81.7811 RDTITL> * VAN DER WAALS = -28.8742 ELECTROSTATIC = -52.9069 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6372" Parameter: CONF_N -> "8002" Comparing "6372" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6373" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755978 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756930 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30141 from a total of 756930 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6373 -80.99946 -0.78165 0.74045 INTE EXTERN> -26.94131 -54.05815 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9995" Parameter: A <- "-80.9995" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9413" Parameter: B <- "-26.9413" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0581" Parameter: C <- "-54.0581" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6373 TOTAL ENERGY = -80.9995 RDTITL> * VAN DER WAALS = -26.9413 ELECTROSTATIC = -54.0581 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6373" Parameter: CONF_N -> "8002" Comparing "6373" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6374" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756930 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761516 ATOM PAIRS WERE FOUND FOR ATOM LIST 41927 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30263 from a total of 761516 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6374 -77.92544 -3.07402 0.68719 INTE EXTERN> -30.91962 -47.00582 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9254" Parameter: A <- "-77.9254" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9196" Parameter: B <- "-30.9196" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0058" Parameter: C <- "-47.0058" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6374 TOTAL ENERGY = -77.9254 RDTITL> * VAN DER WAALS = -30.9196 ELECTROSTATIC = -47.0058 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6374" Parameter: CONF_N -> "8002" Comparing "6374" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6375" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761516 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754583 ATOM PAIRS WERE FOUND FOR ATOM LIST 41537 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30175 from a total of 754583 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6375 -71.71906 -6.20639 0.69853 INTE EXTERN> -30.29331 -41.42575 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7191" Parameter: A <- "-71.7191" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2933" Parameter: B <- "-30.2933" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4257" Parameter: C <- "-41.4257" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6375 TOTAL ENERGY = -71.7191 RDTITL> * VAN DER WAALS = -30.2933 ELECTROSTATIC = -41.4257 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6375" Parameter: CONF_N -> "8002" Comparing "6375" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6376" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754583 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752971 ATOM PAIRS WERE FOUND FOR ATOM LIST 41528 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29869 from a total of 752971 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6376 -83.87050 12.15145 0.70558 INTE EXTERN> -30.17567 -53.69483 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.8705" Parameter: A <- "-83.8705" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1757" Parameter: B <- "-30.1757" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6948" Parameter: C <- "-53.6948" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6376 TOTAL ENERGY = -83.8705 RDTITL> * VAN DER WAALS = -30.1757 ELECTROSTATIC = -53.6948 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6376" Parameter: CONF_N -> "8002" Comparing "6376" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6377" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752971 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759228 ATOM PAIRS WERE FOUND FOR ATOM LIST 41769 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30505 from a total of 759228 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6377 -80.21705 -3.65345 0.68188 INTE EXTERN> -31.26328 -48.95377 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2171" Parameter: A <- "-80.2171" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2633" Parameter: B <- "-31.2633" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9538" Parameter: C <- "-48.9538" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6377 TOTAL ENERGY = -80.2171 RDTITL> * VAN DER WAALS = -31.2633 ELECTROSTATIC = -48.9538 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6377" Parameter: CONF_N -> "8002" Comparing "6377" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6378" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759228 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759379 ATOM PAIRS WERE FOUND FOR ATOM LIST 41821 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30311 from a total of 759379 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6378 -80.67311 0.45606 0.74297 INTE EXTERN> -28.79600 -51.87712 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6731" Parameter: A <- "-80.6731" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.796" Parameter: B <- "-28.796" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8771" Parameter: C <- "-51.8771" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6378 TOTAL ENERGY = -80.6731 RDTITL> * VAN DER WAALS = -28.796 ELECTROSTATIC = -51.8771 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6378" Parameter: CONF_N -> "8002" Comparing "6378" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6379" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759379 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759528 ATOM PAIRS WERE FOUND FOR ATOM LIST 41473 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30134 from a total of 759528 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6379 -82.17710 1.50399 0.77411 INTE EXTERN> -28.58365 -53.59346 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.1771" Parameter: A <- "-82.1771" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5836" Parameter: B <- "-28.5836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.5935" Parameter: C <- "-53.5935" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6379 TOTAL ENERGY = -82.1771 RDTITL> * VAN DER WAALS = -28.5836 ELECTROSTATIC = -53.5935 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6379" Parameter: CONF_N -> "8002" Comparing "6379" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6380" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759528 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765223 ATOM PAIRS WERE FOUND FOR ATOM LIST 42021 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30446 from a total of 765223 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6380 -83.22887 1.05177 0.65597 INTE EXTERN> -33.24824 -49.98064 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.2289" Parameter: A <- "-83.2289" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2482" Parameter: B <- "-33.2482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9806" Parameter: C <- "-49.9806" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6380 TOTAL ENERGY = -83.2289 RDTITL> * VAN DER WAALS = -33.2482 ELECTROSTATIC = -49.9806 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6380" Parameter: CONF_N -> "8002" Comparing "6380" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6381" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765223 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756130 ATOM PAIRS WERE FOUND FOR ATOM LIST 41531 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30065 from a total of 756130 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6381 -82.75442 -0.47445 0.63940 INTE EXTERN> -33.47065 -49.28377 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7544" Parameter: A <- "-82.7544" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4707" Parameter: B <- "-33.4707" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2838" Parameter: C <- "-49.2838" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6381 TOTAL ENERGY = -82.7544 RDTITL> * VAN DER WAALS = -33.4707 ELECTROSTATIC = -49.2838 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6381" Parameter: CONF_N -> "8002" Comparing "6381" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6382" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756130 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752915 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29493 from a total of 752915 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6382 -75.24158 -7.51284 0.61764 INTE EXTERN> -31.86816 -43.37342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2416" Parameter: A <- "-75.2416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8682" Parameter: B <- "-31.8682" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3734" Parameter: C <- "-43.3734" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6382 TOTAL ENERGY = -75.2416 RDTITL> * VAN DER WAALS = -31.8682 ELECTROSTATIC = -43.3734 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6382" Parameter: CONF_N -> "8002" Comparing "6382" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6383" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752915 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757870 ATOM PAIRS WERE FOUND FOR ATOM LIST 41542 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29600 from a total of 757870 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6383 -77.49915 2.25757 0.68547 INTE EXTERN> -30.27284 -47.22631 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4991" Parameter: A <- "-77.4991" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2728" Parameter: B <- "-30.2728" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2263" Parameter: C <- "-47.2263" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6383 TOTAL ENERGY = -77.4991 RDTITL> * VAN DER WAALS = -30.2728 ELECTROSTATIC = -47.2263 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6383" Parameter: CONF_N -> "8002" Comparing "6383" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6384" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757870 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751260 ATOM PAIRS WERE FOUND FOR ATOM LIST 41245 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28884 from a total of 751260 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6384 -72.72811 -4.77104 0.81749 INTE EXTERN> -24.78799 -47.94012 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7281" Parameter: A <- "-72.7281" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.788" Parameter: B <- "-24.788" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9401" Parameter: C <- "-47.9401" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6384 TOTAL ENERGY = -72.7281 RDTITL> * VAN DER WAALS = -24.788 ELECTROSTATIC = -47.9401 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6384" Parameter: CONF_N -> "8002" Comparing "6384" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6385" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751260 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757661 ATOM PAIRS WERE FOUND FOR ATOM LIST 41629 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29834 from a total of 757661 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6385 -73.75119 1.02308 0.68683 INTE EXTERN> -30.39628 -43.35491 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7512" Parameter: A <- "-73.7512" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3963" Parameter: B <- "-30.3963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3549" Parameter: C <- "-43.3549" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6385 TOTAL ENERGY = -73.7512 RDTITL> * VAN DER WAALS = -30.3963 ELECTROSTATIC = -43.3549 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6385" Parameter: CONF_N -> "8002" Comparing "6385" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6386" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757661 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754787 ATOM PAIRS WERE FOUND FOR ATOM LIST 41440 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29374 from a total of 754787 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6386 -84.60207 10.85088 0.78365 INTE EXTERN> -28.22833 -56.37374 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.6021" Parameter: A <- "-84.6021" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2283" Parameter: B <- "-28.2283" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.3737" Parameter: C <- "-56.3737" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6386 TOTAL ENERGY = -84.6021 RDTITL> * VAN DER WAALS = -28.2283 ELECTROSTATIC = -56.3737 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6386" Parameter: CONF_N -> "8002" Comparing "6386" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6387" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754787 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752168 ATOM PAIRS WERE FOUND FOR ATOM LIST 41199 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29811 from a total of 752168 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6387 -72.19070 -12.41136 0.61845 INTE EXTERN> -30.10984 -42.08086 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1907" Parameter: A <- "-72.1907" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1098" Parameter: B <- "-30.1098" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0809" Parameter: C <- "-42.0809" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6387 TOTAL ENERGY = -72.1907 RDTITL> * VAN DER WAALS = -30.1098 ELECTROSTATIC = -42.0809 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6387" Parameter: CONF_N -> "8002" Comparing "6387" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6388" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752168 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757182 ATOM PAIRS WERE FOUND FOR ATOM LIST 41518 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29866 from a total of 757182 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6388 -77.84747 5.65676 0.68508 INTE EXTERN> -27.64358 -50.20388 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8475" Parameter: A <- "-77.8475" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6436" Parameter: B <- "-27.6436" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2039" Parameter: C <- "-50.2039" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6388 TOTAL ENERGY = -77.8475 RDTITL> * VAN DER WAALS = -27.6436 ELECTROSTATIC = -50.2039 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6388" Parameter: CONF_N -> "8002" Comparing "6388" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6389" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757182 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755675 ATOM PAIRS WERE FOUND FOR ATOM LIST 41477 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30005 from a total of 755675 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6389 -77.06032 -0.78715 0.77682 INTE EXTERN> -24.35989 -52.70043 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0603" Parameter: A <- "-77.0603" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3599" Parameter: B <- "-24.3599" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.7004" Parameter: C <- "-52.7004" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6389 TOTAL ENERGY = -77.0603 RDTITL> * VAN DER WAALS = -24.3599 ELECTROSTATIC = -52.7004 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6389" Parameter: CONF_N -> "8002" Comparing "6389" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6390" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755675 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751717 ATOM PAIRS WERE FOUND FOR ATOM LIST 41142 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29569 from a total of 751717 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6390 -76.90084 -0.15948 0.64560 INTE EXTERN> -29.39020 -47.51063 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9008" Parameter: A <- "-76.9008" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3902" Parameter: B <- "-29.3902" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5106" Parameter: C <- "-47.5106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6390 TOTAL ENERGY = -76.9008 RDTITL> * VAN DER WAALS = -29.3902 ELECTROSTATIC = -47.5106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6390" Parameter: CONF_N -> "8002" Comparing "6390" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6391" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751717 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754943 ATOM PAIRS WERE FOUND FOR ATOM LIST 41265 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29681 from a total of 754943 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6391 -70.54573 -6.35511 0.60106 INTE EXTERN> -29.39465 -41.15107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5457" Parameter: A <- "-70.5457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3947" Parameter: B <- "-29.3947" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1511" Parameter: C <- "-41.1511" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6391 TOTAL ENERGY = -70.5457 RDTITL> * VAN DER WAALS = -29.3947 ELECTROSTATIC = -41.1511 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6391" Parameter: CONF_N -> "8002" Comparing "6391" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6392" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754943 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753907 ATOM PAIRS WERE FOUND FOR ATOM LIST 41238 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29247 from a total of 753907 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6392 -78.24856 7.70283 0.56806 INTE EXTERN> -30.65618 -47.59238 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2486" Parameter: A <- "-78.2486" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6562" Parameter: B <- "-30.6562" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5924" Parameter: C <- "-47.5924" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6392 TOTAL ENERGY = -78.2486 RDTITL> * VAN DER WAALS = -30.6562 ELECTROSTATIC = -47.5924 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6392" Parameter: CONF_N -> "8002" Comparing "6392" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6393" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753907 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749615 ATOM PAIRS WERE FOUND FOR ATOM LIST 40975 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29164 from a total of 749615 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6393 -71.85972 -6.38884 0.58106 INTE EXTERN> -27.68234 -44.17738 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8597" Parameter: A <- "-71.8597" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6823" Parameter: B <- "-27.6823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1774" Parameter: C <- "-44.1774" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6393 TOTAL ENERGY = -71.8597 RDTITL> * VAN DER WAALS = -27.6823 ELECTROSTATIC = -44.1774 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6393" Parameter: CONF_N -> "8002" Comparing "6393" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6394" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749615 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752610 ATOM PAIRS WERE FOUND FOR ATOM LIST 41320 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29327 from a total of 752610 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6394 -79.26722 7.40750 0.74398 INTE EXTERN> -25.53898 -53.72824 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2672" Parameter: A <- "-79.2672" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.539" Parameter: B <- "-25.539" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.7282" Parameter: C <- "-53.7282" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6394 TOTAL ENERGY = -79.2672 RDTITL> * VAN DER WAALS = -25.539 ELECTROSTATIC = -53.7282 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6394" Parameter: CONF_N -> "8002" Comparing "6394" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6395" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752610 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753893 ATOM PAIRS WERE FOUND FOR ATOM LIST 41412 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29862 from a total of 753893 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6395 -81.30387 2.03666 0.63560 INTE EXTERN> -29.96636 -51.33751 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.3039" Parameter: A <- "-81.3039" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9664" Parameter: B <- "-29.9664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3375" Parameter: C <- "-51.3375" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6395 TOTAL ENERGY = -81.3039 RDTITL> * VAN DER WAALS = -29.9664 ELECTROSTATIC = -51.3375 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6395" Parameter: CONF_N -> "8002" Comparing "6395" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6396" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753893 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759134 ATOM PAIRS WERE FOUND FOR ATOM LIST 41525 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29851 from a total of 759134 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6396 -79.27392 -2.02995 0.68411 INTE EXTERN> -27.44287 -51.83106 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2739" Parameter: A <- "-79.2739" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4429" Parameter: B <- "-27.4429" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8311" Parameter: C <- "-51.8311" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6396 TOTAL ENERGY = -79.2739 RDTITL> * VAN DER WAALS = -27.4429 ELECTROSTATIC = -51.8311 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6396" Parameter: CONF_N -> "8002" Comparing "6396" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6397" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759134 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760008 ATOM PAIRS WERE FOUND FOR ATOM LIST 41718 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30153 from a total of 760008 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6397 -75.65983 -3.61410 0.53399 INTE EXTERN> -32.62803 -43.03180 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6598" Parameter: A <- "-75.6598" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.628" Parameter: B <- "-32.628" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0318" Parameter: C <- "-43.0318" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6397 TOTAL ENERGY = -75.6598 RDTITL> * VAN DER WAALS = -32.628 ELECTROSTATIC = -43.0318 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6397" Parameter: CONF_N -> "8002" Comparing "6397" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6398" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760008 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761723 ATOM PAIRS WERE FOUND FOR ATOM LIST 41665 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30112 from a total of 761723 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6398 -75.15456 -0.50527 0.71324 INTE EXTERN> -27.96904 -47.18552 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1546" Parameter: A <- "-75.1546" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.969" Parameter: B <- "-27.969" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1855" Parameter: C <- "-47.1855" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6398 TOTAL ENERGY = -75.1546 RDTITL> * VAN DER WAALS = -27.969 ELECTROSTATIC = -47.1855 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6398" Parameter: CONF_N -> "8002" Comparing "6398" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6399" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761723 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759263 ATOM PAIRS WERE FOUND FOR ATOM LIST 41508 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29579 from a total of 759263 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6399 -79.01882 3.86426 0.69469 INTE EXTERN> -26.34246 -52.67637 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0188" Parameter: A <- "-79.0188" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3425" Parameter: B <- "-26.3425" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6764" Parameter: C <- "-52.6764" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6399 TOTAL ENERGY = -79.0188 RDTITL> * VAN DER WAALS = -26.3425 ELECTROSTATIC = -52.6764 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6399" Parameter: CONF_N -> "8002" Comparing "6399" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6400" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759263 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758064 ATOM PAIRS WERE FOUND FOR ATOM LIST 41709 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29808 from a total of 758064 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6400 -74.69396 -4.32486 0.67981 INTE EXTERN> -28.21783 -46.47613 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.694" Parameter: A <- "-74.694" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2178" Parameter: B <- "-28.2178" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4761" Parameter: C <- "-46.4761" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6400 TOTAL ENERGY = -74.694 RDTITL> * VAN DER WAALS = -28.2178 ELECTROSTATIC = -46.4761 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6400" Parameter: CONF_N -> "8002" Comparing "6400" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6401" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758064 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755923 ATOM PAIRS WERE FOUND FOR ATOM LIST 41478 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29276 from a total of 755923 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6401 -73.72750 -0.96647 0.68232 INTE EXTERN> -29.49562 -44.23188 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7275" Parameter: A <- "-73.7275" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4956" Parameter: B <- "-29.4956" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2319" Parameter: C <- "-44.2319" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6401 TOTAL ENERGY = -73.7275 RDTITL> * VAN DER WAALS = -29.4956 ELECTROSTATIC = -44.2319 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6401" Parameter: CONF_N -> "8002" Comparing "6401" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6402" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755923 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753778 ATOM PAIRS WERE FOUND FOR ATOM LIST 41402 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29705 from a total of 753778 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6402 -75.17438 1.44689 0.84204 INTE EXTERN> -24.82309 -50.35130 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1744" Parameter: A <- "-75.1744" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8231" Parameter: B <- "-24.8231" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3513" Parameter: C <- "-50.3513" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6402 TOTAL ENERGY = -75.1744 RDTITL> * VAN DER WAALS = -24.8231 ELECTROSTATIC = -50.3513 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6402" Parameter: CONF_N -> "8002" Comparing "6402" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6403" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753778 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756803 ATOM PAIRS WERE FOUND FOR ATOM LIST 41625 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29512 from a total of 756803 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6403 -78.48663 3.31225 0.71253 INTE EXTERN> -29.69565 -48.79097 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4866" Parameter: A <- "-78.4866" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6957" Parameter: B <- "-29.6957" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.791" Parameter: C <- "-48.791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6403 TOTAL ENERGY = -78.4866 RDTITL> * VAN DER WAALS = -29.6957 ELECTROSTATIC = -48.791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6403" Parameter: CONF_N -> "8002" Comparing "6403" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6404" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756803 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752753 ATOM PAIRS WERE FOUND FOR ATOM LIST 41361 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29154 from a total of 752753 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6404 -79.53944 1.05281 0.74405 INTE EXTERN> -26.16094 -53.37849 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5394" Parameter: A <- "-79.5394" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1609" Parameter: B <- "-26.1609" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3785" Parameter: C <- "-53.3785" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6404 TOTAL ENERGY = -79.5394 RDTITL> * VAN DER WAALS = -26.1609 ELECTROSTATIC = -53.3785 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6404" Parameter: CONF_N -> "8002" Comparing "6404" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6405" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752753 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757989 ATOM PAIRS WERE FOUND FOR ATOM LIST 41679 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28959 from a total of 757989 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6405 -80.41269 0.87325 0.71988 INTE EXTERN> -27.86614 -52.54655 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4127" Parameter: A <- "-80.4127" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8661" Parameter: B <- "-27.8661" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5466" Parameter: C <- "-52.5466" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6405 TOTAL ENERGY = -80.4127 RDTITL> * VAN DER WAALS = -27.8661 ELECTROSTATIC = -52.5466 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6405" Parameter: CONF_N -> "8002" Comparing "6405" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6406" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757989 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761417 ATOM PAIRS WERE FOUND FOR ATOM LIST 41677 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29595 from a total of 761417 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6406 -74.57934 -5.83336 0.60792 INTE EXTERN> -32.20888 -42.37046 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5793" Parameter: A <- "-74.5793" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2089" Parameter: B <- "-32.2089" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3705" Parameter: C <- "-42.3705" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6406 TOTAL ENERGY = -74.5793 RDTITL> * VAN DER WAALS = -32.2089 ELECTROSTATIC = -42.3705 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6406" Parameter: CONF_N -> "8002" Comparing "6406" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6407" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761417 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753786 ATOM PAIRS WERE FOUND FOR ATOM LIST 41470 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29314 from a total of 753786 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6407 -77.66005 3.08072 0.77974 INTE EXTERN> -24.57321 -53.08685 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6601" Parameter: A <- "-77.6601" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5732" Parameter: B <- "-24.5732" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0868" Parameter: C <- "-53.0868" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6407 TOTAL ENERGY = -77.6601 RDTITL> * VAN DER WAALS = -24.5732 ELECTROSTATIC = -53.0868 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6407" Parameter: CONF_N -> "8002" Comparing "6407" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6408" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753786 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753854 ATOM PAIRS WERE FOUND FOR ATOM LIST 41434 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29021 from a total of 753854 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6408 -75.50300 -2.15705 0.64944 INTE EXTERN> -28.49849 -47.00451 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.503" Parameter: A <- "-75.503" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4985" Parameter: B <- "-28.4985" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0045" Parameter: C <- "-47.0045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6408 TOTAL ENERGY = -75.503 RDTITL> * VAN DER WAALS = -28.4985 ELECTROSTATIC = -47.0045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6408" Parameter: CONF_N -> "8002" Comparing "6408" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6409" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753854 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755244 ATOM PAIRS WERE FOUND FOR ATOM LIST 41517 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29289 from a total of 755244 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6409 -77.87994 2.37694 0.55057 INTE EXTERN> -33.06053 -44.81941 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8799" Parameter: A <- "-77.8799" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0605" Parameter: B <- "-33.0605" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8194" Parameter: C <- "-44.8194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6409 TOTAL ENERGY = -77.8799 RDTITL> * VAN DER WAALS = -33.0605 ELECTROSTATIC = -44.8194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6409" Parameter: CONF_N -> "8002" Comparing "6409" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6410" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755244 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758701 ATOM PAIRS WERE FOUND FOR ATOM LIST 41615 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29699 from a total of 758701 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6410 -70.08407 -7.79587 0.70577 INTE EXTERN> -25.23132 -44.85275 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0841" Parameter: A <- "-70.0841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2313" Parameter: B <- "-25.2313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8528" Parameter: C <- "-44.8528" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6410 TOTAL ENERGY = -70.0841 RDTITL> * VAN DER WAALS = -25.2313 ELECTROSTATIC = -44.8528 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6410" Parameter: CONF_N -> "8002" Comparing "6410" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6411" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758701 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751888 ATOM PAIRS WERE FOUND FOR ATOM LIST 41284 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29165 from a total of 751888 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6411 -70.70012 0.61605 0.68858 INTE EXTERN> -27.88707 -42.81305 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7001" Parameter: A <- "-70.7001" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8871" Parameter: B <- "-27.8871" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8131" Parameter: C <- "-42.8131" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6411 TOTAL ENERGY = -70.7001 RDTITL> * VAN DER WAALS = -27.8871 ELECTROSTATIC = -42.8131 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6411" Parameter: CONF_N -> "8002" Comparing "6411" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6412" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751888 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756431 ATOM PAIRS WERE FOUND FOR ATOM LIST 41487 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29293 from a total of 756431 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6412 -78.28272 7.58260 0.80002 INTE EXTERN> -24.38144 -53.90128 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2827" Parameter: A <- "-78.2827" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3814" Parameter: B <- "-24.3814" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.9013" Parameter: C <- "-53.9013" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6412 TOTAL ENERGY = -78.2827 RDTITL> * VAN DER WAALS = -24.3814 ELECTROSTATIC = -53.9013 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6412" Parameter: CONF_N -> "8002" Comparing "6412" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6413" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756431 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756180 ATOM PAIRS WERE FOUND FOR ATOM LIST 41513 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29231 from a total of 756180 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6413 -69.39890 -8.88382 0.61802 INTE EXTERN> -30.14643 -39.25247 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3989" Parameter: A <- "-69.3989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1464" Parameter: B <- "-30.1464" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2525" Parameter: C <- "-39.2525" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6413 TOTAL ENERGY = -69.3989 RDTITL> * VAN DER WAALS = -30.1464 ELECTROSTATIC = -39.2525 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6413" Parameter: CONF_N -> "8002" Comparing "6413" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6414" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756180 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754164 ATOM PAIRS WERE FOUND FOR ATOM LIST 41423 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28845 from a total of 754164 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6414 -72.09216 2.69326 0.63452 INTE EXTERN> -26.83825 -45.25390 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0922" Parameter: A <- "-72.0922" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8383" Parameter: B <- "-26.8383" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2539" Parameter: C <- "-45.2539" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6414 TOTAL ENERGY = -72.0922 RDTITL> * VAN DER WAALS = -26.8383 ELECTROSTATIC = -45.2539 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6414" Parameter: CONF_N -> "8002" Comparing "6414" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6415" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754164 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758554 ATOM PAIRS WERE FOUND FOR ATOM LIST 41603 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29512 from a total of 758554 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6415 -78.16242 6.07027 0.69966 INTE EXTERN> -27.69750 -50.46492 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1624" Parameter: A <- "-78.1624" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6975" Parameter: B <- "-27.6975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4649" Parameter: C <- "-50.4649" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6415 TOTAL ENERGY = -78.1624 RDTITL> * VAN DER WAALS = -27.6975 ELECTROSTATIC = -50.4649 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6415" Parameter: CONF_N -> "8002" Comparing "6415" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6416" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758554 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755868 ATOM PAIRS WERE FOUND FOR ATOM LIST 41511 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29585 from a total of 755868 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6416 -77.49537 -0.66705 0.72059 INTE EXTERN> -23.98346 -53.51191 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4954" Parameter: A <- "-77.4954" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9835" Parameter: B <- "-23.9835" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.5119" Parameter: C <- "-53.5119" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6416 TOTAL ENERGY = -77.4954 RDTITL> * VAN DER WAALS = -23.9835 ELECTROSTATIC = -53.5119 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6416" Parameter: CONF_N -> "8002" Comparing "6416" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6417" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755868 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41253 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29146 from a total of 751009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6417 -77.20587 -0.28950 0.70315 INTE EXTERN> -26.56974 -50.63613 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2059" Parameter: A <- "-77.2059" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5697" Parameter: B <- "-26.5697" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6361" Parameter: C <- "-50.6361" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6417 TOTAL ENERGY = -77.2059 RDTITL> * VAN DER WAALS = -26.5697 ELECTROSTATIC = -50.6361 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6417" Parameter: CONF_N -> "8002" Comparing "6417" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6418" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752804 ATOM PAIRS WERE FOUND FOR ATOM LIST 41205 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29657 from a total of 752804 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6418 -77.64721 0.44134 0.55833 INTE EXTERN> -33.33197 -44.31523 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6472" Parameter: A <- "-77.6472" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.332" Parameter: B <- "-33.332" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3152" Parameter: C <- "-44.3152" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6418 TOTAL ENERGY = -77.6472 RDTITL> * VAN DER WAALS = -33.332 ELECTROSTATIC = -44.3152 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6418" Parameter: CONF_N -> "8002" Comparing "6418" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6419" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752804 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758294 ATOM PAIRS WERE FOUND FOR ATOM LIST 41572 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29215 from a total of 758294 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6419 -70.94575 -6.70146 0.58891 INTE EXTERN> -29.04576 -41.89998 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9457" Parameter: A <- "-70.9457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0458" Parameter: B <- "-29.0458" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9" Parameter: C <- "-41.9" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6419 TOTAL ENERGY = -70.9457 RDTITL> * VAN DER WAALS = -29.0458 ELECTROSTATIC = -41.9 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6419" Parameter: CONF_N -> "8002" Comparing "6419" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6420" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758294 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758343 ATOM PAIRS WERE FOUND FOR ATOM LIST 41338 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28999 from a total of 758343 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6420 -69.93753 -1.00822 0.58654 INTE EXTERN> -29.57345 -40.36408 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9375" Parameter: A <- "-69.9375" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5734" Parameter: B <- "-29.5734" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3641" Parameter: C <- "-40.3641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6420 TOTAL ENERGY = -69.9375 RDTITL> * VAN DER WAALS = -29.5734 ELECTROSTATIC = -40.3641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6420" Parameter: CONF_N -> "8002" Comparing "6420" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6421" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758343 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757333 ATOM PAIRS WERE FOUND FOR ATOM LIST 41369 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29316 from a total of 757333 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6421 -72.20886 2.27133 0.66096 INTE EXTERN> -25.18234 -47.02652 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2089" Parameter: A <- "-72.2089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1823" Parameter: B <- "-25.1823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0265" Parameter: C <- "-47.0265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6421 TOTAL ENERGY = -72.2089 RDTITL> * VAN DER WAALS = -25.1823 ELECTROSTATIC = -47.0265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6421" Parameter: CONF_N -> "8002" Comparing "6421" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6422" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757333 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751577 ATOM PAIRS WERE FOUND FOR ATOM LIST 41140 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29038 from a total of 751577 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6422 -77.75137 5.54252 0.64059 INTE EXTERN> -29.60020 -48.15117 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7514" Parameter: A <- "-77.7514" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6002" Parameter: B <- "-29.6002" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1512" Parameter: C <- "-48.1512" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6422 TOTAL ENERGY = -77.7514 RDTITL> * VAN DER WAALS = -29.6002 ELECTROSTATIC = -48.1512 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6422" Parameter: CONF_N -> "8002" Comparing "6422" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6423" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751577 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750457 ATOM PAIRS WERE FOUND FOR ATOM LIST 41185 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29409 from a total of 750457 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6423 -71.02410 -6.72727 0.70733 INTE EXTERN> -26.45445 -44.56966 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0241" Parameter: A <- "-71.0241" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4544" Parameter: B <- "-26.4544" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5697" Parameter: C <- "-44.5697" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6423 TOTAL ENERGY = -71.0241 RDTITL> * VAN DER WAALS = -26.4544 ELECTROSTATIC = -44.5697 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6423" Parameter: CONF_N -> "8002" Comparing "6423" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6424" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750457 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753655 ATOM PAIRS WERE FOUND FOR ATOM LIST 41277 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29664 from a total of 753655 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6424 -73.57289 2.54878 0.68702 INTE EXTERN> -27.09212 -46.48076 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5729" Parameter: A <- "-73.5729" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0921" Parameter: B <- "-27.0921" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4808" Parameter: C <- "-46.4808" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6424 TOTAL ENERGY = -73.5729 RDTITL> * VAN DER WAALS = -27.0921 ELECTROSTATIC = -46.4808 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6424" Parameter: CONF_N -> "8002" Comparing "6424" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6425" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753655 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748284 ATOM PAIRS WERE FOUND FOR ATOM LIST 40962 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29129 from a total of 748284 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6425 -77.00016 3.42728 0.72718 INTE EXTERN> -27.35618 -49.64398 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0002" Parameter: A <- "-77.0002" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3562" Parameter: B <- "-27.3562" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.644" Parameter: C <- "-49.644" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6425 TOTAL ENERGY = -77.0002 RDTITL> * VAN DER WAALS = -27.3562 ELECTROSTATIC = -49.644 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6425" Parameter: CONF_N -> "8002" Comparing "6425" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6426" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748284 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755418 ATOM PAIRS WERE FOUND FOR ATOM LIST 41399 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29541 from a total of 755418 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6426 -74.16937 -2.83080 0.65604 INTE EXTERN> -29.37669 -44.79267 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1694" Parameter: A <- "-74.1694" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3767" Parameter: B <- "-29.3767" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7927" Parameter: C <- "-44.7927" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6426 TOTAL ENERGY = -74.1694 RDTITL> * VAN DER WAALS = -29.3767 ELECTROSTATIC = -44.7927 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6426" Parameter: CONF_N -> "8002" Comparing "6426" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6427" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755418 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749519 ATOM PAIRS WERE FOUND FOR ATOM LIST 40912 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29603 from a total of 749519 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6427 -71.25078 -2.91858 0.62957 INTE EXTERN> -31.66279 -39.58799 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2508" Parameter: A <- "-71.2508" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6628" Parameter: B <- "-31.6628" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.588" Parameter: C <- "-39.588" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6427 TOTAL ENERGY = -71.2508 RDTITL> * VAN DER WAALS = -31.6628 ELECTROSTATIC = -39.588 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6427" Parameter: CONF_N -> "8002" Comparing "6427" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6428" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749519 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746892 ATOM PAIRS WERE FOUND FOR ATOM LIST 40920 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29196 from a total of 746892 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6428 -70.29887 -0.95191 0.62889 INTE EXTERN> -28.67956 -41.61931 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2989" Parameter: A <- "-70.2989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6796" Parameter: B <- "-28.6796" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6193" Parameter: C <- "-41.6193" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6428 TOTAL ENERGY = -70.2989 RDTITL> * VAN DER WAALS = -28.6796 ELECTROSTATIC = -41.6193 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6428" Parameter: CONF_N -> "8002" Comparing "6428" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6429" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746892 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750953 ATOM PAIRS WERE FOUND FOR ATOM LIST 41195 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29393 from a total of 750953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6429 -73.07378 2.77491 0.71962 INTE EXTERN> -22.76318 -50.31060 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0738" Parameter: A <- "-73.0738" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.7632" Parameter: B <- "-22.7632" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3106" Parameter: C <- "-50.3106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6429 TOTAL ENERGY = -73.0738 RDTITL> * VAN DER WAALS = -22.7632 ELECTROSTATIC = -50.3106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6429" Parameter: CONF_N -> "8002" Comparing "6429" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6430" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748223 ATOM PAIRS WERE FOUND FOR ATOM LIST 40899 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28652 from a total of 748223 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6430 -70.18814 -2.88564 0.53591 INTE EXTERN> -28.51171 -41.67643 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1881" Parameter: A <- "-70.1881" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5117" Parameter: B <- "-28.5117" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6764" Parameter: C <- "-41.6764" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6430 TOTAL ENERGY = -70.1881 RDTITL> * VAN DER WAALS = -28.5117 ELECTROSTATIC = -41.6764 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6430" Parameter: CONF_N -> "8002" Comparing "6430" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6431" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748223 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751862 ATOM PAIRS WERE FOUND FOR ATOM LIST 41165 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28871 from a total of 751862 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6431 -72.72427 2.53613 0.51025 INTE EXTERN> -29.00093 -43.72334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7243" Parameter: A <- "-72.7243" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0009" Parameter: B <- "-29.0009" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7233" Parameter: C <- "-43.7233" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6431 TOTAL ENERGY = -72.7243 RDTITL> * VAN DER WAALS = -29.0009 ELECTROSTATIC = -43.7233 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6431" Parameter: CONF_N -> "8002" Comparing "6431" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6432" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751862 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750544 ATOM PAIRS WERE FOUND FOR ATOM LIST 41046 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28189 from a total of 750544 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6432 -79.72079 6.99652 0.67121 INTE EXTERN> -28.11087 -51.60992 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7208" Parameter: A <- "-79.7208" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1109" Parameter: B <- "-28.1109" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6099" Parameter: C <- "-51.6099" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6432 TOTAL ENERGY = -79.7208 RDTITL> * VAN DER WAALS = -28.1109 ELECTROSTATIC = -51.6099 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6432" Parameter: CONF_N -> "8002" Comparing "6432" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6433" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750544 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746149 ATOM PAIRS WERE FOUND FOR ATOM LIST 40897 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 27878 from a total of 746149 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6433 -73.88631 -5.83448 0.55394 INTE EXTERN> -29.77339 -44.11292 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8863" Parameter: A <- "-73.8863" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7734" Parameter: B <- "-29.7734" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1129" Parameter: C <- "-44.1129" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6433 TOTAL ENERGY = -73.8863 RDTITL> * VAN DER WAALS = -29.7734 ELECTROSTATIC = -44.1129 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6433" Parameter: CONF_N -> "8002" Comparing "6433" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6434" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746149 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746178 ATOM PAIRS WERE FOUND FOR ATOM LIST 41028 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28580 from a total of 746178 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6434 -76.84135 2.95504 0.74296 INTE EXTERN> -26.54795 -50.29340 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8414" Parameter: A <- "-76.8414" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5479" Parameter: B <- "-26.5479" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2934" Parameter: C <- "-50.2934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6434 TOTAL ENERGY = -76.8414 RDTITL> * VAN DER WAALS = -26.5479 ELECTROSTATIC = -50.2934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6434" Parameter: CONF_N -> "8002" Comparing "6434" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6435" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746178 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753683 ATOM PAIRS WERE FOUND FOR ATOM LIST 41219 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28839 from a total of 753683 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6435 -77.50233 0.66097 0.65313 INTE EXTERN> -30.65053 -46.85179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5023" Parameter: A <- "-77.5023" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6505" Parameter: B <- "-30.6505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8518" Parameter: C <- "-46.8518" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6435 TOTAL ENERGY = -77.5023 RDTITL> * VAN DER WAALS = -30.6505 ELECTROSTATIC = -46.8518 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6435" Parameter: CONF_N -> "8002" Comparing "6435" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6436" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753683 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750153 ATOM PAIRS WERE FOUND FOR ATOM LIST 41185 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28707 from a total of 750153 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6436 -66.58077 -10.92155 0.58181 INTE EXTERN> -29.00459 -37.57618 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.5808" Parameter: A <- "-66.5808" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0046" Parameter: B <- "-29.0046" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5762" Parameter: C <- "-37.5762" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6436 TOTAL ENERGY = -66.5808 RDTITL> * VAN DER WAALS = -29.0046 ELECTROSTATIC = -37.5762 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6436" Parameter: CONF_N -> "8002" Comparing "6436" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6437" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750153 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752985 ATOM PAIRS WERE FOUND FOR ATOM LIST 41219 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28667 from a total of 752985 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6437 -78.69270 12.11193 0.63056 INTE EXTERN> -30.00164 -48.69106 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6927" Parameter: A <- "-78.6927" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0016" Parameter: B <- "-30.0016" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6911" Parameter: C <- "-48.6911" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6437 TOTAL ENERGY = -78.6927 RDTITL> * VAN DER WAALS = -30.0016 ELECTROSTATIC = -48.6911 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6437" Parameter: CONF_N -> "8002" Comparing "6437" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6438" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752985 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751571 ATOM PAIRS WERE FOUND FOR ATOM LIST 41204 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28989 from a total of 751571 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6438 -74.50116 -4.19154 0.59500 INTE EXTERN> -29.80868 -44.69248 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5012" Parameter: A <- "-74.5012" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8087" Parameter: B <- "-29.8087" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6925" Parameter: C <- "-44.6925" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6438 TOTAL ENERGY = -74.5012 RDTITL> * VAN DER WAALS = -29.8087 ELECTROSTATIC = -44.6925 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6438" Parameter: CONF_N -> "8002" Comparing "6438" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6439" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751571 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751617 ATOM PAIRS WERE FOUND FOR ATOM LIST 41170 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29259 from a total of 751617 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6439 -74.93502 0.43387 0.65647 INTE EXTERN> -28.96838 -45.96665 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.935" Parameter: A <- "-74.935" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9684" Parameter: B <- "-28.9684" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9666" Parameter: C <- "-45.9666" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6439 TOTAL ENERGY = -74.935 RDTITL> * VAN DER WAALS = -28.9684 ELECTROSTATIC = -45.9666 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6439" Parameter: CONF_N -> "8002" Comparing "6439" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6440" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751617 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748117 ATOM PAIRS WERE FOUND FOR ATOM LIST 40986 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28299 from a total of 748117 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6440 -72.58291 -2.35212 0.63480 INTE EXTERN> -28.52625 -44.05665 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5829" Parameter: A <- "-72.5829" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5263" Parameter: B <- "-28.5263" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0567" Parameter: C <- "-44.0567" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6440 TOTAL ENERGY = -72.5829 RDTITL> * VAN DER WAALS = -28.5263 ELECTROSTATIC = -44.0567 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6440" Parameter: CONF_N -> "8002" Comparing "6440" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6441" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748117 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749875 ATOM PAIRS WERE FOUND FOR ATOM LIST 41062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28867 from a total of 749875 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6441 -82.56884 9.98594 0.73662 INTE EXTERN> -26.27585 -56.29300 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5688" Parameter: A <- "-82.5688" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2758" Parameter: B <- "-26.2758" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.293" Parameter: C <- "-56.293" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6441 TOTAL ENERGY = -82.5688 RDTITL> * VAN DER WAALS = -26.2758 ELECTROSTATIC = -56.293 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6441" Parameter: CONF_N -> "8002" Comparing "6441" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6442" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749875 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753357 ATOM PAIRS WERE FOUND FOR ATOM LIST 41146 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28283 from a total of 753357 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6442 -76.42448 -6.14437 0.67171 INTE EXTERN> -27.55090 -48.87357 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4245" Parameter: A <- "-76.4245" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5509" Parameter: B <- "-27.5509" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8736" Parameter: C <- "-48.8736" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6442 TOTAL ENERGY = -76.4245 RDTITL> * VAN DER WAALS = -27.5509 ELECTROSTATIC = -48.8736 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6442" Parameter: CONF_N -> "8002" Comparing "6442" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6443" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753357 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752217 ATOM PAIRS WERE FOUND FOR ATOM LIST 41276 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28809 from a total of 752217 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6443 -78.21248 1.78800 0.58431 INTE EXTERN> -30.77923 -47.43325 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2125" Parameter: A <- "-78.2125" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7792" Parameter: B <- "-30.7792" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4332" Parameter: C <- "-47.4332" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6443 TOTAL ENERGY = -78.2125 RDTITL> * VAN DER WAALS = -30.7792 ELECTROSTATIC = -47.4332 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6443" Parameter: CONF_N -> "8002" Comparing "6443" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6444" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752217 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757050 ATOM PAIRS WERE FOUND FOR ATOM LIST 41262 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29969 from a total of 757050 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6444 -73.57330 -4.63917 0.61686 INTE EXTERN> -31.10204 -42.47126 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5733" Parameter: A <- "-73.5733" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.102" Parameter: B <- "-31.102" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4713" Parameter: C <- "-42.4713" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6444 TOTAL ENERGY = -73.5733 RDTITL> * VAN DER WAALS = -31.102 ELECTROSTATIC = -42.4713 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6444" Parameter: CONF_N -> "8002" Comparing "6444" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6445" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757050 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756722 ATOM PAIRS WERE FOUND FOR ATOM LIST 41420 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29653 from a total of 756722 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6445 -76.19455 2.62125 0.65620 INTE EXTERN> -27.88396 -48.31059 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1945" Parameter: A <- "-76.1945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.884" Parameter: B <- "-27.884" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3106" Parameter: C <- "-48.3106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6445 TOTAL ENERGY = -76.1945 RDTITL> * VAN DER WAALS = -27.884 ELECTROSTATIC = -48.3106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6445" Parameter: CONF_N -> "8002" Comparing "6445" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6446" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756722 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752120 ATOM PAIRS WERE FOUND FOR ATOM LIST 41325 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28823 from a total of 752120 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6446 -82.82818 6.63363 0.69788 INTE EXTERN> -28.37182 -54.45636 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.8282" Parameter: A <- "-82.8282" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3718" Parameter: B <- "-28.3718" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.4564" Parameter: C <- "-54.4564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6446 TOTAL ENERGY = -82.8282 RDTITL> * VAN DER WAALS = -28.3718 ELECTROSTATIC = -54.4564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6446" Parameter: CONF_N -> "8002" Comparing "6446" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6447" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752120 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757167 ATOM PAIRS WERE FOUND FOR ATOM LIST 41486 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29430 from a total of 757167 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6447 -86.15702 3.32884 0.69629 INTE EXTERN> -31.01438 -55.14264 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.157" Parameter: A <- "-86.157" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0144" Parameter: B <- "-31.0144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.1426" Parameter: C <- "-55.1426" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6447 TOTAL ENERGY = -86.157 RDTITL> * VAN DER WAALS = -31.0144 ELECTROSTATIC = -55.1426 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6447" Parameter: CONF_N -> "8002" Comparing "6447" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6448" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757167 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750931 ATOM PAIRS WERE FOUND FOR ATOM LIST 41036 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29161 from a total of 750931 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6448 -79.91044 -6.24658 0.68762 INTE EXTERN> -30.83373 -49.07671 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9104" Parameter: A <- "-79.9104" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8337" Parameter: B <- "-30.8337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0767" Parameter: C <- "-49.0767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6448 TOTAL ENERGY = -79.9104 RDTITL> * VAN DER WAALS = -30.8337 ELECTROSTATIC = -49.0767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6448" Parameter: CONF_N -> "8002" Comparing "6448" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6449" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750931 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752689 ATOM PAIRS WERE FOUND FOR ATOM LIST 41408 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29538 from a total of 752689 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6449 -83.71053 3.80009 0.63522 INTE EXTERN> -33.28834 -50.42219 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.7105" Parameter: A <- "-83.7105" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2883" Parameter: B <- "-33.2883" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4222" Parameter: C <- "-50.4222" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6449 TOTAL ENERGY = -83.7105 RDTITL> * VAN DER WAALS = -33.2883 ELECTROSTATIC = -50.4222 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6449" Parameter: CONF_N -> "8002" Comparing "6449" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6450" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752689 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758536 ATOM PAIRS WERE FOUND FOR ATOM LIST 41526 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29896 from a total of 758536 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6450 -80.21738 -3.49315 0.71227 INTE EXTERN> -30.68541 -49.53197 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2174" Parameter: A <- "-80.2174" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6854" Parameter: B <- "-30.6854" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.532" Parameter: C <- "-49.532" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6450 TOTAL ENERGY = -80.2174 RDTITL> * VAN DER WAALS = -30.6854 ELECTROSTATIC = -49.532 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6450" Parameter: CONF_N -> "8002" Comparing "6450" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6451" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758536 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755136 ATOM PAIRS WERE FOUND FOR ATOM LIST 41369 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29941 from a total of 755136 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6451 -75.37249 -4.84489 0.68429 INTE EXTERN> -25.96864 -49.40385 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3725" Parameter: A <- "-75.3725" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9686" Parameter: B <- "-25.9686" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4039" Parameter: C <- "-49.4039" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6451 TOTAL ENERGY = -75.3725 RDTITL> * VAN DER WAALS = -25.9686 ELECTROSTATIC = -49.4039 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6451" Parameter: CONF_N -> "8002" Comparing "6451" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6452" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755136 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753215 ATOM PAIRS WERE FOUND FOR ATOM LIST 41215 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29294 from a total of 753215 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6452 -80.55679 5.18430 0.73869 INTE EXTERN> -27.72405 -52.83274 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5568" Parameter: A <- "-80.5568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7241" Parameter: B <- "-27.7241" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8327" Parameter: C <- "-52.8327" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6452 TOTAL ENERGY = -80.5568 RDTITL> * VAN DER WAALS = -27.7241 ELECTROSTATIC = -52.8327 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6452" Parameter: CONF_N -> "8002" Comparing "6452" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6453" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753215 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754087 ATOM PAIRS WERE FOUND FOR ATOM LIST 41207 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29182 from a total of 754087 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6453 -77.31990 -3.23689 0.75000 INTE EXTERN> -26.29743 -51.02248 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3199" Parameter: A <- "-77.3199" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2974" Parameter: B <- "-26.2974" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0225" Parameter: C <- "-51.0225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6453 TOTAL ENERGY = -77.3199 RDTITL> * VAN DER WAALS = -26.2974 ELECTROSTATIC = -51.0225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6453" Parameter: CONF_N -> "8002" Comparing "6453" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6454" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754087 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756071 ATOM PAIRS WERE FOUND FOR ATOM LIST 41194 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28947 from a total of 756071 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6454 -83.44830 6.12840 0.67668 INTE EXTERN> -32.26310 -51.18520 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.4483" Parameter: A <- "-83.4483" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2631" Parameter: B <- "-32.2631" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1852" Parameter: C <- "-51.1852" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6454 TOTAL ENERGY = -83.4483 RDTITL> * VAN DER WAALS = -32.2631 ELECTROSTATIC = -51.1852 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6454" Parameter: CONF_N -> "8002" Comparing "6454" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6455" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756071 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756249 ATOM PAIRS WERE FOUND FOR ATOM LIST 41201 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29422 from a total of 756249 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6455 -78.37018 -5.07813 0.63345 INTE EXTERN> -30.73945 -47.63072 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3702" Parameter: A <- "-78.3702" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7395" Parameter: B <- "-30.7395" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6307" Parameter: C <- "-47.6307" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6455 TOTAL ENERGY = -78.3702 RDTITL> * VAN DER WAALS = -30.7395 ELECTROSTATIC = -47.6307 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6455" Parameter: CONF_N -> "8002" Comparing "6455" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6456" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756249 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755851 ATOM PAIRS WERE FOUND FOR ATOM LIST 41295 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29843 from a total of 755851 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6456 -80.27423 1.90406 0.66931 INTE EXTERN> -29.86307 -50.41116 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2742" Parameter: A <- "-80.2742" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8631" Parameter: B <- "-29.8631" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4112" Parameter: C <- "-50.4112" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6456 TOTAL ENERGY = -80.2742 RDTITL> * VAN DER WAALS = -29.8631 ELECTROSTATIC = -50.4112 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6456" Parameter: CONF_N -> "8002" Comparing "6456" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6457" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755851 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758311 ATOM PAIRS WERE FOUND FOR ATOM LIST 41467 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30402 from a total of 758311 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6457 -82.82799 2.55376 0.71604 INTE EXTERN> -27.98735 -54.84065 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.828" Parameter: A <- "-82.828" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9873" Parameter: B <- "-27.9873" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8406" Parameter: C <- "-54.8406" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6457 TOTAL ENERGY = -82.828 RDTITL> * VAN DER WAALS = -27.9873 ELECTROSTATIC = -54.8406 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6457" Parameter: CONF_N -> "8002" Comparing "6457" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6458" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758311 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754374 ATOM PAIRS WERE FOUND FOR ATOM LIST 41013 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29265 from a total of 754374 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6458 -75.99154 -6.83645 0.62684 INTE EXTERN> -28.19473 -47.79682 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9915" Parameter: A <- "-75.9915" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1947" Parameter: B <- "-28.1947" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7968" Parameter: C <- "-47.7968" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6458 TOTAL ENERGY = -75.9915 RDTITL> * VAN DER WAALS = -28.1947 ELECTROSTATIC = -47.7968 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6458" Parameter: CONF_N -> "8002" Comparing "6458" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6459" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754374 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754357 ATOM PAIRS WERE FOUND FOR ATOM LIST 41120 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29827 from a total of 754357 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6459 -78.90769 2.91615 0.71268 INTE EXTERN> -27.86507 -51.04262 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9077" Parameter: A <- "-78.9077" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8651" Parameter: B <- "-27.8651" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0426" Parameter: C <- "-51.0426" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6459 TOTAL ENERGY = -78.9077 RDTITL> * VAN DER WAALS = -27.8651 ELECTROSTATIC = -51.0426 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6459" Parameter: CONF_N -> "8002" Comparing "6459" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6460" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754357 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759165 ATOM PAIRS WERE FOUND FOR ATOM LIST 41118 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30457 from a total of 759165 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6460 -78.58606 -0.32163 0.64365 INTE EXTERN> -29.10795 -49.47811 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5861" Parameter: A <- "-78.5861" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.108" Parameter: B <- "-29.108" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4781" Parameter: C <- "-49.4781" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6460 TOTAL ENERGY = -78.5861 RDTITL> * VAN DER WAALS = -29.108 ELECTROSTATIC = -49.4781 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6460" Parameter: CONF_N -> "8002" Comparing "6460" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6461" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759165 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750352 ATOM PAIRS WERE FOUND FOR ATOM LIST 40969 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29218 from a total of 750352 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6461 -79.99094 1.40488 0.69276 INTE EXTERN> -27.01219 -52.97875 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9909" Parameter: A <- "-79.9909" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0122" Parameter: B <- "-27.0122" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9788" Parameter: C <- "-52.9788" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6461 TOTAL ENERGY = -79.9909 RDTITL> * VAN DER WAALS = -27.0122 ELECTROSTATIC = -52.9788 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6461" Parameter: CONF_N -> "8002" Comparing "6461" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6462" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750352 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753646 ATOM PAIRS WERE FOUND FOR ATOM LIST 41081 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29327 from a total of 753646 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6462 -71.98167 -8.00928 0.64977 INTE EXTERN> -27.35903 -44.62263 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9817" Parameter: A <- "-71.9817" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.359" Parameter: B <- "-27.359" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6226" Parameter: C <- "-44.6226" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6462 TOTAL ENERGY = -71.9817 RDTITL> * VAN DER WAALS = -27.359 ELECTROSTATIC = -44.6226 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6462" Parameter: CONF_N -> "8002" Comparing "6462" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6463" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753646 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754947 ATOM PAIRS WERE FOUND FOR ATOM LIST 41392 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29880 from a total of 754947 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6463 -83.87166 11.88999 0.79838 INTE EXTERN> -26.06705 -57.80461 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.8717" Parameter: A <- "-83.8717" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.067" Parameter: B <- "-26.067" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.8046" Parameter: C <- "-57.8046" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6463 TOTAL ENERGY = -83.8717 RDTITL> * VAN DER WAALS = -26.067 ELECTROSTATIC = -57.8046 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6463" Parameter: CONF_N -> "8002" Comparing "6463" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6464" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754947 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759514 ATOM PAIRS WERE FOUND FOR ATOM LIST 41578 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30190 from a total of 759514 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6464 -76.94580 -6.92586 0.61497 INTE EXTERN> -31.10423 -45.84156 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9458" Parameter: A <- "-76.9458" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1042" Parameter: B <- "-31.1042" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8416" Parameter: C <- "-45.8416" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6464 TOTAL ENERGY = -76.9458 RDTITL> * VAN DER WAALS = -31.1042 ELECTROSTATIC = -45.8416 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6464" Parameter: CONF_N -> "8002" Comparing "6464" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6465" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759514 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755158 ATOM PAIRS WERE FOUND FOR ATOM LIST 41222 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30415 from a total of 755158 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6465 -81.62910 4.68330 0.79022 INTE EXTERN> -26.84619 -54.78291 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6291" Parameter: A <- "-81.6291" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8462" Parameter: B <- "-26.8462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.7829" Parameter: C <- "-54.7829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6465 TOTAL ENERGY = -81.6291 RDTITL> * VAN DER WAALS = -26.8462 ELECTROSTATIC = -54.7829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6465" Parameter: CONF_N -> "8002" Comparing "6465" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6466" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755158 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754513 ATOM PAIRS WERE FOUND FOR ATOM LIST 41349 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29433 from a total of 754513 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6466 -80.53754 -1.09156 0.74719 INTE EXTERN> -25.21442 -55.32312 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5375" Parameter: A <- "-80.5375" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2144" Parameter: B <- "-25.2144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.3231" Parameter: C <- "-55.3231" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6466 TOTAL ENERGY = -80.5375 RDTITL> * VAN DER WAALS = -25.2144 ELECTROSTATIC = -55.3231 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6466" Parameter: CONF_N -> "8002" Comparing "6466" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6467" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754513 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753723 ATOM PAIRS WERE FOUND FOR ATOM LIST 41341 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29520 from a total of 753723 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6467 -82.25806 1.72052 0.66552 INTE EXTERN> -31.56021 -50.69785 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.2581" Parameter: A <- "-82.2581" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5602" Parameter: B <- "-31.5602" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6978" Parameter: C <- "-50.6978" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6467 TOTAL ENERGY = -82.2581 RDTITL> * VAN DER WAALS = -31.5602 ELECTROSTATIC = -50.6978 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6467" Parameter: CONF_N -> "8002" Comparing "6467" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6468" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753723 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756626 ATOM PAIRS WERE FOUND FOR ATOM LIST 41220 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29524 from a total of 756626 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6468 -73.50887 -8.74919 0.60513 INTE EXTERN> -28.85209 -44.65678 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5089" Parameter: A <- "-73.5089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8521" Parameter: B <- "-28.8521" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6568" Parameter: C <- "-44.6568" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6468 TOTAL ENERGY = -73.5089 RDTITL> * VAN DER WAALS = -28.8521 ELECTROSTATIC = -44.6568 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6468" Parameter: CONF_N -> "8002" Comparing "6468" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6469" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756626 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759335 ATOM PAIRS WERE FOUND FOR ATOM LIST 41423 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30048 from a total of 759335 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6469 -77.42656 3.91768 0.69998 INTE EXTERN> -25.73215 -51.69441 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4266" Parameter: A <- "-77.4266" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7321" Parameter: B <- "-25.7321" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6944" Parameter: C <- "-51.6944" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6469 TOTAL ENERGY = -77.4266 RDTITL> * VAN DER WAALS = -25.7321 ELECTROSTATIC = -51.6944 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6469" Parameter: CONF_N -> "8002" Comparing "6469" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6470" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759335 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759286 ATOM PAIRS WERE FOUND FOR ATOM LIST 41447 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29865 from a total of 759286 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6470 -73.96774 -3.45882 0.76550 INTE EXTERN> -26.72679 -47.24095 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9677" Parameter: A <- "-73.9677" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7268" Parameter: B <- "-26.7268" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2409" Parameter: C <- "-47.2409" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6470 TOTAL ENERGY = -73.9677 RDTITL> * VAN DER WAALS = -26.7268 ELECTROSTATIC = -47.2409 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6470" Parameter: CONF_N -> "8002" Comparing "6470" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6471" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759286 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756474 ATOM PAIRS WERE FOUND FOR ATOM LIST 41166 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29310 from a total of 756474 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6471 -79.29651 5.32877 0.68798 INTE EXTERN> -30.24857 -49.04794 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2965" Parameter: A <- "-79.2965" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2486" Parameter: B <- "-30.2486" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0479" Parameter: C <- "-49.0479" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6471 TOTAL ENERGY = -79.2965 RDTITL> * VAN DER WAALS = -30.2486 ELECTROSTATIC = -49.0479 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6471" Parameter: CONF_N -> "8002" Comparing "6471" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6472" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756474 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751368 ATOM PAIRS WERE FOUND FOR ATOM LIST 41120 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29443 from a total of 751368 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6472 -74.19491 -5.10160 0.60014 INTE EXTERN> -30.65529 -43.53963 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1949" Parameter: A <- "-74.1949" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6553" Parameter: B <- "-30.6553" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5396" Parameter: C <- "-43.5396" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6472 TOTAL ENERGY = -74.1949 RDTITL> * VAN DER WAALS = -30.6553 ELECTROSTATIC = -43.5396 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6472" Parameter: CONF_N -> "8002" Comparing "6472" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6473" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751368 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41246 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29082 from a total of 754009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6473 -79.74379 5.54887 0.56713 INTE EXTERN> -32.91642 -46.82736 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7438" Parameter: A <- "-79.7438" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9164" Parameter: B <- "-32.9164" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8274" Parameter: C <- "-46.8274" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6473 TOTAL ENERGY = -79.7438 RDTITL> * VAN DER WAALS = -32.9164 ELECTROSTATIC = -46.8274 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6473" Parameter: CONF_N -> "8002" Comparing "6473" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6474" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41118 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29071 from a total of 752601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6474 -83.15149 3.40770 0.65600 INTE EXTERN> -30.36076 -52.79072 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.1515" Parameter: A <- "-83.1515" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3608" Parameter: B <- "-30.3608" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.7907" Parameter: C <- "-52.7907" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6474 TOTAL ENERGY = -83.1515 RDTITL> * VAN DER WAALS = -30.3608 ELECTROSTATIC = -52.7907 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6474" Parameter: CONF_N -> "8002" Comparing "6474" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6475" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755522 ATOM PAIRS WERE FOUND FOR ATOM LIST 41316 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29927 from a total of 755522 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6475 -79.42685 -3.72463 0.69646 INTE EXTERN> -28.46739 -50.95946 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4269" Parameter: A <- "-79.4269" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4674" Parameter: B <- "-28.4674" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9595" Parameter: C <- "-50.9595" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6475 TOTAL ENERGY = -79.4269 RDTITL> * VAN DER WAALS = -28.4674 ELECTROSTATIC = -50.9595 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6475" Parameter: CONF_N -> "8002" Comparing "6475" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6476" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755522 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753779 ATOM PAIRS WERE FOUND FOR ATOM LIST 41296 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29841 from a total of 753779 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6476 -75.11689 -4.30996 0.56924 INTE EXTERN> -31.10604 -44.01085 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1169" Parameter: A <- "-75.1169" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.106" Parameter: B <- "-31.106" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0108" Parameter: C <- "-44.0108" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6476 TOTAL ENERGY = -75.1169 RDTITL> * VAN DER WAALS = -31.106 ELECTROSTATIC = -44.0108 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6476" Parameter: CONF_N -> "8002" Comparing "6476" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6477" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753779 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750416 ATOM PAIRS WERE FOUND FOR ATOM LIST 41035 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29585 from a total of 750416 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6477 -79.01827 3.90138 0.74075 INTE EXTERN> -26.95113 -52.06714 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0183" Parameter: A <- "-79.0183" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9511" Parameter: B <- "-26.9511" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0671" Parameter: C <- "-52.0671" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6477 TOTAL ENERGY = -79.0183 RDTITL> * VAN DER WAALS = -26.9511 ELECTROSTATIC = -52.0671 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6477" Parameter: CONF_N -> "8002" Comparing "6477" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6478" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750416 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759251 ATOM PAIRS WERE FOUND FOR ATOM LIST 41564 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30035 from a total of 759251 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6478 -80.07080 1.05253 0.70944 INTE EXTERN> -29.37744 -50.69336 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0708" Parameter: A <- "-80.0708" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3774" Parameter: B <- "-29.3774" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6934" Parameter: C <- "-50.6934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6478 TOTAL ENERGY = -80.0708 RDTITL> * VAN DER WAALS = -29.3774 ELECTROSTATIC = -50.6934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6478" Parameter: CONF_N -> "8002" Comparing "6478" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6479" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759251 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753314 ATOM PAIRS WERE FOUND FOR ATOM LIST 41117 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30157 from a total of 753314 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6479 -74.32222 -5.74858 0.58222 INTE EXTERN> -31.34216 -42.98006 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3222" Parameter: A <- "-74.3222" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3422" Parameter: B <- "-31.3422" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9801" Parameter: C <- "-42.9801" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6479 TOTAL ENERGY = -74.3222 RDTITL> * VAN DER WAALS = -31.3422 ELECTROSTATIC = -42.9801 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6479" Parameter: CONF_N -> "8002" Comparing "6479" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6480" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753314 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758793 ATOM PAIRS WERE FOUND FOR ATOM LIST 41407 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30107 from a total of 758793 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6480 -83.69470 9.37248 0.60185 INTE EXTERN> -32.93723 -50.75746 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.6947" Parameter: A <- "-83.6947" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9372" Parameter: B <- "-32.9372" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7575" Parameter: C <- "-50.7575" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6480 TOTAL ENERGY = -83.6947 RDTITL> * VAN DER WAALS = -32.9372 ELECTROSTATIC = -50.7575 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6480" Parameter: CONF_N -> "8002" Comparing "6480" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6481" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758793 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755798 ATOM PAIRS WERE FOUND FOR ATOM LIST 41194 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30153 from a total of 755798 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6481 -78.90337 -4.79132 0.70060 INTE EXTERN> -27.55098 -51.35239 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9034" Parameter: A <- "-78.9034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.551" Parameter: B <- "-27.551" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3524" Parameter: C <- "-51.3524" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6481 TOTAL ENERGY = -78.9034 RDTITL> * VAN DER WAALS = -27.551 ELECTROSTATIC = -51.3524 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6481" Parameter: CONF_N -> "8002" Comparing "6481" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6482" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755798 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760876 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30410 from a total of 760876 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6482 -75.00951 -3.89387 0.70784 INTE EXTERN> -29.66556 -45.34394 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0095" Parameter: A <- "-75.0095" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6656" Parameter: B <- "-29.6656" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3439" Parameter: C <- "-45.3439" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6482 TOTAL ENERGY = -75.0095 RDTITL> * VAN DER WAALS = -29.6656 ELECTROSTATIC = -45.3439 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6482" Parameter: CONF_N -> "8002" Comparing "6482" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6483" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760876 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756840 ATOM PAIRS WERE FOUND FOR ATOM LIST 41329 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29590 from a total of 756840 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6483 -83.36455 8.35504 0.72494 INTE EXTERN> -27.62164 -55.74291 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.3646" Parameter: A <- "-83.3646" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6216" Parameter: B <- "-27.6216" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.7429" Parameter: C <- "-55.7429" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6483 TOTAL ENERGY = -83.3646 RDTITL> * VAN DER WAALS = -27.6216 ELECTROSTATIC = -55.7429 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6483" Parameter: CONF_N -> "8002" Comparing "6483" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6484" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756840 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757578 ATOM PAIRS WERE FOUND FOR ATOM LIST 41330 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29821 from a total of 757578 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6484 -79.58277 -3.78178 0.75097 INTE EXTERN> -27.91735 -51.66542 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5828" Parameter: A <- "-79.5828" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9174" Parameter: B <- "-27.9174" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6654" Parameter: C <- "-51.6654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6484 TOTAL ENERGY = -79.5828 RDTITL> * VAN DER WAALS = -27.9174 ELECTROSTATIC = -51.6654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6484" Parameter: CONF_N -> "8002" Comparing "6484" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6485" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757578 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757673 ATOM PAIRS WERE FOUND FOR ATOM LIST 41409 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29509 from a total of 757673 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6485 -81.32461 1.74183 0.63653 INTE EXTERN> -30.59967 -50.72494 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.3246" Parameter: A <- "-81.3246" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5997" Parameter: B <- "-30.5997" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7249" Parameter: C <- "-50.7249" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6485 TOTAL ENERGY = -81.3246 RDTITL> * VAN DER WAALS = -30.5997 ELECTROSTATIC = -50.7249 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6485" Parameter: CONF_N -> "8002" Comparing "6485" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6486" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757673 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757093 ATOM PAIRS WERE FOUND FOR ATOM LIST 41357 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29516 from a total of 757093 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6486 -77.41804 -3.90657 0.77852 INTE EXTERN> -27.11862 -50.29941 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.418" Parameter: A <- "-77.418" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1186" Parameter: B <- "-27.1186" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2994" Parameter: C <- "-50.2994" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6486 TOTAL ENERGY = -77.418 RDTITL> * VAN DER WAALS = -27.1186 ELECTROSTATIC = -50.2994 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6486" Parameter: CONF_N -> "8002" Comparing "6486" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6487" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757093 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760798 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29184 from a total of 760798 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6487 -72.95202 -4.46601 0.74532 INTE EXTERN> -25.88990 -47.06213 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.952" Parameter: A <- "-72.952" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8899" Parameter: B <- "-25.8899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0621" Parameter: C <- "-47.0621" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6487 TOTAL ENERGY = -72.952 RDTITL> * VAN DER WAALS = -25.8899 ELECTROSTATIC = -47.0621 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6487" Parameter: CONF_N -> "8002" Comparing "6487" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6488" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760798 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752424 ATOM PAIRS WERE FOUND FOR ATOM LIST 40862 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29461 from a total of 752424 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6488 -74.14270 1.19068 0.71515 INTE EXTERN> -29.07801 -45.06469 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1427" Parameter: A <- "-74.1427" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.078" Parameter: B <- "-29.078" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0647" Parameter: C <- "-45.0647" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6488 TOTAL ENERGY = -74.1427 RDTITL> * VAN DER WAALS = -29.078 ELECTROSTATIC = -45.0647 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6488" Parameter: CONF_N -> "8002" Comparing "6488" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6489" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752424 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751236 ATOM PAIRS WERE FOUND FOR ATOM LIST 40980 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29277 from a total of 751236 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6489 -82.86023 8.71753 0.65587 INTE EXTERN> -30.19508 -52.66515 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.8602" Parameter: A <- "-82.8602" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1951" Parameter: B <- "-30.1951" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6651" Parameter: C <- "-52.6651" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6489 TOTAL ENERGY = -82.8602 RDTITL> * VAN DER WAALS = -30.1951 ELECTROSTATIC = -52.6651 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6489" Parameter: CONF_N -> "8002" Comparing "6489" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6490" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751236 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755603 ATOM PAIRS WERE FOUND FOR ATOM LIST 41356 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29329 from a total of 755603 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6490 -83.08500 0.22477 0.67154 INTE EXTERN> -31.40356 -51.68144 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.085" Parameter: A <- "-83.085" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4036" Parameter: B <- "-31.4036" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6814" Parameter: C <- "-51.6814" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6490 TOTAL ENERGY = -83.085 RDTITL> * VAN DER WAALS = -31.4036 ELECTROSTATIC = -51.6814 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6490" Parameter: CONF_N -> "8002" Comparing "6490" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6491" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755603 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760281 ATOM PAIRS WERE FOUND FOR ATOM LIST 41553 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29226 from a total of 760281 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6491 -81.16874 -1.91626 0.64174 INTE EXTERN> -32.63233 -48.53641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1687" Parameter: A <- "-81.1687" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6323" Parameter: B <- "-32.6323" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5364" Parameter: C <- "-48.5364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6491 TOTAL ENERGY = -81.1687 RDTITL> * VAN DER WAALS = -32.6323 ELECTROSTATIC = -48.5364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6491" Parameter: CONF_N -> "8002" Comparing "6491" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6492" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760281 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753697 ATOM PAIRS WERE FOUND FOR ATOM LIST 41267 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29176 from a total of 753697 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6492 -78.27131 -2.89743 0.65875 INTE EXTERN> -27.77801 -50.49330 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2713" Parameter: A <- "-78.2713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.778" Parameter: B <- "-27.778" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4933" Parameter: C <- "-50.4933" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6492 TOTAL ENERGY = -78.2713 RDTITL> * VAN DER WAALS = -27.778 ELECTROSTATIC = -50.4933 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6492" Parameter: CONF_N -> "8002" Comparing "6492" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6493" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753697 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758739 ATOM PAIRS WERE FOUND FOR ATOM LIST 41487 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29571 from a total of 758739 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6493 -79.43196 1.16065 0.70186 INTE EXTERN> -26.19100 -53.24096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.432" Parameter: A <- "-79.432" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.191" Parameter: B <- "-26.191" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.241" Parameter: C <- "-53.241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6493 TOTAL ENERGY = -79.432 RDTITL> * VAN DER WAALS = -26.191 ELECTROSTATIC = -53.241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6493" Parameter: CONF_N -> "8002" Comparing "6493" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6494" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758739 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757396 ATOM PAIRS WERE FOUND FOR ATOM LIST 41338 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29527 from a total of 757396 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6494 -77.63389 -1.79807 0.70086 INTE EXTERN> -27.98718 -49.64671 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6339" Parameter: A <- "-77.6339" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9872" Parameter: B <- "-27.9872" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6467" Parameter: C <- "-49.6467" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6494 TOTAL ENERGY = -77.6339 RDTITL> * VAN DER WAALS = -27.9872 ELECTROSTATIC = -49.6467 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6494" Parameter: CONF_N -> "8002" Comparing "6494" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6495" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757396 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757931 ATOM PAIRS WERE FOUND FOR ATOM LIST 41689 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29398 from a total of 757931 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6495 -90.33818 12.70430 0.68486 INTE EXTERN> -32.13338 -58.20480 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-90.3382" Parameter: A <- "-90.3382" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1334" Parameter: B <- "-32.1334" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.2048" Parameter: C <- "-58.2048" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6495 TOTAL ENERGY = -90.3382 RDTITL> * VAN DER WAALS = -32.1334 ELECTROSTATIC = -58.2048 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6495" Parameter: CONF_N -> "8002" Comparing "6495" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6496" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757931 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762705 ATOM PAIRS WERE FOUND FOR ATOM LIST 41755 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30121 from a total of 762705 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6496 -81.89663 -8.44155 0.61861 INTE EXTERN> -31.61442 -50.28221 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8966" Parameter: A <- "-81.8966" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6144" Parameter: B <- "-31.6144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2822" Parameter: C <- "-50.2822" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6496 TOTAL ENERGY = -81.8966 RDTITL> * VAN DER WAALS = -31.6144 ELECTROSTATIC = -50.2822 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6496" Parameter: CONF_N -> "8002" Comparing "6496" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6497" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762705 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760392 ATOM PAIRS WERE FOUND FOR ATOM LIST 41631 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29548 from a total of 760392 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6497 -77.77883 -4.11780 0.64646 INTE EXTERN> -30.03141 -47.74743 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7788" Parameter: A <- "-77.7788" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0314" Parameter: B <- "-30.0314" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7474" Parameter: C <- "-47.7474" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6497 TOTAL ENERGY = -77.7788 RDTITL> * VAN DER WAALS = -30.0314 ELECTROSTATIC = -47.7474 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6497" Parameter: CONF_N -> "8002" Comparing "6497" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6498" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760392 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755953 ATOM PAIRS WERE FOUND FOR ATOM LIST 41505 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29625 from a total of 755953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6498 -78.67874 0.89991 0.69352 INTE EXTERN> -28.29752 -50.38122 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6787" Parameter: A <- "-78.6787" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2975" Parameter: B <- "-28.2975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3812" Parameter: C <- "-50.3812" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6498 TOTAL ENERGY = -78.6787 RDTITL> * VAN DER WAALS = -28.2975 ELECTROSTATIC = -50.3812 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6498" Parameter: CONF_N -> "8002" Comparing "6498" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6499" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762105 ATOM PAIRS WERE FOUND FOR ATOM LIST 41697 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29980 from a total of 762105 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6499 -85.79646 7.11772 0.81795 INTE EXTERN> -24.37306 -61.42340 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.7965" Parameter: A <- "-85.7965" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3731" Parameter: B <- "-24.3731" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-61.4234" Parameter: C <- "-61.4234" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6499 TOTAL ENERGY = -85.7965 RDTITL> * VAN DER WAALS = -24.3731 ELECTROSTATIC = -61.4234 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6499" Parameter: CONF_N -> "8002" Comparing "6499" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6500" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762105 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753350 ATOM PAIRS WERE FOUND FOR ATOM LIST 41282 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29943 from a total of 753350 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6500 -78.73982 -7.05664 0.55530 INTE EXTERN> -32.17425 -46.56557 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7398" Parameter: A <- "-78.7398" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1743" Parameter: B <- "-32.1743" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5656" Parameter: C <- "-46.5656" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6500 TOTAL ENERGY = -78.7398 RDTITL> * VAN DER WAALS = -32.1743 ELECTROSTATIC = -46.5656 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6500" Parameter: CONF_N -> "8002" Comparing "6500" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6501" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753350 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748284 ATOM PAIRS WERE FOUND FOR ATOM LIST 41108 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28642 from a total of 748284 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6501 -73.48401 -5.25580 0.71159 INTE EXTERN> -23.02124 -50.46277 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.484" Parameter: A <- "-73.484" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.0212" Parameter: B <- "-23.0212" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4628" Parameter: C <- "-50.4628" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6501 TOTAL ENERGY = -73.484 RDTITL> * VAN DER WAALS = -23.0212 ELECTROSTATIC = -50.4628 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6501" Parameter: CONF_N -> "8002" Comparing "6501" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6502" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748284 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751781 ATOM PAIRS WERE FOUND FOR ATOM LIST 41107 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29124 from a total of 751781 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6502 -78.03244 4.54843 0.76580 INTE EXTERN> -26.49227 -51.54017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0324" Parameter: A <- "-78.0324" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4923" Parameter: B <- "-26.4923" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5402" Parameter: C <- "-51.5402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6502 TOTAL ENERGY = -78.0324 RDTITL> * VAN DER WAALS = -26.4923 ELECTROSTATIC = -51.5402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6502" Parameter: CONF_N -> "8002" Comparing "6502" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6503" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751781 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760090 ATOM PAIRS WERE FOUND FOR ATOM LIST 41669 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29924 from a total of 760090 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6503 -78.86601 0.83357 0.66867 INTE EXTERN> -27.75613 -51.10989 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.866" Parameter: A <- "-78.866" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7561" Parameter: B <- "-27.7561" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1099" Parameter: C <- "-51.1099" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6503 TOTAL ENERGY = -78.866 RDTITL> * VAN DER WAALS = -27.7561 ELECTROSTATIC = -51.1099 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6503" Parameter: CONF_N -> "8002" Comparing "6503" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6504" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760090 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763543 ATOM PAIRS WERE FOUND FOR ATOM LIST 41932 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30342 from a total of 763543 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6504 -83.94994 5.08393 0.71327 INTE EXTERN> -29.07624 -54.87370 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.9499" Parameter: A <- "-83.9499" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0762" Parameter: B <- "-29.0762" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8737" Parameter: C <- "-54.8737" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6504 TOTAL ENERGY = -83.9499 RDTITL> * VAN DER WAALS = -29.0762 ELECTROSTATIC = -54.8737 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6504" Parameter: CONF_N -> "8002" Comparing "6504" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6505" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763543 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754714 ATOM PAIRS WERE FOUND FOR ATOM LIST 41308 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29941 from a total of 754714 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6505 -74.84661 -9.10333 0.75948 INTE EXTERN> -26.33152 -48.51509 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8466" Parameter: A <- "-74.8466" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3315" Parameter: B <- "-26.3315" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5151" Parameter: C <- "-48.5151" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6505 TOTAL ENERGY = -74.8466 RDTITL> * VAN DER WAALS = -26.3315 ELECTROSTATIC = -48.5151 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6505" Parameter: CONF_N -> "8002" Comparing "6505" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6506" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754714 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756687 ATOM PAIRS WERE FOUND FOR ATOM LIST 41560 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29845 from a total of 756687 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6506 -82.71645 7.86984 0.72640 INTE EXTERN> -28.65528 -54.06117 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7164" Parameter: A <- "-82.7164" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6553" Parameter: B <- "-28.6553" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0612" Parameter: C <- "-54.0612" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6506 TOTAL ENERGY = -82.7164 RDTITL> * VAN DER WAALS = -28.6553 ELECTROSTATIC = -54.0612 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6506" Parameter: CONF_N -> "8002" Comparing "6506" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6507" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756687 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763865 ATOM PAIRS WERE FOUND FOR ATOM LIST 41751 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30105 from a total of 763865 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6507 -84.64099 1.92454 0.71848 INTE EXTERN> -30.79056 -53.85043 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.641" Parameter: A <- "-84.641" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7906" Parameter: B <- "-30.7906" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8504" Parameter: C <- "-53.8504" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6507 TOTAL ENERGY = -84.641 RDTITL> * VAN DER WAALS = -30.7906 ELECTROSTATIC = -53.8504 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6507" Parameter: CONF_N -> "8002" Comparing "6507" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6508" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763865 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761448 ATOM PAIRS WERE FOUND FOR ATOM LIST 41704 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30267 from a total of 761448 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6508 -79.58672 -5.05427 0.66949 INTE EXTERN> -29.39740 -50.18932 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5867" Parameter: A <- "-79.5867" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3974" Parameter: B <- "-29.3974" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1893" Parameter: C <- "-50.1893" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6508 TOTAL ENERGY = -79.5867 RDTITL> * VAN DER WAALS = -29.3974 ELECTROSTATIC = -50.1893 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6508" Parameter: CONF_N -> "8002" Comparing "6508" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6509" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761448 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751888 ATOM PAIRS WERE FOUND FOR ATOM LIST 41060 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29658 from a total of 751888 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6509 -72.66269 -6.92403 0.56588 INTE EXTERN> -31.60706 -41.05562 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6627" Parameter: A <- "-72.6627" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6071" Parameter: B <- "-31.6071" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0556" Parameter: C <- "-41.0556" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6509 TOTAL ENERGY = -72.6627 RDTITL> * VAN DER WAALS = -31.6071 ELECTROSTATIC = -41.0556 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6509" Parameter: CONF_N -> "8002" Comparing "6509" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6510" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751888 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753138 ATOM PAIRS WERE FOUND FOR ATOM LIST 41067 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29812 from a total of 753138 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6510 -76.95294 4.29025 0.70817 INTE EXTERN> -27.64442 -49.30852 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9529" Parameter: A <- "-76.9529" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6444" Parameter: B <- "-27.6444" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3085" Parameter: C <- "-49.3085" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6510 TOTAL ENERGY = -76.9529 RDTITL> * VAN DER WAALS = -27.6444 ELECTROSTATIC = -49.3085 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6510" Parameter: CONF_N -> "8002" Comparing "6510" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6511" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753138 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757408 ATOM PAIRS WERE FOUND FOR ATOM LIST 41439 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29443 from a total of 757408 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6511 -79.90053 2.94759 0.77166 INTE EXTERN> -26.48235 -53.41818 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9005" Parameter: A <- "-79.9005" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4823" Parameter: B <- "-26.4823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4182" Parameter: C <- "-53.4182" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6511 TOTAL ENERGY = -79.9005 RDTITL> * VAN DER WAALS = -26.4823 ELECTROSTATIC = -53.4182 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6511" Parameter: CONF_N -> "8002" Comparing "6511" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6512" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757408 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757527 ATOM PAIRS WERE FOUND FOR ATOM LIST 41223 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29384 from a total of 757527 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6512 -75.80137 -4.09915 0.71376 INTE EXTERN> -27.83609 -47.96528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8014" Parameter: A <- "-75.8014" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8361" Parameter: B <- "-27.8361" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9653" Parameter: C <- "-47.9653" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6512 TOTAL ENERGY = -75.8014 RDTITL> * VAN DER WAALS = -27.8361 ELECTROSTATIC = -47.9653 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6512" Parameter: CONF_N -> "8002" Comparing "6512" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6513" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757527 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760701 ATOM PAIRS WERE FOUND FOR ATOM LIST 41375 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30197 from a total of 760701 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6513 -81.46763 5.66626 0.68558 INTE EXTERN> -30.34082 -51.12681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4676" Parameter: A <- "-81.4676" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3408" Parameter: B <- "-30.3408" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1268" Parameter: C <- "-51.1268" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6513 TOTAL ENERGY = -81.4676 RDTITL> * VAN DER WAALS = -30.3408 ELECTROSTATIC = -51.1268 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6513" Parameter: CONF_N -> "8002" Comparing "6513" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6514" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760701 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755677 ATOM PAIRS WERE FOUND FOR ATOM LIST 41276 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29964 from a total of 755677 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6514 -82.96224 1.49461 0.64215 INTE EXTERN> -31.07965 -51.88259 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9622" Parameter: A <- "-82.9622" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0797" Parameter: B <- "-31.0797" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8826" Parameter: C <- "-51.8826" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6514 TOTAL ENERGY = -82.9622 RDTITL> * VAN DER WAALS = -31.0797 ELECTROSTATIC = -51.8826 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6514" Parameter: CONF_N -> "8002" Comparing "6514" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6515" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755677 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41575 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30271 from a total of 762009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6515 -74.03906 -8.92319 0.60473 INTE EXTERN> -34.74304 -39.29602 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0391" Parameter: A <- "-74.0391" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.743" Parameter: B <- "-34.743" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.296" Parameter: C <- "-39.296" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6515 TOTAL ENERGY = -74.0391 RDTITL> * VAN DER WAALS = -34.743 ELECTROSTATIC = -39.296 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6515" Parameter: CONF_N -> "8002" Comparing "6515" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6516" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761455 ATOM PAIRS WERE FOUND FOR ATOM LIST 41564 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30290 from a total of 761455 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6516 -73.84405 -0.19501 0.73599 INTE EXTERN> -28.10447 -45.73958 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.844" Parameter: A <- "-73.844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1045" Parameter: B <- "-28.1045" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7396" Parameter: C <- "-45.7396" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6516 TOTAL ENERGY = -73.844 RDTITL> * VAN DER WAALS = -28.1045 ELECTROSTATIC = -45.7396 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6516" Parameter: CONF_N -> "8002" Comparing "6516" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6517" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761455 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758034 ATOM PAIRS WERE FOUND FOR ATOM LIST 41488 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30011 from a total of 758034 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6517 -76.61117 2.76712 0.60318 INTE EXTERN> -33.38562 -43.22555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6112" Parameter: A <- "-76.6112" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3856" Parameter: B <- "-33.3856" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2256" Parameter: C <- "-43.2256" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6517 TOTAL ENERGY = -76.6112 RDTITL> * VAN DER WAALS = -33.3856 ELECTROSTATIC = -43.2256 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6517" Parameter: CONF_N -> "8002" Comparing "6517" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6518" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758034 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753662 ATOM PAIRS WERE FOUND FOR ATOM LIST 41183 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29497 from a total of 753662 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6518 -76.73540 0.12422 0.64838 INTE EXTERN> -29.30354 -47.43185 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7354" Parameter: A <- "-76.7354" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3035" Parameter: B <- "-29.3035" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4319" Parameter: C <- "-47.4319" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6518 TOTAL ENERGY = -76.7354 RDTITL> * VAN DER WAALS = -29.3035 ELECTROSTATIC = -47.4319 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6518" Parameter: CONF_N -> "8002" Comparing "6518" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6519" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753662 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759634 ATOM PAIRS WERE FOUND FOR ATOM LIST 41384 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30195 from a total of 759634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6519 -80.03543 3.30003 0.70472 INTE EXTERN> -30.89379 -49.14164 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0354" Parameter: A <- "-80.0354" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8938" Parameter: B <- "-30.8938" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1416" Parameter: C <- "-49.1416" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6519 TOTAL ENERGY = -80.0354 RDTITL> * VAN DER WAALS = -30.8938 ELECTROSTATIC = -49.1416 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6519" Parameter: CONF_N -> "8002" Comparing "6519" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6520" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761255 ATOM PAIRS WERE FOUND FOR ATOM LIST 41611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29731 from a total of 761255 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6520 -72.82412 -7.21131 0.66031 INTE EXTERN> -27.59951 -45.22461 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8241" Parameter: A <- "-72.8241" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5995" Parameter: B <- "-27.5995" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2246" Parameter: C <- "-45.2246" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6520 TOTAL ENERGY = -72.8241 RDTITL> * VAN DER WAALS = -27.5995 ELECTROSTATIC = -45.2246 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6520" Parameter: CONF_N -> "8002" Comparing "6520" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6521" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761255 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756619 ATOM PAIRS WERE FOUND FOR ATOM LIST 41479 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29516 from a total of 756619 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6521 -73.93476 1.11064 0.73606 INTE EXTERN> -25.15076 -48.78400 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9348" Parameter: A <- "-73.9348" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1508" Parameter: B <- "-25.1508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.784" Parameter: C <- "-48.784" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6521 TOTAL ENERGY = -73.9348 RDTITL> * VAN DER WAALS = -25.1508 ELECTROSTATIC = -48.784 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6521" Parameter: CONF_N -> "8002" Comparing "6521" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6522" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756619 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752006 ATOM PAIRS WERE FOUND FOR ATOM LIST 41333 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28634 from a total of 752006 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6522 -74.96454 1.02978 0.61548 INTE EXTERN> -28.25715 -46.70739 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9645" Parameter: A <- "-74.9645" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2571" Parameter: B <- "-28.2571" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7074" Parameter: C <- "-46.7074" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6522 TOTAL ENERGY = -74.9645 RDTITL> * VAN DER WAALS = -28.2571 ELECTROSTATIC = -46.7074 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6522" Parameter: CONF_N -> "8002" Comparing "6522" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6523" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752006 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754485 ATOM PAIRS WERE FOUND FOR ATOM LIST 41284 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29279 from a total of 754485 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6523 -73.90545 -1.05909 0.71946 INTE EXTERN> -27.21054 -46.69491 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9055" Parameter: A <- "-73.9055" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2105" Parameter: B <- "-27.2105" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6949" Parameter: C <- "-46.6949" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6523 TOTAL ENERGY = -73.9055 RDTITL> * VAN DER WAALS = -27.2105 ELECTROSTATIC = -46.6949 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6523" Parameter: CONF_N -> "8002" Comparing "6523" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6524" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754485 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758503 ATOM PAIRS WERE FOUND FOR ATOM LIST 41585 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29756 from a total of 758503 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6524 -78.74498 4.83953 0.63105 INTE EXTERN> -32.20577 -46.53921 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.745" Parameter: A <- "-78.745" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2058" Parameter: B <- "-32.2058" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5392" Parameter: C <- "-46.5392" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6524 TOTAL ENERGY = -78.745 RDTITL> * VAN DER WAALS = -32.2058 ELECTROSTATIC = -46.5392 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6524" Parameter: CONF_N -> "8002" Comparing "6524" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6525" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758503 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758041 ATOM PAIRS WERE FOUND FOR ATOM LIST 41322 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29428 from a total of 758041 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6525 -79.31908 0.57410 0.77060 INTE EXTERN> -26.07719 -53.24189 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.3191" Parameter: A <- "-79.3191" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0772" Parameter: B <- "-26.0772" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.2419" Parameter: C <- "-53.2419" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6525 TOTAL ENERGY = -79.3191 RDTITL> * VAN DER WAALS = -26.0772 ELECTROSTATIC = -53.2419 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6525" Parameter: CONF_N -> "8002" Comparing "6525" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6526" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758041 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752226 ATOM PAIRS WERE FOUND FOR ATOM LIST 41179 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28628 from a total of 752226 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6526 -71.97153 -7.34755 0.68697 INTE EXTERN> -29.11640 -42.85513 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9715" Parameter: A <- "-71.9715" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1164" Parameter: B <- "-29.1164" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8551" Parameter: C <- "-42.8551" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6526 TOTAL ENERGY = -71.9715 RDTITL> * VAN DER WAALS = -29.1164 ELECTROSTATIC = -42.8551 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6526" Parameter: CONF_N -> "8002" Comparing "6526" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6527" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752226 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752201 ATOM PAIRS WERE FOUND FOR ATOM LIST 41154 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29320 from a total of 752201 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6527 -72.83494 0.86340 0.71239 INTE EXTERN> -26.73583 -46.09910 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8349" Parameter: A <- "-72.8349" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7358" Parameter: B <- "-26.7358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0991" Parameter: C <- "-46.0991" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6527 TOTAL ENERGY = -72.8349 RDTITL> * VAN DER WAALS = -26.7358 ELECTROSTATIC = -46.0991 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6527" Parameter: CONF_N -> "8002" Comparing "6527" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6528" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752201 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759460 ATOM PAIRS WERE FOUND FOR ATOM LIST 41395 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29896 from a total of 759460 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6528 -75.78241 2.94747 0.65926 INTE EXTERN> -28.30708 -47.47533 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7824" Parameter: A <- "-75.7824" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3071" Parameter: B <- "-28.3071" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4753" Parameter: C <- "-47.4753" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6528 TOTAL ENERGY = -75.7824 RDTITL> * VAN DER WAALS = -28.3071 ELECTROSTATIC = -47.4753 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6528" Parameter: CONF_N -> "8002" Comparing "6528" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6529" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759460 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759895 ATOM PAIRS WERE FOUND FOR ATOM LIST 41524 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30303 from a total of 759895 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6529 -72.72014 -3.06227 0.69955 INTE EXTERN> -24.95303 -47.76711 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7201" Parameter: A <- "-72.7201" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.953" Parameter: B <- "-24.953" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7671" Parameter: C <- "-47.7671" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6529 TOTAL ENERGY = -72.7201 RDTITL> * VAN DER WAALS = -24.953 ELECTROSTATIC = -47.7671 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6529" Parameter: CONF_N -> "8002" Comparing "6529" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6530" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759895 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752560 ATOM PAIRS WERE FOUND FOR ATOM LIST 41029 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29838 from a total of 752560 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6530 -74.59189 1.87175 0.59630 INTE EXTERN> -30.38970 -44.20219 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5919" Parameter: A <- "-74.5919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3897" Parameter: B <- "-30.3897" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2022" Parameter: C <- "-44.2022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6530 TOTAL ENERGY = -74.5919 RDTITL> * VAN DER WAALS = -30.3897 ELECTROSTATIC = -44.2022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6530" Parameter: CONF_N -> "8002" Comparing "6530" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6531" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752560 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757330 ATOM PAIRS WERE FOUND FOR ATOM LIST 41280 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29920 from a total of 757330 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6531 -77.25674 2.66485 0.56817 INTE EXTERN> -30.88147 -46.37526 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2567" Parameter: A <- "-77.2567" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8815" Parameter: B <- "-30.8815" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3753" Parameter: C <- "-46.3753" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6531 TOTAL ENERGY = -77.2567 RDTITL> * VAN DER WAALS = -30.8815 ELECTROSTATIC = -46.3753 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6531" Parameter: CONF_N -> "8002" Comparing "6531" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6532" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757330 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756250 ATOM PAIRS WERE FOUND FOR ATOM LIST 41272 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29549 from a total of 756250 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6532 -65.49542 -11.76131 0.48229 INTE EXTERN> -32.71446 -32.78096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4954" Parameter: A <- "-65.4954" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7145" Parameter: B <- "-32.7145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.781" Parameter: C <- "-32.781" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6532 TOTAL ENERGY = -65.4954 RDTITL> * VAN DER WAALS = -32.7145 ELECTROSTATIC = -32.781 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6532" Parameter: CONF_N -> "8002" Comparing "6532" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6533" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756250 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754854 ATOM PAIRS WERE FOUND FOR ATOM LIST 41441 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29649 from a total of 754854 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6533 -76.30038 10.80496 0.51877 INTE EXTERN> -34.25148 -42.04890 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3004" Parameter: A <- "-76.3004" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.2515" Parameter: B <- "-34.2515" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0489" Parameter: C <- "-42.0489" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6533 TOTAL ENERGY = -76.3004 RDTITL> * VAN DER WAALS = -34.2515 ELECTROSTATIC = -42.0489 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6533" Parameter: CONF_N -> "8002" Comparing "6533" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6534" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754854 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753413 ATOM PAIRS WERE FOUND FOR ATOM LIST 41071 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29679 from a total of 753413 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6534 -73.72114 -2.57924 0.62226 INTE EXTERN> -30.48735 -43.23380 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7211" Parameter: A <- "-73.7211" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4873" Parameter: B <- "-30.4873" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2338" Parameter: C <- "-43.2338" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6534 TOTAL ENERGY = -73.7211 RDTITL> * VAN DER WAALS = -30.4873 ELECTROSTATIC = -43.2338 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6534" Parameter: CONF_N -> "8002" Comparing "6534" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6535" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753413 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753643 ATOM PAIRS WERE FOUND FOR ATOM LIST 41043 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29290 from a total of 753643 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6535 -75.84654 2.12540 0.63392 INTE EXTERN> -29.96534 -45.88120 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8465" Parameter: A <- "-75.8465" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9653" Parameter: B <- "-29.9653" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8812" Parameter: C <- "-45.8812" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6535 TOTAL ENERGY = -75.8465 RDTITL> * VAN DER WAALS = -29.9653 ELECTROSTATIC = -45.8812 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6535" Parameter: CONF_N -> "8002" Comparing "6535" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6536" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753643 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757656 ATOM PAIRS WERE FOUND FOR ATOM LIST 41264 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29802 from a total of 757656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6536 -82.35061 6.50408 0.55617 INTE EXTERN> -32.81022 -49.54040 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3506" Parameter: A <- "-82.3506" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8102" Parameter: B <- "-32.8102" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5404" Parameter: C <- "-49.5404" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6536 TOTAL ENERGY = -82.3506 RDTITL> * VAN DER WAALS = -32.8102 ELECTROSTATIC = -49.5404 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6536" Parameter: CONF_N -> "8002" Comparing "6536" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6537" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757938 ATOM PAIRS WERE FOUND FOR ATOM LIST 41197 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28978 from a total of 757938 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6537 -73.63564 -8.71498 0.61667 INTE EXTERN> -28.87812 -44.75752 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6356" Parameter: A <- "-73.6356" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8781" Parameter: B <- "-28.8781" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7575" Parameter: C <- "-44.7575" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6537 TOTAL ENERGY = -73.6356 RDTITL> * VAN DER WAALS = -28.8781 ELECTROSTATIC = -44.7575 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6537" Parameter: CONF_N -> "8002" Comparing "6537" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6538" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757938 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756124 ATOM PAIRS WERE FOUND FOR ATOM LIST 41293 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29476 from a total of 756124 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6538 -73.82767 0.19203 0.64367 INTE EXTERN> -27.22333 -46.60434 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8277" Parameter: A <- "-73.8277" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2233" Parameter: B <- "-27.2233" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6043" Parameter: C <- "-46.6043" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6538 TOTAL ENERGY = -73.8277 RDTITL> * VAN DER WAALS = -27.2233 ELECTROSTATIC = -46.6043 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6538" Parameter: CONF_N -> "8002" Comparing "6538" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6539" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756124 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759986 ATOM PAIRS WERE FOUND FOR ATOM LIST 41256 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30214 from a total of 759986 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6539 -73.96429 0.13662 0.59834 INTE EXTERN> -32.08954 -41.87475 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9643" Parameter: A <- "-73.9643" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0895" Parameter: B <- "-32.0895" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8747" Parameter: C <- "-41.8747" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6539 TOTAL ENERGY = -73.9643 RDTITL> * VAN DER WAALS = -32.0895 ELECTROSTATIC = -41.8747 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6539" Parameter: CONF_N -> "8002" Comparing "6539" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6540" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759986 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755521 ATOM PAIRS WERE FOUND FOR ATOM LIST 41457 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30181 from a total of 755521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6540 -76.10420 2.13991 0.75029 INTE EXTERN> -23.12056 -52.98364 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1042" Parameter: A <- "-76.1042" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.1206" Parameter: B <- "-23.1206" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9836" Parameter: C <- "-52.9836" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6540 TOTAL ENERGY = -76.1042 RDTITL> * VAN DER WAALS = -23.1206 ELECTROSTATIC = -52.9836 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6540" Parameter: CONF_N -> "8002" Comparing "6540" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6541" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759933 ATOM PAIRS WERE FOUND FOR ATOM LIST 41749 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30245 from a total of 759933 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6541 -76.87791 0.77371 0.55908 INTE EXTERN> -31.57478 -45.30312 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8779" Parameter: A <- "-76.8779" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5748" Parameter: B <- "-31.5748" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3031" Parameter: C <- "-45.3031" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6541 TOTAL ENERGY = -76.8779 RDTITL> * VAN DER WAALS = -31.5748 ELECTROSTATIC = -45.3031 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6541" Parameter: CONF_N -> "8002" Comparing "6541" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6542" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759933 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756409 ATOM PAIRS WERE FOUND FOR ATOM LIST 41371 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30271 from a total of 756409 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6542 -83.04528 6.16737 0.66952 INTE EXTERN> -31.43042 -51.61485 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.0453" Parameter: A <- "-83.0453" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4304" Parameter: B <- "-31.4304" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6149" Parameter: C <- "-51.6149" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6542 TOTAL ENERGY = -83.0453 RDTITL> * VAN DER WAALS = -31.4304 ELECTROSTATIC = -51.6149 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6542" Parameter: CONF_N -> "8002" Comparing "6542" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6543" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756409 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754247 ATOM PAIRS WERE FOUND FOR ATOM LIST 41372 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29626 from a total of 754247 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6543 -77.67285 -5.37243 0.61738 INTE EXTERN> -30.82205 -46.85080 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6728" Parameter: A <- "-77.6728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.822" Parameter: B <- "-30.822" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8508" Parameter: C <- "-46.8508" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6543 TOTAL ENERGY = -77.6728 RDTITL> * VAN DER WAALS = -30.822 ELECTROSTATIC = -46.8508 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6543" Parameter: CONF_N -> "8002" Comparing "6543" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6544" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754247 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759522 ATOM PAIRS WERE FOUND FOR ATOM LIST 41590 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30195 from a total of 759522 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6544 -79.12688 1.45404 0.63827 INTE EXTERN> -33.75246 -45.37442 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1269" Parameter: A <- "-79.1269" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7525" Parameter: B <- "-33.7525" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3744" Parameter: C <- "-45.3744" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6544 TOTAL ENERGY = -79.1269 RDTITL> * VAN DER WAALS = -33.7525 ELECTROSTATIC = -45.3744 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6544" Parameter: CONF_N -> "8002" Comparing "6544" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6545" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759522 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751045 ATOM PAIRS WERE FOUND FOR ATOM LIST 41064 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29818 from a total of 751045 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6545 -76.09282 -3.03407 0.67208 INTE EXTERN> -28.10200 -47.99082 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0928" Parameter: A <- "-76.0928" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.102" Parameter: B <- "-28.102" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9908" Parameter: C <- "-47.9908" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6545 TOTAL ENERGY = -76.0928 RDTITL> * VAN DER WAALS = -28.102 ELECTROSTATIC = -47.9908 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6545" Parameter: CONF_N -> "8002" Comparing "6545" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6546" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751045 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754206 ATOM PAIRS WERE FOUND FOR ATOM LIST 41277 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30139 from a total of 754206 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6546 -70.45756 -5.63526 0.82504 INTE EXTERN> -23.98427 -46.47329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4576" Parameter: A <- "-70.4576" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9843" Parameter: B <- "-23.9843" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4733" Parameter: C <- "-46.4733" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6546 TOTAL ENERGY = -70.4576 RDTITL> * VAN DER WAALS = -23.9843 ELECTROSTATIC = -46.4733 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6546" Parameter: CONF_N -> "8002" Comparing "6546" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6547" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754206 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756605 ATOM PAIRS WERE FOUND FOR ATOM LIST 41277 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29991 from a total of 756605 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6547 -83.97021 13.51265 0.70419 INTE EXTERN> -31.98253 -51.98769 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.9702" Parameter: A <- "-83.9702" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9825" Parameter: B <- "-31.9825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.9877" Parameter: C <- "-51.9877" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6547 TOTAL ENERGY = -83.9702 RDTITL> * VAN DER WAALS = -31.9825 ELECTROSTATIC = -51.9877 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6547" Parameter: CONF_N -> "8002" Comparing "6547" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6548" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756605 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764862 ATOM PAIRS WERE FOUND FOR ATOM LIST 41933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30225 from a total of 764862 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6548 -76.16870 -7.80151 0.63133 INTE EXTERN> -29.80055 -46.36815 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1687" Parameter: A <- "-76.1687" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8006" Parameter: B <- "-29.8006" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3681" Parameter: C <- "-46.3681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6548 TOTAL ENERGY = -76.1687 RDTITL> * VAN DER WAALS = -29.8006 ELECTROSTATIC = -46.3681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6548" Parameter: CONF_N -> "8002" Comparing "6548" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6549" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764862 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758899 ATOM PAIRS WERE FOUND FOR ATOM LIST 41534 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29847 from a total of 758899 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6549 -70.71648 -5.45222 0.68063 INTE EXTERN> -25.59925 -45.11722 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7165" Parameter: A <- "-70.7165" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5993" Parameter: B <- "-25.5993" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1172" Parameter: C <- "-45.1172" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6549 TOTAL ENERGY = -70.7165 RDTITL> * VAN DER WAALS = -25.5993 ELECTROSTATIC = -45.1172 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6549" Parameter: CONF_N -> "8002" Comparing "6549" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6550" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758899 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756653 ATOM PAIRS WERE FOUND FOR ATOM LIST 41082 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29011 from a total of 756653 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6550 -77.48159 6.76511 0.66818 INTE EXTERN> -27.02046 -50.46114 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4816" Parameter: A <- "-77.4816" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0205" Parameter: B <- "-27.0205" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4611" Parameter: C <- "-50.4611" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6550 TOTAL ENERGY = -77.4816 RDTITL> * VAN DER WAALS = -27.0205 ELECTROSTATIC = -50.4611 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6550" Parameter: CONF_N -> "8002" Comparing "6550" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6551" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756653 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754598 ATOM PAIRS WERE FOUND FOR ATOM LIST 41172 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29428 from a total of 754598 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6551 -73.73905 -3.74254 0.61660 INTE EXTERN> -32.34009 -41.39896 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.739" Parameter: A <- "-73.739" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3401" Parameter: B <- "-32.3401" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.399" Parameter: C <- "-41.399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6551 TOTAL ENERGY = -73.739 RDTITL> * VAN DER WAALS = -32.3401 ELECTROSTATIC = -41.399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6551" Parameter: CONF_N -> "8002" Comparing "6551" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6552" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754598 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749685 ATOM PAIRS WERE FOUND FOR ATOM LIST 41181 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28806 from a total of 749685 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6552 -75.68715 1.94810 0.64714 INTE EXTERN> -29.37042 -46.31674 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6872" Parameter: A <- "-75.6872" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3704" Parameter: B <- "-29.3704" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3167" Parameter: C <- "-46.3167" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6552 TOTAL ENERGY = -75.6872 RDTITL> * VAN DER WAALS = -29.3704 ELECTROSTATIC = -46.3167 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6552" Parameter: CONF_N -> "8002" Comparing "6552" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6553" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749685 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751054 ATOM PAIRS WERE FOUND FOR ATOM LIST 41015 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28918 from a total of 751054 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6553 -80.52792 4.84076 0.68684 INTE EXTERN> -27.88019 -52.64772 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5279" Parameter: A <- "-80.5279" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8802" Parameter: B <- "-27.8802" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6477" Parameter: C <- "-52.6477" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6553 TOTAL ENERGY = -80.5279 RDTITL> * VAN DER WAALS = -27.8802 ELECTROSTATIC = -52.6477 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6553" Parameter: CONF_N -> "8002" Comparing "6553" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6554" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751054 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756921 ATOM PAIRS WERE FOUND FOR ATOM LIST 41261 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29563 from a total of 756921 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6554 -80.28828 -0.23964 0.79271 INTE EXTERN> -25.40921 -54.87907 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2883" Parameter: A <- "-80.2883" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4092" Parameter: B <- "-25.4092" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8791" Parameter: C <- "-54.8791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6554 TOTAL ENERGY = -80.2883 RDTITL> * VAN DER WAALS = -25.4092 ELECTROSTATIC = -54.8791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6554" Parameter: CONF_N -> "8002" Comparing "6554" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6555" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756921 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753366 ATOM PAIRS WERE FOUND FOR ATOM LIST 41224 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29106 from a total of 753366 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6555 -75.02948 -5.25880 0.70266 INTE EXTERN> -26.55760 -48.47188 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0295" Parameter: A <- "-75.0295" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5576" Parameter: B <- "-26.5576" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4719" Parameter: C <- "-48.4719" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6555 TOTAL ENERGY = -75.0295 RDTITL> * VAN DER WAALS = -26.5576 ELECTROSTATIC = -48.4719 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6555" Parameter: CONF_N -> "8002" Comparing "6555" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6556" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753366 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758577 ATOM PAIRS WERE FOUND FOR ATOM LIST 41233 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29532 from a total of 758577 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6556 -72.32959 -2.69990 0.71281 INTE EXTERN> -26.87043 -45.45916 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3296" Parameter: A <- "-72.3296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8704" Parameter: B <- "-26.8704" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4592" Parameter: C <- "-45.4592" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6556 TOTAL ENERGY = -72.3296 RDTITL> * VAN DER WAALS = -26.8704 ELECTROSTATIC = -45.4592 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6556" Parameter: CONF_N -> "8002" Comparing "6556" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6557" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758577 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752508 ATOM PAIRS WERE FOUND FOR ATOM LIST 41124 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29212 from a total of 752508 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6557 -76.25987 3.93028 0.57818 INTE EXTERN> -31.90300 -44.35687 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2599" Parameter: A <- "-76.2599" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.903" Parameter: B <- "-31.903" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3569" Parameter: C <- "-44.3569" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6557 TOTAL ENERGY = -76.2599 RDTITL> * VAN DER WAALS = -31.903 ELECTROSTATIC = -44.3569 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6557" Parameter: CONF_N -> "8002" Comparing "6557" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6558" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752508 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750464 ATOM PAIRS WERE FOUND FOR ATOM LIST 41039 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29120 from a total of 750464 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6558 -74.28032 -1.97955 0.60888 INTE EXTERN> -30.95625 -43.32407 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2803" Parameter: A <- "-74.2803" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9562" Parameter: B <- "-30.9562" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3241" Parameter: C <- "-43.3241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6558 TOTAL ENERGY = -74.2803 RDTITL> * VAN DER WAALS = -30.9562 ELECTROSTATIC = -43.3241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6558" Parameter: CONF_N -> "8002" Comparing "6558" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6559" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750464 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749776 ATOM PAIRS WERE FOUND FOR ATOM LIST 41071 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29173 from a total of 749776 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6559 -71.35115 -2.92917 0.58307 INTE EXTERN> -29.59713 -41.75401 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3511" Parameter: A <- "-71.3511" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5971" Parameter: B <- "-29.5971" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.754" Parameter: C <- "-41.754" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6559 TOTAL ENERGY = -71.3511 RDTITL> * VAN DER WAALS = -29.5971 ELECTROSTATIC = -41.754 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6559" Parameter: CONF_N -> "8002" Comparing "6559" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6560" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749776 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748302 ATOM PAIRS WERE FOUND FOR ATOM LIST 40939 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29095 from a total of 748302 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6560 -67.86582 -3.48533 0.67738 INTE EXTERN> -26.49125 -41.37457 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8658" Parameter: A <- "-67.8658" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4913" Parameter: B <- "-26.4913" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3746" Parameter: C <- "-41.3746" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6560 TOTAL ENERGY = -67.8658 RDTITL> * VAN DER WAALS = -26.4913 ELECTROSTATIC = -41.3746 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6560" Parameter: CONF_N -> "8002" Comparing "6560" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6561" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748302 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752464 ATOM PAIRS WERE FOUND FOR ATOM LIST 41159 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29384 from a total of 752464 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6561 -78.10790 10.24208 0.67320 INTE EXTERN> -29.57841 -48.52950 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1079" Parameter: A <- "-78.1079" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5784" Parameter: B <- "-29.5784" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5295" Parameter: C <- "-48.5295" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6561 TOTAL ENERGY = -78.1079 RDTITL> * VAN DER WAALS = -29.5784 ELECTROSTATIC = -48.5295 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6561" Parameter: CONF_N -> "8002" Comparing "6561" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6562" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752464 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749390 ATOM PAIRS WERE FOUND FOR ATOM LIST 41194 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29729 from a total of 749390 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6562 -69.55173 -8.55617 0.78916 INTE EXTERN> -24.46947 -45.08226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5517" Parameter: A <- "-69.5517" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4695" Parameter: B <- "-24.4695" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0823" Parameter: C <- "-45.0823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6562 TOTAL ENERGY = -69.5517 RDTITL> * VAN DER WAALS = -24.4695 ELECTROSTATIC = -45.0823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6562" Parameter: CONF_N -> "8002" Comparing "6562" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6563" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749390 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757270 ATOM PAIRS WERE FOUND FOR ATOM LIST 41233 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29844 from a total of 757270 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6563 -77.48883 7.93710 0.70364 INTE EXTERN> -31.21556 -46.27327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4888" Parameter: A <- "-77.4888" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2156" Parameter: B <- "-31.2156" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2733" Parameter: C <- "-46.2733" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6563 TOTAL ENERGY = -77.4888 RDTITL> * VAN DER WAALS = -31.2156 ELECTROSTATIC = -46.2733 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6563" Parameter: CONF_N -> "8002" Comparing "6563" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6564" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757270 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754480 ATOM PAIRS WERE FOUND FOR ATOM LIST 41354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29611 from a total of 754480 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6564 -81.96993 4.48111 0.72361 INTE EXTERN> -28.32210 -53.64783 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9699" Parameter: A <- "-81.9699" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3221" Parameter: B <- "-28.3221" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6478" Parameter: C <- "-53.6478" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6564 TOTAL ENERGY = -81.9699 RDTITL> * VAN DER WAALS = -28.3221 ELECTROSTATIC = -53.6478 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6564" Parameter: CONF_N -> "8002" Comparing "6564" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6565" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754480 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761144 ATOM PAIRS WERE FOUND FOR ATOM LIST 41488 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29598 from a total of 761144 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6565 -84.94837 2.97844 0.73951 INTE EXTERN> -28.62386 -56.32451 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.9484" Parameter: A <- "-84.9484" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6239" Parameter: B <- "-28.6239" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.3245" Parameter: C <- "-56.3245" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6565 TOTAL ENERGY = -84.9484 RDTITL> * VAN DER WAALS = -28.6239 ELECTROSTATIC = -56.3245 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6565" Parameter: CONF_N -> "8002" Comparing "6565" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6566" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761144 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758146 ATOM PAIRS WERE FOUND FOR ATOM LIST 41528 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28963 from a total of 758146 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6566 -75.70202 -9.24635 0.67453 INTE EXTERN> -29.09808 -46.60394 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.702" Parameter: A <- "-75.702" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0981" Parameter: B <- "-29.0981" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6039" Parameter: C <- "-46.6039" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6566 TOTAL ENERGY = -75.702 RDTITL> * VAN DER WAALS = -29.0981 ELECTROSTATIC = -46.6039 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6566" Parameter: CONF_N -> "8002" Comparing "6566" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6567" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758146 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758887 ATOM PAIRS WERE FOUND FOR ATOM LIST 41466 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29650 from a total of 758887 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6567 -76.39339 0.69136 0.63614 INTE EXTERN> -32.22400 -44.16938 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3934" Parameter: A <- "-76.3934" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.224" Parameter: B <- "-32.224" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1694" Parameter: C <- "-44.1694" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6567 TOTAL ENERGY = -76.3934 RDTITL> * VAN DER WAALS = -32.224 ELECTROSTATIC = -44.1694 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6567" Parameter: CONF_N -> "8002" Comparing "6567" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6568" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758887 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756608 ATOM PAIRS WERE FOUND FOR ATOM LIST 41423 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29966 from a total of 756608 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6568 -76.53975 0.14636 0.70289 INTE EXTERN> -29.79887 -46.74088 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5397" Parameter: A <- "-76.5397" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7989" Parameter: B <- "-29.7989" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7409" Parameter: C <- "-46.7409" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6568 TOTAL ENERGY = -76.5397 RDTITL> * VAN DER WAALS = -29.7989 ELECTROSTATIC = -46.7409 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6568" Parameter: CONF_N -> "8002" Comparing "6568" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6569" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756608 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756727 ATOM PAIRS WERE FOUND FOR ATOM LIST 41397 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29858 from a total of 756727 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6569 -80.23398 3.69423 0.72361 INTE EXTERN> -29.70785 -50.52612 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.234" Parameter: A <- "-80.234" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7079" Parameter: B <- "-29.7079" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5261" Parameter: C <- "-50.5261" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6569 TOTAL ENERGY = -80.234 RDTITL> * VAN DER WAALS = -29.7079 ELECTROSTATIC = -50.5261 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6569" Parameter: CONF_N -> "8002" Comparing "6569" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6570" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756727 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754534 ATOM PAIRS WERE FOUND FOR ATOM LIST 41290 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29194 from a total of 754534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6570 -77.67945 -2.55452 0.82340 INTE EXTERN> -26.01161 -51.66784 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6795" Parameter: A <- "-77.6795" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0116" Parameter: B <- "-26.0116" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6678" Parameter: C <- "-51.6678" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6570 TOTAL ENERGY = -77.6795 RDTITL> * VAN DER WAALS = -26.0116 ELECTROSTATIC = -51.6678 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6570" Parameter: CONF_N -> "8002" Comparing "6570" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6571" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754353 ATOM PAIRS WERE FOUND FOR ATOM LIST 41288 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29510 from a total of 754353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6571 -77.52274 -0.15672 0.81875 INTE EXTERN> -26.19796 -51.32478 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5227" Parameter: A <- "-77.5227" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.198" Parameter: B <- "-26.198" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3248" Parameter: C <- "-51.3248" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6571 TOTAL ENERGY = -77.5227 RDTITL> * VAN DER WAALS = -26.198 ELECTROSTATIC = -51.3248 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6571" Parameter: CONF_N -> "8002" Comparing "6571" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6572" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756393 ATOM PAIRS WERE FOUND FOR ATOM LIST 41230 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29127 from a total of 756393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6572 -84.57863 7.05590 0.67712 INTE EXTERN> -29.34133 -55.23730 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.5786" Parameter: A <- "-84.5786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3413" Parameter: B <- "-29.3413" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.2373" Parameter: C <- "-55.2373" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6572 TOTAL ENERGY = -84.5786 RDTITL> * VAN DER WAALS = -29.3413 ELECTROSTATIC = -55.2373 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6572" Parameter: CONF_N -> "8002" Comparing "6572" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6573" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758054 ATOM PAIRS WERE FOUND FOR ATOM LIST 41334 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29460 from a total of 758054 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6573 -84.69788 0.11924 0.77552 INTE EXTERN> -27.41504 -57.28284 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.6979" Parameter: A <- "-84.6979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.415" Parameter: B <- "-27.415" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.2828" Parameter: C <- "-57.2828" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6573 TOTAL ENERGY = -84.6979 RDTITL> * VAN DER WAALS = -27.415 ELECTROSTATIC = -57.2828 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6573" Parameter: CONF_N -> "8002" Comparing "6573" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6574" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758054 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756432 ATOM PAIRS WERE FOUND FOR ATOM LIST 41468 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29904 from a total of 756432 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6574 -73.59473 -11.10315 0.68285 INTE EXTERN> -28.10059 -45.49414 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5947" Parameter: A <- "-73.5947" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1006" Parameter: B <- "-28.1006" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4941" Parameter: C <- "-45.4941" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6574 TOTAL ENERGY = -73.5947 RDTITL> * VAN DER WAALS = -28.1006 ELECTROSTATIC = -45.4941 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6574" Parameter: CONF_N -> "8002" Comparing "6574" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6575" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756432 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753662 ATOM PAIRS WERE FOUND FOR ATOM LIST 41242 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29663 from a total of 753662 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6575 -81.67024 8.07551 0.71740 INTE EXTERN> -27.16438 -54.50586 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6702" Parameter: A <- "-81.6702" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1644" Parameter: B <- "-27.1644" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.5059" Parameter: C <- "-54.5059" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6575 TOTAL ENERGY = -81.6702 RDTITL> * VAN DER WAALS = -27.1644 ELECTROSTATIC = -54.5059 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6575" Parameter: CONF_N -> "8002" Comparing "6575" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6576" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753662 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758050 ATOM PAIRS WERE FOUND FOR ATOM LIST 41289 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29792 from a total of 758050 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6576 -72.80669 -8.86355 0.65790 INTE EXTERN> -29.98712 -42.81957 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8067" Parameter: A <- "-72.8067" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9871" Parameter: B <- "-29.9871" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8196" Parameter: C <- "-42.8196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6576 TOTAL ENERGY = -72.8067 RDTITL> * VAN DER WAALS = -29.9871 ELECTROSTATIC = -42.8196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6576" Parameter: CONF_N -> "8002" Comparing "6576" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6577" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758050 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747965 ATOM PAIRS WERE FOUND FOR ATOM LIST 41110 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29327 from a total of 747965 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6577 -75.35887 2.55219 0.69889 INTE EXTERN> -28.02364 -47.33523 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3589" Parameter: A <- "-75.3589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0236" Parameter: B <- "-28.0236" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3352" Parameter: C <- "-47.3352" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6577 TOTAL ENERGY = -75.3589 RDTITL> * VAN DER WAALS = -28.0236 ELECTROSTATIC = -47.3352 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6577" Parameter: CONF_N -> "8002" Comparing "6577" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6578" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747965 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749559 ATOM PAIRS WERE FOUND FOR ATOM LIST 41163 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29104 from a total of 749559 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6578 -80.38588 5.02701 0.65655 INTE EXTERN> -30.08244 -50.30345 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3859" Parameter: A <- "-80.3859" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0824" Parameter: B <- "-30.0824" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3034" Parameter: C <- "-50.3034" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6578 TOTAL ENERGY = -80.3859 RDTITL> * VAN DER WAALS = -30.0824 ELECTROSTATIC = -50.3034 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6578" Parameter: CONF_N -> "8002" Comparing "6578" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6579" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749559 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752011 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29597 from a total of 752011 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6579 -75.61011 -4.77578 0.81000 INTE EXTERN> -24.79460 -50.81551 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6101" Parameter: A <- "-75.6101" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7946" Parameter: B <- "-24.7946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8155" Parameter: C <- "-50.8155" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6579 TOTAL ENERGY = -75.6101 RDTITL> * VAN DER WAALS = -24.7946 ELECTROSTATIC = -50.8155 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6579" Parameter: CONF_N -> "8002" Comparing "6579" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6580" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752011 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749908 ATOM PAIRS WERE FOUND FOR ATOM LIST 41058 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29458 from a total of 749908 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6580 -79.41304 3.80293 0.62315 INTE EXTERN> -32.25102 -47.16202 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.413" Parameter: A <- "-79.413" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.251" Parameter: B <- "-32.251" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.162" Parameter: C <- "-47.162" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6580 TOTAL ENERGY = -79.413 RDTITL> * VAN DER WAALS = -32.251 ELECTROSTATIC = -47.162 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6580" Parameter: CONF_N -> "8002" Comparing "6580" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6581" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749908 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754772 ATOM PAIRS WERE FOUND FOR ATOM LIST 41490 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30011 from a total of 754772 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6581 -78.18322 -1.22982 0.79339 INTE EXTERN> -26.61168 -51.57154 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1832" Parameter: A <- "-78.1832" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6117" Parameter: B <- "-26.6117" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5715" Parameter: C <- "-51.5715" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6581 TOTAL ENERGY = -78.1832 RDTITL> * VAN DER WAALS = -26.6117 ELECTROSTATIC = -51.5715 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6581" Parameter: CONF_N -> "8002" Comparing "6581" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6582" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754772 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760117 ATOM PAIRS WERE FOUND FOR ATOM LIST 41752 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29690 from a total of 760117 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6582 -78.94052 0.75730 0.56075 INTE EXTERN> -34.58751 -44.35301 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9405" Parameter: A <- "-78.9405" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.5875" Parameter: B <- "-34.5875" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.353" Parameter: C <- "-44.353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6582 TOTAL ENERGY = -78.9405 RDTITL> * VAN DER WAALS = -34.5875 ELECTROSTATIC = -44.353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6582" Parameter: CONF_N -> "8002" Comparing "6582" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6583" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760117 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748055 ATOM PAIRS WERE FOUND FOR ATOM LIST 41141 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29165 from a total of 748055 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6583 -71.18422 -7.75630 0.52256 INTE EXTERN> -31.37623 -39.80798 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1842" Parameter: A <- "-71.1842" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3762" Parameter: B <- "-31.3762" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.808" Parameter: C <- "-39.808" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6583 TOTAL ENERGY = -71.1842 RDTITL> * VAN DER WAALS = -31.3762 ELECTROSTATIC = -39.808 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6583" Parameter: CONF_N -> "8002" Comparing "6583" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6584" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748055 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748909 ATOM PAIRS WERE FOUND FOR ATOM LIST 41163 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29809 from a total of 748909 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6584 -82.77312 11.58890 0.73069 INTE EXTERN> -28.48339 -54.28973 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7731" Parameter: A <- "-82.7731" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4834" Parameter: B <- "-28.4834" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2897" Parameter: C <- "-54.2897" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6584 TOTAL ENERGY = -82.7731 RDTITL> * VAN DER WAALS = -28.4834 ELECTROSTATIC = -54.2897 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6584" Parameter: CONF_N -> "8002" Comparing "6584" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6585" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748909 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751735 ATOM PAIRS WERE FOUND FOR ATOM LIST 41226 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29303 from a total of 751735 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6585 -77.69810 -5.07502 0.59307 INTE EXTERN> -29.71940 -47.97870 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6981" Parameter: A <- "-77.6981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7194" Parameter: B <- "-29.7194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9787" Parameter: C <- "-47.9787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6585 TOTAL ENERGY = -77.6981 RDTITL> * VAN DER WAALS = -29.7194 ELECTROSTATIC = -47.9787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6585" Parameter: CONF_N -> "8002" Comparing "6585" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6586" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751735 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752088 ATOM PAIRS WERE FOUND FOR ATOM LIST 41313 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29125 from a total of 752088 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6586 -79.34138 1.64328 0.64141 INTE EXTERN> -30.10361 -49.23778 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.3414" Parameter: A <- "-79.3414" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1036" Parameter: B <- "-30.1036" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2378" Parameter: C <- "-49.2378" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6586 TOTAL ENERGY = -79.3414 RDTITL> * VAN DER WAALS = -30.1036 ELECTROSTATIC = -49.2378 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6586" Parameter: CONF_N -> "8002" Comparing "6586" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6587" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752088 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756106 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29849 from a total of 756106 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6587 -85.23384 5.89246 0.77799 INTE EXTERN> -27.13022 -58.10362 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.2338" Parameter: A <- "-85.2338" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1302" Parameter: B <- "-27.1302" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.1036" Parameter: C <- "-58.1036" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6587 TOTAL ENERGY = -85.2338 RDTITL> * VAN DER WAALS = -27.1302 ELECTROSTATIC = -58.1036 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6587" Parameter: CONF_N -> "8002" Comparing "6587" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6588" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756106 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757295 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29983 from a total of 757295 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6588 -75.67490 -9.55894 0.67765 INTE EXTERN> -28.94975 -46.72515 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6749" Parameter: A <- "-75.6749" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9497" Parameter: B <- "-28.9497" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7252" Parameter: C <- "-46.7252" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6588 TOTAL ENERGY = -75.6749 RDTITL> * VAN DER WAALS = -28.9497 ELECTROSTATIC = -46.7252 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6588" Parameter: CONF_N -> "8002" Comparing "6588" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6589" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757295 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755189 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 755189 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6589 -74.67200 -1.00290 0.77226 INTE EXTERN> -22.80422 -51.86778 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.672" Parameter: A <- "-74.672" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.8042" Parameter: B <- "-22.8042" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8678" Parameter: C <- "-51.8678" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6589 TOTAL ENERGY = -74.672 RDTITL> * VAN DER WAALS = -22.8042 ELECTROSTATIC = -51.8678 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6589" Parameter: CONF_N -> "8002" Comparing "6589" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6590" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755189 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752289 ATOM PAIRS WERE FOUND FOR ATOM LIST 41272 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30413 from a total of 752289 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6590 -86.46610 11.79410 0.62361 INTE EXTERN> -34.56639 -51.89971 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.4661" Parameter: A <- "-86.4661" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.5664" Parameter: B <- "-34.5664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8997" Parameter: C <- "-51.8997" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6590 TOTAL ENERGY = -86.4661 RDTITL> * VAN DER WAALS = -34.5664 ELECTROSTATIC = -51.8997 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6590" Parameter: CONF_N -> "8002" Comparing "6590" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6591" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752289 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754445 ATOM PAIRS WERE FOUND FOR ATOM LIST 41426 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29749 from a total of 754445 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6591 -82.21644 -4.24966 0.65477 INTE EXTERN> -29.59774 -52.61871 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.2164" Parameter: A <- "-82.2164" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5977" Parameter: B <- "-29.5977" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6187" Parameter: C <- "-52.6187" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6591 TOTAL ENERGY = -82.2164 RDTITL> * VAN DER WAALS = -29.5977 ELECTROSTATIC = -52.6187 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6591" Parameter: CONF_N -> "8002" Comparing "6591" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6592" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754445 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754307 ATOM PAIRS WERE FOUND FOR ATOM LIST 41385 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29781 from a total of 754307 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6592 -75.75827 -6.45818 0.69183 INTE EXTERN> -30.12175 -45.63652 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7583" Parameter: A <- "-75.7583" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1218" Parameter: B <- "-30.1218" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6365" Parameter: C <- "-45.6365" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6592 TOTAL ENERGY = -75.7583 RDTITL> * VAN DER WAALS = -30.1218 ELECTROSTATIC = -45.6365 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6592" Parameter: CONF_N -> "8002" Comparing "6592" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6593" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754307 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756442 ATOM PAIRS WERE FOUND FOR ATOM LIST 41611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29659 from a total of 756442 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6593 -84.29602 8.53776 0.72004 INTE EXTERN> -29.92621 -54.36982 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.296" Parameter: A <- "-84.296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9262" Parameter: B <- "-29.9262" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.3698" Parameter: C <- "-54.3698" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6593 TOTAL ENERGY = -84.296 RDTITL> * VAN DER WAALS = -29.9262 ELECTROSTATIC = -54.3698 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6593" Parameter: CONF_N -> "8002" Comparing "6593" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6594" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756442 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757490 ATOM PAIRS WERE FOUND FOR ATOM LIST 41518 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30443 from a total of 757490 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6594 -80.56469 -3.73133 0.60605 INTE EXTERN> -33.08768 -47.47702 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5647" Parameter: A <- "-80.5647" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0877" Parameter: B <- "-33.0877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.477" Parameter: C <- "-47.477" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6594 TOTAL ENERGY = -80.5647 RDTITL> * VAN DER WAALS = -33.0877 ELECTROSTATIC = -47.477 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6594" Parameter: CONF_N -> "8002" Comparing "6594" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6595" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757490 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755906 ATOM PAIRS WERE FOUND FOR ATOM LIST 41529 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30436 from a total of 755906 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6595 -84.91877 4.35407 0.81326 INTE EXTERN> -27.87045 -57.04831 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.9188" Parameter: A <- "-84.9188" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8705" Parameter: B <- "-27.8705" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.0483" Parameter: C <- "-57.0483" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6595 TOTAL ENERGY = -84.9188 RDTITL> * VAN DER WAALS = -27.8705 ELECTROSTATIC = -57.0483 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6595" Parameter: CONF_N -> "8002" Comparing "6595" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6596" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755906 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758328 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29663 from a total of 758328 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6596 -80.36254 -4.55623 0.73015 INTE EXTERN> -28.01605 -52.34649 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3625" Parameter: A <- "-80.3625" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.016" Parameter: B <- "-28.016" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3465" Parameter: C <- "-52.3465" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6596 TOTAL ENERGY = -80.3625 RDTITL> * VAN DER WAALS = -28.016 ELECTROSTATIC = -52.3465 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6596" Parameter: CONF_N -> "8002" Comparing "6596" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6597" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758328 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757928 ATOM PAIRS WERE FOUND FOR ATOM LIST 41673 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30065 from a total of 757928 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6597 -80.96638 0.60384 0.64479 INTE EXTERN> -29.26665 -51.69973 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9664" Parameter: A <- "-80.9664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2666" Parameter: B <- "-29.2666" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6997" Parameter: C <- "-51.6997" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6597 TOTAL ENERGY = -80.9664 RDTITL> * VAN DER WAALS = -29.2666 ELECTROSTATIC = -51.6997 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6597" Parameter: CONF_N -> "8002" Comparing "6597" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6598" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757928 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757433 ATOM PAIRS WERE FOUND FOR ATOM LIST 41615 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30400 from a total of 757433 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6598 -84.78062 3.81424 0.70803 INTE EXTERN> -31.17265 -53.60798 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.7806" Parameter: A <- "-84.7806" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1726" Parameter: B <- "-31.1726" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.608" Parameter: C <- "-53.608" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6598 TOTAL ENERGY = -84.7806 RDTITL> * VAN DER WAALS = -31.1726 ELECTROSTATIC = -53.608 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6598" Parameter: CONF_N -> "8002" Comparing "6598" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6599" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757433 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754012 ATOM PAIRS WERE FOUND FOR ATOM LIST 41178 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30147 from a total of 754012 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6599 -82.09726 -2.68336 0.75259 INTE EXTERN> -25.91895 -56.17832 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.0973" Parameter: A <- "-82.0973" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9189" Parameter: B <- "-25.9189" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.1783" Parameter: C <- "-56.1783" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6599 TOTAL ENERGY = -82.0973 RDTITL> * VAN DER WAALS = -25.9189 ELECTROSTATIC = -56.1783 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6599" Parameter: CONF_N -> "8002" Comparing "6599" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6600" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754012 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761877 ATOM PAIRS WERE FOUND FOR ATOM LIST 41705 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30683 from a total of 761877 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6600 -74.35779 -7.73947 0.73458 INTE EXTERN> -26.04085 -48.31695 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3578" Parameter: A <- "-74.3578" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0408" Parameter: B <- "-26.0408" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3169" Parameter: C <- "-48.3169" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6600 TOTAL ENERGY = -74.3578 RDTITL> * VAN DER WAALS = -26.0408 ELECTROSTATIC = -48.3169 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6600" Parameter: CONF_N -> "8002" Comparing "6600" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6601" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761877 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757289 ATOM PAIRS WERE FOUND FOR ATOM LIST 41631 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30194 from a total of 757289 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6601 -83.51235 9.15455 0.60128 INTE EXTERN> -31.94092 -51.57143 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.5123" Parameter: A <- "-83.5123" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9409" Parameter: B <- "-31.9409" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5714" Parameter: C <- "-51.5714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6601 TOTAL ENERGY = -83.5123 RDTITL> * VAN DER WAALS = -31.9409 ELECTROSTATIC = -51.5714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6601" Parameter: CONF_N -> "8002" Comparing "6601" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6602" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757289 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757973 ATOM PAIRS WERE FOUND FOR ATOM LIST 41593 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30133 from a total of 757973 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6602 -89.61526 6.10291 0.70677 INTE EXTERN> -31.69362 -57.92164 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-89.6153" Parameter: A <- "-89.6153" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6936" Parameter: B <- "-31.6936" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.9216" Parameter: C <- "-57.9216" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6602 TOTAL ENERGY = -89.6153 RDTITL> * VAN DER WAALS = -31.6936 ELECTROSTATIC = -57.9216 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6602" Parameter: CONF_N -> "8002" Comparing "6602" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6603" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757973 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754820 ATOM PAIRS WERE FOUND FOR ATOM LIST 41508 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29815 from a total of 754820 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6603 -83.00513 -6.61013 0.67781 INTE EXTERN> -30.75186 -52.25327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.0051" Parameter: A <- "-83.0051" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7519" Parameter: B <- "-30.7519" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2533" Parameter: C <- "-52.2533" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6603 TOTAL ENERGY = -83.0051 RDTITL> * VAN DER WAALS = -30.7519 ELECTROSTATIC = -52.2533 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6603" Parameter: CONF_N -> "8002" Comparing "6603" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6604" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754820 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760755 ATOM PAIRS WERE FOUND FOR ATOM LIST 41834 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30597 from a total of 760755 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6604 -77.07915 -5.92597 0.78854 INTE EXTERN> -23.83073 -53.24842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0792" Parameter: A <- "-77.0792" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8307" Parameter: B <- "-23.8307" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.2484" Parameter: C <- "-53.2484" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6604 TOTAL ENERGY = -77.0792 RDTITL> * VAN DER WAALS = -23.8307 ELECTROSTATIC = -53.2484 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6604" Parameter: CONF_N -> "8002" Comparing "6604" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6605" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760755 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754404 ATOM PAIRS WERE FOUND FOR ATOM LIST 41500 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30003 from a total of 754404 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6605 -83.54755 6.46840 0.68618 INTE EXTERN> -31.11929 -52.42826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.5476" Parameter: A <- "-83.5476" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1193" Parameter: B <- "-31.1193" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.4283" Parameter: C <- "-52.4283" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6605 TOTAL ENERGY = -83.5476 RDTITL> * VAN DER WAALS = -31.1193 ELECTROSTATIC = -52.4283 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6605" Parameter: CONF_N -> "8002" Comparing "6605" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6606" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754404 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755854 ATOM PAIRS WERE FOUND FOR ATOM LIST 41363 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29823 from a total of 755854 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6606 -82.30223 -1.24533 0.73012 INTE EXTERN> -29.59753 -52.70469 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3022" Parameter: A <- "-82.3022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5975" Parameter: B <- "-29.5975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.7047" Parameter: C <- "-52.7047" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6606 TOTAL ENERGY = -82.3022 RDTITL> * VAN DER WAALS = -29.5975 ELECTROSTATIC = -52.7047 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6606" Parameter: CONF_N -> "8002" Comparing "6606" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6607" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755854 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760673 ATOM PAIRS WERE FOUND FOR ATOM LIST 41565 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30535 from a total of 760673 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6607 -82.04061 -0.26162 0.78114 INTE EXTERN> -27.55444 -54.48616 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.0406" Parameter: A <- "-82.0406" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5544" Parameter: B <- "-27.5544" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.4862" Parameter: C <- "-54.4862" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6607 TOTAL ENERGY = -82.0406 RDTITL> * VAN DER WAALS = -27.5544 ELECTROSTATIC = -54.4862 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6607" Parameter: CONF_N -> "8002" Comparing "6607" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6608" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760673 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756213 ATOM PAIRS WERE FOUND FOR ATOM LIST 41516 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30154 from a total of 756213 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6608 -76.85991 -5.18069 0.80849 INTE EXTERN> -23.18931 -53.67060 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8599" Parameter: A <- "-76.8599" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.1893" Parameter: B <- "-23.1893" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6706" Parameter: C <- "-53.6706" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6608 TOTAL ENERGY = -76.8599 RDTITL> * VAN DER WAALS = -23.1893 ELECTROSTATIC = -53.6706 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6608" Parameter: CONF_N -> "8002" Comparing "6608" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6609" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756213 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756585 ATOM PAIRS WERE FOUND FOR ATOM LIST 41654 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30305 from a total of 756585 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6609 -81.77879 4.91888 0.65825 INTE EXTERN> -32.41070 -49.36809 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.7788" Parameter: A <- "-81.7788" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4107" Parameter: B <- "-32.4107" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3681" Parameter: C <- "-49.3681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6609 TOTAL ENERGY = -81.7788 RDTITL> * VAN DER WAALS = -32.4107 ELECTROSTATIC = -49.3681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6609" Parameter: CONF_N -> "8002" Comparing "6609" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6610" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756585 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760104 ATOM PAIRS WERE FOUND FOR ATOM LIST 41597 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30306 from a total of 760104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6610 -76.60820 -5.17058 0.58822 INTE EXTERN> -33.32932 -43.27888 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6082" Parameter: A <- "-76.6082" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3293" Parameter: B <- "-33.3293" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2789" Parameter: C <- "-43.2789" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6610 TOTAL ENERGY = -76.6082 RDTITL> * VAN DER WAALS = -33.3293 ELECTROSTATIC = -43.2789 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6610" Parameter: CONF_N -> "8002" Comparing "6610" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6611" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41967 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30483 from a total of 764586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6611 -75.48594 -1.12226 0.73638 INTE EXTERN> -28.18751 -47.29843 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4859" Parameter: A <- "-75.4859" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1875" Parameter: B <- "-28.1875" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2984" Parameter: C <- "-47.2984" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6611 TOTAL ENERGY = -75.4859 RDTITL> * VAN DER WAALS = -28.1875 ELECTROSTATIC = -47.2984 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6611" Parameter: CONF_N -> "8002" Comparing "6611" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6612" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761011 ATOM PAIRS WERE FOUND FOR ATOM LIST 41770 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29905 from a total of 761011 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6612 -75.20354 -0.28240 0.61290 INTE EXTERN> -31.47916 -43.72438 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2035" Parameter: A <- "-75.2035" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4792" Parameter: B <- "-31.4792" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7244" Parameter: C <- "-43.7244" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6612 TOTAL ENERGY = -75.2035 RDTITL> * VAN DER WAALS = -31.4792 ELECTROSTATIC = -43.7244 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6612" Parameter: CONF_N -> "8002" Comparing "6612" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6613" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761011 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762022 ATOM PAIRS WERE FOUND FOR ATOM LIST 41692 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30091 from a total of 762022 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6613 -83.08137 7.87783 0.67155 INTE EXTERN> -30.90192 -52.17945 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.0814" Parameter: A <- "-83.0814" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9019" Parameter: B <- "-30.9019" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1794" Parameter: C <- "-52.1794" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6613 TOTAL ENERGY = -83.0814 RDTITL> * VAN DER WAALS = -30.9019 ELECTROSTATIC = -52.1794 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6613" Parameter: CONF_N -> "8002" Comparing "6613" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6614" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762022 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762920 ATOM PAIRS WERE FOUND FOR ATOM LIST 41936 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30370 from a total of 762920 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6614 -77.88271 -5.19866 0.85773 INTE EXTERN> -23.27826 -54.60445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8827" Parameter: A <- "-77.8827" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.2783" Parameter: B <- "-23.2783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.6045" Parameter: C <- "-54.6045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6614 TOTAL ENERGY = -77.8827 RDTITL> * VAN DER WAALS = -23.2783 ELECTROSTATIC = -54.6045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6614" Parameter: CONF_N -> "8002" Comparing "6614" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6615" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762920 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760839 ATOM PAIRS WERE FOUND FOR ATOM LIST 41833 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30171 from a total of 760839 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6615 -82.65300 4.77029 0.73180 INTE EXTERN> -28.81684 -53.83616 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.653" Parameter: A <- "-82.653" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8168" Parameter: B <- "-28.8168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8362" Parameter: C <- "-53.8362" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6615 TOTAL ENERGY = -82.653 RDTITL> * VAN DER WAALS = -28.8168 ELECTROSTATIC = -53.8362 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6615" Parameter: CONF_N -> "8002" Comparing "6615" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6616" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760839 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760021 ATOM PAIRS WERE FOUND FOR ATOM LIST 41516 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30424 from a total of 760021 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6616 -79.26918 -3.38382 0.78035 INTE EXTERN> -26.50200 -52.76718 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2692" Parameter: A <- "-79.2692" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.502" Parameter: B <- "-26.502" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.7672" Parameter: C <- "-52.7672" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6616 TOTAL ENERGY = -79.2692 RDTITL> * VAN DER WAALS = -26.502 ELECTROSTATIC = -52.7672 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6616" Parameter: CONF_N -> "8002" Comparing "6616" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6617" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760021 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756769 ATOM PAIRS WERE FOUND FOR ATOM LIST 41551 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29764 from a total of 756769 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6617 -72.40155 -6.86763 0.68408 INTE EXTERN> -28.63302 -43.76853 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4015" Parameter: A <- "-72.4015" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.633" Parameter: B <- "-28.633" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7685" Parameter: C <- "-43.7685" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6617 TOTAL ENERGY = -72.4015 RDTITL> * VAN DER WAALS = -28.633 ELECTROSTATIC = -43.7685 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6617" Parameter: CONF_N -> "8002" Comparing "6617" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6618" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756769 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753611 ATOM PAIRS WERE FOUND FOR ATOM LIST 41450 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29481 from a total of 753611 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6618 -79.30751 6.90596 0.69772 INTE EXTERN> -27.50025 -51.80726 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.3075" Parameter: A <- "-79.3075" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5002" Parameter: B <- "-27.5002" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8073" Parameter: C <- "-51.8073" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6618 TOTAL ENERGY = -79.3075 RDTITL> * VAN DER WAALS = -27.5002 ELECTROSTATIC = -51.8073 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6618" Parameter: CONF_N -> "8002" Comparing "6618" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6619" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753611 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752439 ATOM PAIRS WERE FOUND FOR ATOM LIST 41364 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29839 from a total of 752439 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6619 -84.73334 5.42583 0.73344 INTE EXTERN> -30.11941 -54.61393 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.7333" Parameter: A <- "-84.7333" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1194" Parameter: B <- "-30.1194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.6139" Parameter: C <- "-54.6139" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6619 TOTAL ENERGY = -84.7333 RDTITL> * VAN DER WAALS = -30.1194 ELECTROSTATIC = -54.6139 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6619" Parameter: CONF_N -> "8002" Comparing "6619" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6620" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752439 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751307 ATOM PAIRS WERE FOUND FOR ATOM LIST 41391 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29137 from a total of 751307 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6620 -67.45905 -17.27428 0.80467 INTE EXTERN> -27.00279 -40.45626 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4591" Parameter: A <- "-67.4591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0028" Parameter: B <- "-27.0028" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4563" Parameter: C <- "-40.4563" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6620 TOTAL ENERGY = -67.4591 RDTITL> * VAN DER WAALS = -27.0028 ELECTROSTATIC = -40.4563 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6620" Parameter: CONF_N -> "8002" Comparing "6620" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6621" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751307 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750202 ATOM PAIRS WERE FOUND FOR ATOM LIST 41169 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29138 from a total of 750202 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6621 -73.57431 6.11526 0.77730 INTE EXTERN> -26.59880 -46.97551 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5743" Parameter: A <- "-73.5743" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5988" Parameter: B <- "-26.5988" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9755" Parameter: C <- "-46.9755" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6621 TOTAL ENERGY = -73.5743 RDTITL> * VAN DER WAALS = -26.5988 ELECTROSTATIC = -46.9755 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6621" Parameter: CONF_N -> "8002" Comparing "6621" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6622" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750202 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755258 ATOM PAIRS WERE FOUND FOR ATOM LIST 41555 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29444 from a total of 755258 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6622 -75.89458 2.32026 0.74861 INTE EXTERN> -25.78783 -50.10675 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8946" Parameter: A <- "-75.8946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7878" Parameter: B <- "-25.7878" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1067" Parameter: C <- "-50.1067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6622 TOTAL ENERGY = -75.8946 RDTITL> * VAN DER WAALS = -25.7878 ELECTROSTATIC = -50.1067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6622" Parameter: CONF_N -> "8002" Comparing "6622" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6623" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755258 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754939 ATOM PAIRS WERE FOUND FOR ATOM LIST 41581 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29408 from a total of 754939 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6623 -76.67159 0.77701 0.61911 INTE EXTERN> -32.37514 -44.29645 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6716" Parameter: A <- "-76.6716" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3751" Parameter: B <- "-32.3751" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2965" Parameter: C <- "-44.2965" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6623 TOTAL ENERGY = -76.6716 RDTITL> * VAN DER WAALS = -32.3751 ELECTROSTATIC = -44.2965 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6623" Parameter: CONF_N -> "8002" Comparing "6623" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6624" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754939 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756800 ATOM PAIRS WERE FOUND FOR ATOM LIST 41503 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29918 from a total of 756800 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6624 -74.84743 -1.82416 0.74173 INTE EXTERN> -26.31106 -48.53637 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8474" Parameter: A <- "-74.8474" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3111" Parameter: B <- "-26.3111" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5364" Parameter: C <- "-48.5364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6624 TOTAL ENERGY = -74.8474 RDTITL> * VAN DER WAALS = -26.3111 ELECTROSTATIC = -48.5364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6624" Parameter: CONF_N -> "8002" Comparing "6624" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6625" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756800 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755476 ATOM PAIRS WERE FOUND FOR ATOM LIST 41344 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29342 from a total of 755476 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6625 -78.63526 3.78783 0.75137 INTE EXTERN> -27.14578 -51.48948 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6353" Parameter: A <- "-78.6353" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1458" Parameter: B <- "-27.1458" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4895" Parameter: C <- "-51.4895" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6625 TOTAL ENERGY = -78.6353 RDTITL> * VAN DER WAALS = -27.1458 ELECTROSTATIC = -51.4895 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6625" Parameter: CONF_N -> "8002" Comparing "6625" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6626" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755476 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758669 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30052 from a total of 758669 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6626 -81.70542 3.07016 0.60723 INTE EXTERN> -32.67952 -49.02590 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.7054" Parameter: A <- "-81.7054" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6795" Parameter: B <- "-32.6795" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0259" Parameter: C <- "-49.0259" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6626 TOTAL ENERGY = -81.7054 RDTITL> * VAN DER WAALS = -32.6795 ELECTROSTATIC = -49.0259 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6626" Parameter: CONF_N -> "8002" Comparing "6626" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6627" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758669 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755956 ATOM PAIRS WERE FOUND FOR ATOM LIST 41631 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30211 from a total of 755956 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6627 -79.64850 -2.05691 0.71211 INTE EXTERN> -26.19792 -53.45058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6485" Parameter: A <- "-79.6485" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1979" Parameter: B <- "-26.1979" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4506" Parameter: C <- "-53.4506" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6627 TOTAL ENERGY = -79.6485 RDTITL> * VAN DER WAALS = -26.1979 ELECTROSTATIC = -53.4506 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6627" Parameter: CONF_N -> "8002" Comparing "6627" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6628" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755956 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758729 ATOM PAIRS WERE FOUND FOR ATOM LIST 41711 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29846 from a total of 758729 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6628 -78.00777 -1.64073 0.69833 INTE EXTERN> -29.12063 -48.88714 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0078" Parameter: A <- "-78.0078" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1206" Parameter: B <- "-29.1206" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8871" Parameter: C <- "-48.8871" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6628 TOTAL ENERGY = -78.0078 RDTITL> * VAN DER WAALS = -29.1206 ELECTROSTATIC = -48.8871 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6628" Parameter: CONF_N -> "8002" Comparing "6628" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6629" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758729 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758756 ATOM PAIRS WERE FOUND FOR ATOM LIST 41695 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30621 from a total of 758756 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6629 -79.78437 1.77660 0.60459 INTE EXTERN> -31.74120 -48.04317 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7844" Parameter: A <- "-79.7844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7412" Parameter: B <- "-31.7412" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0432" Parameter: C <- "-48.0432" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6629 TOTAL ENERGY = -79.7844 RDTITL> * VAN DER WAALS = -31.7412 ELECTROSTATIC = -48.0432 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6629" Parameter: CONF_N -> "8002" Comparing "6629" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6630" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758756 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760012 ATOM PAIRS WERE FOUND FOR ATOM LIST 41854 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30773 from a total of 760012 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6630 -82.58374 2.79937 0.71961 INTE EXTERN> -28.83510 -53.74864 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5837" Parameter: A <- "-82.5837" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8351" Parameter: B <- "-28.8351" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.7486" Parameter: C <- "-53.7486" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6630 TOTAL ENERGY = -82.5837 RDTITL> * VAN DER WAALS = -28.8351 ELECTROSTATIC = -53.7486 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6630" Parameter: CONF_N -> "8002" Comparing "6630" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6631" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760012 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756382 ATOM PAIRS WERE FOUND FOR ATOM LIST 41580 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30525 from a total of 756382 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6631 -79.67457 -2.90917 0.69403 INTE EXTERN> -28.57921 -51.09536 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6746" Parameter: A <- "-79.6746" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5792" Parameter: B <- "-28.5792" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0954" Parameter: C <- "-51.0954" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6631 TOTAL ENERGY = -79.6746 RDTITL> * VAN DER WAALS = -28.5792 ELECTROSTATIC = -51.0954 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6631" Parameter: CONF_N -> "8002" Comparing "6631" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6632" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756382 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751599 ATOM PAIRS WERE FOUND FOR ATOM LIST 41193 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29926 from a total of 751599 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6632 -79.26933 -0.40524 0.62900 INTE EXTERN> -29.26410 -50.00523 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2693" Parameter: A <- "-79.2693" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2641" Parameter: B <- "-29.2641" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0052" Parameter: C <- "-50.0052" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6632 TOTAL ENERGY = -79.2693 RDTITL> * VAN DER WAALS = -29.2641 ELECTROSTATIC = -50.0052 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6632" Parameter: CONF_N -> "8002" Comparing "6632" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6633" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751599 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751898 ATOM PAIRS WERE FOUND FOR ATOM LIST 41161 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30079 from a total of 751898 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6633 -78.94185 -0.32748 0.73949 INTE EXTERN> -27.42586 -51.51599 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9418" Parameter: A <- "-78.9418" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4259" Parameter: B <- "-27.4259" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.516" Parameter: C <- "-51.516" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6633 TOTAL ENERGY = -78.9418 RDTITL> * VAN DER WAALS = -27.4259 ELECTROSTATIC = -51.516 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6633" Parameter: CONF_N -> "8002" Comparing "6633" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6634" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751898 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753218 ATOM PAIRS WERE FOUND FOR ATOM LIST 41314 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30216 from a total of 753218 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6634 -76.40068 -2.54117 0.60278 INTE EXTERN> -34.48268 -41.91800 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4007" Parameter: A <- "-76.4007" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.4827" Parameter: B <- "-34.4827" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.918" Parameter: C <- "-41.918" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6634 TOTAL ENERGY = -76.4007 RDTITL> * VAN DER WAALS = -34.4827 ELECTROSTATIC = -41.918 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6634" Parameter: CONF_N -> "8002" Comparing "6634" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6635" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753218 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758574 ATOM PAIRS WERE FOUND FOR ATOM LIST 41773 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30282 from a total of 758574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6635 -70.90213 -5.49855 0.79834 INTE EXTERN> -27.62375 -43.27838 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9021" Parameter: A <- "-70.9021" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6238" Parameter: B <- "-27.6238" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2784" Parameter: C <- "-43.2784" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6635 TOTAL ENERGY = -70.9021 RDTITL> * VAN DER WAALS = -27.6238 ELECTROSTATIC = -43.2784 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6635" Parameter: CONF_N -> "8002" Comparing "6635" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6636" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756248 ATOM PAIRS WERE FOUND FOR ATOM LIST 41525 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29865 from a total of 756248 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6636 -71.86870 0.96657 0.70293 INTE EXTERN> -28.82744 -43.04125 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8687" Parameter: A <- "-71.8687" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8274" Parameter: B <- "-28.8274" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0413" Parameter: C <- "-43.0413" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6636 TOTAL ENERGY = -71.8687 RDTITL> * VAN DER WAALS = -28.8274 ELECTROSTATIC = -43.0413 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6636" Parameter: CONF_N -> "8002" Comparing "6636" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6637" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756248 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759214 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29969 from a total of 759214 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6637 -71.81917 -0.04953 0.79078 INTE EXTERN> -28.01148 -43.80769 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8192" Parameter: A <- "-71.8192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0115" Parameter: B <- "-28.0115" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8077" Parameter: C <- "-43.8077" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6637 TOTAL ENERGY = -71.8192 RDTITL> * VAN DER WAALS = -28.0115 ELECTROSTATIC = -43.8077 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6637" Parameter: CONF_N -> "8002" Comparing "6637" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6638" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759214 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758671 ATOM PAIRS WERE FOUND FOR ATOM LIST 41649 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30162 from a total of 758671 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6638 -76.71554 4.89637 0.78324 INTE EXTERN> -25.56072 -51.15482 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7155" Parameter: A <- "-76.7155" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5607" Parameter: B <- "-25.5607" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1548" Parameter: C <- "-51.1548" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6638 TOTAL ENERGY = -76.7155 RDTITL> * VAN DER WAALS = -25.5607 ELECTROSTATIC = -51.1548 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6638" Parameter: CONF_N -> "8002" Comparing "6638" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6639" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758671 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759397 ATOM PAIRS WERE FOUND FOR ATOM LIST 41750 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29486 from a total of 759397 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6639 -75.32795 -1.38759 0.59333 INTE EXTERN> -31.88914 -43.43881 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.328" Parameter: A <- "-75.328" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8891" Parameter: B <- "-31.8891" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4388" Parameter: C <- "-43.4388" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6639 TOTAL ENERGY = -75.328 RDTITL> * VAN DER WAALS = -31.8891 ELECTROSTATIC = -43.4388 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6639" Parameter: CONF_N -> "8002" Comparing "6639" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6640" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759397 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760332 ATOM PAIRS WERE FOUND FOR ATOM LIST 41862 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30047 from a total of 760332 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6640 -83.71523 8.38728 0.63058 INTE EXTERN> -30.94255 -52.77268 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.7152" Parameter: A <- "-83.7152" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9425" Parameter: B <- "-30.9425" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.7727" Parameter: C <- "-52.7727" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6640 TOTAL ENERGY = -83.7152 RDTITL> * VAN DER WAALS = -30.9425 ELECTROSTATIC = -52.7727 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6640" Parameter: CONF_N -> "8002" Comparing "6640" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6641" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760332 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764796 ATOM PAIRS WERE FOUND FOR ATOM LIST 42133 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30222 from a total of 764796 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6641 -78.42624 -5.28899 0.65430 INTE EXTERN> -32.76059 -45.66565 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4262" Parameter: A <- "-78.4262" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7606" Parameter: B <- "-32.7606" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6656" Parameter: C <- "-45.6656" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6641 TOTAL ENERGY = -78.4262 RDTITL> * VAN DER WAALS = -32.7606 ELECTROSTATIC = -45.6656 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6641" Parameter: CONF_N -> "8002" Comparing "6641" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6642" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764796 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758636 ATOM PAIRS WERE FOUND FOR ATOM LIST 41527 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30349 from a total of 758636 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6642 -80.09575 1.66952 0.66601 INTE EXTERN> -29.87425 -50.22151 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0958" Parameter: A <- "-80.0958" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8742" Parameter: B <- "-29.8742" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2215" Parameter: C <- "-50.2215" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6642 TOTAL ENERGY = -80.0958 RDTITL> * VAN DER WAALS = -29.8742 ELECTROSTATIC = -50.2215 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6642" Parameter: CONF_N -> "8002" Comparing "6642" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6643" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758636 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759173 ATOM PAIRS WERE FOUND FOR ATOM LIST 41642 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30070 from a total of 759173 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6643 -79.16977 -0.92598 0.61057 INTE EXTERN> -35.17781 -43.99196 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1698" Parameter: A <- "-79.1698" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-35.1778" Parameter: B <- "-35.1778" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.992" Parameter: C <- "-43.992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6643 TOTAL ENERGY = -79.1698 RDTITL> * VAN DER WAALS = -35.1778 ELECTROSTATIC = -43.992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6643" Parameter: CONF_N -> "8002" Comparing "6643" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6644" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759173 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755927 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29682 from a total of 755927 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6644 -74.02901 -5.14076 0.62275 INTE EXTERN> -31.73992 -42.28908 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.029" Parameter: A <- "-74.029" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7399" Parameter: B <- "-31.7399" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2891" Parameter: C <- "-42.2891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6644 TOTAL ENERGY = -74.029 RDTITL> * VAN DER WAALS = -31.7399 ELECTROSTATIC = -42.2891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6644" Parameter: CONF_N -> "8002" Comparing "6644" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6645" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755927 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751726 ATOM PAIRS WERE FOUND FOR ATOM LIST 41214 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30280 from a total of 751726 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6645 -73.72535 -0.30365 0.73134 INTE EXTERN> -28.83217 -44.89318 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7254" Parameter: A <- "-73.7254" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8322" Parameter: B <- "-28.8322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8932" Parameter: C <- "-44.8932" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6645 TOTAL ENERGY = -73.7254 RDTITL> * VAN DER WAALS = -28.8322 ELECTROSTATIC = -44.8932 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6645" Parameter: CONF_N -> "8002" Comparing "6645" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6646" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751726 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752303 ATOM PAIRS WERE FOUND FOR ATOM LIST 41246 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29893 from a total of 752303 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6646 -72.59087 -1.13448 0.65562 INTE EXTERN> -31.92729 -40.66358 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5909" Parameter: A <- "-72.5909" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9273" Parameter: B <- "-31.9273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6636" Parameter: C <- "-40.6636" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6646 TOTAL ENERGY = -72.5909 RDTITL> * VAN DER WAALS = -31.9273 ELECTROSTATIC = -40.6636 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6646" Parameter: CONF_N -> "8002" Comparing "6646" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6647" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752303 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756851 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30063 from a total of 756851 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6647 -77.04348 4.45261 0.63430 INTE EXTERN> -31.52147 -45.52201 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0435" Parameter: A <- "-77.0435" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5215" Parameter: B <- "-31.5215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.522" Parameter: C <- "-45.522" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6647 TOTAL ENERGY = -77.0435 RDTITL> * VAN DER WAALS = -31.5215 ELECTROSTATIC = -45.522 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6647" Parameter: CONF_N -> "8002" Comparing "6647" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6648" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756851 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752420 ATOM PAIRS WERE FOUND FOR ATOM LIST 41535 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29969 from a total of 752420 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6648 -69.23493 -7.80855 0.68442 INTE EXTERN> -23.79397 -45.44096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.2349" Parameter: A <- "-69.2349" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.794" Parameter: B <- "-23.794" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.441" Parameter: C <- "-45.441" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6648 TOTAL ENERGY = -69.2349 RDTITL> * VAN DER WAALS = -23.794 ELECTROSTATIC = -45.441 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6648" Parameter: CONF_N -> "8002" Comparing "6648" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6649" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752420 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753638 ATOM PAIRS WERE FOUND FOR ATOM LIST 41524 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29444 from a total of 753638 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6649 -79.18307 9.94814 0.60123 INTE EXTERN> -33.49999 -45.68308 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1831" Parameter: A <- "-79.1831" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5" Parameter: B <- "-33.5" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6831" Parameter: C <- "-45.6831" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6649 TOTAL ENERGY = -79.1831 RDTITL> * VAN DER WAALS = -33.5 ELECTROSTATIC = -45.6831 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6649" Parameter: CONF_N -> "8002" Comparing "6649" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6650" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753638 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759112 ATOM PAIRS WERE FOUND FOR ATOM LIST 41690 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30025 from a total of 759112 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6650 -71.64892 -7.53415 0.67084 INTE EXTERN> -29.42664 -42.22228 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6489" Parameter: A <- "-71.6489" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4266" Parameter: B <- "-29.4266" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2223" Parameter: C <- "-42.2223" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6650 TOTAL ENERGY = -71.6489 RDTITL> * VAN DER WAALS = -29.4266 ELECTROSTATIC = -42.2223 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6650" Parameter: CONF_N -> "8002" Comparing "6650" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6651" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759112 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758031 ATOM PAIRS WERE FOUND FOR ATOM LIST 41718 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30057 from a total of 758031 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6651 -78.30627 6.65735 0.61620 INTE EXTERN> -31.22143 -47.08485 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3063" Parameter: A <- "-78.3063" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2214" Parameter: B <- "-31.2214" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0848" Parameter: C <- "-47.0848" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6651 TOTAL ENERGY = -78.3063 RDTITL> * VAN DER WAALS = -31.2214 ELECTROSTATIC = -47.0848 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6651" Parameter: CONF_N -> "8002" Comparing "6651" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6652" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758031 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753587 ATOM PAIRS WERE FOUND FOR ATOM LIST 41307 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29271 from a total of 753587 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6652 -70.36855 -7.93772 0.62782 INTE EXTERN> -30.22708 -40.14147 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3686" Parameter: A <- "-70.3686" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2271" Parameter: B <- "-30.2271" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1415" Parameter: C <- "-40.1415" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6652 TOTAL ENERGY = -70.3686 RDTITL> * VAN DER WAALS = -30.2271 ELECTROSTATIC = -40.1415 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6652" Parameter: CONF_N -> "8002" Comparing "6652" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6653" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753587 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750893 ATOM PAIRS WERE FOUND FOR ATOM LIST 41400 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29373 from a total of 750893 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6653 -72.34574 1.97719 0.62054 INTE EXTERN> -28.68711 -43.65864 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3457" Parameter: A <- "-72.3457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6871" Parameter: B <- "-28.6871" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6586" Parameter: C <- "-43.6586" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6653 TOTAL ENERGY = -72.3457 RDTITL> * VAN DER WAALS = -28.6871 ELECTROSTATIC = -43.6586 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6653" Parameter: CONF_N -> "8002" Comparing "6653" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6654" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750893 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755581 ATOM PAIRS WERE FOUND FOR ATOM LIST 41608 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29628 from a total of 755581 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6654 -78.95356 6.60782 0.68494 INTE EXTERN> -29.21338 -49.74018 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9536" Parameter: A <- "-78.9536" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2134" Parameter: B <- "-29.2134" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7402" Parameter: C <- "-49.7402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6654 TOTAL ENERGY = -78.9536 RDTITL> * VAN DER WAALS = -29.2134 ELECTROSTATIC = -49.7402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6654" Parameter: CONF_N -> "8002" Comparing "6654" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6655" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755581 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754637 ATOM PAIRS WERE FOUND FOR ATOM LIST 41265 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29817 from a total of 754637 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6655 -81.88100 2.92744 0.83257 INTE EXTERN> -22.18326 -59.69774 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.881" Parameter: A <- "-81.881" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.1833" Parameter: B <- "-22.1833" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.6977" Parameter: C <- "-59.6977" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6655 TOTAL ENERGY = -81.881 RDTITL> * VAN DER WAALS = -22.1833 ELECTROSTATIC = -59.6977 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6655" Parameter: CONF_N -> "8002" Comparing "6655" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6656" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754637 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755747 ATOM PAIRS WERE FOUND FOR ATOM LIST 41504 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30092 from a total of 755747 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6656 -74.15459 -7.72640 0.63524 INTE EXTERN> -29.20768 -44.94691 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1546" Parameter: A <- "-74.1546" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2077" Parameter: B <- "-29.2077" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9469" Parameter: C <- "-44.9469" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6656 TOTAL ENERGY = -74.1546 RDTITL> * VAN DER WAALS = -29.2077 ELECTROSTATIC = -44.9469 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6656" Parameter: CONF_N -> "8002" Comparing "6656" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6657" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755747 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759307 ATOM PAIRS WERE FOUND FOR ATOM LIST 41742 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29933 from a total of 759307 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6657 -78.76487 4.61028 0.69170 INTE EXTERN> -31.50421 -47.26066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7649" Parameter: A <- "-78.7649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5042" Parameter: B <- "-31.5042" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2607" Parameter: C <- "-47.2607" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6657 TOTAL ENERGY = -78.7649 RDTITL> * VAN DER WAALS = -31.5042 ELECTROSTATIC = -47.2607 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6657" Parameter: CONF_N -> "8002" Comparing "6657" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6658" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759307 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754328 ATOM PAIRS WERE FOUND FOR ATOM LIST 41513 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29836 from a total of 754328 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6658 -80.62639 1.86152 0.71046 INTE EXTERN> -29.52284 -51.10355 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6264" Parameter: A <- "-80.6264" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5228" Parameter: B <- "-29.5228" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1036" Parameter: C <- "-51.1036" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6658 TOTAL ENERGY = -80.6264 RDTITL> * VAN DER WAALS = -29.5228 ELECTROSTATIC = -51.1036 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6658" Parameter: CONF_N -> "8002" Comparing "6658" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6659" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754328 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758722 ATOM PAIRS WERE FOUND FOR ATOM LIST 41733 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29571 from a total of 758722 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6659 -76.00696 -4.61943 0.68534 INTE EXTERN> -29.05497 -46.95198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.007" Parameter: A <- "-76.007" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.055" Parameter: B <- "-29.055" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.952" Parameter: C <- "-46.952" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6659 TOTAL ENERGY = -76.007 RDTITL> * VAN DER WAALS = -29.055 ELECTROSTATIC = -46.952 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6659" Parameter: CONF_N -> "8002" Comparing "6659" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6660" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758722 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759317 ATOM PAIRS WERE FOUND FOR ATOM LIST 41801 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30169 from a total of 759317 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6660 -72.23793 -3.76903 0.77994 INTE EXTERN> -26.13494 -46.10299 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2379" Parameter: A <- "-72.2379" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1349" Parameter: B <- "-26.1349" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.103" Parameter: C <- "-46.103" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6660 TOTAL ENERGY = -72.2379 RDTITL> * VAN DER WAALS = -26.1349 ELECTROSTATIC = -46.103 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6660" Parameter: CONF_N -> "8002" Comparing "6660" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6661" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759317 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762626 ATOM PAIRS WERE FOUND FOR ATOM LIST 41757 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30177 from a total of 762626 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6661 -76.25128 4.01335 0.67611 INTE EXTERN> -31.54976 -44.70152 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2513" Parameter: A <- "-76.2513" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5498" Parameter: B <- "-31.5498" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7015" Parameter: C <- "-44.7015" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6661 TOTAL ENERGY = -76.2513 RDTITL> * VAN DER WAALS = -31.5498 ELECTROSTATIC = -44.7015 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6661" Parameter: CONF_N -> "8002" Comparing "6661" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6662" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762626 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753989 ATOM PAIRS WERE FOUND FOR ATOM LIST 41298 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29804 from a total of 753989 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6662 -74.54790 -1.70338 0.65876 INTE EXTERN> -31.47493 -43.07297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5479" Parameter: A <- "-74.5479" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4749" Parameter: B <- "-31.4749" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.073" Parameter: C <- "-43.073" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6662 TOTAL ENERGY = -74.5479 RDTITL> * VAN DER WAALS = -31.4749 ELECTROSTATIC = -43.073 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6662" Parameter: CONF_N -> "8002" Comparing "6662" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6663" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753989 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749452 ATOM PAIRS WERE FOUND FOR ATOM LIST 41057 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29762 from a total of 749452 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6663 -78.37990 3.83200 0.68765 INTE EXTERN> -30.05063 -48.32927 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3799" Parameter: A <- "-78.3799" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0506" Parameter: B <- "-30.0506" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3293" Parameter: C <- "-48.3293" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6663 TOTAL ENERGY = -78.3799 RDTITL> * VAN DER WAALS = -30.0506 ELECTROSTATIC = -48.3293 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6663" Parameter: CONF_N -> "8002" Comparing "6663" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6664" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749452 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756476 ATOM PAIRS WERE FOUND FOR ATOM LIST 41632 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30490 from a total of 756476 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6664 -75.96041 -2.41949 0.68416 INTE EXTERN> -30.98918 -44.97123 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9604" Parameter: A <- "-75.9604" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9892" Parameter: B <- "-30.9892" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9712" Parameter: C <- "-44.9712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6664 TOTAL ENERGY = -75.9604 RDTITL> * VAN DER WAALS = -30.9892 ELECTROSTATIC = -44.9712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6664" Parameter: CONF_N -> "8002" Comparing "6664" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6665" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756476 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755349 ATOM PAIRS WERE FOUND FOR ATOM LIST 41502 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30003 from a total of 755349 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6665 -77.12578 1.16537 0.69050 INTE EXTERN> -28.06251 -49.06328 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1258" Parameter: A <- "-77.1258" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0625" Parameter: B <- "-28.0625" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0633" Parameter: C <- "-49.0633" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6665 TOTAL ENERGY = -77.1258 RDTITL> * VAN DER WAALS = -28.0625 ELECTROSTATIC = -49.0633 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6665" Parameter: CONF_N -> "8002" Comparing "6665" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6666" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755349 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752808 ATOM PAIRS WERE FOUND FOR ATOM LIST 41301 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29874 from a total of 752808 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6666 -75.20342 -1.92236 0.69031 INTE EXTERN> -31.61916 -43.58426 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2034" Parameter: A <- "-75.2034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6192" Parameter: B <- "-31.6192" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5843" Parameter: C <- "-43.5843" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6666 TOTAL ENERGY = -75.2034 RDTITL> * VAN DER WAALS = -31.6192 ELECTROSTATIC = -43.5843 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6666" Parameter: CONF_N -> "8002" Comparing "6666" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6667" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752808 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754477 ATOM PAIRS WERE FOUND FOR ATOM LIST 41591 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30007 from a total of 754477 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6667 -75.80445 0.60102 0.67482 INTE EXTERN> -29.29779 -46.50666 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8044" Parameter: A <- "-75.8044" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2978" Parameter: B <- "-29.2978" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5067" Parameter: C <- "-46.5067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6667 TOTAL ENERGY = -75.8044 RDTITL> * VAN DER WAALS = -29.2978 ELECTROSTATIC = -46.5067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6667" Parameter: CONF_N -> "8002" Comparing "6667" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6668" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754477 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749833 ATOM PAIRS WERE FOUND FOR ATOM LIST 41140 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29594 from a total of 749833 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6668 -77.41047 1.60602 0.72202 INTE EXTERN> -28.63905 -48.77142 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4105" Parameter: A <- "-77.4105" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6391" Parameter: B <- "-28.6391" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7714" Parameter: C <- "-48.7714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6668 TOTAL ENERGY = -77.4105 RDTITL> * VAN DER WAALS = -28.6391 ELECTROSTATIC = -48.7714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6668" Parameter: CONF_N -> "8002" Comparing "6668" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6669" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749833 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752731 ATOM PAIRS WERE FOUND FOR ATOM LIST 41108 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29422 from a total of 752731 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6669 -74.40675 -3.00372 0.81081 INTE EXTERN> -26.60536 -47.80139 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4068" Parameter: A <- "-74.4068" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6054" Parameter: B <- "-26.6054" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8014" Parameter: C <- "-47.8014" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6669 TOTAL ENERGY = -74.4068 RDTITL> * VAN DER WAALS = -26.6054 ELECTROSTATIC = -47.8014 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6669" Parameter: CONF_N -> "8002" Comparing "6669" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6670" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752731 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755848 ATOM PAIRS WERE FOUND FOR ATOM LIST 41544 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29631 from a total of 755848 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6670 -82.27961 7.87286 0.75728 INTE EXTERN> -28.01279 -54.26682 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.2796" Parameter: A <- "-82.2796" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0128" Parameter: B <- "-28.0128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2668" Parameter: C <- "-54.2668" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6670 TOTAL ENERGY = -82.2796 RDTITL> * VAN DER WAALS = -28.0128 ELECTROSTATIC = -54.2668 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6670" Parameter: CONF_N -> "8002" Comparing "6670" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6671" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755848 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 766260 ATOM PAIRS WERE FOUND FOR ATOM LIST 41969 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29964 from a total of 766260 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6671 -66.40664 -15.87297 0.87194 INTE EXTERN> -24.38553 -42.02111 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4066" Parameter: A <- "-66.4066" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3855" Parameter: B <- "-24.3855" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0211" Parameter: C <- "-42.0211" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6671 TOTAL ENERGY = -66.4066 RDTITL> * VAN DER WAALS = -24.3855 ELECTROSTATIC = -42.0211 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6671" Parameter: CONF_N -> "8002" Comparing "6671" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6672" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 766260 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753862 ATOM PAIRS WERE FOUND FOR ATOM LIST 41357 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29733 from a total of 753862 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6672 -75.82234 9.41570 0.69526 INTE EXTERN> -27.33315 -48.48920 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8223" Parameter: A <- "-75.8223" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3331" Parameter: B <- "-27.3331" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4892" Parameter: C <- "-48.4892" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6672 TOTAL ENERGY = -75.8223 RDTITL> * VAN DER WAALS = -27.3331 ELECTROSTATIC = -48.4892 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6672" Parameter: CONF_N -> "8002" Comparing "6672" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6673" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753862 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751427 ATOM PAIRS WERE FOUND FOR ATOM LIST 41199 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29667 from a total of 751427 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6673 -75.12684 -0.69550 0.66969 INTE EXTERN> -29.97406 -45.15278 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1268" Parameter: A <- "-75.1268" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9741" Parameter: B <- "-29.9741" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1528" Parameter: C <- "-45.1528" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6673 TOTAL ENERGY = -75.1268 RDTITL> * VAN DER WAALS = -29.9741 ELECTROSTATIC = -45.1528 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6673" Parameter: CONF_N -> "8002" Comparing "6673" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6674" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751427 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746563 ATOM PAIRS WERE FOUND FOR ATOM LIST 41261 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28916 from a total of 746563 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6674 -71.16415 -3.96269 0.65686 INTE EXTERN> -29.60112 -41.56303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1642" Parameter: A <- "-71.1642" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6011" Parameter: B <- "-29.6011" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.563" Parameter: C <- "-41.563" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6674 TOTAL ENERGY = -71.1642 RDTITL> * VAN DER WAALS = -29.6011 ELECTROSTATIC = -41.563 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6674" Parameter: CONF_N -> "8002" Comparing "6674" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6675" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746563 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753753 ATOM PAIRS WERE FOUND FOR ATOM LIST 41276 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29607 from a total of 753753 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6675 -77.63130 6.46715 0.73941 INTE EXTERN> -30.34992 -47.28138 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6313" Parameter: A <- "-77.6313" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3499" Parameter: B <- "-30.3499" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2814" Parameter: C <- "-47.2814" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6675 TOTAL ENERGY = -77.6313 RDTITL> * VAN DER WAALS = -30.3499 ELECTROSTATIC = -47.2814 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6675" Parameter: CONF_N -> "8002" Comparing "6675" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6676" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753753 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756304 ATOM PAIRS WERE FOUND FOR ATOM LIST 41389 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29663 from a total of 756304 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6676 -69.79284 -7.83846 0.70452 INTE EXTERN> -25.91518 -43.87766 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7928" Parameter: A <- "-69.7928" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9152" Parameter: B <- "-25.9152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8777" Parameter: C <- "-43.8777" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6676 TOTAL ENERGY = -69.7928 RDTITL> * VAN DER WAALS = -25.9152 ELECTROSTATIC = -43.8777 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6676" Parameter: CONF_N -> "8002" Comparing "6676" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6677" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756304 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752481 ATOM PAIRS WERE FOUND FOR ATOM LIST 41524 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29602 from a total of 752481 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6677 -77.14998 7.35714 0.62803 INTE EXTERN> -30.98670 -46.16328 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.15" Parameter: A <- "-77.15" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9867" Parameter: B <- "-30.9867" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1633" Parameter: C <- "-46.1633" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6677 TOTAL ENERGY = -77.15 RDTITL> * VAN DER WAALS = -30.9867 ELECTROSTATIC = -46.1633 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6677" Parameter: CONF_N -> "8002" Comparing "6677" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6678" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752481 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752529 ATOM PAIRS WERE FOUND FOR ATOM LIST 41244 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29918 from a total of 752529 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6678 -78.57672 1.42674 0.68449 INTE EXTERN> -30.68446 -47.89226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5767" Parameter: A <- "-78.5767" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6845" Parameter: B <- "-30.6845" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8923" Parameter: C <- "-47.8923" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6678 TOTAL ENERGY = -78.5767 RDTITL> * VAN DER WAALS = -30.6845 ELECTROSTATIC = -47.8923 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6678" Parameter: CONF_N -> "8002" Comparing "6678" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6679" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752529 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749777 ATOM PAIRS WERE FOUND FOR ATOM LIST 41322 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29846 from a total of 749777 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6679 -69.80366 -8.77306 0.69974 INTE EXTERN> -26.67136 -43.13230 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8037" Parameter: A <- "-69.8037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6714" Parameter: B <- "-26.6714" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1323" Parameter: C <- "-43.1323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6679 TOTAL ENERGY = -69.8037 RDTITL> * VAN DER WAALS = -26.6714 ELECTROSTATIC = -43.1323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6679" Parameter: CONF_N -> "8002" Comparing "6679" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6680" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749777 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751683 ATOM PAIRS WERE FOUND FOR ATOM LIST 41314 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30026 from a total of 751683 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6680 -71.90460 2.10094 0.70366 INTE EXTERN> -28.34978 -43.55482 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9046" Parameter: A <- "-71.9046" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3498" Parameter: B <- "-28.3498" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5548" Parameter: C <- "-43.5548" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6680 TOTAL ENERGY = -71.9046 RDTITL> * VAN DER WAALS = -28.3498 ELECTROSTATIC = -43.5548 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6680" Parameter: CONF_N -> "8002" Comparing "6680" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6681" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751683 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748034 ATOM PAIRS WERE FOUND FOR ATOM LIST 41117 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30397 from a total of 748034 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6681 -73.27407 1.36947 0.69061 INTE EXTERN> -31.76259 -41.51148 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2741" Parameter: A <- "-73.2741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7626" Parameter: B <- "-31.7626" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5115" Parameter: C <- "-41.5115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6681 TOTAL ENERGY = -73.2741 RDTITL> * VAN DER WAALS = -31.7626 ELECTROSTATIC = -41.5115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6681" Parameter: CONF_N -> "8002" Comparing "6681" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6682" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748034 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751062 ATOM PAIRS WERE FOUND FOR ATOM LIST 41318 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30567 from a total of 751062 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6682 -74.28799 1.01392 0.67576 INTE EXTERN> -29.39626 -44.89173 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.288" Parameter: A <- "-74.288" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3963" Parameter: B <- "-29.3963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8917" Parameter: C <- "-44.8917" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6682 TOTAL ENERGY = -74.288 RDTITL> * VAN DER WAALS = -29.3963 ELECTROSTATIC = -44.8917 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6682" Parameter: CONF_N -> "8002" Comparing "6682" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6683" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751062 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751491 ATOM PAIRS WERE FOUND FOR ATOM LIST 41359 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29841 from a total of 751491 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6683 -63.08603 -11.20195 0.62857 INTE EXTERN> -30.29131 -32.79472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.086" Parameter: A <- "-63.086" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2913" Parameter: B <- "-30.2913" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.7947" Parameter: C <- "-32.7947" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6683 TOTAL ENERGY = -63.086 RDTITL> * VAN DER WAALS = -30.2913 ELECTROSTATIC = -32.7947 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6683" Parameter: CONF_N -> "8002" Comparing "6683" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6684" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751491 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752647 ATOM PAIRS WERE FOUND FOR ATOM LIST 41573 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30237 from a total of 752647 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6684 -68.30463 5.21860 0.89069 INTE EXTERN> -20.23601 -48.06862 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3046" Parameter: A <- "-68.3046" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.236" Parameter: B <- "-20.236" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0686" Parameter: C <- "-48.0686" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6684 TOTAL ENERGY = -68.3046 RDTITL> * VAN DER WAALS = -20.236 ELECTROSTATIC = -48.0686 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6684" Parameter: CONF_N -> "8002" Comparing "6684" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6685" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752647 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754731 ATOM PAIRS WERE FOUND FOR ATOM LIST 41355 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30153 from a total of 754731 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6685 -68.04540 -0.25923 0.63108 INTE EXTERN> -31.07270 -36.97270 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0454" Parameter: A <- "-68.0454" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0727" Parameter: B <- "-31.0727" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9727" Parameter: C <- "-36.9727" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6685 TOTAL ENERGY = -68.0454 RDTITL> * VAN DER WAALS = -31.0727 ELECTROSTATIC = -36.9727 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6685" Parameter: CONF_N -> "8002" Comparing "6685" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6686" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754731 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759764 ATOM PAIRS WERE FOUND FOR ATOM LIST 41674 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30401 from a total of 759764 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6686 -79.99370 11.94831 0.67935 INTE EXTERN> -30.29275 -49.70095 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9937" Parameter: A <- "-79.9937" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2928" Parameter: B <- "-30.2928" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7009" Parameter: C <- "-49.7009" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6686 TOTAL ENERGY = -79.9937 RDTITL> * VAN DER WAALS = -30.2928 ELECTROSTATIC = -49.7009 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6686" Parameter: CONF_N -> "8002" Comparing "6686" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6687" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759764 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753736 ATOM PAIRS WERE FOUND FOR ATOM LIST 41436 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30245 from a total of 753736 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6687 -75.26512 -4.72858 0.73978 INTE EXTERN> -26.03933 -49.22579 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2651" Parameter: A <- "-75.2651" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0393" Parameter: B <- "-26.0393" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2258" Parameter: C <- "-49.2258" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6687 TOTAL ENERGY = -75.2651 RDTITL> * VAN DER WAALS = -26.0393 ELECTROSTATIC = -49.2258 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6687" Parameter: CONF_N -> "8002" Comparing "6687" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6688" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753736 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751591 ATOM PAIRS WERE FOUND FOR ATOM LIST 41353 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29578 from a total of 751591 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6688 -72.99869 -2.26644 0.87105 INTE EXTERN> -25.44757 -47.55111 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9987" Parameter: A <- "-72.9987" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4476" Parameter: B <- "-25.4476" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5511" Parameter: C <- "-47.5511" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6688 TOTAL ENERGY = -72.9987 RDTITL> * VAN DER WAALS = -25.4476 ELECTROSTATIC = -47.5511 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6688" Parameter: CONF_N -> "8002" Comparing "6688" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6689" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751591 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757343 ATOM PAIRS WERE FOUND FOR ATOM LIST 41614 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30438 from a total of 757343 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6689 -69.77882 -3.21987 0.72244 INTE EXTERN> -22.96666 -46.81215 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7788" Parameter: A <- "-69.7788" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.9667" Parameter: B <- "-22.9667" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8122" Parameter: C <- "-46.8122" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6689 TOTAL ENERGY = -69.7788 RDTITL> * VAN DER WAALS = -22.9667 ELECTROSTATIC = -46.8122 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6689" Parameter: CONF_N -> "8002" Comparing "6689" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6690" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757343 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755862 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29988 from a total of 755862 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6690 -64.96364 -4.81517 0.67022 INTE EXTERN> -24.89608 -40.06756 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9636" Parameter: A <- "-64.9636" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8961" Parameter: B <- "-24.8961" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0676" Parameter: C <- "-40.0676" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6690 TOTAL ENERGY = -64.9636 RDTITL> * VAN DER WAALS = -24.8961 ELECTROSTATIC = -40.0676 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6690" Parameter: CONF_N -> "8002" Comparing "6690" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6691" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755862 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754713 ATOM PAIRS WERE FOUND FOR ATOM LIST 41555 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29746 from a total of 754713 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6691 -62.94621 -2.01743 0.56776 INTE EXTERN> -30.68122 -32.26499 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9462" Parameter: A <- "-62.9462" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6812" Parameter: B <- "-30.6812" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.265" Parameter: C <- "-32.265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6691 TOTAL ENERGY = -62.9462 RDTITL> * VAN DER WAALS = -30.6812 ELECTROSTATIC = -32.265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6691" Parameter: CONF_N -> "8002" Comparing "6691" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6692" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754713 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755092 ATOM PAIRS WERE FOUND FOR ATOM LIST 41484 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29859 from a total of 755092 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6692 -62.30161 -0.64459 0.69066 INTE EXTERN> -27.87828 -34.42333 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.3016" Parameter: A <- "-62.3016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8783" Parameter: B <- "-27.8783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.4233" Parameter: C <- "-34.4233" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6692 TOTAL ENERGY = -62.3016 RDTITL> * VAN DER WAALS = -27.8783 ELECTROSTATIC = -34.4233 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6692" Parameter: CONF_N -> "8002" Comparing "6692" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6693" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755092 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759000 ATOM PAIRS WERE FOUND FOR ATOM LIST 41652 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29951 from a total of 759000 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6693 -77.25992 14.95830 0.65522 INTE EXTERN> -31.15546 -46.10446 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2599" Parameter: A <- "-77.2599" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1555" Parameter: B <- "-31.1555" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1045" Parameter: C <- "-46.1045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6693 TOTAL ENERGY = -77.2599 RDTITL> * VAN DER WAALS = -31.1555 ELECTROSTATIC = -46.1045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6693" Parameter: CONF_N -> "8002" Comparing "6693" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6694" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759000 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757609 ATOM PAIRS WERE FOUND FOR ATOM LIST 41907 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30500 from a total of 757609 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6694 -74.06966 -3.19026 0.74764 INTE EXTERN> -28.06720 -46.00246 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0697" Parameter: A <- "-74.0697" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0672" Parameter: B <- "-28.0672" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0025" Parameter: C <- "-46.0025" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6694 TOTAL ENERGY = -74.0697 RDTITL> * VAN DER WAALS = -28.0672 ELECTROSTATIC = -46.0025 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6694" Parameter: CONF_N -> "8002" Comparing "6694" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6695" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757609 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756777 ATOM PAIRS WERE FOUND FOR ATOM LIST 41806 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30411 from a total of 756777 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6695 -74.48842 0.41876 0.73085 INTE EXTERN> -30.68972 -43.79869 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4884" Parameter: A <- "-74.4884" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6897" Parameter: B <- "-30.6897" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7987" Parameter: C <- "-43.7987" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6695 TOTAL ENERGY = -74.4884 RDTITL> * VAN DER WAALS = -30.6897 ELECTROSTATIC = -43.7987 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6695" Parameter: CONF_N -> "8002" Comparing "6695" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6696" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756777 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756413 ATOM PAIRS WERE FOUND FOR ATOM LIST 41647 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30153 from a total of 756413 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6696 -72.57400 -1.91441 0.64417 INTE EXTERN> -26.76703 -45.80698 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.574" Parameter: A <- "-72.574" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.767" Parameter: B <- "-26.767" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.807" Parameter: C <- "-45.807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6696 TOTAL ENERGY = -72.574 RDTITL> * VAN DER WAALS = -26.767 ELECTROSTATIC = -45.807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6696" Parameter: CONF_N -> "8002" Comparing "6696" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6697" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756413 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761063 ATOM PAIRS WERE FOUND FOR ATOM LIST 41982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30579 from a total of 761063 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6697 -77.90945 5.33544 0.61323 INTE EXTERN> -31.94649 -45.96296 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9094" Parameter: A <- "-77.9094" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9465" Parameter: B <- "-31.9465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.963" Parameter: C <- "-45.963" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6697 TOTAL ENERGY = -77.9094 RDTITL> * VAN DER WAALS = -31.9465 ELECTROSTATIC = -45.963 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6697" Parameter: CONF_N -> "8002" Comparing "6697" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6698" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761063 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757435 ATOM PAIRS WERE FOUND FOR ATOM LIST 41614 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29851 from a total of 757435 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6698 -78.63578 0.72634 0.70974 INTE EXTERN> -26.92419 -51.71160 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6358" Parameter: A <- "-78.6358" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9242" Parameter: B <- "-26.9242" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7116" Parameter: C <- "-51.7116" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6698 TOTAL ENERGY = -78.6358 RDTITL> * VAN DER WAALS = -26.9242 ELECTROSTATIC = -51.7116 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6698" Parameter: CONF_N -> "8002" Comparing "6698" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6699" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757435 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754474 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29732 from a total of 754474 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6699 -71.49082 -7.14496 0.66432 INTE EXTERN> -31.75135 -39.73947 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4908" Parameter: A <- "-71.4908" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7514" Parameter: B <- "-31.7514" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7395" Parameter: C <- "-39.7395" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6699 TOTAL ENERGY = -71.4908 RDTITL> * VAN DER WAALS = -31.7514 ELECTROSTATIC = -39.7395 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6699" Parameter: CONF_N -> "8002" Comparing "6699" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6700" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754474 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752153 ATOM PAIRS WERE FOUND FOR ATOM LIST 41302 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29898 from a total of 752153 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6700 -73.32773 1.83691 0.62647 INTE EXTERN> -28.62263 -44.70510 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3277" Parameter: A <- "-73.3277" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6226" Parameter: B <- "-28.6226" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7051" Parameter: C <- "-44.7051" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6700 TOTAL ENERGY = -73.3277 RDTITL> * VAN DER WAALS = -28.6226 ELECTROSTATIC = -44.7051 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6700" Parameter: CONF_N -> "8002" Comparing "6700" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6701" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752153 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753566 ATOM PAIRS WERE FOUND FOR ATOM LIST 41467 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29966 from a total of 753566 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6701 -72.47789 -0.84984 0.60846 INTE EXTERN> -29.84276 -42.63513 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4779" Parameter: A <- "-72.4779" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8428" Parameter: B <- "-29.8428" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6351" Parameter: C <- "-42.6351" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6701 TOTAL ENERGY = -72.4779 RDTITL> * VAN DER WAALS = -29.8428 ELECTROSTATIC = -42.6351 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6701" Parameter: CONF_N -> "8002" Comparing "6701" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6702" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753566 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754198 ATOM PAIRS WERE FOUND FOR ATOM LIST 41499 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29652 from a total of 754198 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6702 -67.75048 -4.72740 0.60874 INTE EXTERN> -29.73531 -38.01518 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7505" Parameter: A <- "-67.7505" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7353" Parameter: B <- "-29.7353" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0152" Parameter: C <- "-38.0152" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6702 TOTAL ENERGY = -67.7505 RDTITL> * VAN DER WAALS = -29.7353 ELECTROSTATIC = -38.0152 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6702" Parameter: CONF_N -> "8002" Comparing "6702" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6703" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754198 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753151 ATOM PAIRS WERE FOUND FOR ATOM LIST 41403 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29500 from a total of 753151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6703 -76.44867 8.69818 0.58913 INTE EXTERN> -29.12650 -47.32216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4487" Parameter: A <- "-76.4487" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1265" Parameter: B <- "-29.1265" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3222" Parameter: C <- "-47.3222" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6703 TOTAL ENERGY = -76.4487 RDTITL> * VAN DER WAALS = -29.1265 ELECTROSTATIC = -47.3222 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6703" Parameter: CONF_N -> "8002" Comparing "6703" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6704" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749740 ATOM PAIRS WERE FOUND FOR ATOM LIST 41287 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29832 from a total of 749740 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6704 -75.86731 -0.58135 0.53346 INTE EXTERN> -32.94409 -42.92322 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8673" Parameter: A <- "-75.8673" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9441" Parameter: B <- "-32.9441" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9232" Parameter: C <- "-42.9232" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6704 TOTAL ENERGY = -75.8673 RDTITL> * VAN DER WAALS = -32.9441 ELECTROSTATIC = -42.9232 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6704" Parameter: CONF_N -> "8002" Comparing "6704" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6705" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749740 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748035 ATOM PAIRS WERE FOUND FOR ATOM LIST 41310 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29231 from a total of 748035 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6705 -72.11194 -3.75537 0.60676 INTE EXTERN> -27.77661 -44.33533 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1119" Parameter: A <- "-72.1119" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7766" Parameter: B <- "-27.7766" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3353" Parameter: C <- "-44.3353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6705 TOTAL ENERGY = -72.1119 RDTITL> * VAN DER WAALS = -27.7766 ELECTROSTATIC = -44.3353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6705" Parameter: CONF_N -> "8002" Comparing "6705" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6706" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748035 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752089 ATOM PAIRS WERE FOUND FOR ATOM LIST 41399 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30023 from a total of 752089 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6706 -78.40946 6.29752 0.91072 INTE EXTERN> -22.88308 -55.52639 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4095" Parameter: A <- "-78.4095" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.8831" Parameter: B <- "-22.8831" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.5264" Parameter: C <- "-55.5264" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6706 TOTAL ENERGY = -78.4095 RDTITL> * VAN DER WAALS = -22.8831 ELECTROSTATIC = -55.5264 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6706" Parameter: CONF_N -> "8002" Comparing "6706" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6707" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752089 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754599 ATOM PAIRS WERE FOUND FOR ATOM LIST 41530 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29427 from a total of 754599 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6707 -76.83100 -1.57846 0.63914 INTE EXTERN> -29.64624 -47.18476 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.831" Parameter: A <- "-76.831" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6462" Parameter: B <- "-29.6462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1848" Parameter: C <- "-47.1848" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6707 TOTAL ENERGY = -76.831 RDTITL> * VAN DER WAALS = -29.6462 ELECTROSTATIC = -47.1848 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6707" Parameter: CONF_N -> "8002" Comparing "6707" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6708" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754599 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753603 ATOM PAIRS WERE FOUND FOR ATOM LIST 41800 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29560 from a total of 753603 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6708 -73.52954 -3.30146 0.68500 INTE EXTERN> -27.45474 -46.07480 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5295" Parameter: A <- "-73.5295" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4547" Parameter: B <- "-27.4547" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0748" Parameter: C <- "-46.0748" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6708 TOTAL ENERGY = -73.5295 RDTITL> * VAN DER WAALS = -27.4547 ELECTROSTATIC = -46.0748 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6708" Parameter: CONF_N -> "8002" Comparing "6708" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6709" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753603 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755141 ATOM PAIRS WERE FOUND FOR ATOM LIST 41548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29663 from a total of 755141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6709 -74.00473 0.47519 0.66013 INTE EXTERN> -29.91509 -44.08964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0047" Parameter: A <- "-74.0047" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9151" Parameter: B <- "-29.9151" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0896" Parameter: C <- "-44.0896" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6709 TOTAL ENERGY = -74.0047 RDTITL> * VAN DER WAALS = -29.9151 ELECTROSTATIC = -44.0896 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6709" Parameter: CONF_N -> "8002" Comparing "6709" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6710" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753533 ATOM PAIRS WERE FOUND FOR ATOM LIST 41481 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29823 from a total of 753533 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6710 -75.06085 1.05612 0.57458 INTE EXTERN> -32.15561 -42.90524 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0608" Parameter: A <- "-75.0608" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1556" Parameter: B <- "-32.1556" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9052" Parameter: C <- "-42.9052" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6710 TOTAL ENERGY = -75.0608 RDTITL> * VAN DER WAALS = -32.1556 ELECTROSTATIC = -42.9052 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6710" Parameter: CONF_N -> "8002" Comparing "6710" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6711" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753533 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755491 ATOM PAIRS WERE FOUND FOR ATOM LIST 41514 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30024 from a total of 755491 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6711 -79.61464 4.55379 0.69119 INTE EXTERN> -28.52909 -51.08555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6146" Parameter: A <- "-79.6146" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5291" Parameter: B <- "-28.5291" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0856" Parameter: C <- "-51.0856" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6711 TOTAL ENERGY = -79.6146 RDTITL> * VAN DER WAALS = -28.5291 ELECTROSTATIC = -51.0856 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6711" Parameter: CONF_N -> "8002" Comparing "6711" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6712" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755491 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752898 ATOM PAIRS WERE FOUND FOR ATOM LIST 41471 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30147 from a total of 752898 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6712 -63.15422 -16.46043 0.51054 INTE EXTERN> -31.20726 -31.94696 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1542" Parameter: A <- "-63.1542" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2073" Parameter: B <- "-31.2073" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.947" Parameter: C <- "-31.947" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6712 TOTAL ENERGY = -63.1542 RDTITL> * VAN DER WAALS = -31.2073 ELECTROSTATIC = -31.947 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6712" Parameter: CONF_N -> "8002" Comparing "6712" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6713" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752898 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752218 ATOM PAIRS WERE FOUND FOR ATOM LIST 41432 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29722 from a total of 752218 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6713 -64.29893 1.14471 0.62550 INTE EXTERN> -27.84936 -36.44957 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2989" Parameter: A <- "-64.2989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8494" Parameter: B <- "-27.8494" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.4496" Parameter: C <- "-36.4496" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6713 TOTAL ENERGY = -64.2989 RDTITL> * VAN DER WAALS = -27.8494 ELECTROSTATIC = -36.4496 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6713" Parameter: CONF_N -> "8002" Comparing "6713" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6714" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752218 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751461 ATOM PAIRS WERE FOUND FOR ATOM LIST 41332 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29770 from a total of 751461 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6714 -68.82313 4.52420 0.62560 INTE EXTERN> -30.00014 -38.82299 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8231" Parameter: A <- "-68.8231" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0001" Parameter: B <- "-30.0001" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.823" Parameter: C <- "-38.823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6714 TOTAL ENERGY = -68.8231 RDTITL> * VAN DER WAALS = -30.0001 ELECTROSTATIC = -38.823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6714" Parameter: CONF_N -> "8002" Comparing "6714" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6715" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751461 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749389 ATOM PAIRS WERE FOUND FOR ATOM LIST 41217 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29520 from a total of 749389 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6715 -65.17346 -3.64966 0.52048 INTE EXTERN> -31.78390 -33.38957 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1735" Parameter: A <- "-65.1735" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7839" Parameter: B <- "-31.7839" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.3896" Parameter: C <- "-33.3896" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6715 TOTAL ENERGY = -65.1735 RDTITL> * VAN DER WAALS = -31.7839 ELECTROSTATIC = -33.3896 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6715" Parameter: CONF_N -> "8002" Comparing "6715" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6716" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749389 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750452 ATOM PAIRS WERE FOUND FOR ATOM LIST 41304 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29108 from a total of 750452 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6716 -67.34045 2.16698 0.66677 INTE EXTERN> -28.78719 -38.55326 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3404" Parameter: A <- "-67.3404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7872" Parameter: B <- "-28.7872" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5533" Parameter: C <- "-38.5533" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6716 TOTAL ENERGY = -67.3404 RDTITL> * VAN DER WAALS = -28.7872 ELECTROSTATIC = -38.5533 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6716" Parameter: CONF_N -> "8002" Comparing "6716" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6717" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750452 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747484 ATOM PAIRS WERE FOUND FOR ATOM LIST 41204 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29217 from a total of 747484 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6717 -71.69384 4.35339 0.60805 INTE EXTERN> -27.55422 -44.13962 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6938" Parameter: A <- "-71.6938" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5542" Parameter: B <- "-27.5542" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1396" Parameter: C <- "-44.1396" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6717 TOTAL ENERGY = -71.6938 RDTITL> * VAN DER WAALS = -27.5542 ELECTROSTATIC = -44.1396 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6717" Parameter: CONF_N -> "8002" Comparing "6717" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6718" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747484 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753415 ATOM PAIRS WERE FOUND FOR ATOM LIST 41467 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29854 from a total of 753415 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6718 -68.94699 -2.74685 0.76776 INTE EXTERN> -25.91339 -43.03360 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.947" Parameter: A <- "-68.947" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9134" Parameter: B <- "-25.9134" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0336" Parameter: C <- "-43.0336" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6718 TOTAL ENERGY = -68.947 RDTITL> * VAN DER WAALS = -25.9134 ELECTROSTATIC = -43.0336 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6718" Parameter: CONF_N -> "8002" Comparing "6718" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6719" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753415 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750273 ATOM PAIRS WERE FOUND FOR ATOM LIST 41452 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29912 from a total of 750273 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6719 -72.67978 3.73279 0.66809 INTE EXTERN> -26.64071 -46.03907 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6798" Parameter: A <- "-72.6798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6407" Parameter: B <- "-26.6407" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0391" Parameter: C <- "-46.0391" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6719 TOTAL ENERGY = -72.6798 RDTITL> * VAN DER WAALS = -26.6407 ELECTROSTATIC = -46.0391 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6719" Parameter: CONF_N -> "8002" Comparing "6719" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6720" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750273 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751034 ATOM PAIRS WERE FOUND FOR ATOM LIST 41325 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29676 from a total of 751034 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6720 -75.44030 2.76052 0.70056 INTE EXTERN> -29.80432 -45.63598 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4403" Parameter: A <- "-75.4403" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8043" Parameter: B <- "-29.8043" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.636" Parameter: C <- "-45.636" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6720 TOTAL ENERGY = -75.4403 RDTITL> * VAN DER WAALS = -29.8043 ELECTROSTATIC = -45.636 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6720" Parameter: CONF_N -> "8002" Comparing "6720" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6721" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751034 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758639 ATOM PAIRS WERE FOUND FOR ATOM LIST 41832 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30653 from a total of 758639 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6721 -72.55415 -2.88615 0.66979 INTE EXTERN> -28.35165 -44.20251 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5542" Parameter: A <- "-72.5542" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3516" Parameter: B <- "-28.3516" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2025" Parameter: C <- "-44.2025" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6721 TOTAL ENERGY = -72.5542 RDTITL> * VAN DER WAALS = -28.3516 ELECTROSTATIC = -44.2025 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6721" Parameter: CONF_N -> "8002" Comparing "6721" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6722" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758639 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758465 ATOM PAIRS WERE FOUND FOR ATOM LIST 41745 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30653 from a total of 758465 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6722 -78.28977 5.73562 0.60041 INTE EXTERN> -30.80967 -47.48010 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2898" Parameter: A <- "-78.2898" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8097" Parameter: B <- "-30.8097" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4801" Parameter: C <- "-47.4801" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6722 TOTAL ENERGY = -78.2898 RDTITL> * VAN DER WAALS = -30.8097 ELECTROSTATIC = -47.4801 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6722" Parameter: CONF_N -> "8002" Comparing "6722" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6723" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758465 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757626 ATOM PAIRS WERE FOUND FOR ATOM LIST 41725 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29896 from a total of 757626 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6723 -81.26655 2.97678 0.64967 INTE EXTERN> -30.88790 -50.37866 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.2666" Parameter: A <- "-81.2666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8879" Parameter: B <- "-30.8879" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3787" Parameter: C <- "-50.3787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6723 TOTAL ENERGY = -81.2666 RDTITL> * VAN DER WAALS = -30.8879 ELECTROSTATIC = -50.3787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6723" Parameter: CONF_N -> "8002" Comparing "6723" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6724" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757626 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755523 ATOM PAIRS WERE FOUND FOR ATOM LIST 41472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30289 from a total of 755523 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6724 -74.98612 -6.28044 0.53880 INTE EXTERN> -33.05455 -41.93157 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9861" Parameter: A <- "-74.9861" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0545" Parameter: B <- "-33.0545" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9316" Parameter: C <- "-41.9316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6724 TOTAL ENERGY = -74.9861 RDTITL> * VAN DER WAALS = -33.0545 ELECTROSTATIC = -41.9316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6724" Parameter: CONF_N -> "8002" Comparing "6724" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6725" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755523 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759328 ATOM PAIRS WERE FOUND FOR ATOM LIST 41635 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30238 from a total of 759328 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6725 -78.62575 3.63963 0.66945 INTE EXTERN> -29.81321 -48.81254 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6257" Parameter: A <- "-78.6257" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8132" Parameter: B <- "-29.8132" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8125" Parameter: C <- "-48.8125" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6725 TOTAL ENERGY = -78.6257 RDTITL> * VAN DER WAALS = -29.8132 ELECTROSTATIC = -48.8125 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6725" Parameter: CONF_N -> "8002" Comparing "6725" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6726" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759328 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754331 ATOM PAIRS WERE FOUND FOR ATOM LIST 41341 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30366 from a total of 754331 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6726 -74.81793 -3.80782 0.55587 INTE EXTERN> -33.79276 -41.02516 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8179" Parameter: A <- "-74.8179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7928" Parameter: B <- "-33.7928" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0252" Parameter: C <- "-41.0252" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6726 TOTAL ENERGY = -74.8179 RDTITL> * VAN DER WAALS = -33.7928 ELECTROSTATIC = -41.0252 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6726" Parameter: CONF_N -> "8002" Comparing "6726" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6727" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754331 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752593 ATOM PAIRS WERE FOUND FOR ATOM LIST 41228 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30377 from a total of 752593 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6727 -77.55520 2.73727 0.56676 INTE EXTERN> -31.67221 -45.88298 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5552" Parameter: A <- "-77.5552" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6722" Parameter: B <- "-31.6722" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.883" Parameter: C <- "-45.883" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6727 TOTAL ENERGY = -77.5552 RDTITL> * VAN DER WAALS = -31.6722 ELECTROSTATIC = -45.883 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6727" Parameter: CONF_N -> "8002" Comparing "6727" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6728" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752593 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754761 ATOM PAIRS WERE FOUND FOR ATOM LIST 41468 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30158 from a total of 754761 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6728 -80.55557 3.00037 0.59558 INTE EXTERN> -31.96539 -48.59018 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5556" Parameter: A <- "-80.5556" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9654" Parameter: B <- "-31.9654" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5902" Parameter: C <- "-48.5902" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6728 TOTAL ENERGY = -80.5556 RDTITL> * VAN DER WAALS = -31.9654 ELECTROSTATIC = -48.5902 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6728" Parameter: CONF_N -> "8002" Comparing "6728" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6729" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754761 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755165 ATOM PAIRS WERE FOUND FOR ATOM LIST 41549 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30232 from a total of 755165 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6729 -76.51622 -4.03935 0.55427 INTE EXTERN> -33.31914 -43.19708 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5162" Parameter: A <- "-76.5162" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3191" Parameter: B <- "-33.3191" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1971" Parameter: C <- "-43.1971" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6729 TOTAL ENERGY = -76.5162 RDTITL> * VAN DER WAALS = -33.3191 ELECTROSTATIC = -43.1971 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6729" Parameter: CONF_N -> "8002" Comparing "6729" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6730" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755165 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751964 ATOM PAIRS WERE FOUND FOR ATOM LIST 41444 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29302 from a total of 751964 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6730 -75.80280 -0.71342 0.65711 INTE EXTERN> -29.48583 -46.31697 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8028" Parameter: A <- "-75.8028" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4858" Parameter: B <- "-29.4858" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.317" Parameter: C <- "-46.317" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6730 TOTAL ENERGY = -75.8028 RDTITL> * VAN DER WAALS = -29.4858 ELECTROSTATIC = -46.317 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6730" Parameter: CONF_N -> "8002" Comparing "6730" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6731" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751964 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754919 ATOM PAIRS WERE FOUND FOR ATOM LIST 41733 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29800 from a total of 754919 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6731 -75.02588 -0.77692 0.66390 INTE EXTERN> -27.07054 -47.95534 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0259" Parameter: A <- "-75.0259" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0705" Parameter: B <- "-27.0705" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9553" Parameter: C <- "-47.9553" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6731 TOTAL ENERGY = -75.0259 RDTITL> * VAN DER WAALS = -27.0705 ELECTROSTATIC = -47.9553 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6731" Parameter: CONF_N -> "8002" Comparing "6731" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6732" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754919 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757454 ATOM PAIRS WERE FOUND FOR ATOM LIST 41646 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30133 from a total of 757454 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6732 -84.60833 9.58245 0.72292 INTE EXTERN> -27.75939 -56.84894 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.6083" Parameter: A <- "-84.6083" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7594" Parameter: B <- "-27.7594" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.8489" Parameter: C <- "-56.8489" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6732 TOTAL ENERGY = -84.6083 RDTITL> * VAN DER WAALS = -27.7594 ELECTROSTATIC = -56.8489 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6732" Parameter: CONF_N -> "8002" Comparing "6732" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6733" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757454 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757615 ATOM PAIRS WERE FOUND FOR ATOM LIST 41666 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29299 from a total of 757615 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6733 -87.29564 2.68731 0.72803 INTE EXTERN> -28.43514 -58.86049 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.2956" Parameter: A <- "-87.2956" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4351" Parameter: B <- "-28.4351" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.8605" Parameter: C <- "-58.8605" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6733 TOTAL ENERGY = -87.2956 RDTITL> * VAN DER WAALS = -28.4351 ELECTROSTATIC = -58.8605 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6733" Parameter: CONF_N -> "8002" Comparing "6733" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6734" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757615 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757465 ATOM PAIRS WERE FOUND FOR ATOM LIST 41497 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29620 from a total of 757465 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6734 -81.01042 -6.28522 0.63984 INTE EXTERN> -30.09502 -50.91539 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.0104" Parameter: A <- "-81.0104" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.095" Parameter: B <- "-30.095" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9154" Parameter: C <- "-50.9154" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6734 TOTAL ENERGY = -81.0104 RDTITL> * VAN DER WAALS = -30.095 ELECTROSTATIC = -50.9154 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6734" Parameter: CONF_N -> "8002" Comparing "6734" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6735" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757465 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750377 ATOM PAIRS WERE FOUND FOR ATOM LIST 41288 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29462 from a total of 750377 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6735 -82.32793 1.31751 0.66462 INTE EXTERN> -30.59256 -51.73537 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3279" Parameter: A <- "-82.3279" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5926" Parameter: B <- "-30.5926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7354" Parameter: C <- "-51.7354" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6735 TOTAL ENERGY = -82.3279 RDTITL> * VAN DER WAALS = -30.5926 ELECTROSTATIC = -51.7354 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6735" Parameter: CONF_N -> "8002" Comparing "6735" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6736" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750377 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752656 ATOM PAIRS WERE FOUND FOR ATOM LIST 41200 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29562 from a total of 752656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6736 -85.92121 3.59328 0.69290 INTE EXTERN> -28.18761 -57.73359 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.9212" Parameter: A <- "-85.9212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1876" Parameter: B <- "-28.1876" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.7336" Parameter: C <- "-57.7336" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6736 TOTAL ENERGY = -85.9212 RDTITL> * VAN DER WAALS = -28.1876 ELECTROSTATIC = -57.7336 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6736" Parameter: CONF_N -> "8002" Comparing "6736" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6737" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752457 ATOM PAIRS WERE FOUND FOR ATOM LIST 41328 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29887 from a total of 752457 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6737 -77.57825 -8.34296 0.78096 INTE EXTERN> -24.20431 -53.37394 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5782" Parameter: A <- "-77.5782" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2043" Parameter: B <- "-24.2043" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3739" Parameter: C <- "-53.3739" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6737 TOTAL ENERGY = -77.5782 RDTITL> * VAN DER WAALS = -24.2043 ELECTROSTATIC = -53.3739 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6737" Parameter: CONF_N -> "8002" Comparing "6737" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6738" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752457 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760923 ATOM PAIRS WERE FOUND FOR ATOM LIST 41731 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30620 from a total of 760923 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6738 -79.66140 2.08315 0.64936 INTE EXTERN> -30.11492 -49.54647 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6614" Parameter: A <- "-79.6614" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1149" Parameter: B <- "-30.1149" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5465" Parameter: C <- "-49.5465" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6738 TOTAL ENERGY = -79.6614 RDTITL> * VAN DER WAALS = -30.1149 ELECTROSTATIC = -49.5465 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6738" Parameter: CONF_N -> "8002" Comparing "6738" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6739" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760923 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757231 ATOM PAIRS WERE FOUND FOR ATOM LIST 41724 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29697 from a total of 757231 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6739 -75.49470 -4.16670 0.64061 INTE EXTERN> -29.09621 -46.39848 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4947" Parameter: A <- "-75.4947" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0962" Parameter: B <- "-29.0962" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3985" Parameter: C <- "-46.3985" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6739 TOTAL ENERGY = -75.4947 RDTITL> * VAN DER WAALS = -29.0962 ELECTROSTATIC = -46.3985 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6739" Parameter: CONF_N -> "8002" Comparing "6739" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6740" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757231 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758399 ATOM PAIRS WERE FOUND FOR ATOM LIST 41398 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29131 from a total of 758399 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6740 -81.71583 6.22113 0.72636 INTE EXTERN> -24.48130 -57.23453 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.7158" Parameter: A <- "-81.7158" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4813" Parameter: B <- "-24.4813" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.2345" Parameter: C <- "-57.2345" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6740 TOTAL ENERGY = -81.7158 RDTITL> * VAN DER WAALS = -24.4813 ELECTROSTATIC = -57.2345 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6740" Parameter: CONF_N -> "8002" Comparing "6740" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6741" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758399 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756736 ATOM PAIRS WERE FOUND FOR ATOM LIST 41585 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29823 from a total of 756736 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6741 -80.93619 -0.77964 0.65745 INTE EXTERN> -30.07277 -50.86342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9362" Parameter: A <- "-80.9362" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0728" Parameter: B <- "-30.0728" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8634" Parameter: C <- "-50.8634" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6741 TOTAL ENERGY = -80.9362 RDTITL> * VAN DER WAALS = -30.0728 ELECTROSTATIC = -50.8634 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6741" Parameter: CONF_N -> "8002" Comparing "6741" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6742" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756736 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758011 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29281 from a total of 758011 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6742 -79.71456 -1.22162 0.66150 INTE EXTERN> -29.53839 -50.17618 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7146" Parameter: A <- "-79.7146" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5384" Parameter: B <- "-29.5384" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1762" Parameter: C <- "-50.1762" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6742 TOTAL ENERGY = -79.7146 RDTITL> * VAN DER WAALS = -29.5384 ELECTROSTATIC = -50.1762 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6742" Parameter: CONF_N -> "8002" Comparing "6742" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6743" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758011 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760337 ATOM PAIRS WERE FOUND FOR ATOM LIST 41928 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29869 from a total of 760337 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6743 -88.46161 8.74705 0.71481 INTE EXTERN> -28.45901 -60.00260 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.4616" Parameter: A <- "-88.4616" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.459" Parameter: B <- "-28.459" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-60.0026" Parameter: C <- "-60.0026" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6743 TOTAL ENERGY = -88.4616 RDTITL> * VAN DER WAALS = -28.459 ELECTROSTATIC = -60.0026 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6743" Parameter: CONF_N -> "8002" Comparing "6743" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6744" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760337 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760689 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30141 from a total of 760689 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6744 -83.71642 -4.74520 0.64350 INTE EXTERN> -32.56300 -51.15342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.7164" Parameter: A <- "-83.7164" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.563" Parameter: B <- "-32.563" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1534" Parameter: C <- "-51.1534" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6744 TOTAL ENERGY = -83.7164 RDTITL> * VAN DER WAALS = -32.563 ELECTROSTATIC = -51.1534 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6744" Parameter: CONF_N -> "8002" Comparing "6744" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6745" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760689 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755876 ATOM PAIRS WERE FOUND FOR ATOM LIST 41469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29311 from a total of 755876 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6745 -82.99136 -0.72506 0.67096 INTE EXTERN> -31.18722 -51.80414 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9914" Parameter: A <- "-82.9914" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1872" Parameter: B <- "-31.1872" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8041" Parameter: C <- "-51.8041" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6745 TOTAL ENERGY = -82.9914 RDTITL> * VAN DER WAALS = -31.1872 ELECTROSTATIC = -51.8041 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6745" Parameter: CONF_N -> "8002" Comparing "6745" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6746" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755876 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755619 ATOM PAIRS WERE FOUND FOR ATOM LIST 41609 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29440 from a total of 755619 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6746 -76.02236 -6.96900 0.60765 INTE EXTERN> -28.84123 -47.18113 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0224" Parameter: A <- "-76.0224" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8412" Parameter: B <- "-28.8412" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1811" Parameter: C <- "-47.1811" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6746 TOTAL ENERGY = -76.0224 RDTITL> * VAN DER WAALS = -28.8412 ELECTROSTATIC = -47.1811 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6746" Parameter: CONF_N -> "8002" Comparing "6746" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6747" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755619 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764454 ATOM PAIRS WERE FOUND FOR ATOM LIST 41943 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 764454 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6747 -80.46991 4.44755 0.57242 INTE EXTERN> -33.80726 -46.66265 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4699" Parameter: A <- "-80.4699" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.8073" Parameter: B <- "-33.8073" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6626" Parameter: C <- "-46.6626" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6747 TOTAL ENERGY = -80.4699 RDTITL> * VAN DER WAALS = -33.8073 ELECTROSTATIC = -46.6626 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6747" Parameter: CONF_N -> "8002" Comparing "6747" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6748" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764454 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756452 ATOM PAIRS WERE FOUND FOR ATOM LIST 41435 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29540 from a total of 756452 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6748 -77.51647 -2.95343 0.58182 INTE EXTERN> -32.63555 -44.88092 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5165" Parameter: A <- "-77.5165" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6356" Parameter: B <- "-32.6356" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8809" Parameter: C <- "-44.8809" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6748 TOTAL ENERGY = -77.5165 RDTITL> * VAN DER WAALS = -32.6356 ELECTROSTATIC = -44.8809 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6748" Parameter: CONF_N -> "8002" Comparing "6748" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6749" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756452 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753997 ATOM PAIRS WERE FOUND FOR ATOM LIST 41340 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29647 from a total of 753997 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6749 -71.01193 -6.50454 0.65044 INTE EXTERN> -27.96084 -43.05109 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0119" Parameter: A <- "-71.0119" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9608" Parameter: B <- "-27.9608" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0511" Parameter: C <- "-43.0511" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6749 TOTAL ENERGY = -71.0119 RDTITL> * VAN DER WAALS = -27.9608 ELECTROSTATIC = -43.0511 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6749" Parameter: CONF_N -> "8002" Comparing "6749" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6750" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753997 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750888 ATOM PAIRS WERE FOUND FOR ATOM LIST 41304 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29917 from a total of 750888 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6750 -79.44071 8.42878 0.65052 INTE EXTERN> -30.21544 -49.22527 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4407" Parameter: A <- "-79.4407" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2154" Parameter: B <- "-30.2154" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2253" Parameter: C <- "-49.2253" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6750 TOTAL ENERGY = -79.4407 RDTITL> * VAN DER WAALS = -30.2154 ELECTROSTATIC = -49.2253 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6750" Parameter: CONF_N -> "8002" Comparing "6750" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6751" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750888 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760661 ATOM PAIRS WERE FOUND FOR ATOM LIST 41690 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30539 from a total of 760661 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6751 -84.29808 4.85737 0.74453 INTE EXTERN> -27.66340 -56.63469 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.2981" Parameter: A <- "-84.2981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6634" Parameter: B <- "-27.6634" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.6347" Parameter: C <- "-56.6347" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6751 TOTAL ENERGY = -84.2981 RDTITL> * VAN DER WAALS = -27.6634 ELECTROSTATIC = -56.6347 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6751" Parameter: CONF_N -> "8002" Comparing "6751" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6752" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760661 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756500 ATOM PAIRS WERE FOUND FOR ATOM LIST 41369 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29792 from a total of 756500 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6752 -80.48294 -3.81514 0.68658 INTE EXTERN> -26.46063 -54.02231 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4829" Parameter: A <- "-80.4829" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4606" Parameter: B <- "-26.4606" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0223" Parameter: C <- "-54.0223" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6752 TOTAL ENERGY = -80.4829 RDTITL> * VAN DER WAALS = -26.4606 ELECTROSTATIC = -54.0223 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6752" Parameter: CONF_N -> "8002" Comparing "6752" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6753" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756500 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761602 ATOM PAIRS WERE FOUND FOR ATOM LIST 41811 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30209 from a total of 761602 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6753 -81.11576 0.63282 0.64386 INTE EXTERN> -30.59556 -50.52020 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1158" Parameter: A <- "-81.1158" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5956" Parameter: B <- "-30.5956" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5202" Parameter: C <- "-50.5202" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6753 TOTAL ENERGY = -81.1158 RDTITL> * VAN DER WAALS = -30.5956 ELECTROSTATIC = -50.5202 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6753" Parameter: CONF_N -> "8002" Comparing "6753" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6754" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761602 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762302 ATOM PAIRS WERE FOUND FOR ATOM LIST 41778 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30727 from a total of 762302 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6754 -78.59665 -2.51911 0.69120 INTE EXTERN> -30.76343 -47.83322 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5967" Parameter: A <- "-78.5967" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7634" Parameter: B <- "-30.7634" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8332" Parameter: C <- "-47.8332" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6754 TOTAL ENERGY = -78.5967 RDTITL> * VAN DER WAALS = -30.7634 ELECTROSTATIC = -47.8332 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6754" Parameter: CONF_N -> "8002" Comparing "6754" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6755" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762302 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755677 ATOM PAIRS WERE FOUND FOR ATOM LIST 41366 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29803 from a total of 755677 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6755 -73.45715 -5.13950 0.53424 INTE EXTERN> -31.97232 -41.48483 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4571" Parameter: A <- "-73.4571" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9723" Parameter: B <- "-31.9723" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4848" Parameter: C <- "-41.4848" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6755 TOTAL ENERGY = -73.4571 RDTITL> * VAN DER WAALS = -31.9723 ELECTROSTATIC = -41.4848 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6755" Parameter: CONF_N -> "8002" Comparing "6755" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6756" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755677 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749191 ATOM PAIRS WERE FOUND FOR ATOM LIST 41108 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29771 from a total of 749191 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6756 -81.69575 8.23860 0.66592 INTE EXTERN> -31.73515 -49.96060 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6957" Parameter: A <- "-81.6957" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7351" Parameter: B <- "-31.7351" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9606" Parameter: C <- "-49.9606" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6756 TOTAL ENERGY = -81.6957 RDTITL> * VAN DER WAALS = -31.7351 ELECTROSTATIC = -49.9606 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6756" Parameter: CONF_N -> "8002" Comparing "6756" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6757" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749191 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753169 ATOM PAIRS WERE FOUND FOR ATOM LIST 41498 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29344 from a total of 753169 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6757 -69.93669 -11.75906 0.56816 INTE EXTERN> -31.93599 -38.00070 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9367" Parameter: A <- "-69.9367" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.936" Parameter: B <- "-31.936" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0007" Parameter: C <- "-38.0007" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6757 TOTAL ENERGY = -69.9367 RDTITL> * VAN DER WAALS = -31.936 ELECTROSTATIC = -38.0007 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6757" Parameter: CONF_N -> "8002" Comparing "6757" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6758" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753169 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754137 ATOM PAIRS WERE FOUND FOR ATOM LIST 41360 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29718 from a total of 754137 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6758 -75.80699 5.87030 0.63406 INTE EXTERN> -30.28142 -45.52558 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.807" Parameter: A <- "-75.807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2814" Parameter: B <- "-30.2814" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5256" Parameter: C <- "-45.5256" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6758 TOTAL ENERGY = -75.807 RDTITL> * VAN DER WAALS = -30.2814 ELECTROSTATIC = -45.5256 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6758" Parameter: CONF_N -> "8002" Comparing "6758" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6759" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754137 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755824 ATOM PAIRS WERE FOUND FOR ATOM LIST 41452 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30239 from a total of 755824 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6759 -79.98949 4.18250 0.69656 INTE EXTERN> -28.76384 -51.22565 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9895" Parameter: A <- "-79.9895" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7638" Parameter: B <- "-28.7638" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2256" Parameter: C <- "-51.2256" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6759 TOTAL ENERGY = -79.9895 RDTITL> * VAN DER WAALS = -28.7638 ELECTROSTATIC = -51.2256 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6759" Parameter: CONF_N -> "8002" Comparing "6759" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6760" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755824 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754752 ATOM PAIRS WERE FOUND FOR ATOM LIST 41223 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29829 from a total of 754752 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6760 -77.41254 -2.57695 0.59601 INTE EXTERN> -30.50747 -46.90507 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4125" Parameter: A <- "-77.4125" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5075" Parameter: B <- "-30.5075" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9051" Parameter: C <- "-46.9051" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6760 TOTAL ENERGY = -77.4125 RDTITL> * VAN DER WAALS = -30.5075 ELECTROSTATIC = -46.9051 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6760" Parameter: CONF_N -> "8002" Comparing "6760" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6761" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754752 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757481 ATOM PAIRS WERE FOUND FOR ATOM LIST 41569 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29915 from a total of 757481 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6761 -81.22417 3.81163 0.75241 INTE EXTERN> -26.11216 -55.11200 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.2242" Parameter: A <- "-81.2242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1122" Parameter: B <- "-26.1122" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.112" Parameter: C <- "-55.112" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6761 TOTAL ENERGY = -81.2242 RDTITL> * VAN DER WAALS = -26.1122 ELECTROSTATIC = -55.112 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6761" Parameter: CONF_N -> "8002" Comparing "6761" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6762" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757481 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755954 ATOM PAIRS WERE FOUND FOR ATOM LIST 41395 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29851 from a total of 755954 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6762 -85.59729 4.37313 0.69718 INTE EXTERN> -30.18939 -55.40790 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.5973" Parameter: A <- "-85.5973" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1894" Parameter: B <- "-30.1894" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.4079" Parameter: C <- "-55.4079" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6762 TOTAL ENERGY = -85.5973 RDTITL> * VAN DER WAALS = -30.1894 ELECTROSTATIC = -55.4079 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6762" Parameter: CONF_N -> "8002" Comparing "6762" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6763" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755954 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754365 ATOM PAIRS WERE FOUND FOR ATOM LIST 41553 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29792 from a total of 754365 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6763 -76.69535 -8.90195 0.80932 INTE EXTERN> -27.84267 -48.85268 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6953" Parameter: A <- "-76.6953" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8427" Parameter: B <- "-27.8427" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8527" Parameter: C <- "-48.8527" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6763 TOTAL ENERGY = -76.6953 RDTITL> * VAN DER WAALS = -27.8427 ELECTROSTATIC = -48.8527 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6763" Parameter: CONF_N -> "8002" Comparing "6763" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6764" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754365 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754699 ATOM PAIRS WERE FOUND FOR ATOM LIST 41421 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29852 from a total of 754699 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6764 -83.62610 6.93075 0.64657 INTE EXTERN> -33.04931 -50.57678 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.6261" Parameter: A <- "-83.6261" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0493" Parameter: B <- "-33.0493" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5768" Parameter: C <- "-50.5768" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6764 TOTAL ENERGY = -83.6261 RDTITL> * VAN DER WAALS = -33.0493 ELECTROSTATIC = -50.5768 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6764" Parameter: CONF_N -> "8002" Comparing "6764" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6765" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754699 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759905 ATOM PAIRS WERE FOUND FOR ATOM LIST 41576 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30042 from a total of 759905 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6765 -70.05837 -13.56773 0.59202 INTE EXTERN> -32.30364 -37.75473 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0584" Parameter: A <- "-70.0584" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3036" Parameter: B <- "-32.3036" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7547" Parameter: C <- "-37.7547" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6765 TOTAL ENERGY = -70.0584 RDTITL> * VAN DER WAALS = -32.3036 ELECTROSTATIC = -37.7547 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6765" Parameter: CONF_N -> "8002" Comparing "6765" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6766" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759905 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756595 ATOM PAIRS WERE FOUND FOR ATOM LIST 41570 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29703 from a total of 756595 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6766 -86.65375 16.59538 0.71314 INTE EXTERN> -31.06002 -55.59372 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.6537" Parameter: A <- "-86.6537" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.06" Parameter: B <- "-31.06" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.5937" Parameter: C <- "-55.5937" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6766 TOTAL ENERGY = -86.6537 RDTITL> * VAN DER WAALS = -31.06 ELECTROSTATIC = -55.5937 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6766" Parameter: CONF_N -> "8002" Comparing "6766" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6767" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756595 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753228 ATOM PAIRS WERE FOUND FOR ATOM LIST 41272 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29452 from a total of 753228 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6767 -81.89645 -4.75730 0.56574 INTE EXTERN> -32.62992 -49.26653 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8965" Parameter: A <- "-81.8965" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6299" Parameter: B <- "-32.6299" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2665" Parameter: C <- "-49.2665" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6767 TOTAL ENERGY = -81.8965 RDTITL> * VAN DER WAALS = -32.6299 ELECTROSTATIC = -49.2665 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6767" Parameter: CONF_N -> "8002" Comparing "6767" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6768" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753228 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750052 ATOM PAIRS WERE FOUND FOR ATOM LIST 41088 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28791 from a total of 750052 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6768 -76.96494 -4.93151 0.69435 INTE EXTERN> -28.88772 -48.07722 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9649" Parameter: A <- "-76.9649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8877" Parameter: B <- "-28.8877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0772" Parameter: C <- "-48.0772" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6768 TOTAL ENERGY = -76.9649 RDTITL> * VAN DER WAALS = -28.8877 ELECTROSTATIC = -48.0772 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6768" Parameter: CONF_N -> "8002" Comparing "6768" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6769" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750052 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755802 ATOM PAIRS WERE FOUND FOR ATOM LIST 41612 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30001 from a total of 755802 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6769 -81.65933 4.69439 0.63944 INTE EXTERN> -32.31098 -49.34835 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6593" Parameter: A <- "-81.6593" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.311" Parameter: B <- "-32.311" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3483" Parameter: C <- "-49.3483" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6769 TOTAL ENERGY = -81.6593 RDTITL> * VAN DER WAALS = -32.311 ELECTROSTATIC = -49.3483 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6769" Parameter: CONF_N -> "8002" Comparing "6769" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6770" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755802 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756805 ATOM PAIRS WERE FOUND FOR ATOM LIST 41436 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29538 from a total of 756805 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6770 -80.39523 -1.26410 0.66174 INTE EXTERN> -29.22447 -51.17076 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3952" Parameter: A <- "-80.3952" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2245" Parameter: B <- "-29.2245" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1708" Parameter: C <- "-51.1708" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6770 TOTAL ENERGY = -80.3952 RDTITL> * VAN DER WAALS = -29.2245 ELECTROSTATIC = -51.1708 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6770" Parameter: CONF_N -> "8002" Comparing "6770" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6771" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756805 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757490 ATOM PAIRS WERE FOUND FOR ATOM LIST 41682 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29608 from a total of 757490 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6771 -86.25531 5.86008 0.72891 INTE EXTERN> -27.94369 -58.31162 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.2553" Parameter: A <- "-86.2553" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9437" Parameter: B <- "-27.9437" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.3116" Parameter: C <- "-58.3116" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6771 TOTAL ENERGY = -86.2553 RDTITL> * VAN DER WAALS = -27.9437 ELECTROSTATIC = -58.3116 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6771" Parameter: CONF_N -> "8002" Comparing "6771" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6772" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757490 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752896 ATOM PAIRS WERE FOUND FOR ATOM LIST 41378 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29766 from a total of 752896 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6772 -76.67139 -9.58392 0.59911 INTE EXTERN> -31.74880 -44.92259 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6714" Parameter: A <- "-76.6714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7488" Parameter: B <- "-31.7488" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9226" Parameter: C <- "-44.9226" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6772 TOTAL ENERGY = -76.6714 RDTITL> * VAN DER WAALS = -31.7488 ELECTROSTATIC = -44.9226 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6772" Parameter: CONF_N -> "8002" Comparing "6772" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6773" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752896 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756075 ATOM PAIRS WERE FOUND FOR ATOM LIST 41594 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29976 from a total of 756075 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6773 -75.44285 -1.22854 0.75069 INTE EXTERN> -28.80628 -46.63657 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4429" Parameter: A <- "-75.4429" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8063" Parameter: B <- "-28.8063" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6366" Parameter: C <- "-46.6366" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6773 TOTAL ENERGY = -75.4429 RDTITL> * VAN DER WAALS = -28.8063 ELECTROSTATIC = -46.6366 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6773" Parameter: CONF_N -> "8002" Comparing "6773" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6774" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756075 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752516 ATOM PAIRS WERE FOUND FOR ATOM LIST 41431 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29449 from a total of 752516 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6774 -79.28727 3.84441 0.80977 INTE EXTERN> -23.70903 -55.57824 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2873" Parameter: A <- "-79.2873" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.709" Parameter: B <- "-23.709" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.5782" Parameter: C <- "-55.5782" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6774 TOTAL ENERGY = -79.2873 RDTITL> * VAN DER WAALS = -23.709 ELECTROSTATIC = -55.5782 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6774" Parameter: CONF_N -> "8002" Comparing "6774" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6775" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752516 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754947 ATOM PAIRS WERE FOUND FOR ATOM LIST 41560 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30070 from a total of 754947 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6775 -81.75721 2.46995 0.70130 INTE EXTERN> -32.01943 -49.73778 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.7572" Parameter: A <- "-81.7572" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0194" Parameter: B <- "-32.0194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7378" Parameter: C <- "-49.7378" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6775 TOTAL ENERGY = -81.7572 RDTITL> * VAN DER WAALS = -32.0194 ELECTROSTATIC = -49.7378 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6775" Parameter: CONF_N -> "8002" Comparing "6775" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6776" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754947 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748292 ATOM PAIRS WERE FOUND FOR ATOM LIST 41044 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29457 from a total of 748292 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6776 -69.62769 -12.12952 0.64494 INTE EXTERN> -29.36075 -40.26694 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6277" Parameter: A <- "-69.6277" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3608" Parameter: B <- "-29.3608" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2669" Parameter: C <- "-40.2669" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6776 TOTAL ENERGY = -69.6277 RDTITL> * VAN DER WAALS = -29.3608 ELECTROSTATIC = -40.2669 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6776" Parameter: CONF_N -> "8002" Comparing "6776" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6777" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748292 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753528 ATOM PAIRS WERE FOUND FOR ATOM LIST 41344 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29212 from a total of 753528 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6777 -76.90845 7.28075 0.62294 INTE EXTERN> -31.43178 -45.47667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9084" Parameter: A <- "-76.9084" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4318" Parameter: B <- "-31.4318" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4767" Parameter: C <- "-45.4767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6777 TOTAL ENERGY = -76.9084 RDTITL> * VAN DER WAALS = -31.4318 ELECTROSTATIC = -45.4767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6777" Parameter: CONF_N -> "8002" Comparing "6777" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6778" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753528 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751050 ATOM PAIRS WERE FOUND FOR ATOM LIST 41205 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29775 from a total of 751050 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6778 -77.31912 0.41067 0.56483 INTE EXTERN> -30.69108 -46.62804 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3191" Parameter: A <- "-77.3191" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6911" Parameter: B <- "-30.6911" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.628" Parameter: C <- "-46.628" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6778 TOTAL ENERGY = -77.3191 RDTITL> * VAN DER WAALS = -30.6911 ELECTROSTATIC = -46.628 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6778" Parameter: CONF_N -> "8002" Comparing "6778" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6779" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751050 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760904 ATOM PAIRS WERE FOUND FOR ATOM LIST 41670 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29817 from a total of 760904 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6779 -80.30361 2.98449 0.65178 INTE EXTERN> -32.71785 -47.58576 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3036" Parameter: A <- "-80.3036" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7178" Parameter: B <- "-32.7178" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5858" Parameter: C <- "-47.5858" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6779 TOTAL ENERGY = -80.3036 RDTITL> * VAN DER WAALS = -32.7178 ELECTROSTATIC = -47.5858 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6779" Parameter: CONF_N -> "8002" Comparing "6779" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6780" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760904 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754633 ATOM PAIRS WERE FOUND FOR ATOM LIST 41607 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30266 from a total of 754633 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6780 -76.64355 -3.66006 0.62262 INTE EXTERN> -29.68359 -46.95996 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6436" Parameter: A <- "-76.6436" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6836" Parameter: B <- "-29.6836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.96" Parameter: C <- "-46.96" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6780 TOTAL ENERGY = -76.6436 RDTITL> * VAN DER WAALS = -29.6836 ELECTROSTATIC = -46.96 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6780" Parameter: CONF_N -> "8002" Comparing "6780" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6781" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754633 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755329 ATOM PAIRS WERE FOUND FOR ATOM LIST 41618 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30032 from a total of 755329 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6781 -68.43542 -8.20813 0.68408 INTE EXTERN> -26.38265 -42.05277 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4354" Parameter: A <- "-68.4354" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3827" Parameter: B <- "-26.3827" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0528" Parameter: C <- "-42.0528" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6781 TOTAL ENERGY = -68.4354 RDTITL> * VAN DER WAALS = -26.3827 ELECTROSTATIC = -42.0528 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6781" Parameter: CONF_N -> "8002" Comparing "6781" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6782" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755329 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755390 ATOM PAIRS WERE FOUND FOR ATOM LIST 41440 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29337 from a total of 755390 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6782 -75.35613 6.92071 0.59657 INTE EXTERN> -33.76637 -41.58976 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3561" Parameter: A <- "-75.3561" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7664" Parameter: B <- "-33.7664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5898" Parameter: C <- "-41.5898" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6782 TOTAL ENERGY = -75.3561 RDTITL> * VAN DER WAALS = -33.7664 ELECTROSTATIC = -41.5898 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6782" Parameter: CONF_N -> "8002" Comparing "6782" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6783" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755390 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753966 ATOM PAIRS WERE FOUND FOR ATOM LIST 41402 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29225 from a total of 753966 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6783 -76.69026 1.33412 0.55229 INTE EXTERN> -32.42017 -44.27009 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6903" Parameter: A <- "-76.6903" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4202" Parameter: B <- "-32.4202" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2701" Parameter: C <- "-44.2701" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6783 TOTAL ENERGY = -76.6903 RDTITL> * VAN DER WAALS = -32.4202 ELECTROSTATIC = -44.2701 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6783" Parameter: CONF_N -> "8002" Comparing "6783" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6784" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753966 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756901 ATOM PAIRS WERE FOUND FOR ATOM LIST 41508 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29997 from a total of 756901 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6784 -75.33330 -1.35695 0.81984 INTE EXTERN> -23.46819 -51.86511 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3333" Parameter: A <- "-75.3333" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4682" Parameter: B <- "-23.4682" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8651" Parameter: C <- "-51.8651" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6784 TOTAL ENERGY = -75.3333 RDTITL> * VAN DER WAALS = -23.4682 ELECTROSTATIC = -51.8651 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6784" Parameter: CONF_N -> "8002" Comparing "6784" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6785" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756901 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757279 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29089 from a total of 757279 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6785 -75.64100 0.30770 0.70936 INTE EXTERN> -26.29448 -49.34652 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.641" Parameter: A <- "-75.641" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2945" Parameter: B <- "-26.2945" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3465" Parameter: C <- "-49.3465" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6785 TOTAL ENERGY = -75.641 RDTITL> * VAN DER WAALS = -26.2945 ELECTROSTATIC = -49.3465 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6785" Parameter: CONF_N -> "8002" Comparing "6785" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6786" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757279 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758434 ATOM PAIRS WERE FOUND FOR ATOM LIST 41737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29506 from a total of 758434 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6786 -74.56966 -1.07134 0.70752 INTE EXTERN> -28.32643 -46.24323 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5697" Parameter: A <- "-74.5697" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3264" Parameter: B <- "-28.3264" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2432" Parameter: C <- "-46.2432" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6786 TOTAL ENERGY = -74.5697 RDTITL> * VAN DER WAALS = -28.3264 ELECTROSTATIC = -46.2432 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6786" Parameter: CONF_N -> "8002" Comparing "6786" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6787" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758434 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757754 ATOM PAIRS WERE FOUND FOR ATOM LIST 41503 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29911 from a total of 757754 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6787 -80.58282 6.01316 0.63723 INTE EXTERN> -32.08469 -48.49814 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5828" Parameter: A <- "-80.5828" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0847" Parameter: B <- "-32.0847" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4981" Parameter: C <- "-48.4981" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6787 TOTAL ENERGY = -80.5828 RDTITL> * VAN DER WAALS = -32.0847 ELECTROSTATIC = -48.4981 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6787" Parameter: CONF_N -> "8002" Comparing "6787" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6788" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757754 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755646 ATOM PAIRS WERE FOUND FOR ATOM LIST 41601 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29297 from a total of 755646 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6788 -78.84519 -1.73764 0.61843 INTE EXTERN> -30.00545 -48.83973 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8452" Parameter: A <- "-78.8452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0055" Parameter: B <- "-30.0055" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8397" Parameter: C <- "-48.8397" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6788 TOTAL ENERGY = -78.8452 RDTITL> * VAN DER WAALS = -30.0055 ELECTROSTATIC = -48.8397 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6788" Parameter: CONF_N -> "8002" Comparing "6788" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6789" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755646 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755081 ATOM PAIRS WERE FOUND FOR ATOM LIST 41611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29526 from a total of 755081 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6789 -73.67344 -5.17174 0.68175 INTE EXTERN> -26.03165 -47.64179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6734" Parameter: A <- "-73.6734" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0317" Parameter: B <- "-26.0317" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6418" Parameter: C <- "-47.6418" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6789 TOTAL ENERGY = -73.6734 RDTITL> * VAN DER WAALS = -26.0317 ELECTROSTATIC = -47.6418 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6789" Parameter: CONF_N -> "8002" Comparing "6789" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6790" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755081 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758008 ATOM PAIRS WERE FOUND FOR ATOM LIST 41634 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28723 from a total of 758008 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6790 -77.23123 3.55779 0.72810 INTE EXTERN> -26.96953 -50.26171 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2312" Parameter: A <- "-77.2312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9695" Parameter: B <- "-26.9695" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2617" Parameter: C <- "-50.2617" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6790 TOTAL ENERGY = -77.2312 RDTITL> * VAN DER WAALS = -26.9695 ELECTROSTATIC = -50.2617 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6790" Parameter: CONF_N -> "8002" Comparing "6790" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6791" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758008 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754858 ATOM PAIRS WERE FOUND FOR ATOM LIST 41492 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28840 from a total of 754858 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6791 -74.65094 -2.58030 0.66794 INTE EXTERN> -29.17975 -45.47119 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6509" Parameter: A <- "-74.6509" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1797" Parameter: B <- "-29.1797" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4712" Parameter: C <- "-45.4712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6791 TOTAL ENERGY = -74.6509 RDTITL> * VAN DER WAALS = -29.1797 ELECTROSTATIC = -45.4712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6791" Parameter: CONF_N -> "8002" Comparing "6791" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6792" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754858 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757076 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28834 from a total of 757076 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6792 -84.46236 9.81142 0.62108 INTE EXTERN> -31.21406 -53.24830 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.4624" Parameter: A <- "-84.4624" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2141" Parameter: B <- "-31.2141" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.2483" Parameter: C <- "-53.2483" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6792 TOTAL ENERGY = -84.4624 RDTITL> * VAN DER WAALS = -31.2141 ELECTROSTATIC = -53.2483 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6792" Parameter: CONF_N -> "8002" Comparing "6792" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6793" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757076 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763840 ATOM PAIRS WERE FOUND FOR ATOM LIST 41906 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29634 from a total of 763840 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6793 -78.65112 -5.81123 0.79361 INTE EXTERN> -27.39952 -51.25160 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6511" Parameter: A <- "-78.6511" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3995" Parameter: B <- "-27.3995" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2516" Parameter: C <- "-51.2516" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6793 TOTAL ENERGY = -78.6511 RDTITL> * VAN DER WAALS = -27.3995 ELECTROSTATIC = -51.2516 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6793" Parameter: CONF_N -> "8002" Comparing "6793" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6794" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763840 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756976 ATOM PAIRS WERE FOUND FOR ATOM LIST 41883 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29628 from a total of 756976 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6794 -81.89132 3.24020 0.61989 INTE EXTERN> -32.11876 -49.77256 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8913" Parameter: A <- "-81.8913" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1188" Parameter: B <- "-32.1188" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7726" Parameter: C <- "-49.7726" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6794 TOTAL ENERGY = -81.8913 RDTITL> * VAN DER WAALS = -32.1188 ELECTROSTATIC = -49.7726 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6794" Parameter: CONF_N -> "8002" Comparing "6794" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6795" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756976 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753237 ATOM PAIRS WERE FOUND FOR ATOM LIST 41567 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28883 from a total of 753237 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6795 -79.27906 -2.61226 0.70191 INTE EXTERN> -27.84742 -51.43164 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2791" Parameter: A <- "-79.2791" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8474" Parameter: B <- "-27.8474" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4316" Parameter: C <- "-51.4316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6795 TOTAL ENERGY = -79.2791 RDTITL> * VAN DER WAALS = -27.8474 ELECTROSTATIC = -51.4316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6795" Parameter: CONF_N -> "8002" Comparing "6795" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6796" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753237 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751350 ATOM PAIRS WERE FOUND FOR ATOM LIST 41234 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28873 from a total of 751350 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6796 -81.71495 2.43589 0.69015 INTE EXTERN> -29.43622 -52.27873 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.715" Parameter: A <- "-81.715" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4362" Parameter: B <- "-29.4362" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2787" Parameter: C <- "-52.2787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6796 TOTAL ENERGY = -81.715 RDTITL> * VAN DER WAALS = -29.4362 ELECTROSTATIC = -52.2787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6796" Parameter: CONF_N -> "8002" Comparing "6796" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6797" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751350 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752240 ATOM PAIRS WERE FOUND FOR ATOM LIST 41419 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28705 from a total of 752240 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6797 -78.30899 -3.40596 0.64698 INTE EXTERN> -29.55727 -48.75173 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.309" Parameter: A <- "-78.309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5573" Parameter: B <- "-29.5573" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7517" Parameter: C <- "-48.7517" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6797 TOTAL ENERGY = -78.309 RDTITL> * VAN DER WAALS = -29.5573 ELECTROSTATIC = -48.7517 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6797" Parameter: CONF_N -> "8002" Comparing "6797" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6798" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752240 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757344 ATOM PAIRS WERE FOUND FOR ATOM LIST 41596 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28934 from a total of 757344 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6798 -74.60583 -3.70317 0.74685 INTE EXTERN> -27.02154 -47.58428 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6058" Parameter: A <- "-74.6058" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0215" Parameter: B <- "-27.0215" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5843" Parameter: C <- "-47.5843" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6798 TOTAL ENERGY = -74.6058 RDTITL> * VAN DER WAALS = -27.0215 ELECTROSTATIC = -47.5843 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6798" Parameter: CONF_N -> "8002" Comparing "6798" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6799" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757344 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757536 ATOM PAIRS WERE FOUND FOR ATOM LIST 41854 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29164 from a total of 757536 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6799 -72.70540 -1.90042 0.60067 INTE EXTERN> -32.05525 -40.65015 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7054" Parameter: A <- "-72.7054" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0553" Parameter: B <- "-32.0553" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6502" Parameter: C <- "-40.6502" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6799 TOTAL ENERGY = -72.7054 RDTITL> * VAN DER WAALS = -32.0553 ELECTROSTATIC = -40.6502 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6799" Parameter: CONF_N -> "8002" Comparing "6799" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6800" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757536 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752285 ATOM PAIRS WERE FOUND FOR ATOM LIST 41350 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28231 from a total of 752285 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6800 -75.09549 2.39009 0.61282 INTE EXTERN> -30.06130 -45.03419 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0955" Parameter: A <- "-75.0955" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0613" Parameter: B <- "-30.0613" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0342" Parameter: C <- "-45.0342" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6800 TOTAL ENERGY = -75.0955 RDTITL> * VAN DER WAALS = -30.0613 ELECTROSTATIC = -45.0342 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6800" Parameter: CONF_N -> "8002" Comparing "6800" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6801" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752285 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756028 ATOM PAIRS WERE FOUND FOR ATOM LIST 41524 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29295 from a total of 756028 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6801 -78.12016 3.02467 0.64706 INTE EXTERN> -29.48349 -48.63667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1202" Parameter: A <- "-78.1202" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4835" Parameter: B <- "-29.4835" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6367" Parameter: C <- "-48.6367" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6801 TOTAL ENERGY = -78.1202 RDTITL> * VAN DER WAALS = -29.4835 ELECTROSTATIC = -48.6367 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6801" Parameter: CONF_N -> "8002" Comparing "6801" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6802" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756028 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757171 ATOM PAIRS WERE FOUND FOR ATOM LIST 41426 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29028 from a total of 757171 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6802 -76.31359 -1.80657 0.65291 INTE EXTERN> -28.19235 -48.12124 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3136" Parameter: A <- "-76.3136" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1924" Parameter: B <- "-28.1924" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1212" Parameter: C <- "-48.1212" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6802 TOTAL ENERGY = -76.3136 RDTITL> * VAN DER WAALS = -28.1924 ELECTROSTATIC = -48.1212 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6802" Parameter: CONF_N -> "8002" Comparing "6802" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6803" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757171 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756320 ATOM PAIRS WERE FOUND FOR ATOM LIST 41554 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29988 from a total of 756320 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6803 -74.24650 -2.06709 0.71364 INTE EXTERN> -26.92354 -47.32296 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2465" Parameter: A <- "-74.2465" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9235" Parameter: B <- "-26.9235" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.323" Parameter: C <- "-47.323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6803 TOTAL ENERGY = -74.2465 RDTITL> * VAN DER WAALS = -26.9235 ELECTROSTATIC = -47.323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6803" Parameter: CONF_N -> "8002" Comparing "6803" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6804" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756320 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756577 ATOM PAIRS WERE FOUND FOR ATOM LIST 41515 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29908 from a total of 756577 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6804 -82.13766 7.89116 0.63645 INTE EXTERN> -33.00719 -49.13047 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.1377" Parameter: A <- "-82.1377" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0072" Parameter: B <- "-33.0072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1305" Parameter: C <- "-49.1305" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6804 TOTAL ENERGY = -82.1377 RDTITL> * VAN DER WAALS = -33.0072 ELECTROSTATIC = -49.1305 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6804" Parameter: CONF_N -> "8002" Comparing "6804" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6805" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756577 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759510 ATOM PAIRS WERE FOUND FOR ATOM LIST 41641 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29772 from a total of 759510 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6805 -77.98937 -4.14828 0.66561 INTE EXTERN> -30.00479 -47.98458 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9894" Parameter: A <- "-77.9894" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0048" Parameter: B <- "-30.0048" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9846" Parameter: C <- "-47.9846" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6805 TOTAL ENERGY = -77.9894 RDTITL> * VAN DER WAALS = -30.0048 ELECTROSTATIC = -47.9846 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6805" Parameter: CONF_N -> "8002" Comparing "6805" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6806" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759510 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756588 ATOM PAIRS WERE FOUND FOR ATOM LIST 41553 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29697 from a total of 756588 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6806 -76.52477 -1.46461 0.75512 INTE EXTERN> -25.26121 -51.26356 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5248" Parameter: A <- "-76.5248" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2612" Parameter: B <- "-25.2612" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2636" Parameter: C <- "-51.2636" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6806 TOTAL ENERGY = -76.5248 RDTITL> * VAN DER WAALS = -25.2612 ELECTROSTATIC = -51.2636 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6806" Parameter: CONF_N -> "8002" Comparing "6806" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6807" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756588 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41457 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29894 from a total of 754009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6807 -76.74708 0.22231 0.53474 INTE EXTERN> -34.18457 -42.56251 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7471" Parameter: A <- "-76.7471" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.1846" Parameter: B <- "-34.1846" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5625" Parameter: C <- "-42.5625" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6807 TOTAL ENERGY = -76.7471 RDTITL> * VAN DER WAALS = -34.1846 ELECTROSTATIC = -42.5625 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6807" Parameter: CONF_N -> "8002" Comparing "6807" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6808" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749280 ATOM PAIRS WERE FOUND FOR ATOM LIST 41029 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28962 from a total of 749280 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6808 -82.96021 6.21313 0.62063 INTE EXTERN> -32.88191 -50.07830 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9602" Parameter: A <- "-82.9602" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8819" Parameter: B <- "-32.8819" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0783" Parameter: C <- "-50.0783" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6808 TOTAL ENERGY = -82.9602 RDTITL> * VAN DER WAALS = -32.8819 ELECTROSTATIC = -50.0783 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6808" Parameter: CONF_N -> "8002" Comparing "6808" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6809" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749280 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 743825 ATOM PAIRS WERE FOUND FOR ATOM LIST 40958 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28577 from a total of 743825 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6809 -86.64301 3.68280 0.69634 INTE EXTERN> -28.66285 -57.98016 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.643" Parameter: A <- "-86.643" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6628" Parameter: B <- "-28.6628" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.9802" Parameter: C <- "-57.9802" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6809 TOTAL ENERGY = -86.643 RDTITL> * VAN DER WAALS = -28.6628 ELECTROSTATIC = -57.9802 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6809" Parameter: CONF_N -> "8002" Comparing "6809" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6810" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 743825 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757784 ATOM PAIRS WERE FOUND FOR ATOM LIST 41487 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29985 from a total of 757784 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6810 -77.88373 -8.75928 0.79774 INTE EXTERN> -26.92479 -50.95894 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8837" Parameter: A <- "-77.8837" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9248" Parameter: B <- "-26.9248" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9589" Parameter: C <- "-50.9589" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6810 TOTAL ENERGY = -77.8837 RDTITL> * VAN DER WAALS = -26.9248 ELECTROSTATIC = -50.9589 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6810" Parameter: CONF_N -> "8002" Comparing "6810" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6811" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757784 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758230 ATOM PAIRS WERE FOUND FOR ATOM LIST 41527 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28911 from a total of 758230 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6811 -77.11759 -0.76613 0.61531 INTE EXTERN> -31.09490 -46.02270 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1176" Parameter: A <- "-77.1176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0949" Parameter: B <- "-31.0949" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0227" Parameter: C <- "-46.0227" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6811 TOTAL ENERGY = -77.1176 RDTITL> * VAN DER WAALS = -31.0949 ELECTROSTATIC = -46.0227 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6811" Parameter: CONF_N -> "8002" Comparing "6811" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6812" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758230 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755362 ATOM PAIRS WERE FOUND FOR ATOM LIST 41354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29254 from a total of 755362 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6812 -79.95007 2.83248 0.70967 INTE EXTERN> -28.40201 -51.54806 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9501" Parameter: A <- "-79.9501" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.402" Parameter: B <- "-28.402" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5481" Parameter: C <- "-51.5481" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6812 TOTAL ENERGY = -79.9501 RDTITL> * VAN DER WAALS = -28.402 ELECTROSTATIC = -51.5481 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6812" Parameter: CONF_N -> "8002" Comparing "6812" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6813" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755362 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754714 ATOM PAIRS WERE FOUND FOR ATOM LIST 41611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29722 from a total of 754714 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6813 -78.51836 -1.43171 0.88250 INTE EXTERN> -21.97460 -56.54377 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5184" Parameter: A <- "-78.5184" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.9746" Parameter: B <- "-21.9746" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.5438" Parameter: C <- "-56.5438" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6813 TOTAL ENERGY = -78.5184 RDTITL> * VAN DER WAALS = -21.9746 ELECTROSTATIC = -56.5438 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6813" Parameter: CONF_N -> "8002" Comparing "6813" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6814" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754714 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759966 ATOM PAIRS WERE FOUND FOR ATOM LIST 42022 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29878 from a total of 759966 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6814 -79.25684 0.73848 0.72372 INTE EXTERN> -31.04739 -48.20945 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2568" Parameter: A <- "-79.2568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0474" Parameter: B <- "-31.0474" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2095" Parameter: C <- "-48.2095" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6814 TOTAL ENERGY = -79.2568 RDTITL> * VAN DER WAALS = -31.0474 ELECTROSTATIC = -48.2095 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6814" Parameter: CONF_N -> "8002" Comparing "6814" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6815" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759966 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758628 ATOM PAIRS WERE FOUND FOR ATOM LIST 41823 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29665 from a total of 758628 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6815 -82.13522 2.87838 0.70991 INTE EXTERN> -28.78571 -53.34951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.1352" Parameter: A <- "-82.1352" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7857" Parameter: B <- "-28.7857" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3495" Parameter: C <- "-53.3495" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6815 TOTAL ENERGY = -82.1352 RDTITL> * VAN DER WAALS = -28.7857 ELECTROSTATIC = -53.3495 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6815" Parameter: CONF_N -> "8002" Comparing "6815" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6816" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758628 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754804 ATOM PAIRS WERE FOUND FOR ATOM LIST 41427 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29101 from a total of 754804 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6816 -77.73266 -4.40256 0.64105 INTE EXTERN> -31.05437 -46.67828 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7327" Parameter: A <- "-77.7327" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0544" Parameter: B <- "-31.0544" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6783" Parameter: C <- "-46.6783" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6816 TOTAL ENERGY = -77.7327 RDTITL> * VAN DER WAALS = -31.0544 ELECTROSTATIC = -46.6783 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6816" Parameter: CONF_N -> "8002" Comparing "6816" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6817" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754804 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754293 ATOM PAIRS WERE FOUND FOR ATOM LIST 41494 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29429 from a total of 754293 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6817 -77.81919 0.08653 0.72680 INTE EXTERN> -26.55218 -51.26701 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8192" Parameter: A <- "-77.8192" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5522" Parameter: B <- "-26.5522" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.267" Parameter: C <- "-51.267" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6817 TOTAL ENERGY = -77.8192 RDTITL> * VAN DER WAALS = -26.5522 ELECTROSTATIC = -51.267 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6817" Parameter: CONF_N -> "8002" Comparing "6817" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6818" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754293 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755841 ATOM PAIRS WERE FOUND FOR ATOM LIST 41758 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29265 from a total of 755841 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6818 -82.48173 4.66254 0.62673 INTE EXTERN> -31.99907 -50.48267 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.4817" Parameter: A <- "-82.4817" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9991" Parameter: B <- "-31.9991" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4827" Parameter: C <- "-50.4827" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6818 TOTAL ENERGY = -82.4817 RDTITL> * VAN DER WAALS = -31.9991 ELECTROSTATIC = -50.4827 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6818" Parameter: CONF_N -> "8002" Comparing "6818" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6819" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755841 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758091 ATOM PAIRS WERE FOUND FOR ATOM LIST 41588 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29393 from a total of 758091 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6819 -78.79605 -3.68568 0.63720 INTE EXTERN> -31.54857 -47.24748 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7961" Parameter: A <- "-78.7961" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5486" Parameter: B <- "-31.5486" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2475" Parameter: C <- "-47.2475" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6819 TOTAL ENERGY = -78.7961 RDTITL> * VAN DER WAALS = -31.5486 ELECTROSTATIC = -47.2475 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6819" Parameter: CONF_N -> "8002" Comparing "6819" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6820" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758091 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755981 ATOM PAIRS WERE FOUND FOR ATOM LIST 41623 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28875 from a total of 755981 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6820 -73.55210 -5.24395 0.73996 INTE EXTERN> -26.41436 -47.13774 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5521" Parameter: A <- "-73.5521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4144" Parameter: B <- "-26.4144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1377" Parameter: C <- "-47.1377" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6820 TOTAL ENERGY = -73.5521 RDTITL> * VAN DER WAALS = -26.4144 ELECTROSTATIC = -47.1377 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6820" Parameter: CONF_N -> "8002" Comparing "6820" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6821" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755981 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751216 ATOM PAIRS WERE FOUND FOR ATOM LIST 41272 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29185 from a total of 751216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6821 -84.81902 11.26692 0.68102 INTE EXTERN> -29.34087 -55.47815 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.819" Parameter: A <- "-84.819" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3409" Parameter: B <- "-29.3409" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.4782" Parameter: C <- "-55.4782" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6821 TOTAL ENERGY = -84.819 RDTITL> * VAN DER WAALS = -29.3409 ELECTROSTATIC = -55.4782 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6821" Parameter: CONF_N -> "8002" Comparing "6821" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6822" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755819 ATOM PAIRS WERE FOUND FOR ATOM LIST 41612 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29418 from a total of 755819 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6822 -78.95889 -5.86013 0.65665 INTE EXTERN> -28.56380 -50.39509 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9589" Parameter: A <- "-78.9589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5638" Parameter: B <- "-28.5638" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3951" Parameter: C <- "-50.3951" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6822 TOTAL ENERGY = -78.9589 RDTITL> * VAN DER WAALS = -28.5638 ELECTROSTATIC = -50.3951 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6822" Parameter: CONF_N -> "8002" Comparing "6822" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6823" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755819 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750694 ATOM PAIRS WERE FOUND FOR ATOM LIST 41404 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29268 from a total of 750694 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6823 -78.99429 0.03539 0.66580 INTE EXTERN> -30.18057 -48.81372 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9943" Parameter: A <- "-78.9943" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1806" Parameter: B <- "-30.1806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8137" Parameter: C <- "-48.8137" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6823 TOTAL ENERGY = -78.9943 RDTITL> * VAN DER WAALS = -30.1806 ELECTROSTATIC = -48.8137 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6823" Parameter: CONF_N -> "8002" Comparing "6823" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6824" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750694 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753475 ATOM PAIRS WERE FOUND FOR ATOM LIST 41525 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29449 from a total of 753475 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6824 -80.82294 1.82866 0.78347 INTE EXTERN> -22.42391 -58.39904 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.8229" Parameter: A <- "-80.8229" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.4239" Parameter: B <- "-22.4239" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.399" Parameter: C <- "-58.399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6824 TOTAL ENERGY = -80.8229 RDTITL> * VAN DER WAALS = -22.4239 ELECTROSTATIC = -58.399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6824" Parameter: CONF_N -> "8002" Comparing "6824" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6825" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753475 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754140 ATOM PAIRS WERE FOUND FOR ATOM LIST 41658 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29428 from a total of 754140 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6825 -79.83329 -0.98966 0.75232 INTE EXTERN> -22.71633 -57.11695 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8333" Parameter: A <- "-79.8333" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.7163" Parameter: B <- "-22.7163" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.117" Parameter: C <- "-57.117" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6825 TOTAL ENERGY = -79.8333 RDTITL> * VAN DER WAALS = -22.7163 ELECTROSTATIC = -57.117 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6825" Parameter: CONF_N -> "8002" Comparing "6825" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6826" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754140 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757904 ATOM PAIRS WERE FOUND FOR ATOM LIST 41803 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29321 from a total of 757904 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6826 -78.42554 -1.40775 0.62331 INTE EXTERN> -31.65893 -46.76661 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4255" Parameter: A <- "-78.4255" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6589" Parameter: B <- "-31.6589" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7666" Parameter: C <- "-46.7666" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6826 TOTAL ENERGY = -78.4255 RDTITL> * VAN DER WAALS = -31.6589 ELECTROSTATIC = -46.7666 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6826" Parameter: CONF_N -> "8002" Comparing "6826" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6827" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757904 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755001 ATOM PAIRS WERE FOUND FOR ATOM LIST 41462 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29819 from a total of 755001 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6827 -81.44325 3.01772 0.68807 INTE EXTERN> -29.68091 -51.76234 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4433" Parameter: A <- "-81.4433" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6809" Parameter: B <- "-29.6809" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7623" Parameter: C <- "-51.7623" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6827 TOTAL ENERGY = -81.4433 RDTITL> * VAN DER WAALS = -29.6809 ELECTROSTATIC = -51.7623 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6827" Parameter: CONF_N -> "8002" Comparing "6827" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6828" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755001 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753279 ATOM PAIRS WERE FOUND FOR ATOM LIST 41525 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28976 from a total of 753279 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6828 -77.00629 -4.43696 0.71668 INTE EXTERN> -26.28137 -50.72492 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0063" Parameter: A <- "-77.0063" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2814" Parameter: B <- "-26.2814" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7249" Parameter: C <- "-50.7249" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6828 TOTAL ENERGY = -77.0063 RDTITL> * VAN DER WAALS = -26.2814 ELECTROSTATIC = -50.7249 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6828" Parameter: CONF_N -> "8002" Comparing "6828" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6829" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753279 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744243 ATOM PAIRS WERE FOUND FOR ATOM LIST 41062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29453 from a total of 744243 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6829 -77.64659 0.64030 0.65079 INTE EXTERN> -29.53041 -48.11619 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6466" Parameter: A <- "-77.6466" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5304" Parameter: B <- "-29.5304" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1162" Parameter: C <- "-48.1162" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6829 TOTAL ENERGY = -77.6466 RDTITL> * VAN DER WAALS = -29.5304 ELECTROSTATIC = -48.1162 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6829" Parameter: CONF_N -> "8002" Comparing "6829" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6830" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744243 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754394 ATOM PAIRS WERE FOUND FOR ATOM LIST 41389 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29763 from a total of 754394 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6830 -78.08065 0.43406 0.62130 INTE EXTERN> -29.55292 -48.52773 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0807" Parameter: A <- "-78.0807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5529" Parameter: B <- "-29.5529" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5277" Parameter: C <- "-48.5277" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6830 TOTAL ENERGY = -78.0807 RDTITL> * VAN DER WAALS = -29.5529 ELECTROSTATIC = -48.5277 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6830" Parameter: CONF_N -> "8002" Comparing "6830" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6831" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754394 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750616 ATOM PAIRS WERE FOUND FOR ATOM LIST 41103 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29718 from a total of 750616 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6831 -86.04599 7.96534 0.71604 INTE EXTERN> -33.49385 -52.55214 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.046" Parameter: A <- "-86.046" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4939" Parameter: B <- "-33.4939" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5521" Parameter: C <- "-52.5521" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6831 TOTAL ENERGY = -86.046 RDTITL> * VAN DER WAALS = -33.4939 ELECTROSTATIC = -52.5521 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6831" Parameter: CONF_N -> "8002" Comparing "6831" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6832" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750616 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754846 ATOM PAIRS WERE FOUND FOR ATOM LIST 41581 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29864 from a total of 754846 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6832 -77.60009 -8.44590 0.72048 INTE EXTERN> -27.97387 -49.62622 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6001" Parameter: A <- "-77.6001" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9739" Parameter: B <- "-27.9739" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6262" Parameter: C <- "-49.6262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6832 TOTAL ENERGY = -77.6001 RDTITL> * VAN DER WAALS = -27.9739 ELECTROSTATIC = -49.6262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6832" Parameter: CONF_N -> "8002" Comparing "6832" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6833" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754846 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753355 ATOM PAIRS WERE FOUND FOR ATOM LIST 41313 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30037 from a total of 753355 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6833 -77.06276 -0.53732 0.62604 INTE EXTERN> -30.22418 -46.83859 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0628" Parameter: A <- "-77.0628" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2242" Parameter: B <- "-30.2242" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8386" Parameter: C <- "-46.8386" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6833 TOTAL ENERGY = -77.0628 RDTITL> * VAN DER WAALS = -30.2242 ELECTROSTATIC = -46.8386 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6833" Parameter: CONF_N -> "8002" Comparing "6833" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6834" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753355 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754949 ATOM PAIRS WERE FOUND FOR ATOM LIST 41543 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29641 from a total of 754949 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6834 -76.15407 -0.90870 0.92559 INTE EXTERN> -21.31647 -54.83759 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1541" Parameter: A <- "-76.1541" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.3165" Parameter: B <- "-21.3165" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8376" Parameter: C <- "-54.8376" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6834 TOTAL ENERGY = -76.1541 RDTITL> * VAN DER WAALS = -21.3165 ELECTROSTATIC = -54.8376 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6834" Parameter: CONF_N -> "8002" Comparing "6834" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6835" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754949 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753284 ATOM PAIRS WERE FOUND FOR ATOM LIST 41527 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29075 from a total of 753284 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6835 -78.28402 2.12996 0.74633 INTE EXTERN> -28.41338 -49.87064 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.284" Parameter: A <- "-78.284" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4134" Parameter: B <- "-28.4134" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8706" Parameter: C <- "-49.8706" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6835 TOTAL ENERGY = -78.284 RDTITL> * VAN DER WAALS = -28.4134 ELECTROSTATIC = -49.8706 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6835" Parameter: CONF_N -> "8002" Comparing "6835" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6836" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753284 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754461 ATOM PAIRS WERE FOUND FOR ATOM LIST 41536 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29342 from a total of 754461 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6836 -80.17019 1.88617 0.63029 INTE EXTERN> -34.95948 -45.21071 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1702" Parameter: A <- "-80.1702" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.9595" Parameter: B <- "-34.9595" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2107" Parameter: C <- "-45.2107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6836 TOTAL ENERGY = -80.1702 RDTITL> * VAN DER WAALS = -34.9595 ELECTROSTATIC = -45.2107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6836" Parameter: CONF_N -> "8002" Comparing "6836" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6837" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754461 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749665 ATOM PAIRS WERE FOUND FOR ATOM LIST 41278 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29206 from a total of 749665 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6837 -77.23561 -2.93458 0.58626 INTE EXTERN> -31.46008 -45.77553 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2356" Parameter: A <- "-77.2356" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4601" Parameter: B <- "-31.4601" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7755" Parameter: C <- "-45.7755" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6837 TOTAL ENERGY = -77.2356 RDTITL> * VAN DER WAALS = -31.4601 ELECTROSTATIC = -45.7755 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6837" Parameter: CONF_N -> "8002" Comparing "6837" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6838" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749665 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750685 ATOM PAIRS WERE FOUND FOR ATOM LIST 41446 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28929 from a total of 750685 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6838 -75.43705 -1.79856 0.71749 INTE EXTERN> -27.81427 -47.62278 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4371" Parameter: A <- "-75.4371" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8143" Parameter: B <- "-27.8143" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6228" Parameter: C <- "-47.6228" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6838 TOTAL ENERGY = -75.4371 RDTITL> * VAN DER WAALS = -27.8143 ELECTROSTATIC = -47.6228 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6838" Parameter: CONF_N -> "8002" Comparing "6838" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6839" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750685 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754562 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29578 from a total of 754562 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6839 -77.85015 2.41309 0.71482 INTE EXTERN> -28.44271 -49.40744 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8501" Parameter: A <- "-77.8501" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4427" Parameter: B <- "-28.4427" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4074" Parameter: C <- "-49.4074" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6839 TOTAL ENERGY = -77.8501 RDTITL> * VAN DER WAALS = -28.4427 ELECTROSTATIC = -49.4074 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6839" Parameter: CONF_N -> "8002" Comparing "6839" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6840" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754562 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745631 ATOM PAIRS WERE FOUND FOR ATOM LIST 41266 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29793 from a total of 745631 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6840 -74.95822 -2.89192 0.81648 INTE EXTERN> -24.75341 -50.20481 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9582" Parameter: A <- "-74.9582" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7534" Parameter: B <- "-24.7534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2048" Parameter: C <- "-50.2048" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6840 TOTAL ENERGY = -74.9582 RDTITL> * VAN DER WAALS = -24.7534 ELECTROSTATIC = -50.2048 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6840" Parameter: CONF_N -> "8002" Comparing "6840" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6841" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745631 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750249 ATOM PAIRS WERE FOUND FOR ATOM LIST 41448 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30456 from a total of 750249 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6841 -84.53874 9.58052 0.70070 INTE EXTERN> -32.34547 -52.19327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.5387" Parameter: A <- "-84.5387" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3455" Parameter: B <- "-32.3455" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1933" Parameter: C <- "-52.1933" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6841 TOTAL ENERGY = -84.5387 RDTITL> * VAN DER WAALS = -32.3455 ELECTROSTATIC = -52.1933 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6841" Parameter: CONF_N -> "8002" Comparing "6841" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6842" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750249 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749208 ATOM PAIRS WERE FOUND FOR ATOM LIST 41202 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29821 from a total of 749208 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6842 -76.52376 -8.01499 0.60713 INTE EXTERN> -31.78843 -44.73532 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5238" Parameter: A <- "-76.5238" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7884" Parameter: B <- "-31.7884" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7353" Parameter: C <- "-44.7353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6842 TOTAL ENERGY = -76.5238 RDTITL> * VAN DER WAALS = -31.7884 ELECTROSTATIC = -44.7353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6842" Parameter: CONF_N -> "8002" Comparing "6842" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6843" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749208 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748799 ATOM PAIRS WERE FOUND FOR ATOM LIST 41541 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29534 from a total of 748799 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6843 -75.16477 -1.35899 0.70623 INTE EXTERN> -28.83998 -46.32479 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1648" Parameter: A <- "-75.1648" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.84" Parameter: B <- "-28.84" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3248" Parameter: C <- "-46.3248" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6843 TOTAL ENERGY = -75.1648 RDTITL> * VAN DER WAALS = -28.84 ELECTROSTATIC = -46.3248 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6843" Parameter: CONF_N -> "8002" Comparing "6843" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6844" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748799 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747647 ATOM PAIRS WERE FOUND FOR ATOM LIST 41191 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29191 from a total of 747647 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6844 -76.09230 0.92753 0.60542 INTE EXTERN> -33.64522 -42.44707 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0923" Parameter: A <- "-76.0923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6452" Parameter: B <- "-33.6452" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4471" Parameter: C <- "-42.4471" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6844 TOTAL ENERGY = -76.0923 RDTITL> * VAN DER WAALS = -33.6452 ELECTROSTATIC = -42.4471 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6844" Parameter: CONF_N -> "8002" Comparing "6844" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6845" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747647 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747298 ATOM PAIRS WERE FOUND FOR ATOM LIST 41313 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29201 from a total of 747298 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6845 -78.43839 2.34609 0.70083 INTE EXTERN> -31.30197 -47.13642 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4384" Parameter: A <- "-78.4384" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.302" Parameter: B <- "-31.302" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1364" Parameter: C <- "-47.1364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6845 TOTAL ENERGY = -78.4384 RDTITL> * VAN DER WAALS = -31.302 ELECTROSTATIC = -47.1364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6845" Parameter: CONF_N -> "8002" Comparing "6845" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6846" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747298 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753712 ATOM PAIRS WERE FOUND FOR ATOM LIST 41536 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29281 from a total of 753712 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6846 -73.96964 -4.46875 0.64229 INTE EXTERN> -30.37579 -43.59385 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9696" Parameter: A <- "-73.9696" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3758" Parameter: B <- "-30.3758" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5939" Parameter: C <- "-43.5939" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6846 TOTAL ENERGY = -73.9696 RDTITL> * VAN DER WAALS = -30.3758 ELECTROSTATIC = -43.5939 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6846" Parameter: CONF_N -> "8002" Comparing "6846" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6847" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753712 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744254 ATOM PAIRS WERE FOUND FOR ATOM LIST 41028 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29348 from a total of 744254 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6847 -76.25832 2.28868 0.54700 INTE EXTERN> -32.22291 -44.03541 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2583" Parameter: A <- "-76.2583" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2229" Parameter: B <- "-32.2229" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0354" Parameter: C <- "-44.0354" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6847 TOTAL ENERGY = -76.2583 RDTITL> * VAN DER WAALS = -32.2229 ELECTROSTATIC = -44.0354 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6847" Parameter: CONF_N -> "8002" Comparing "6847" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6848" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744254 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754050 ATOM PAIRS WERE FOUND FOR ATOM LIST 41472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29451 from a total of 754050 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6848 -83.71160 7.45328 0.69742 INTE EXTERN> -29.90221 -53.80938 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.7116" Parameter: A <- "-83.7116" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9022" Parameter: B <- "-29.9022" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8094" Parameter: C <- "-53.8094" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6848 TOTAL ENERGY = -83.7116 RDTITL> * VAN DER WAALS = -29.9022 ELECTROSTATIC = -53.8094 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6848" Parameter: CONF_N -> "8002" Comparing "6848" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6849" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754050 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748635 ATOM PAIRS WERE FOUND FOR ATOM LIST 41232 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29944 from a total of 748635 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6849 -73.55209 -10.15951 0.62115 INTE EXTERN> -29.21540 -44.33668 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5521" Parameter: A <- "-73.5521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2154" Parameter: B <- "-29.2154" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3367" Parameter: C <- "-44.3367" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6849 TOTAL ENERGY = -73.5521 RDTITL> * VAN DER WAALS = -29.2154 ELECTROSTATIC = -44.3367 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6849" Parameter: CONF_N -> "8002" Comparing "6849" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6850" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748635 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752010 ATOM PAIRS WERE FOUND FOR ATOM LIST 41465 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29059 from a total of 752010 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6850 -80.44644 6.89435 0.68237 INTE EXTERN> -27.67115 -52.77529 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4464" Parameter: A <- "-80.4464" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6711" Parameter: B <- "-27.6711" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.7753" Parameter: C <- "-52.7753" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6850 TOTAL ENERGY = -80.4464 RDTITL> * VAN DER WAALS = -27.6711 ELECTROSTATIC = -52.7753 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6850" Parameter: CONF_N -> "8002" Comparing "6850" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6851" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752010 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759742 ATOM PAIRS WERE FOUND FOR ATOM LIST 41795 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29860 from a total of 759742 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6851 -76.68191 -3.76453 0.72507 INTE EXTERN> -27.29420 -49.38771 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6819" Parameter: A <- "-76.6819" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2942" Parameter: B <- "-27.2942" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3877" Parameter: C <- "-49.3877" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6851 TOTAL ENERGY = -76.6819 RDTITL> * VAN DER WAALS = -27.2942 ELECTROSTATIC = -49.3877 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6851" Parameter: CONF_N -> "8002" Comparing "6851" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6852" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759742 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752351 ATOM PAIRS WERE FOUND FOR ATOM LIST 41377 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30086 from a total of 752351 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6852 -79.19118 2.50927 0.59086 INTE EXTERN> -33.46964 -45.72154 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1912" Parameter: A <- "-79.1912" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4696" Parameter: B <- "-33.4696" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7215" Parameter: C <- "-45.7215" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6852 TOTAL ENERGY = -79.1912 RDTITL> * VAN DER WAALS = -33.4696 ELECTROSTATIC = -45.7215 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6852" Parameter: CONF_N -> "8002" Comparing "6852" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6853" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752351 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752639 ATOM PAIRS WERE FOUND FOR ATOM LIST 41419 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28951 from a total of 752639 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6853 -77.61017 -1.58101 0.62290 INTE EXTERN> -27.51648 -50.09369 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6102" Parameter: A <- "-77.6102" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5165" Parameter: B <- "-27.5165" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0937" Parameter: C <- "-50.0937" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6853 TOTAL ENERGY = -77.6102 RDTITL> * VAN DER WAALS = -27.5165 ELECTROSTATIC = -50.0937 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6853" Parameter: CONF_N -> "8002" Comparing "6853" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6854" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752639 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753673 ATOM PAIRS WERE FOUND FOR ATOM LIST 41400 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29541 from a total of 753673 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6854 -73.99181 -3.61836 0.89243 INTE EXTERN> -27.11312 -46.87869 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9918" Parameter: A <- "-73.9918" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1131" Parameter: B <- "-27.1131" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8787" Parameter: C <- "-46.8787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6854 TOTAL ENERGY = -73.9918 RDTITL> * VAN DER WAALS = -27.1131 ELECTROSTATIC = -46.8787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6854" Parameter: CONF_N -> "8002" Comparing "6854" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6855" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753673 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753306 ATOM PAIRS WERE FOUND FOR ATOM LIST 41685 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29761 from a total of 753306 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6855 -75.69605 1.70424 0.77198 INTE EXTERN> -28.24342 -47.45263 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.696" Parameter: A <- "-75.696" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2434" Parameter: B <- "-28.2434" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4526" Parameter: C <- "-47.4526" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6855 TOTAL ENERGY = -75.696 RDTITL> * VAN DER WAALS = -28.2434 ELECTROSTATIC = -47.4526 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6855" Parameter: CONF_N -> "8002" Comparing "6855" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6856" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753306 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750617 ATOM PAIRS WERE FOUND FOR ATOM LIST 41259 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28847 from a total of 750617 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6856 -78.26324 2.56719 0.72582 INTE EXTERN> -27.39300 -50.87024 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2632" Parameter: A <- "-78.2632" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.393" Parameter: B <- "-27.393" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8702" Parameter: C <- "-50.8702" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6856 TOTAL ENERGY = -78.2632 RDTITL> * VAN DER WAALS = -27.393 ELECTROSTATIC = -50.8702 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6856" Parameter: CONF_N -> "8002" Comparing "6856" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6857" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750617 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751567 ATOM PAIRS WERE FOUND FOR ATOM LIST 41559 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30058 from a total of 751567 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6857 -81.64060 3.37737 0.77262 INTE EXTERN> -25.42564 -56.21496 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6406" Parameter: A <- "-81.6406" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4256" Parameter: B <- "-25.4256" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.215" Parameter: C <- "-56.215" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6857 TOTAL ENERGY = -81.6406 RDTITL> * VAN DER WAALS = -25.4256 ELECTROSTATIC = -56.215 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6857" Parameter: CONF_N -> "8002" Comparing "6857" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6858" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751567 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759413 ATOM PAIRS WERE FOUND FOR ATOM LIST 41962 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30118 from a total of 759413 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6858 -87.24360 5.60299 0.72237 INTE EXTERN> -30.14190 -57.10170 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.2436" Parameter: A <- "-87.2436" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1419" Parameter: B <- "-30.1419" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.1017" Parameter: C <- "-57.1017" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6858 TOTAL ENERGY = -87.2436 RDTITL> * VAN DER WAALS = -30.1419 ELECTROSTATIC = -57.1017 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6858" Parameter: CONF_N -> "8002" Comparing "6858" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6859" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759413 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757655 ATOM PAIRS WERE FOUND FOR ATOM LIST 41761 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29753 from a total of 757655 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6859 -79.36902 -7.87458 0.72167 INTE EXTERN> -28.90135 -50.46767 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.369" Parameter: A <- "-79.369" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9014" Parameter: B <- "-28.9014" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4677" Parameter: C <- "-50.4677" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6859 TOTAL ENERGY = -79.369 RDTITL> * VAN DER WAALS = -28.9014 ELECTROSTATIC = -50.4677 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6859" Parameter: CONF_N -> "8002" Comparing "6859" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6860" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757655 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750141 ATOM PAIRS WERE FOUND FOR ATOM LIST 41470 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29627 from a total of 750141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6860 -81.59675 2.22773 0.71796 INTE EXTERN> -30.61762 -50.97912 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5967" Parameter: A <- "-81.5967" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6176" Parameter: B <- "-30.6176" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9791" Parameter: C <- "-50.9791" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6860 TOTAL ENERGY = -81.5967 RDTITL> * VAN DER WAALS = -30.6176 ELECTROSTATIC = -50.9791 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6860" Parameter: CONF_N -> "8002" Comparing "6860" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6861" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749507 ATOM PAIRS WERE FOUND FOR ATOM LIST 41380 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29541 from a total of 749507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6861 -83.29993 1.70318 0.70067 INTE EXTERN> -29.69219 -53.60773 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.2999" Parameter: A <- "-83.2999" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6922" Parameter: B <- "-29.6922" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6077" Parameter: C <- "-53.6077" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6861 TOTAL ENERGY = -83.2999 RDTITL> * VAN DER WAALS = -29.6922 ELECTROSTATIC = -53.6077 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6861" Parameter: CONF_N -> "8002" Comparing "6861" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6862" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754122 ATOM PAIRS WERE FOUND FOR ATOM LIST 41629 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29784 from a total of 754122 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6862 -70.54497 -12.75495 0.65345 INTE EXTERN> -28.06266 -42.48231 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.545" Parameter: A <- "-70.545" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0627" Parameter: B <- "-28.0627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4823" Parameter: C <- "-42.4823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6862 TOTAL ENERGY = -70.545 RDTITL> * VAN DER WAALS = -28.0627 ELECTROSTATIC = -42.4823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6862" Parameter: CONF_N -> "8002" Comparing "6862" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6863" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754122 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751455 ATOM PAIRS WERE FOUND FOR ATOM LIST 41630 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29294 from a total of 751455 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6863 -83.98746 13.44249 0.72811 INTE EXTERN> -29.17735 -54.81011 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.9875" Parameter: A <- "-83.9875" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1774" Parameter: B <- "-29.1774" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8101" Parameter: C <- "-54.8101" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6863 TOTAL ENERGY = -83.9875 RDTITL> * VAN DER WAALS = -29.1774 ELECTROSTATIC = -54.8101 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6863" Parameter: CONF_N -> "8002" Comparing "6863" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6864" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751455 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754244 ATOM PAIRS WERE FOUND FOR ATOM LIST 41587 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29875 from a total of 754244 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6864 -74.90801 -9.07945 0.73878 INTE EXTERN> -25.38741 -49.52060 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.908" Parameter: A <- "-74.908" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3874" Parameter: B <- "-25.3874" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5206" Parameter: C <- "-49.5206" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6864 TOTAL ENERGY = -74.908 RDTITL> * VAN DER WAALS = -25.3874 ELECTROSTATIC = -49.5206 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6864" Parameter: CONF_N -> "8002" Comparing "6864" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6865" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754244 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750050 ATOM PAIRS WERE FOUND FOR ATOM LIST 41469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29259 from a total of 750050 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6865 -80.13768 5.22966 0.67377 INTE EXTERN> -29.11528 -51.02240 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1377" Parameter: A <- "-80.1377" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1153" Parameter: B <- "-29.1153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0224" Parameter: C <- "-51.0224" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6865 TOTAL ENERGY = -80.1377 RDTITL> * VAN DER WAALS = -29.1153 ELECTROSTATIC = -51.0224 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6865" Parameter: CONF_N -> "8002" Comparing "6865" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6866" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750050 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41344 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29635 from a total of 748009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6866 -77.99009 -2.14759 0.70843 INTE EXTERN> -31.14404 -46.84605 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9901" Parameter: A <- "-77.9901" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.144" Parameter: B <- "-31.144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8461" Parameter: C <- "-46.8461" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6866 TOTAL ENERGY = -77.9901 RDTITL> * VAN DER WAALS = -31.144 ELECTROSTATIC = -46.8461 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6866" Parameter: CONF_N -> "8002" Comparing "6866" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6867" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747453 ATOM PAIRS WERE FOUND FOR ATOM LIST 41202 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29715 from a total of 747453 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6867 -77.66512 -0.32497 0.72346 INTE EXTERN> -29.24289 -48.42223 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6651" Parameter: A <- "-77.6651" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2429" Parameter: B <- "-29.2429" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4222" Parameter: C <- "-48.4222" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6867 TOTAL ENERGY = -77.6651 RDTITL> * VAN DER WAALS = -29.2429 ELECTROSTATIC = -48.4222 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6867" Parameter: CONF_N -> "8002" Comparing "6867" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6868" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747453 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752996 ATOM PAIRS WERE FOUND FOR ATOM LIST 41491 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29849 from a total of 752996 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6868 -84.55489 6.88977 0.76297 INTE EXTERN> -27.21938 -57.33551 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.5549" Parameter: A <- "-84.5549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2194" Parameter: B <- "-27.2194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.3355" Parameter: C <- "-57.3355" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6868 TOTAL ENERGY = -84.5549 RDTITL> * VAN DER WAALS = -27.2194 ELECTROSTATIC = -57.3355 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6868" Parameter: CONF_N -> "8002" Comparing "6868" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6869" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752996 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755218 ATOM PAIRS WERE FOUND FOR ATOM LIST 41531 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30320 from a total of 755218 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6869 -79.99193 -4.56296 0.70615 INTE EXTERN> -30.08367 -49.90826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9919" Parameter: A <- "-79.9919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0837" Parameter: B <- "-30.0837" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9083" Parameter: C <- "-49.9083" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6869 TOTAL ENERGY = -79.9919 RDTITL> * VAN DER WAALS = -30.0837 ELECTROSTATIC = -49.9083 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6869" Parameter: CONF_N -> "8002" Comparing "6869" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6870" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755218 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749380 ATOM PAIRS WERE FOUND FOR ATOM LIST 41301 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29809 from a total of 749380 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6870 -79.73471 -0.25722 0.67781 INTE EXTERN> -31.60865 -48.12606 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7347" Parameter: A <- "-79.7347" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6086" Parameter: B <- "-31.6086" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1261" Parameter: C <- "-48.1261" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6870 TOTAL ENERGY = -79.7347 RDTITL> * VAN DER WAALS = -31.6086 ELECTROSTATIC = -48.1261 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6870" Parameter: CONF_N -> "8002" Comparing "6870" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6871" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749380 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749346 ATOM PAIRS WERE FOUND FOR ATOM LIST 41134 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29961 from a total of 749346 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6871 -79.14050 -0.59421 0.69848 INTE EXTERN> -28.60188 -50.53862 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1405" Parameter: A <- "-79.1405" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6019" Parameter: B <- "-28.6019" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5386" Parameter: C <- "-50.5386" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6871 TOTAL ENERGY = -79.1405 RDTITL> * VAN DER WAALS = -28.6019 ELECTROSTATIC = -50.5386 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6871" Parameter: CONF_N -> "8002" Comparing "6871" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6872" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749346 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753049 ATOM PAIRS WERE FOUND FOR ATOM LIST 41600 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29804 from a total of 753049 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6872 -75.24168 -3.89882 0.74893 INTE EXTERN> -24.92307 -50.31862 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2417" Parameter: A <- "-75.2417" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9231" Parameter: B <- "-24.9231" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3186" Parameter: C <- "-50.3186" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6872 TOTAL ENERGY = -75.2417 RDTITL> * VAN DER WAALS = -24.9231 ELECTROSTATIC = -50.3186 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6872" Parameter: CONF_N -> "8002" Comparing "6872" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6873" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753049 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756330 ATOM PAIRS WERE FOUND FOR ATOM LIST 41653 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30196 from a total of 756330 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6873 -78.10798 2.86630 0.74697 INTE EXTERN> -26.00242 -52.10556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.108" Parameter: A <- "-78.108" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0024" Parameter: B <- "-26.0024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1056" Parameter: C <- "-52.1056" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6873 TOTAL ENERGY = -78.108 RDTITL> * VAN DER WAALS = -26.0024 ELECTROSTATIC = -52.1056 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6873" Parameter: CONF_N -> "8002" Comparing "6873" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6874" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756330 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752789 ATOM PAIRS WERE FOUND FOR ATOM LIST 41235 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29396 from a total of 752789 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6874 -73.98897 -4.11901 0.65618 INTE EXTERN> -30.16611 -43.82287 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.989" Parameter: A <- "-73.989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1661" Parameter: B <- "-30.1661" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8229" Parameter: C <- "-43.8229" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6874 TOTAL ENERGY = -73.989 RDTITL> * VAN DER WAALS = -30.1661 ELECTROSTATIC = -43.8229 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6874" Parameter: CONF_N -> "8002" Comparing "6874" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6875" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752789 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749708 ATOM PAIRS WERE FOUND FOR ATOM LIST 41382 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29229 from a total of 749708 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6875 -78.75458 4.76560 0.59824 INTE EXTERN> -31.45649 -47.29808 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7546" Parameter: A <- "-78.7546" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4565" Parameter: B <- "-31.4565" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2981" Parameter: C <- "-47.2981" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6875 TOTAL ENERGY = -78.7546 RDTITL> * VAN DER WAALS = -31.4565 ELECTROSTATIC = -47.2981 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6875" Parameter: CONF_N -> "8002" Comparing "6875" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6876" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749708 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753354 ATOM PAIRS WERE FOUND FOR ATOM LIST 41281 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29279 from a total of 753354 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6876 -73.91083 -4.84375 0.61056 INTE EXTERN> -29.56747 -44.34335 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9108" Parameter: A <- "-73.9108" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5675" Parameter: B <- "-29.5675" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3434" Parameter: C <- "-44.3434" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6876 TOTAL ENERGY = -73.9108 RDTITL> * VAN DER WAALS = -29.5675 ELECTROSTATIC = -44.3434 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6876" Parameter: CONF_N -> "8002" Comparing "6876" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6877" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753354 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755343 ATOM PAIRS WERE FOUND FOR ATOM LIST 41539 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29787 from a total of 755343 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6877 -78.19280 4.28197 0.72739 INTE EXTERN> -28.53774 -49.65506 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1928" Parameter: A <- "-78.1928" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5377" Parameter: B <- "-28.5377" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6551" Parameter: C <- "-49.6551" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6877 TOTAL ENERGY = -78.1928 RDTITL> * VAN DER WAALS = -28.5377 ELECTROSTATIC = -49.6551 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6877" Parameter: CONF_N -> "8002" Comparing "6877" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6878" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755343 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747860 ATOM PAIRS WERE FOUND FOR ATOM LIST 41043 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28825 from a total of 747860 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6878 -76.25384 -1.93896 0.65488 INTE EXTERN> -30.62527 -45.62856 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2538" Parameter: A <- "-76.2538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6253" Parameter: B <- "-30.6253" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6286" Parameter: C <- "-45.6286" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6878 TOTAL ENERGY = -76.2538 RDTITL> * VAN DER WAALS = -30.6253 ELECTROSTATIC = -45.6286 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6878" Parameter: CONF_N -> "8002" Comparing "6878" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6879" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747860 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750164 ATOM PAIRS WERE FOUND FOR ATOM LIST 41332 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28740 from a total of 750164 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6879 -81.12412 4.87028 0.74168 INTE EXTERN> -29.29873 -51.82538 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1241" Parameter: A <- "-81.1241" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2987" Parameter: B <- "-29.2987" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8254" Parameter: C <- "-51.8254" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6879 TOTAL ENERGY = -81.1241 RDTITL> * VAN DER WAALS = -29.2987 ELECTROSTATIC = -51.8254 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6879" Parameter: CONF_N -> "8002" Comparing "6879" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6880" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750164 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755452 ATOM PAIRS WERE FOUND FOR ATOM LIST 41540 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 755452 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6880 -76.87492 -4.24920 0.58696 INTE EXTERN> -33.71962 -43.15530 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8749" Parameter: A <- "-76.8749" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7196" Parameter: B <- "-33.7196" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1553" Parameter: C <- "-43.1553" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6880 TOTAL ENERGY = -76.8749 RDTITL> * VAN DER WAALS = -33.7196 ELECTROSTATIC = -43.1553 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6880" Parameter: CONF_N -> "8002" Comparing "6880" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6881" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755452 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754521 ATOM PAIRS WERE FOUND FOR ATOM LIST 41706 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30034 from a total of 754521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6881 -79.98427 3.10935 0.72117 INTE EXTERN> -27.99962 -51.98464 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9843" Parameter: A <- "-79.9843" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9996" Parameter: B <- "-27.9996" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.9846" Parameter: C <- "-51.9846" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6881 TOTAL ENERGY = -79.9843 RDTITL> * VAN DER WAALS = -27.9996 ELECTROSTATIC = -51.9846 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6881" Parameter: CONF_N -> "8002" Comparing "6881" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6882" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750460 ATOM PAIRS WERE FOUND FOR ATOM LIST 41476 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29669 from a total of 750460 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6882 -78.34836 -1.63590 0.74956 INTE EXTERN> -27.67852 -50.66985 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3484" Parameter: A <- "-78.3484" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6785" Parameter: B <- "-27.6785" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6698" Parameter: C <- "-50.6698" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6882 TOTAL ENERGY = -78.3484 RDTITL> * VAN DER WAALS = -27.6785 ELECTROSTATIC = -50.6698 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6882" Parameter: CONF_N -> "8002" Comparing "6882" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6883" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750460 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752883 ATOM PAIRS WERE FOUND FOR ATOM LIST 41623 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29819 from a total of 752883 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6883 -69.53249 -8.81587 0.64004 INTE EXTERN> -30.08222 -39.45028 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5325" Parameter: A <- "-69.5325" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0822" Parameter: B <- "-30.0822" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4503" Parameter: C <- "-39.4503" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6883 TOTAL ENERGY = -69.5325 RDTITL> * VAN DER WAALS = -30.0822 ELECTROSTATIC = -39.4503 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6883" Parameter: CONF_N -> "8002" Comparing "6883" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6884" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752883 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41543 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29485 from a total of 755601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6884 -73.37801 3.84552 0.60083 INTE EXTERN> -29.82174 -43.55627 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.378" Parameter: A <- "-73.378" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8217" Parameter: B <- "-29.8217" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5563" Parameter: C <- "-43.5563" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6884 TOTAL ENERGY = -73.378 RDTITL> * VAN DER WAALS = -29.8217 ELECTROSTATIC = -43.5563 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6884" Parameter: CONF_N -> "8002" Comparing "6884" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6885" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754521 ATOM PAIRS WERE FOUND FOR ATOM LIST 41595 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29707 from a total of 754521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6885 -79.62044 6.24243 0.70855 INTE EXTERN> -28.91649 -50.70395 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6204" Parameter: A <- "-79.6204" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9165" Parameter: B <- "-28.9165" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7039" Parameter: C <- "-50.7039" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6885 TOTAL ENERGY = -79.6204 RDTITL> * VAN DER WAALS = -28.9165 ELECTROSTATIC = -50.7039 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6885" Parameter: CONF_N -> "8002" Comparing "6885" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6886" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754957 ATOM PAIRS WERE FOUND FOR ATOM LIST 41594 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29541 from a total of 754957 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6886 -86.93214 7.31170 0.81462 INTE EXTERN> -24.35829 -62.57384 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.9321" Parameter: A <- "-86.9321" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3583" Parameter: B <- "-24.3583" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-62.5738" Parameter: C <- "-62.5738" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6886 TOTAL ENERGY = -86.9321 RDTITL> * VAN DER WAALS = -24.3583 ELECTROSTATIC = -62.5738 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6886" Parameter: CONF_N -> "8002" Comparing "6886" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6887" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754957 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755435 ATOM PAIRS WERE FOUND FOR ATOM LIST 41722 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30173 from a total of 755435 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6887 -82.86594 -4.06619 0.64422 INTE EXTERN> -31.48325 -51.38269 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.8659" Parameter: A <- "-82.8659" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4833" Parameter: B <- "-31.4833" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3827" Parameter: C <- "-51.3827" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6887 TOTAL ENERGY = -82.8659 RDTITL> * VAN DER WAALS = -31.4833 ELECTROSTATIC = -51.3827 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6887" Parameter: CONF_N -> "8002" Comparing "6887" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6888" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755435 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754685 ATOM PAIRS WERE FOUND FOR ATOM LIST 41607 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29884 from a total of 754685 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6888 -76.87401 -5.99193 0.66731 INTE EXTERN> -30.75715 -46.11686 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.874" Parameter: A <- "-76.874" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7572" Parameter: B <- "-30.7572" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1169" Parameter: C <- "-46.1169" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6888 TOTAL ENERGY = -76.874 RDTITL> * VAN DER WAALS = -30.7572 ELECTROSTATIC = -46.1169 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6888" Parameter: CONF_N -> "8002" Comparing "6888" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6889" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754685 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761634 ATOM PAIRS WERE FOUND FOR ATOM LIST 41988 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29854 from a total of 761634 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6889 -74.80162 -2.07239 0.72016 INTE EXTERN> -29.32720 -45.47442 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8016" Parameter: A <- "-74.8016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3272" Parameter: B <- "-29.3272" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4744" Parameter: C <- "-45.4744" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6889 TOTAL ENERGY = -74.8016 RDTITL> * VAN DER WAALS = -29.3272 ELECTROSTATIC = -45.4744 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6889" Parameter: CONF_N -> "8002" Comparing "6889" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6890" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761634 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756386 ATOM PAIRS WERE FOUND FOR ATOM LIST 41626 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29233 from a total of 756386 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6890 -75.73476 0.93313 0.73069 INTE EXTERN> -25.88776 -49.84700 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7348" Parameter: A <- "-75.7348" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8878" Parameter: B <- "-25.8878" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.847" Parameter: C <- "-49.847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6890 TOTAL ENERGY = -75.7348 RDTITL> * VAN DER WAALS = -25.8878 ELECTROSTATIC = -49.847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6890" Parameter: CONF_N -> "8002" Comparing "6890" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6891" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756386 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755100 ATOM PAIRS WERE FOUND FOR ATOM LIST 41630 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29320 from a total of 755100 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6891 -80.63422 4.89946 0.89578 INTE EXTERN> -24.31458 -56.31964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6342" Parameter: A <- "-80.6342" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3146" Parameter: B <- "-24.3146" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.3196" Parameter: C <- "-56.3196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6891 TOTAL ENERGY = -80.6342 RDTITL> * VAN DER WAALS = -24.3146 ELECTROSTATIC = -56.3196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6891" Parameter: CONF_N -> "8002" Comparing "6891" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6892" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755100 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758937 ATOM PAIRS WERE FOUND FOR ATOM LIST 41714 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29553 from a total of 758937 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6892 -81.29361 0.65940 0.69168 INTE EXTERN> -29.48248 -51.81113 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.2936" Parameter: A <- "-81.2936" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4825" Parameter: B <- "-29.4825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8111" Parameter: C <- "-51.8111" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6892 TOTAL ENERGY = -81.2936 RDTITL> * VAN DER WAALS = -29.4825 ELECTROSTATIC = -51.8111 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6892" Parameter: CONF_N -> "8002" Comparing "6892" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6893" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758937 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756656 ATOM PAIRS WERE FOUND FOR ATOM LIST 41623 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29279 from a total of 756656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6893 -76.99149 -4.30212 0.66441 INTE EXTERN> -31.22717 -45.76433 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9915" Parameter: A <- "-76.9915" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2272" Parameter: B <- "-31.2272" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7643" Parameter: C <- "-45.7643" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6893 TOTAL ENERGY = -76.9915 RDTITL> * VAN DER WAALS = -31.2272 ELECTROSTATIC = -45.7643 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6893" Parameter: CONF_N -> "8002" Comparing "6893" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6894" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752405 ATOM PAIRS WERE FOUND FOR ATOM LIST 41352 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29220 from a total of 752405 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6894 -82.01475 5.02325 0.69101 INTE EXTERN> -31.06167 -50.95308 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.0147" Parameter: A <- "-82.0147" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0617" Parameter: B <- "-31.0617" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9531" Parameter: C <- "-50.9531" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6894 TOTAL ENERGY = -82.0147 RDTITL> * VAN DER WAALS = -31.0617 ELECTROSTATIC = -50.9531 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6894" Parameter: CONF_N -> "8002" Comparing "6894" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6895" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752405 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754175 ATOM PAIRS WERE FOUND FOR ATOM LIST 41581 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29493 from a total of 754175 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6895 -79.26482 -2.74993 0.61780 INTE EXTERN> -31.68996 -47.57485 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2648" Parameter: A <- "-79.2648" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.69" Parameter: B <- "-31.69" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5749" Parameter: C <- "-47.5749" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6895 TOTAL ENERGY = -79.2648 RDTITL> * VAN DER WAALS = -31.69 ELECTROSTATIC = -47.5749 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6895" Parameter: CONF_N -> "8002" Comparing "6895" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6896" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754175 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755383 ATOM PAIRS WERE FOUND FOR ATOM LIST 41494 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29285 from a total of 755383 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6896 -75.62071 -3.64411 0.72069 INTE EXTERN> -26.33576 -49.28495 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6207" Parameter: A <- "-75.6207" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3358" Parameter: B <- "-26.3358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.285" Parameter: C <- "-49.285" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6896 TOTAL ENERGY = -75.6207 RDTITL> * VAN DER WAALS = -26.3358 ELECTROSTATIC = -49.285 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6896" Parameter: CONF_N -> "8002" Comparing "6896" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6897" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755383 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757038 ATOM PAIRS WERE FOUND FOR ATOM LIST 41619 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29391 from a total of 757038 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6897 -78.89750 3.27679 0.66064 INTE EXTERN> -29.52432 -49.37318 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8975" Parameter: A <- "-78.8975" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5243" Parameter: B <- "-29.5243" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3732" Parameter: C <- "-49.3732" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6897 TOTAL ENERGY = -78.8975 RDTITL> * VAN DER WAALS = -29.5243 ELECTROSTATIC = -49.3732 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6897" Parameter: CONF_N -> "8002" Comparing "6897" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6898" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757038 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751992 ATOM PAIRS WERE FOUND FOR ATOM LIST 41301 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28766 from a total of 751992 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6898 -79.92114 1.02364 0.74719 INTE EXTERN> -27.50808 -52.41307 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9211" Parameter: A <- "-79.9211" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5081" Parameter: B <- "-27.5081" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.4131" Parameter: C <- "-52.4131" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6898 TOTAL ENERGY = -79.9211 RDTITL> * VAN DER WAALS = -27.5081 ELECTROSTATIC = -52.4131 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6898" Parameter: CONF_N -> "8002" Comparing "6898" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6899" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751992 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752154 ATOM PAIRS WERE FOUND FOR ATOM LIST 41171 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29789 from a total of 752154 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6899 -84.23458 4.31344 0.62379 INTE EXTERN> -30.60024 -53.63434 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.2346" Parameter: A <- "-84.2346" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6002" Parameter: B <- "-30.6002" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6343" Parameter: C <- "-53.6343" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6899 TOTAL ENERGY = -84.2346 RDTITL> * VAN DER WAALS = -30.6002 ELECTROSTATIC = -53.6343 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6899" Parameter: CONF_N -> "8002" Comparing "6899" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6900" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752154 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756643 ATOM PAIRS WERE FOUND FOR ATOM LIST 41666 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30579 from a total of 756643 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6900 -73.32208 -10.91250 0.61474 INTE EXTERN> -30.10493 -43.21716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3221" Parameter: A <- "-73.3221" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1049" Parameter: B <- "-30.1049" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2172" Parameter: C <- "-43.2172" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6900 TOTAL ENERGY = -73.3221 RDTITL> * VAN DER WAALS = -30.1049 ELECTROSTATIC = -43.2172 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6900" Parameter: CONF_N -> "8002" Comparing "6900" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6901" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756643 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756401 ATOM PAIRS WERE FOUND FOR ATOM LIST 41484 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30089 from a total of 756401 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6901 -76.21532 2.89324 0.70325 INTE EXTERN> -28.36642 -47.84890 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2153" Parameter: A <- "-76.2153" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3664" Parameter: B <- "-28.3664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8489" Parameter: C <- "-47.8489" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6901 TOTAL ENERGY = -76.2153 RDTITL> * VAN DER WAALS = -28.3664 ELECTROSTATIC = -47.8489 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6901" Parameter: CONF_N -> "8002" Comparing "6901" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6902" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756401 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757876 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29675 from a total of 757876 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6902 -78.80281 2.58748 0.67936 INTE EXTERN> -28.52534 -50.27747 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8028" Parameter: A <- "-78.8028" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5253" Parameter: B <- "-28.5253" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2775" Parameter: C <- "-50.2775" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6902 TOTAL ENERGY = -78.8028 RDTITL> * VAN DER WAALS = -28.5253 ELECTROSTATIC = -50.2775 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6902" Parameter: CONF_N -> "8002" Comparing "6902" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6903" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757876 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753029 ATOM PAIRS WERE FOUND FOR ATOM LIST 41303 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29158 from a total of 753029 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6903 -73.55085 -5.25196 0.71619 INTE EXTERN> -25.61782 -47.93303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5508" Parameter: A <- "-73.5508" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6178" Parameter: B <- "-25.6178" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.933" Parameter: C <- "-47.933" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6903 TOTAL ENERGY = -73.5508 RDTITL> * VAN DER WAALS = -25.6178 ELECTROSTATIC = -47.933 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6903" Parameter: CONF_N -> "8002" Comparing "6903" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6904" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753029 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757389 ATOM PAIRS WERE FOUND FOR ATOM LIST 41574 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29214 from a total of 757389 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6904 -73.59947 0.04862 0.64106 INTE EXTERN> -28.78733 -44.81214 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5995" Parameter: A <- "-73.5995" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7873" Parameter: B <- "-28.7873" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8121" Parameter: C <- "-44.8121" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6904 TOTAL ENERGY = -73.5995 RDTITL> * VAN DER WAALS = -28.7873 ELECTROSTATIC = -44.8121 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6904" Parameter: CONF_N -> "8002" Comparing "6904" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6905" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757389 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757332 ATOM PAIRS WERE FOUND FOR ATOM LIST 41664 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29615 from a total of 757332 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6905 -76.79785 3.19838 0.67001 INTE EXTERN> -29.75584 -47.04202 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7979" Parameter: A <- "-76.7979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7558" Parameter: B <- "-29.7558" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.042" Parameter: C <- "-47.042" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6905 TOTAL ENERGY = -76.7979 RDTITL> * VAN DER WAALS = -29.7558 ELECTROSTATIC = -47.042 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6905" Parameter: CONF_N -> "8002" Comparing "6905" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6906" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757332 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757903 ATOM PAIRS WERE FOUND FOR ATOM LIST 41539 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29753 from a total of 757903 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6906 -73.83195 -2.96590 0.78769 INTE EXTERN> -24.83901 -48.99295 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.832" Parameter: A <- "-73.832" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.839" Parameter: B <- "-24.839" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9929" Parameter: C <- "-48.9929" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6906 TOTAL ENERGY = -73.832 RDTITL> * VAN DER WAALS = -24.839 ELECTROSTATIC = -48.9929 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6906" Parameter: CONF_N -> "8002" Comparing "6906" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6907" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757903 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749270 ATOM PAIRS WERE FOUND FOR ATOM LIST 41294 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29890 from a total of 749270 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6907 -77.31053 3.47857 0.66958 INTE EXTERN> -27.33578 -49.97474 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3105" Parameter: A <- "-77.3105" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3358" Parameter: B <- "-27.3358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9747" Parameter: C <- "-49.9747" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6907 TOTAL ENERGY = -77.3105 RDTITL> * VAN DER WAALS = -27.3358 ELECTROSTATIC = -49.9747 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6907" Parameter: CONF_N -> "8002" Comparing "6907" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6908" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749270 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757777 ATOM PAIRS WERE FOUND FOR ATOM LIST 41761 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29946 from a total of 757777 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6908 -70.66827 -6.64226 0.68944 INTE EXTERN> -27.05629 -43.61198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6683" Parameter: A <- "-70.6683" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0563" Parameter: B <- "-27.0563" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.612" Parameter: C <- "-43.612" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6908 TOTAL ENERGY = -70.6683 RDTITL> * VAN DER WAALS = -27.0563 ELECTROSTATIC = -43.612 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6908" Parameter: CONF_N -> "8002" Comparing "6908" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6909" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757777 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761988 ATOM PAIRS WERE FOUND FOR ATOM LIST 41670 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29669 from a total of 761988 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6909 -80.07649 9.40823 0.74991 INTE EXTERN> -25.71131 -54.36519 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0765" Parameter: A <- "-80.0765" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7113" Parameter: B <- "-25.7113" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.3652" Parameter: C <- "-54.3652" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6909 TOTAL ENERGY = -80.0765 RDTITL> * VAN DER WAALS = -25.7113 ELECTROSTATIC = -54.3652 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6909" Parameter: CONF_N -> "8002" Comparing "6909" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6910" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761988 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754673 ATOM PAIRS WERE FOUND FOR ATOM LIST 41475 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29748 from a total of 754673 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6910 -82.64198 2.56548 0.70340 INTE EXTERN> -28.38805 -54.25393 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.642" Parameter: A <- "-82.642" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.388" Parameter: B <- "-28.388" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2539" Parameter: C <- "-54.2539" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6910 TOTAL ENERGY = -82.642 RDTITL> * VAN DER WAALS = -28.388 ELECTROSTATIC = -54.2539 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6910" Parameter: CONF_N -> "8002" Comparing "6910" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6911" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754673 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753594 ATOM PAIRS WERE FOUND FOR ATOM LIST 41457 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29840 from a total of 753594 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6911 -82.57407 -0.06791 0.69661 INTE EXTERN> -28.30168 -54.27238 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5741" Parameter: A <- "-82.5741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3017" Parameter: B <- "-28.3017" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2724" Parameter: C <- "-54.2724" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6911 TOTAL ENERGY = -82.5741 RDTITL> * VAN DER WAALS = -28.3017 ELECTROSTATIC = -54.2724 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6911" Parameter: CONF_N -> "8002" Comparing "6911" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6912" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753594 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759249 ATOM PAIRS WERE FOUND FOR ATOM LIST 41824 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29886 from a total of 759249 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6912 -79.68544 -2.88863 0.60770 INTE EXTERN> -31.44056 -48.24487 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6854" Parameter: A <- "-79.6854" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4406" Parameter: B <- "-31.4406" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2449" Parameter: C <- "-48.2449" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6912 TOTAL ENERGY = -79.6854 RDTITL> * VAN DER WAALS = -31.4406 ELECTROSTATIC = -48.2449 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6912" Parameter: CONF_N -> "8002" Comparing "6912" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6913" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759249 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758496 ATOM PAIRS WERE FOUND FOR ATOM LIST 41743 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29988 from a total of 758496 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6913 -74.78598 -4.89946 0.72022 INTE EXTERN> -26.95328 -47.83270 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.786" Parameter: A <- "-74.786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9533" Parameter: B <- "-26.9533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8327" Parameter: C <- "-47.8327" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6913 TOTAL ENERGY = -74.786 RDTITL> * VAN DER WAALS = -26.9533 ELECTROSTATIC = -47.8327 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6913" Parameter: CONF_N -> "8002" Comparing "6913" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6914" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758496 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756709 ATOM PAIRS WERE FOUND FOR ATOM LIST 41627 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30362 from a total of 756709 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6914 -74.62435 -0.16163 0.61144 INTE EXTERN> -32.32783 -42.29653 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6244" Parameter: A <- "-74.6244" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3278" Parameter: B <- "-32.3278" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2965" Parameter: C <- "-42.2965" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6914 TOTAL ENERGY = -74.6244 RDTITL> * VAN DER WAALS = -32.3278 ELECTROSTATIC = -42.2965 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6914" Parameter: CONF_N -> "8002" Comparing "6914" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6915" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756709 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756955 ATOM PAIRS WERE FOUND FOR ATOM LIST 41724 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29519 from a total of 756955 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6915 -77.98627 3.36192 0.66641 INTE EXTERN> -30.95430 -47.03197 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9863" Parameter: A <- "-77.9863" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9543" Parameter: B <- "-30.9543" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.032" Parameter: C <- "-47.032" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6915 TOTAL ENERGY = -77.9863 RDTITL> * VAN DER WAALS = -30.9543 ELECTROSTATIC = -47.032 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6915" Parameter: CONF_N -> "8002" Comparing "6915" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6916" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756955 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756772 ATOM PAIRS WERE FOUND FOR ATOM LIST 41481 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30006 from a total of 756772 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6916 -87.25723 9.27096 0.62960 INTE EXTERN> -33.25268 -54.00455 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.2572" Parameter: A <- "-87.2572" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2527" Parameter: B <- "-33.2527" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0046" Parameter: C <- "-54.0046" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6916 TOTAL ENERGY = -87.2572 RDTITL> * VAN DER WAALS = -33.2527 ELECTROSTATIC = -54.0046 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6916" Parameter: CONF_N -> "8002" Comparing "6916" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6917" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756772 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754646 ATOM PAIRS WERE FOUND FOR ATOM LIST 41480 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29693 from a total of 754646 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6917 -77.51677 -9.74045 0.55106 INTE EXTERN> -32.80954 -44.70723 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5168" Parameter: A <- "-77.5168" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8095" Parameter: B <- "-32.8095" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7072" Parameter: C <- "-44.7072" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6917 TOTAL ENERGY = -77.5168 RDTITL> * VAN DER WAALS = -32.8095 ELECTROSTATIC = -44.7072 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6917" Parameter: CONF_N -> "8002" Comparing "6917" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6918" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754646 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751804 ATOM PAIRS WERE FOUND FOR ATOM LIST 41371 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29778 from a total of 751804 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6918 -82.48260 4.96582 0.68421 INTE EXTERN> -28.79788 -53.68472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.4826" Parameter: A <- "-82.4826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7979" Parameter: B <- "-28.7979" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6847" Parameter: C <- "-53.6847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6918 TOTAL ENERGY = -82.4826 RDTITL> * VAN DER WAALS = -28.7979 ELECTROSTATIC = -53.6847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6918" Parameter: CONF_N -> "8002" Comparing "6918" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6919" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751804 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748213 ATOM PAIRS WERE FOUND FOR ATOM LIST 41085 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30190 from a total of 748213 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6919 -74.73157 -7.75103 0.64351 INTE EXTERN> -30.15613 -44.57544 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7316" Parameter: A <- "-74.7316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1561" Parameter: B <- "-30.1561" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5754" Parameter: C <- "-44.5754" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6919 TOTAL ENERGY = -74.7316 RDTITL> * VAN DER WAALS = -30.1561 ELECTROSTATIC = -44.5754 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6919" Parameter: CONF_N -> "8002" Comparing "6919" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6920" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748213 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756200 ATOM PAIRS WERE FOUND FOR ATOM LIST 41603 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30184 from a total of 756200 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6920 -77.38577 2.65420 0.66257 INTE EXTERN> -30.27120 -47.11457 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3858" Parameter: A <- "-77.3858" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2712" Parameter: B <- "-30.2712" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1146" Parameter: C <- "-47.1146" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6920 TOTAL ENERGY = -77.3858 RDTITL> * VAN DER WAALS = -30.2712 ELECTROSTATIC = -47.1146 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6920" Parameter: CONF_N -> "8002" Comparing "6920" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6921" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756200 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757856 ATOM PAIRS WERE FOUND FOR ATOM LIST 41610 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29189 from a total of 757856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6921 -86.25079 8.86502 0.72330 INTE EXTERN> -29.86505 -56.38574 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.2508" Parameter: A <- "-86.2508" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.865" Parameter: B <- "-29.865" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.3857" Parameter: C <- "-56.3857" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6921 TOTAL ENERGY = -86.2508 RDTITL> * VAN DER WAALS = -29.865 ELECTROSTATIC = -56.3857 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6921" Parameter: CONF_N -> "8002" Comparing "6921" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6922" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750423 ATOM PAIRS WERE FOUND FOR ATOM LIST 41233 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29985 from a total of 750423 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6922 -78.94381 -7.30698 0.63359 INTE EXTERN> -30.33244 -48.61137 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9438" Parameter: A <- "-78.9438" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3324" Parameter: B <- "-30.3324" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6114" Parameter: C <- "-48.6114" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6922 TOTAL ENERGY = -78.9438 RDTITL> * VAN DER WAALS = -30.3324 ELECTROSTATIC = -48.6114 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6922" Parameter: CONF_N -> "8002" Comparing "6922" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6923" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750423 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754058 ATOM PAIRS WERE FOUND FOR ATOM LIST 41540 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29731 from a total of 754058 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6923 -74.54423 -4.39957 0.65653 INTE EXTERN> -30.70832 -43.83591 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5442" Parameter: A <- "-74.5442" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7083" Parameter: B <- "-30.7083" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8359" Parameter: C <- "-43.8359" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6923 TOTAL ENERGY = -74.5442 RDTITL> * VAN DER WAALS = -30.7083 ELECTROSTATIC = -43.8359 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6923" Parameter: CONF_N -> "8002" Comparing "6923" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6924" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754058 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760844 ATOM PAIRS WERE FOUND FOR ATOM LIST 41741 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30118 from a total of 760844 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6924 -70.49367 -4.05057 0.84722 INTE EXTERN> -26.92909 -43.56458 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4937" Parameter: A <- "-70.4937" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9291" Parameter: B <- "-26.9291" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5646" Parameter: C <- "-43.5646" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6924 TOTAL ENERGY = -70.4937 RDTITL> * VAN DER WAALS = -26.9291 ELECTROSTATIC = -43.5646 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6924" Parameter: CONF_N -> "8002" Comparing "6924" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6925" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760844 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754400 ATOM PAIRS WERE FOUND FOR ATOM LIST 41262 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29766 from a total of 754400 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6925 -76.16102 5.66735 0.59275 INTE EXTERN> -33.01634 -43.14468 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.161" Parameter: A <- "-76.161" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0163" Parameter: B <- "-33.0163" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1447" Parameter: C <- "-43.1447" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6925 TOTAL ENERGY = -76.161 RDTITL> * VAN DER WAALS = -33.0163 ELECTROSTATIC = -43.1447 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6925" Parameter: CONF_N -> "8002" Comparing "6925" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6926" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754400 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757368 ATOM PAIRS WERE FOUND FOR ATOM LIST 41805 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29476 from a total of 757368 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6926 -77.55493 1.39391 0.64062 INTE EXTERN> -31.69754 -45.85739 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5549" Parameter: A <- "-77.5549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6975" Parameter: B <- "-31.6975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8574" Parameter: C <- "-45.8574" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6926 TOTAL ENERGY = -77.5549 RDTITL> * VAN DER WAALS = -31.6975 ELECTROSTATIC = -45.8574 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6926" Parameter: CONF_N -> "8002" Comparing "6926" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6927" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757368 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751647 ATOM PAIRS WERE FOUND FOR ATOM LIST 41401 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29536 from a total of 751647 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6927 -81.56414 4.00921 0.69243 INTE EXTERN> -29.89948 -51.66466 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5641" Parameter: A <- "-81.5641" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8995" Parameter: B <- "-29.8995" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6647" Parameter: C <- "-51.6647" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6927 TOTAL ENERGY = -81.5641 RDTITL> * VAN DER WAALS = -29.8995 ELECTROSTATIC = -51.6647 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6927" Parameter: CONF_N -> "8002" Comparing "6927" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6928" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751647 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753157 ATOM PAIRS WERE FOUND FOR ATOM LIST 41400 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29295 from a total of 753157 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6928 -78.30156 -3.26258 0.61260 INTE EXTERN> -32.22448 -46.07708 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3016" Parameter: A <- "-78.3016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2245" Parameter: B <- "-32.2245" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0771" Parameter: C <- "-46.0771" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6928 TOTAL ENERGY = -78.3016 RDTITL> * VAN DER WAALS = -32.2245 ELECTROSTATIC = -46.0771 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6928" Parameter: CONF_N -> "8002" Comparing "6928" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6929" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753157 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751783 ATOM PAIRS WERE FOUND FOR ATOM LIST 41415 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30001 from a total of 751783 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6929 -80.76368 2.46212 0.64590 INTE EXTERN> -32.34348 -48.42020 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7637" Parameter: A <- "-80.7637" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3435" Parameter: B <- "-32.3435" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4202" Parameter: C <- "-48.4202" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6929 TOTAL ENERGY = -80.7637 RDTITL> * VAN DER WAALS = -32.3435 ELECTROSTATIC = -48.4202 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6929" Parameter: CONF_N -> "8002" Comparing "6929" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6930" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751783 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751203 ATOM PAIRS WERE FOUND FOR ATOM LIST 41271 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28972 from a total of 751203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6930 -86.41240 5.64873 0.69674 INTE EXTERN> -30.80098 -55.61143 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.4124" Parameter: A <- "-86.4124" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.801" Parameter: B <- "-30.801" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.6114" Parameter: C <- "-55.6114" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6930 TOTAL ENERGY = -86.4124 RDTITL> * VAN DER WAALS = -30.801 ELECTROSTATIC = -55.6114 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6930" Parameter: CONF_N -> "8002" Comparing "6930" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6931" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751407 ATOM PAIRS WERE FOUND FOR ATOM LIST 41133 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28988 from a total of 751407 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6931 -77.14101 -9.27139 0.67079 INTE EXTERN> -28.85189 -48.28912 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.141" Parameter: A <- "-77.141" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8519" Parameter: B <- "-28.8519" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2891" Parameter: C <- "-48.2891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6931 TOTAL ENERGY = -77.141 RDTITL> * VAN DER WAALS = -28.8519 ELECTROSTATIC = -48.2891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6931" Parameter: CONF_N -> "8002" Comparing "6931" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6932" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751407 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754316 ATOM PAIRS WERE FOUND FOR ATOM LIST 41329 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29297 from a total of 754316 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6932 -75.17681 -1.96420 0.79848 INTE EXTERN> -21.42170 -53.75511 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1768" Parameter: A <- "-75.1768" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.4217" Parameter: B <- "-21.4217" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.7551" Parameter: C <- "-53.7551" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6932 TOTAL ENERGY = -75.1768 RDTITL> * VAN DER WAALS = -21.4217 ELECTROSTATIC = -53.7551 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6932" Parameter: CONF_N -> "8002" Comparing "6932" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6933" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754316 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761407 ATOM PAIRS WERE FOUND FOR ATOM LIST 41582 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29600 from a total of 761407 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6933 -76.42007 1.24326 1.07176 INTE EXTERN> -21.02931 -55.39076 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4201" Parameter: A <- "-76.4201" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.0293" Parameter: B <- "-21.0293" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.3908" Parameter: C <- "-55.3908" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6933 TOTAL ENERGY = -76.4201 RDTITL> * VAN DER WAALS = -21.0293 ELECTROSTATIC = -55.3908 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6933" Parameter: CONF_N -> "8002" Comparing "6933" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6934" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761407 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748062 ATOM PAIRS WERE FOUND FOR ATOM LIST 41283 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29019 from a total of 748062 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6934 -74.81097 -1.60910 0.75737 INTE EXTERN> -23.81010 -51.00087 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.811" Parameter: A <- "-74.811" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8101" Parameter: B <- "-23.8101" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0009" Parameter: C <- "-51.0009" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6934 TOTAL ENERGY = -74.811 RDTITL> * VAN DER WAALS = -23.8101 ELECTROSTATIC = -51.0009 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6934" Parameter: CONF_N -> "8002" Comparing "6934" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6935" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748062 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757874 ATOM PAIRS WERE FOUND FOR ATOM LIST 41612 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29640 from a total of 757874 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6935 -80.31739 5.50642 0.71961 INTE EXTERN> -30.32960 -49.98779 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3174" Parameter: A <- "-80.3174" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3296" Parameter: B <- "-30.3296" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9878" Parameter: C <- "-49.9878" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6935 TOTAL ENERGY = -80.3174 RDTITL> * VAN DER WAALS = -30.3296 ELECTROSTATIC = -49.9878 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6935" Parameter: CONF_N -> "8002" Comparing "6935" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6936" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757874 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755567 ATOM PAIRS WERE FOUND FOR ATOM LIST 41442 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30136 from a total of 755567 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6936 -77.06294 -3.25444 0.77666 INTE EXTERN> -25.67681 -51.38614 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0629" Parameter: A <- "-77.0629" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6768" Parameter: B <- "-25.6768" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3861" Parameter: C <- "-51.3861" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6936 TOTAL ENERGY = -77.0629 RDTITL> * VAN DER WAALS = -25.6768 ELECTROSTATIC = -51.3861 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6936" Parameter: CONF_N -> "8002" Comparing "6936" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6937" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755567 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756887 ATOM PAIRS WERE FOUND FOR ATOM LIST 41691 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29511 from a total of 756887 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6937 -83.46627 6.40333 0.64521 INTE EXTERN> -31.06999 -52.39628 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.4663" Parameter: A <- "-83.4663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.07" Parameter: B <- "-31.07" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3963" Parameter: C <- "-52.3963" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6937 TOTAL ENERGY = -83.4663 RDTITL> * VAN DER WAALS = -31.07 ELECTROSTATIC = -52.3963 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6937" Parameter: CONF_N -> "8002" Comparing "6937" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6938" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756887 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760629 ATOM PAIRS WERE FOUND FOR ATOM LIST 41743 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30171 from a total of 760629 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6938 -77.68611 -5.78016 0.72109 INTE EXTERN> -28.81116 -48.87494 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6861" Parameter: A <- "-77.6861" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8112" Parameter: B <- "-28.8112" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8749" Parameter: C <- "-48.8749" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6938 TOTAL ENERGY = -77.6861 RDTITL> * VAN DER WAALS = -28.8112 ELECTROSTATIC = -48.8749 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6938" Parameter: CONF_N -> "8002" Comparing "6938" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6939" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760629 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757185 ATOM PAIRS WERE FOUND FOR ATOM LIST 41579 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29515 from a total of 757185 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6939 -76.89332 -0.79279 0.59894 INTE EXTERN> -30.66198 -46.23134 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8933" Parameter: A <- "-76.8933" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.662" Parameter: B <- "-30.662" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2313" Parameter: C <- "-46.2313" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6939 TOTAL ENERGY = -76.8933 RDTITL> * VAN DER WAALS = -30.662 ELECTROSTATIC = -46.2313 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6939" Parameter: CONF_N -> "8002" Comparing "6939" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6940" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757185 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760170 ATOM PAIRS WERE FOUND FOR ATOM LIST 41508 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30022 from a total of 760170 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6940 -77.47525 0.58193 0.73366 INTE EXTERN> -29.32994 -48.14531 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4753" Parameter: A <- "-77.4753" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3299" Parameter: B <- "-29.3299" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1453" Parameter: C <- "-48.1453" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6940 TOTAL ENERGY = -77.4753 RDTITL> * VAN DER WAALS = -29.3299 ELECTROSTATIC = -48.1453 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6940" Parameter: CONF_N -> "8002" Comparing "6940" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6941" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760170 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761693 ATOM PAIRS WERE FOUND FOR ATOM LIST 41639 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29828 from a total of 761693 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6941 -73.37757 -4.09768 0.64238 INTE EXTERN> -27.40880 -45.96878 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3776" Parameter: A <- "-73.3776" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4088" Parameter: B <- "-27.4088" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9688" Parameter: C <- "-45.9688" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6941 TOTAL ENERGY = -73.3776 RDTITL> * VAN DER WAALS = -27.4088 ELECTROSTATIC = -45.9688 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6941" Parameter: CONF_N -> "8002" Comparing "6941" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6942" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761693 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754443 ATOM PAIRS WERE FOUND FOR ATOM LIST 41315 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29345 from a total of 754443 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6942 -67.71745 -5.66012 0.68320 INTE EXTERN> -27.25313 -40.46432 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7175" Parameter: A <- "-67.7175" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2531" Parameter: B <- "-27.2531" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4643" Parameter: C <- "-40.4643" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6942 TOTAL ENERGY = -67.7175 RDTITL> * VAN DER WAALS = -27.2531 ELECTROSTATIC = -40.4643 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6942" Parameter: CONF_N -> "8002" Comparing "6942" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6943" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754443 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754614 ATOM PAIRS WERE FOUND FOR ATOM LIST 41378 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29659 from a total of 754614 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6943 -70.48770 2.77025 0.73371 INTE EXTERN> -24.11406 -46.37364 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4877" Parameter: A <- "-70.4877" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1141" Parameter: B <- "-24.1141" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3736" Parameter: C <- "-46.3736" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6943 TOTAL ENERGY = -70.4877 RDTITL> * VAN DER WAALS = -24.1141 ELECTROSTATIC = -46.3736 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6943" Parameter: CONF_N -> "8002" Comparing "6943" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6944" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754614 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757699 ATOM PAIRS WERE FOUND FOR ATOM LIST 41596 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29836 from a total of 757699 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6944 -76.67124 6.18354 0.71425 INTE EXTERN> -28.57383 -48.09741 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6712" Parameter: A <- "-76.6712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5738" Parameter: B <- "-28.5738" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0974" Parameter: C <- "-48.0974" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6944 TOTAL ENERGY = -76.6712 RDTITL> * VAN DER WAALS = -28.5738 ELECTROSTATIC = -48.0974 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6944" Parameter: CONF_N -> "8002" Comparing "6944" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6945" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757699 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748845 ATOM PAIRS WERE FOUND FOR ATOM LIST 41104 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28791 from a total of 748845 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6945 -72.96099 -3.71025 0.62230 INTE EXTERN> -29.48362 -43.47737 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.961" Parameter: A <- "-72.961" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4836" Parameter: B <- "-29.4836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4774" Parameter: C <- "-43.4774" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6945 TOTAL ENERGY = -72.961 RDTITL> * VAN DER WAALS = -29.4836 ELECTROSTATIC = -43.4774 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6945" Parameter: CONF_N -> "8002" Comparing "6945" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6946" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748845 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749502 ATOM PAIRS WERE FOUND FOR ATOM LIST 41078 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28818 from a total of 749502 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6946 -76.86475 3.90376 0.62752 INTE EXTERN> -28.32360 -48.54115 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8647" Parameter: A <- "-76.8647" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3236" Parameter: B <- "-28.3236" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5412" Parameter: C <- "-48.5412" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6946 TOTAL ENERGY = -76.8647 RDTITL> * VAN DER WAALS = -28.3236 ELECTROSTATIC = -48.5412 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6946" Parameter: CONF_N -> "8002" Comparing "6946" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6947" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749502 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759239 ATOM PAIRS WERE FOUND FOR ATOM LIST 41609 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29294 from a total of 759239 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6947 -71.79367 -5.07108 0.62791 INTE EXTERN> -31.14269 -40.65098 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7937" Parameter: A <- "-71.7937" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1427" Parameter: B <- "-31.1427" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.651" Parameter: C <- "-40.651" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6947 TOTAL ENERGY = -71.7937 RDTITL> * VAN DER WAALS = -31.1427 ELECTROSTATIC = -40.651 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6947" Parameter: CONF_N -> "8002" Comparing "6947" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6948" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759239 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758393 ATOM PAIRS WERE FOUND FOR ATOM LIST 41580 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29960 from a total of 758393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6948 -82.56705 10.77338 0.62812 INTE EXTERN> -30.48605 -52.08100 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5671" Parameter: A <- "-82.5671" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.486" Parameter: B <- "-30.486" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.081" Parameter: C <- "-52.081" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6948 TOTAL ENERGY = -82.5671 RDTITL> * VAN DER WAALS = -30.486 ELECTROSTATIC = -52.081 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6948" Parameter: CONF_N -> "8002" Comparing "6948" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6949" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754248 ATOM PAIRS WERE FOUND FOR ATOM LIST 41381 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29502 from a total of 754248 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6949 -78.94515 -3.62191 0.76259 INTE EXTERN> -25.71632 -53.22883 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9451" Parameter: A <- "-78.9451" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7163" Parameter: B <- "-25.7163" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.2288" Parameter: C <- "-53.2288" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6949 TOTAL ENERGY = -78.9451 RDTITL> * VAN DER WAALS = -25.7163 ELECTROSTATIC = -53.2288 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6949" Parameter: CONF_N -> "8002" Comparing "6949" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6950" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754248 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749049 ATOM PAIRS WERE FOUND FOR ATOM LIST 41484 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29729 from a total of 749049 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6950 -77.27256 -1.67259 0.63709 INTE EXTERN> -29.85400 -47.41855 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2726" Parameter: A <- "-77.2726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.854" Parameter: B <- "-29.854" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4186" Parameter: C <- "-47.4186" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6950 TOTAL ENERGY = -77.2726 RDTITL> * VAN DER WAALS = -29.854 ELECTROSTATIC = -47.4186 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6950" Parameter: CONF_N -> "8002" Comparing "6950" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6951" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749049 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754166 ATOM PAIRS WERE FOUND FOR ATOM LIST 41392 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29395 from a total of 754166 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6951 -79.69125 2.41869 0.70495 INTE EXTERN> -28.05176 -51.63949 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6912" Parameter: A <- "-79.6912" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0518" Parameter: B <- "-28.0518" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6395" Parameter: C <- "-51.6395" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6951 TOTAL ENERGY = -79.6912 RDTITL> * VAN DER WAALS = -28.0518 ELECTROSTATIC = -51.6395 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6951" Parameter: CONF_N -> "8002" Comparing "6951" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6952" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754166 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753390 ATOM PAIRS WERE FOUND FOR ATOM LIST 41252 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29553 from a total of 753390 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6952 -69.92481 -9.76644 0.65461 INTE EXTERN> -26.87785 -43.04695 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9248" Parameter: A <- "-69.9248" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8779" Parameter: B <- "-26.8779" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.047" Parameter: C <- "-43.047" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6952 TOTAL ENERGY = -69.9248 RDTITL> * VAN DER WAALS = -26.8779 ELECTROSTATIC = -43.047 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6952" Parameter: CONF_N -> "8002" Comparing "6952" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6953" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753390 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762212 ATOM PAIRS WERE FOUND FOR ATOM LIST 41548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29879 from a total of 762212 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6953 -76.33402 6.40922 0.65070 INTE EXTERN> -28.72905 -47.60497 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.334" Parameter: A <- "-76.334" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.729" Parameter: B <- "-28.729" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.605" Parameter: C <- "-47.605" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6953 TOTAL ENERGY = -76.334 RDTITL> * VAN DER WAALS = -28.729 ELECTROSTATIC = -47.605 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6953" Parameter: CONF_N -> "8002" Comparing "6953" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6954" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762212 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759274 ATOM PAIRS WERE FOUND FOR ATOM LIST 41355 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29203 from a total of 759274 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6954 -75.02188 -1.31215 0.58948 INTE EXTERN> -30.52790 -44.49397 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0219" Parameter: A <- "-75.0219" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5279" Parameter: B <- "-30.5279" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.494" Parameter: C <- "-44.494" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6954 TOTAL ENERGY = -75.0219 RDTITL> * VAN DER WAALS = -30.5279 ELECTROSTATIC = -44.494 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6954" Parameter: CONF_N -> "8002" Comparing "6954" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6955" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759274 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751523 ATOM PAIRS WERE FOUND FOR ATOM LIST 41409 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29661 from a total of 751523 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6955 -70.11743 -4.90444 0.62075 INTE EXTERN> -30.69999 -39.41744 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1174" Parameter: A <- "-70.1174" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7" Parameter: B <- "-30.7" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4174" Parameter: C <- "-39.4174" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6955 TOTAL ENERGY = -70.1174 RDTITL> * VAN DER WAALS = -30.7 ELECTROSTATIC = -39.4174 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6955" Parameter: CONF_N -> "8002" Comparing "6955" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6956" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751523 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757604 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30400 from a total of 757604 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6956 -74.91420 4.79677 0.59783 INTE EXTERN> -32.36081 -42.55339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9142" Parameter: A <- "-74.9142" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3608" Parameter: B <- "-32.3608" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5534" Parameter: C <- "-42.5534" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6956 TOTAL ENERGY = -74.9142 RDTITL> * VAN DER WAALS = -32.3608 ELECTROSTATIC = -42.5534 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6956" Parameter: CONF_N -> "8002" Comparing "6956" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6957" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757604 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757304 ATOM PAIRS WERE FOUND FOR ATOM LIST 41332 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29367 from a total of 757304 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6957 -75.68565 0.77144 0.65892 INTE EXTERN> -30.09856 -45.58708 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6856" Parameter: A <- "-75.6856" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0986" Parameter: B <- "-30.0986" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5871" Parameter: C <- "-45.5871" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6957 TOTAL ENERGY = -75.6856 RDTITL> * VAN DER WAALS = -30.0986 ELECTROSTATIC = -45.5871 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6957" Parameter: CONF_N -> "8002" Comparing "6957" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6958" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757304 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755811 ATOM PAIRS WERE FOUND FOR ATOM LIST 41402 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29706 from a total of 755811 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6958 -76.87161 1.18597 0.60748 INTE EXTERN> -31.11292 -45.75869 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8716" Parameter: A <- "-76.8716" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1129" Parameter: B <- "-31.1129" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7587" Parameter: C <- "-45.7587" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6958 TOTAL ENERGY = -76.8716 RDTITL> * VAN DER WAALS = -31.1129 ELECTROSTATIC = -45.7587 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6958" Parameter: CONF_N -> "8002" Comparing "6958" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6959" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755811 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755368 ATOM PAIRS WERE FOUND FOR ATOM LIST 41435 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29640 from a total of 755368 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6959 -79.61704 2.74543 0.77176 INTE EXTERN> -25.66707 -53.94997 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.617" Parameter: A <- "-79.617" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6671" Parameter: B <- "-25.6671" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.95" Parameter: C <- "-53.95" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6959 TOTAL ENERGY = -79.617 RDTITL> * VAN DER WAALS = -25.6671 ELECTROSTATIC = -53.95 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6959" Parameter: CONF_N -> "8002" Comparing "6959" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6960" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755368 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755345 ATOM PAIRS WERE FOUND FOR ATOM LIST 41405 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29133 from a total of 755345 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6960 -69.64886 -9.96818 0.65421 INTE EXTERN> -27.26126 -42.38760 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6489" Parameter: A <- "-69.6489" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2613" Parameter: B <- "-27.2613" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3876" Parameter: C <- "-42.3876" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6960 TOTAL ENERGY = -69.6489 RDTITL> * VAN DER WAALS = -27.2613 ELECTROSTATIC = -42.3876 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6960" Parameter: CONF_N -> "8002" Comparing "6960" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6961" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755345 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748942 ATOM PAIRS WERE FOUND FOR ATOM LIST 41075 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28962 from a total of 748942 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6961 -72.43504 2.78618 0.58123 INTE EXTERN> -31.78391 -40.65113 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.435" Parameter: A <- "-72.435" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7839" Parameter: B <- "-31.7839" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6511" Parameter: C <- "-40.6511" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6961 TOTAL ENERGY = -72.435 RDTITL> * VAN DER WAALS = -31.7839 ELECTROSTATIC = -40.6511 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6961" Parameter: CONF_N -> "8002" Comparing "6961" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6962" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748942 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752221 ATOM PAIRS WERE FOUND FOR ATOM LIST 41248 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29516 from a total of 752221 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6962 -76.87489 4.43985 0.68747 INTE EXTERN> -27.28181 -49.59308 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8749" Parameter: A <- "-76.8749" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2818" Parameter: B <- "-27.2818" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5931" Parameter: C <- "-49.5931" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6962 TOTAL ENERGY = -76.8749 RDTITL> * VAN DER WAALS = -27.2818 ELECTROSTATIC = -49.5931 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6962" Parameter: CONF_N -> "8002" Comparing "6962" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6963" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752221 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749667 ATOM PAIRS WERE FOUND FOR ATOM LIST 41187 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29340 from a total of 749667 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6963 -73.17271 -3.70218 0.62039 INTE EXTERN> -28.01268 -45.16003 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1727" Parameter: A <- "-73.1727" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0127" Parameter: B <- "-28.0127" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.16" Parameter: C <- "-45.16" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6963 TOTAL ENERGY = -73.1727 RDTITL> * VAN DER WAALS = -28.0127 ELECTROSTATIC = -45.16 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6963" Parameter: CONF_N -> "8002" Comparing "6963" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6964" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749667 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 741284 ATOM PAIRS WERE FOUND FOR ATOM LIST 40588 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28589 from a total of 741284 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6964 -74.48678 1.31407 0.63519 INTE EXTERN> -29.63939 -44.84739 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4868" Parameter: A <- "-74.4868" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6394" Parameter: B <- "-29.6394" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8474" Parameter: C <- "-44.8474" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6964 TOTAL ENERGY = -74.4868 RDTITL> * VAN DER WAALS = -29.6394 ELECTROSTATIC = -44.8474 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6964" Parameter: CONF_N -> "8002" Comparing "6964" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6965" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 741284 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 738438 ATOM PAIRS WERE FOUND FOR ATOM LIST 40613 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28657 from a total of 738438 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6965 -78.37049 3.88371 0.66548 INTE EXTERN> -29.86767 -48.50282 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3705" Parameter: A <- "-78.3705" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8677" Parameter: B <- "-29.8677" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5028" Parameter: C <- "-48.5028" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6965 TOTAL ENERGY = -78.3705 RDTITL> * VAN DER WAALS = -29.8677 ELECTROSTATIC = -48.5028 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6965" Parameter: CONF_N -> "8002" Comparing "6965" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6966" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 738438 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748930 ATOM PAIRS WERE FOUND FOR ATOM LIST 41088 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29816 from a total of 748930 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6966 -77.30898 -1.06151 0.56766 INTE EXTERN> -31.68533 -45.62365 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.309" Parameter: A <- "-77.309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6853" Parameter: B <- "-31.6853" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6237" Parameter: C <- "-45.6237" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6966 TOTAL ENERGY = -77.309 RDTITL> * VAN DER WAALS = -31.6853 ELECTROSTATIC = -45.6237 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6966" Parameter: CONF_N -> "8002" Comparing "6966" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6967" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748930 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752963 ATOM PAIRS WERE FOUND FOR ATOM LIST 41145 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29112 from a total of 752963 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6967 -76.00533 -1.30365 0.59585 INTE EXTERN> -30.58987 -45.41546 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0053" Parameter: A <- "-76.0053" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5899" Parameter: B <- "-30.5899" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4155" Parameter: C <- "-45.4155" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6967 TOTAL ENERGY = -76.0053 RDTITL> * VAN DER WAALS = -30.5899 ELECTROSTATIC = -45.4155 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6967" Parameter: CONF_N -> "8002" Comparing "6967" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6968" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752963 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754511 ATOM PAIRS WERE FOUND FOR ATOM LIST 41330 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29865 from a total of 754511 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6968 -74.56182 -1.44350 0.64585 INTE EXTERN> -28.23691 -46.32491 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5618" Parameter: A <- "-74.5618" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2369" Parameter: B <- "-28.2369" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3249" Parameter: C <- "-46.3249" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6968 TOTAL ENERGY = -74.5618 RDTITL> * VAN DER WAALS = -28.2369 ELECTROSTATIC = -46.3249 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6968" Parameter: CONF_N -> "8002" Comparing "6968" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6969" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754511 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755055 ATOM PAIRS WERE FOUND FOR ATOM LIST 41539 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28904 from a total of 755055 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6969 -70.63894 -3.92288 0.62494 INTE EXTERN> -26.07860 -44.56034 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6389" Parameter: A <- "-70.6389" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0786" Parameter: B <- "-26.0786" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5603" Parameter: C <- "-44.5603" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6969 TOTAL ENERGY = -70.6389 RDTITL> * VAN DER WAALS = -26.0786 ELECTROSTATIC = -44.5603 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6969" Parameter: CONF_N -> "8002" Comparing "6969" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6970" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755055 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757655 ATOM PAIRS WERE FOUND FOR ATOM LIST 41537 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29996 from a total of 757655 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6970 -73.30832 2.66938 0.80973 INTE EXTERN> -25.11119 -48.19714 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3083" Parameter: A <- "-73.3083" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1112" Parameter: B <- "-25.1112" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1971" Parameter: C <- "-48.1971" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6970 TOTAL ENERGY = -73.3083 RDTITL> * VAN DER WAALS = -25.1112 ELECTROSTATIC = -48.1971 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6970" Parameter: CONF_N -> "8002" Comparing "6970" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6971" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757655 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760443 ATOM PAIRS WERE FOUND FOR ATOM LIST 41580 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29991 from a total of 760443 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6971 -80.30511 6.99678 0.70332 INTE EXTERN> -26.46380 -53.84130 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3051" Parameter: A <- "-80.3051" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4638" Parameter: B <- "-26.4638" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8413" Parameter: C <- "-53.8413" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6971 TOTAL ENERGY = -80.3051 RDTITL> * VAN DER WAALS = -26.4638 ELECTROSTATIC = -53.8413 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6971" Parameter: CONF_N -> "8002" Comparing "6971" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6972" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760443 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759269 ATOM PAIRS WERE FOUND FOR ATOM LIST 41659 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29568 from a total of 759269 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6972 -72.06906 -8.23604 0.66161 INTE EXTERN> -27.58189 -44.48717 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0691" Parameter: A <- "-72.0691" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5819" Parameter: B <- "-27.5819" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4872" Parameter: C <- "-44.4872" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6972 TOTAL ENERGY = -72.0691 RDTITL> * VAN DER WAALS = -27.5819 ELECTROSTATIC = -44.4872 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6972" Parameter: CONF_N -> "8002" Comparing "6972" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6973" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759269 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755006 ATOM PAIRS WERE FOUND FOR ATOM LIST 41391 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29798 from a total of 755006 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6973 -77.22914 5.16008 0.58605 INTE EXTERN> -31.76579 -45.46335 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2291" Parameter: A <- "-77.2291" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7658" Parameter: B <- "-31.7658" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4633" Parameter: C <- "-45.4633" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6973 TOTAL ENERGY = -77.2291 RDTITL> * VAN DER WAALS = -31.7658 ELECTROSTATIC = -45.4633 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6973" Parameter: CONF_N -> "8002" Comparing "6973" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6974" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755006 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751363 ATOM PAIRS WERE FOUND FOR ATOM LIST 41354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29518 from a total of 751363 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6974 -71.32202 -5.90711 0.64450 INTE EXTERN> -26.18034 -45.14168 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.322" Parameter: A <- "-71.322" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1803" Parameter: B <- "-26.1803" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1417" Parameter: C <- "-45.1417" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6974 TOTAL ENERGY = -71.322 RDTITL> * VAN DER WAALS = -26.1803 ELECTROSTATIC = -45.1417 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6974" Parameter: CONF_N -> "8002" Comparing "6974" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6975" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751363 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755267 ATOM PAIRS WERE FOUND FOR ATOM LIST 41392 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29456 from a total of 755267 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6975 -72.29272 0.97070 0.91935 INTE EXTERN> -18.63775 -53.65497 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2927" Parameter: A <- "-72.2927" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-18.6378" Parameter: B <- "-18.6378" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.655" Parameter: C <- "-53.655" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6975 TOTAL ENERGY = -72.2927 RDTITL> * VAN DER WAALS = -18.6378 ELECTROSTATIC = -53.655 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6975" Parameter: CONF_N -> "8002" Comparing "6975" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6976" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755267 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752617 ATOM PAIRS WERE FOUND FOR ATOM LIST 41362 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29217 from a total of 752617 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6976 -74.31390 2.02118 0.68948 INTE EXTERN> -25.83033 -48.48357 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3139" Parameter: A <- "-74.3139" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8303" Parameter: B <- "-25.8303" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4836" Parameter: C <- "-48.4836" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6976 TOTAL ENERGY = -74.3139 RDTITL> * VAN DER WAALS = -25.8303 ELECTROSTATIC = -48.4836 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6976" Parameter: CONF_N -> "8002" Comparing "6976" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6977" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752617 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759693 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29535 from a total of 759693 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6977 -72.87359 -1.44031 0.71135 INTE EXTERN> -26.37554 -46.49805 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8736" Parameter: A <- "-72.8736" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3755" Parameter: B <- "-26.3755" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.498" Parameter: C <- "-46.498" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6977 TOTAL ENERGY = -72.8736 RDTITL> * VAN DER WAALS = -26.3755 ELECTROSTATIC = -46.498 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6977" Parameter: CONF_N -> "8002" Comparing "6977" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6978" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759693 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758910 ATOM PAIRS WERE FOUND FOR ATOM LIST 41788 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29512 from a total of 758910 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6978 -72.98356 0.10997 0.60846 INTE EXTERN> -30.94280 -42.04076 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9836" Parameter: A <- "-72.9836" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9428" Parameter: B <- "-30.9428" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0408" Parameter: C <- "-42.0408" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6978 TOTAL ENERGY = -72.9836 RDTITL> * VAN DER WAALS = -30.9428 ELECTROSTATIC = -42.0408 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6978" Parameter: CONF_N -> "8002" Comparing "6978" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6979" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758910 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755419 ATOM PAIRS WERE FOUND FOR ATOM LIST 41467 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30026 from a total of 755419 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6979 -73.05889 0.07533 0.68629 INTE EXTERN> -25.76224 -47.29665 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0589" Parameter: A <- "-73.0589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7622" Parameter: B <- "-25.7622" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2966" Parameter: C <- "-47.2966" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6979 TOTAL ENERGY = -73.0589 RDTITL> * VAN DER WAALS = -25.7622 ELECTROSTATIC = -47.2966 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6979" Parameter: CONF_N -> "8002" Comparing "6979" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6980" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755419 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754738 ATOM PAIRS WERE FOUND FOR ATOM LIST 41634 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29107 from a total of 754738 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6980 -79.91088 6.85199 0.78548 INTE EXTERN> -24.70506 -55.20582 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9109" Parameter: A <- "-79.9109" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7051" Parameter: B <- "-24.7051" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.2058" Parameter: C <- "-55.2058" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6980 TOTAL ENERGY = -79.9109 RDTITL> * VAN DER WAALS = -24.7051 ELECTROSTATIC = -55.2058 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6980" Parameter: CONF_N -> "8002" Comparing "6980" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6981" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754738 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752822 ATOM PAIRS WERE FOUND FOR ATOM LIST 41315 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29915 from a total of 752822 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6981 -72.54006 -7.37082 0.69165 INTE EXTERN> -25.71704 -46.82302 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5401" Parameter: A <- "-72.5401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.717" Parameter: B <- "-25.717" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.823" Parameter: C <- "-46.823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6981 TOTAL ENERGY = -72.5401 RDTITL> * VAN DER WAALS = -25.717 ELECTROSTATIC = -46.823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6981" Parameter: CONF_N -> "8002" Comparing "6981" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6982" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752822 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750867 ATOM PAIRS WERE FOUND FOR ATOM LIST 41216 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29804 from a total of 750867 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6982 -69.60158 -2.93848 0.74323 INTE EXTERN> -25.21434 -44.38725 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6016" Parameter: A <- "-69.6016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2143" Parameter: B <- "-25.2143" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3872" Parameter: C <- "-44.3872" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6982 TOTAL ENERGY = -69.6016 RDTITL> * VAN DER WAALS = -25.2143 ELECTROSTATIC = -44.3872 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6982" Parameter: CONF_N -> "8002" Comparing "6982" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6983" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750867 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753344 ATOM PAIRS WERE FOUND FOR ATOM LIST 41476 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29778 from a total of 753344 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6983 -71.15695 1.55537 0.84736 INTE EXTERN> -23.78571 -47.37124 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1569" Parameter: A <- "-71.1569" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7857" Parameter: B <- "-23.7857" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3712" Parameter: C <- "-47.3712" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6983 TOTAL ENERGY = -71.1569 RDTITL> * VAN DER WAALS = -23.7857 ELECTROSTATIC = -47.3712 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6983" Parameter: CONF_N -> "8002" Comparing "6983" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6984" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753344 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754284 ATOM PAIRS WERE FOUND FOR ATOM LIST 41313 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30039 from a total of 754284 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6984 -80.64969 9.49274 0.66934 INTE EXTERN> -31.63260 -49.01709 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6497" Parameter: A <- "-80.6497" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6326" Parameter: B <- "-31.6326" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0171" Parameter: C <- "-49.0171" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6984 TOTAL ENERGY = -80.6497 RDTITL> * VAN DER WAALS = -31.6326 ELECTROSTATIC = -49.0171 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6984" Parameter: CONF_N -> "8002" Comparing "6984" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6985" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754284 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756925 ATOM PAIRS WERE FOUND FOR ATOM LIST 41656 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30055 from a total of 756925 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6985 -74.16572 -6.48397 0.66881 INTE EXTERN> -31.95347 -42.21224 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1657" Parameter: A <- "-74.1657" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9535" Parameter: B <- "-31.9535" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2122" Parameter: C <- "-42.2122" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6985 TOTAL ENERGY = -74.1657 RDTITL> * VAN DER WAALS = -31.9535 ELECTROSTATIC = -42.2122 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6985" Parameter: CONF_N -> "8002" Comparing "6985" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6986" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756925 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754462 ATOM PAIRS WERE FOUND FOR ATOM LIST 41406 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29967 from a total of 754462 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6986 -77.90160 3.73588 0.67404 INTE EXTERN> -28.98313 -48.91847 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9016" Parameter: A <- "-77.9016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9831" Parameter: B <- "-28.9831" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9185" Parameter: C <- "-48.9185" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6986 TOTAL ENERGY = -77.9016 RDTITL> * VAN DER WAALS = -28.9831 ELECTROSTATIC = -48.9185 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6986" Parameter: CONF_N -> "8002" Comparing "6986" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6987" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754462 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751768 ATOM PAIRS WERE FOUND FOR ATOM LIST 41198 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30133 from a total of 751768 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6987 -73.88428 -4.01732 0.79202 INTE EXTERN> -26.50741 -47.37688 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8843" Parameter: A <- "-73.8843" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5074" Parameter: B <- "-26.5074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3769" Parameter: C <- "-47.3769" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6987 TOTAL ENERGY = -73.8843 RDTITL> * VAN DER WAALS = -26.5074 ELECTROSTATIC = -47.3769 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6987" Parameter: CONF_N -> "8002" Comparing "6987" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6988" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751768 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752709 ATOM PAIRS WERE FOUND FOR ATOM LIST 41421 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29891 from a total of 752709 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6988 -71.96394 -1.92035 0.73874 INTE EXTERN> -23.89260 -48.07133 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9639" Parameter: A <- "-71.9639" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8926" Parameter: B <- "-23.8926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0713" Parameter: C <- "-48.0713" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6988 TOTAL ENERGY = -71.9639 RDTITL> * VAN DER WAALS = -23.8926 ELECTROSTATIC = -48.0713 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6988" Parameter: CONF_N -> "8002" Comparing "6988" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6989" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752709 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749174 ATOM PAIRS WERE FOUND FOR ATOM LIST 41218 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29683 from a total of 749174 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6989 -78.83222 6.86829 0.67752 INTE EXTERN> -28.77578 -50.05644 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8322" Parameter: A <- "-78.8322" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7758" Parameter: B <- "-28.7758" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0564" Parameter: C <- "-50.0564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6989 TOTAL ENERGY = -78.8322 RDTITL> * VAN DER WAALS = -28.7758 ELECTROSTATIC = -50.0564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6989" Parameter: CONF_N -> "8002" Comparing "6989" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6990" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749174 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754495 ATOM PAIRS WERE FOUND FOR ATOM LIST 41291 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30173 from a total of 754495 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6990 -75.57735 -3.25487 0.62470 INTE EXTERN> -29.61109 -45.96626 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5774" Parameter: A <- "-75.5774" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6111" Parameter: B <- "-29.6111" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9663" Parameter: C <- "-45.9663" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6990 TOTAL ENERGY = -75.5774 RDTITL> * VAN DER WAALS = -29.6111 ELECTROSTATIC = -45.9663 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6990" Parameter: CONF_N -> "8002" Comparing "6990" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6991" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754495 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747695 ATOM PAIRS WERE FOUND FOR ATOM LIST 41324 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29776 from a total of 747695 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6991 -76.64017 1.06281 0.65090 INTE EXTERN> -27.29135 -49.34882 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6402" Parameter: A <- "-76.6402" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2913" Parameter: B <- "-27.2913" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3488" Parameter: C <- "-49.3488" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6991 TOTAL ENERGY = -76.6402 RDTITL> * VAN DER WAALS = -27.2913 ELECTROSTATIC = -49.3488 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6991" Parameter: CONF_N -> "8002" Comparing "6991" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6992" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747695 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755346 ATOM PAIRS WERE FOUND FOR ATOM LIST 41472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29321 from a total of 755346 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6992 -76.37124 -0.26893 0.68997 INTE EXTERN> -27.19352 -49.17772 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3712" Parameter: A <- "-76.3712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1935" Parameter: B <- "-27.1935" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1777" Parameter: C <- "-49.1777" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6992 TOTAL ENERGY = -76.3712 RDTITL> * VAN DER WAALS = -27.1935 ELECTROSTATIC = -49.1777 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6992" Parameter: CONF_N -> "8002" Comparing "6992" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6993" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755346 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746290 ATOM PAIRS WERE FOUND FOR ATOM LIST 41159 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28851 from a total of 746290 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6993 -77.87650 1.50526 0.70136 INTE EXTERN> -27.39378 -50.48272 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8765" Parameter: A <- "-77.8765" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3938" Parameter: B <- "-27.3938" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4827" Parameter: C <- "-50.4827" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6993 TOTAL ENERGY = -77.8765 RDTITL> * VAN DER WAALS = -27.3938 ELECTROSTATIC = -50.4827 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6993" Parameter: CONF_N -> "8002" Comparing "6993" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6994" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746290 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744790 ATOM PAIRS WERE FOUND FOR ATOM LIST 40938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28839 from a total of 744790 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6994 -82.83434 4.95785 0.60617 INTE EXTERN> -29.69031 -53.14403 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.8343" Parameter: A <- "-82.8343" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6903" Parameter: B <- "-29.6903" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.144" Parameter: C <- "-53.144" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6994 TOTAL ENERGY = -82.8343 RDTITL> * VAN DER WAALS = -29.6903 ELECTROSTATIC = -53.144 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6994" Parameter: CONF_N -> "8002" Comparing "6994" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6995" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744790 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749166 ATOM PAIRS WERE FOUND FOR ATOM LIST 41233 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29145 from a total of 749166 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6995 -72.38056 -10.45379 0.75541 INTE EXTERN> -23.28650 -49.09406 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3806" Parameter: A <- "-72.3806" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.2865" Parameter: B <- "-23.2865" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0941" Parameter: C <- "-49.0941" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6995 TOTAL ENERGY = -72.3806 RDTITL> * VAN DER WAALS = -23.2865 ELECTROSTATIC = -49.0941 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6995" Parameter: CONF_N -> "8002" Comparing "6995" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6996" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749166 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750678 ATOM PAIRS WERE FOUND FOR ATOM LIST 41314 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29870 from a total of 750678 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6996 -77.30790 4.92735 0.72077 INTE EXTERN> -24.05136 -53.25654 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3079" Parameter: A <- "-77.3079" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0514" Parameter: B <- "-24.0514" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.2565" Parameter: C <- "-53.2565" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6996 TOTAL ENERGY = -77.3079 RDTITL> * VAN DER WAALS = -24.0514 ELECTROSTATIC = -53.2565 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6996" Parameter: CONF_N -> "8002" Comparing "6996" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6997" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750678 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755091 ATOM PAIRS WERE FOUND FOR ATOM LIST 41518 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28820 from a total of 755091 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6997 -82.99390 5.68600 0.61939 INTE EXTERN> -27.84863 -55.14527 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9939" Parameter: A <- "-82.9939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8486" Parameter: B <- "-27.8486" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.1453" Parameter: C <- "-55.1453" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6997 TOTAL ENERGY = -82.9939 RDTITL> * VAN DER WAALS = -27.8486 ELECTROSTATIC = -55.1453 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6997" Parameter: CONF_N -> "8002" Comparing "6997" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6998" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755091 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755854 ATOM PAIRS WERE FOUND FOR ATOM LIST 41582 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29163 from a total of 755854 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6998 -81.67327 -1.32064 0.77728 INTE EXTERN> -24.24650 -57.42677 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6733" Parameter: A <- "-81.6733" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2465" Parameter: B <- "-24.2465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.4268" Parameter: C <- "-57.4268" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6998 TOTAL ENERGY = -81.6733 RDTITL> * VAN DER WAALS = -24.2465 ELECTROSTATIC = -57.4268 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6998" Parameter: CONF_N -> "8002" Comparing "6998" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "6999" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755854 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756315 ATOM PAIRS WERE FOUND FOR ATOM LIST 41485 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29113 from a total of 756315 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 6999 -81.55183 -0.12143 0.80736 INTE EXTERN> -22.35523 -59.19661 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5518" Parameter: A <- "-81.5518" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.3552" Parameter: B <- "-22.3552" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.1966" Parameter: C <- "-59.1966" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 6999 TOTAL ENERGY = -81.5518 RDTITL> * VAN DER WAALS = -22.3552 ELECTROSTATIC = -59.1966 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "6999" Parameter: CONF_N -> "8002" Comparing "6999" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7000" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756315 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750112 ATOM PAIRS WERE FOUND FOR ATOM LIST 41329 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29269 from a total of 750112 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7000 -88.55597 7.00414 0.79558 INTE EXTERN> -24.02847 -64.52750 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.556" Parameter: A <- "-88.556" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0285" Parameter: B <- "-24.0285" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-64.5275" Parameter: C <- "-64.5275" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7000 TOTAL ENERGY = -88.556 RDTITL> * VAN DER WAALS = -24.0285 ELECTROSTATIC = -64.5275 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7000" Parameter: CONF_N -> "8002" Comparing "7000" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7001" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750112 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749201 ATOM PAIRS WERE FOUND FOR ATOM LIST 41049 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28820 from a total of 749201 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7001 -72.26699 -16.28899 0.68661 INTE EXTERN> -27.41048 -44.85650 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.267" Parameter: A <- "-72.267" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4105" Parameter: B <- "-27.4105" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8565" Parameter: C <- "-44.8565" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7001 TOTAL ENERGY = -72.267 RDTITL> * VAN DER WAALS = -27.4105 ELECTROSTATIC = -44.8565 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7001" Parameter: CONF_N -> "8002" Comparing "7001" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7002" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749201 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752362 ATOM PAIRS WERE FOUND FOR ATOM LIST 41127 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29150 from a total of 752362 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7002 -76.88566 4.61867 0.71336 INTE EXTERN> -27.83497 -49.05069 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8857" Parameter: A <- "-76.8857" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.835" Parameter: B <- "-27.835" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0507" Parameter: C <- "-49.0507" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7002 TOTAL ENERGY = -76.8857 RDTITL> * VAN DER WAALS = -27.835 ELECTROSTATIC = -49.0507 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7002" Parameter: CONF_N -> "8002" Comparing "7002" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7003" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752362 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751718 ATOM PAIRS WERE FOUND FOR ATOM LIST 41569 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28750 from a total of 751718 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7003 -76.98264 0.09698 0.60871 INTE EXTERN> -31.14851 -45.83413 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9826" Parameter: A <- "-76.9826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1485" Parameter: B <- "-31.1485" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8341" Parameter: C <- "-45.8341" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7003 TOTAL ENERGY = -76.9826 RDTITL> * VAN DER WAALS = -31.1485 ELECTROSTATIC = -45.8341 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7003" Parameter: CONF_N -> "8002" Comparing "7003" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7004" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751718 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751069 ATOM PAIRS WERE FOUND FOR ATOM LIST 41339 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28776 from a total of 751069 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7004 -79.09519 2.11254 0.65107 INTE EXTERN> -30.89643 -48.19875 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0952" Parameter: A <- "-79.0952" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8964" Parameter: B <- "-30.8964" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1988" Parameter: C <- "-48.1988" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7004 TOTAL ENERGY = -79.0952 RDTITL> * VAN DER WAALS = -30.8964 ELECTROSTATIC = -48.1988 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7004" Parameter: CONF_N -> "8002" Comparing "7004" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7005" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751069 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744195 ATOM PAIRS WERE FOUND FOR ATOM LIST 40825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28832 from a total of 744195 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7005 -73.56718 -5.52801 0.63565 INTE EXTERN> -27.41467 -46.15251 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5672" Parameter: A <- "-73.5672" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4147" Parameter: B <- "-27.4147" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1525" Parameter: C <- "-46.1525" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7005 TOTAL ENERGY = -73.5672 RDTITL> * VAN DER WAALS = -27.4147 ELECTROSTATIC = -46.1525 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7005" Parameter: CONF_N -> "8002" Comparing "7005" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7006" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744195 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746152 ATOM PAIRS WERE FOUND FOR ATOM LIST 40875 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28962 from a total of 746152 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7006 -76.19435 2.62717 0.67570 INTE EXTERN> -28.43973 -47.75462 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1944" Parameter: A <- "-76.1944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4397" Parameter: B <- "-28.4397" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7546" Parameter: C <- "-47.7546" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7006 TOTAL ENERGY = -76.1944 RDTITL> * VAN DER WAALS = -28.4397 ELECTROSTATIC = -47.7546 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7006" Parameter: CONF_N -> "8002" Comparing "7006" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7007" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746152 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 742447 ATOM PAIRS WERE FOUND FOR ATOM LIST 40825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29092 from a total of 742447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7007 -80.87232 4.67796 0.75046 INTE EXTERN> -25.43522 -55.43710 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.8723" Parameter: A <- "-80.8723" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4352" Parameter: B <- "-25.4352" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.4371" Parameter: C <- "-55.4371" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7007 TOTAL ENERGY = -80.8723 RDTITL> * VAN DER WAALS = -25.4352 ELECTROSTATIC = -55.4371 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7007" Parameter: CONF_N -> "8002" Comparing "7007" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7008" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 742447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746479 ATOM PAIRS WERE FOUND FOR ATOM LIST 40872 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28792 from a total of 746479 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7008 -75.57123 -5.30108 0.80536 INTE EXTERN> -23.25005 -52.32118 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5712" Parameter: A <- "-75.5712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.2501" Parameter: B <- "-23.2501" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3212" Parameter: C <- "-52.3212" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7008 TOTAL ENERGY = -75.5712 RDTITL> * VAN DER WAALS = -23.2501 ELECTROSTATIC = -52.3212 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7008" Parameter: CONF_N -> "8002" Comparing "7008" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7009" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746479 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745942 ATOM PAIRS WERE FOUND FOR ATOM LIST 41162 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28735 from a total of 745942 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7009 -70.70465 -4.86659 0.63247 INTE EXTERN> -30.41536 -40.28929 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7046" Parameter: A <- "-70.7046" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4154" Parameter: B <- "-30.4154" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2893" Parameter: C <- "-40.2893" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7009 TOTAL ENERGY = -70.7046 RDTITL> * VAN DER WAALS = -30.4154 ELECTROSTATIC = -40.2893 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7009" Parameter: CONF_N -> "8002" Comparing "7009" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7010" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745942 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744315 ATOM PAIRS WERE FOUND FOR ATOM LIST 40821 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28707 from a total of 744315 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7010 -78.45566 7.75101 0.69261 INTE EXTERN> -25.94510 -52.51056 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4557" Parameter: A <- "-78.4557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9451" Parameter: B <- "-25.9451" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5106" Parameter: C <- "-52.5106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7010 TOTAL ENERGY = -78.4557 RDTITL> * VAN DER WAALS = -25.9451 ELECTROSTATIC = -52.5106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7010" Parameter: CONF_N -> "8002" Comparing "7010" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7011" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744315 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747913 ATOM PAIRS WERE FOUND FOR ATOM LIST 40938 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29242 from a total of 747913 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7011 -77.95800 -0.49765 0.69093 INTE EXTERN> -27.14650 -50.81150 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.958" Parameter: A <- "-77.958" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1465" Parameter: B <- "-27.1465" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8115" Parameter: C <- "-50.8115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7011 TOTAL ENERGY = -77.958 RDTITL> * VAN DER WAALS = -27.1465 ELECTROSTATIC = -50.8115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7011" Parameter: CONF_N -> "8002" Comparing "7011" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7012" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747913 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749383 ATOM PAIRS WERE FOUND FOR ATOM LIST 41202 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30065 from a total of 749383 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7012 -74.67126 -3.28674 0.77721 INTE EXTERN> -26.06222 -48.60904 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6713" Parameter: A <- "-74.6713" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0622" Parameter: B <- "-26.0622" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.609" Parameter: C <- "-48.609" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7012 TOTAL ENERGY = -74.6713 RDTITL> * VAN DER WAALS = -26.0622 ELECTROSTATIC = -48.609 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7012" Parameter: CONF_N -> "8002" Comparing "7012" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7013" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749383 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748720 ATOM PAIRS WERE FOUND FOR ATOM LIST 41330 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29214 from a total of 748720 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7013 -74.90041 0.22915 0.59295 INTE EXTERN> -32.48239 -42.41801 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9004" Parameter: A <- "-74.9004" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4824" Parameter: B <- "-32.4824" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.418" Parameter: C <- "-42.418" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7013 TOTAL ENERGY = -74.9004 RDTITL> * VAN DER WAALS = -32.4824 ELECTROSTATIC = -42.418 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7013" Parameter: CONF_N -> "8002" Comparing "7013" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7014" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748720 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748314 ATOM PAIRS WERE FOUND FOR ATOM LIST 41157 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29201 from a total of 748314 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7014 -70.42776 -4.47265 0.69995 INTE EXTERN> -28.06980 -42.35796 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4278" Parameter: A <- "-70.4278" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0698" Parameter: B <- "-28.0698" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.358" Parameter: C <- "-42.358" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7014 TOTAL ENERGY = -70.4278 RDTITL> * VAN DER WAALS = -28.0698 ELECTROSTATIC = -42.358 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7014" Parameter: CONF_N -> "8002" Comparing "7014" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7015" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748314 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748451 ATOM PAIRS WERE FOUND FOR ATOM LIST 41150 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28891 from a total of 748451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7015 -74.75528 4.32752 0.63522 INTE EXTERN> -29.97330 -44.78198 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7553" Parameter: A <- "-74.7553" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9733" Parameter: B <- "-29.9733" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.782" Parameter: C <- "-44.782" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7015 TOTAL ENERGY = -74.7553 RDTITL> * VAN DER WAALS = -29.9733 ELECTROSTATIC = -44.782 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7015" Parameter: CONF_N -> "8002" Comparing "7015" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7016" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 743900 ATOM PAIRS WERE FOUND FOR ATOM LIST 40928 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28283 from a total of 743900 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7016 -68.81978 -5.93551 0.62840 INTE EXTERN> -28.27935 -40.54043 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8198" Parameter: A <- "-68.8198" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2793" Parameter: B <- "-28.2793" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5404" Parameter: C <- "-40.5404" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7016 TOTAL ENERGY = -68.8198 RDTITL> * VAN DER WAALS = -28.2793 ELECTROSTATIC = -40.5404 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7016" Parameter: CONF_N -> "8002" Comparing "7016" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7017" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 743900 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751514 ATOM PAIRS WERE FOUND FOR ATOM LIST 41280 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28949 from a total of 751514 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7017 -80.02329 11.20352 0.66663 INTE EXTERN> -28.46641 -51.55688 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0233" Parameter: A <- "-80.0233" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4664" Parameter: B <- "-28.4664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5569" Parameter: C <- "-51.5569" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7017 TOTAL ENERGY = -80.0233 RDTITL> * VAN DER WAALS = -28.4664 ELECTROSTATIC = -51.5569 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7017" Parameter: CONF_N -> "8002" Comparing "7017" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7018" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751514 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751408 ATOM PAIRS WERE FOUND FOR ATOM LIST 41216 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29469 from a total of 751408 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7018 -78.90349 -1.11980 0.60330 INTE EXTERN> -32.43910 -46.46439 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9035" Parameter: A <- "-78.9035" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4391" Parameter: B <- "-32.4391" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4644" Parameter: C <- "-46.4644" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7018 TOTAL ENERGY = -78.9035 RDTITL> * VAN DER WAALS = -32.4391 ELECTROSTATIC = -46.4644 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7018" Parameter: CONF_N -> "8002" Comparing "7018" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7019" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751408 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755171 ATOM PAIRS WERE FOUND FOR ATOM LIST 41365 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29875 from a total of 755171 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7019 -77.28311 -1.62038 0.73347 INTE EXTERN> -25.68632 -51.59679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2831" Parameter: A <- "-77.2831" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6863" Parameter: B <- "-25.6863" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5968" Parameter: C <- "-51.5968" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7019 TOTAL ENERGY = -77.2831 RDTITL> * VAN DER WAALS = -25.6863 ELECTROSTATIC = -51.5968 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7019" Parameter: CONF_N -> "8002" Comparing "7019" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7020" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755171 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749215 ATOM PAIRS WERE FOUND FOR ATOM LIST 41241 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29052 from a total of 749215 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7020 -77.88782 0.60471 0.68241 INTE EXTERN> -28.56309 -49.32473 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8878" Parameter: A <- "-77.8878" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5631" Parameter: B <- "-28.5631" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3247" Parameter: C <- "-49.3247" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7020 TOTAL ENERGY = -77.8878 RDTITL> * VAN DER WAALS = -28.5631 ELECTROSTATIC = -49.3247 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7020" Parameter: CONF_N -> "8002" Comparing "7020" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7021" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749215 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744655 ATOM PAIRS WERE FOUND FOR ATOM LIST 40941 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29511 from a total of 744655 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7021 -84.53549 6.64768 0.74431 INTE EXTERN> -26.61529 -57.92020 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.5355" Parameter: A <- "-84.5355" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6153" Parameter: B <- "-26.6153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.9202" Parameter: C <- "-57.9202" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7021 TOTAL ENERGY = -84.5355 RDTITL> * VAN DER WAALS = -26.6153 ELECTROSTATIC = -57.9202 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7021" Parameter: CONF_N -> "8002" Comparing "7021" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7022" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744655 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748355 ATOM PAIRS WERE FOUND FOR ATOM LIST 40952 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29194 from a total of 748355 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7022 -69.13349 -15.40200 0.60903 INTE EXTERN> -27.60145 -41.53204 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1335" Parameter: A <- "-69.1335" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6015" Parameter: B <- "-27.6015" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.532" Parameter: C <- "-41.532" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7022 TOTAL ENERGY = -69.1335 RDTITL> * VAN DER WAALS = -27.6015 ELECTROSTATIC = -41.532 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7022" Parameter: CONF_N -> "8002" Comparing "7022" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7023" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748355 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754441 ATOM PAIRS WERE FOUND FOR ATOM LIST 41416 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29135 from a total of 754441 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7023 -81.42541 12.29192 0.71036 INTE EXTERN> -26.90844 -54.51697 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4254" Parameter: A <- "-81.4254" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9084" Parameter: B <- "-26.9084" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.517" Parameter: C <- "-54.517" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7023 TOTAL ENERGY = -81.4254 RDTITL> * VAN DER WAALS = -26.9084 ELECTROSTATIC = -54.517 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7023" Parameter: CONF_N -> "8002" Comparing "7023" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7024" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754441 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755645 ATOM PAIRS WERE FOUND FOR ATOM LIST 41284 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29462 from a total of 755645 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7024 -78.09152 -3.33390 0.56746 INTE EXTERN> -31.54665 -46.54487 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0915" Parameter: A <- "-78.0915" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5466" Parameter: B <- "-31.5466" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5449" Parameter: C <- "-46.5449" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7024 TOTAL ENERGY = -78.0915 RDTITL> * VAN DER WAALS = -31.5466 ELECTROSTATIC = -46.5449 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7024" Parameter: CONF_N -> "8002" Comparing "7024" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7025" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755645 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748722 ATOM PAIRS WERE FOUND FOR ATOM LIST 41113 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29327 from a total of 748722 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7025 -80.17867 2.08715 0.62185 INTE EXTERN> -31.49202 -48.68664 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1787" Parameter: A <- "-80.1787" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.492" Parameter: B <- "-31.492" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6866" Parameter: C <- "-48.6866" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7025 TOTAL ENERGY = -80.1787 RDTITL> * VAN DER WAALS = -31.492 ELECTROSTATIC = -48.6866 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7025" Parameter: CONF_N -> "8002" Comparing "7025" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7026" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748722 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753021 ATOM PAIRS WERE FOUND FOR ATOM LIST 41259 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29934 from a total of 753021 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7026 -77.04042 -3.13825 0.65786 INTE EXTERN> -26.76177 -50.27865 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0404" Parameter: A <- "-77.0404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7618" Parameter: B <- "-26.7618" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2786" Parameter: C <- "-50.2786" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7026 TOTAL ENERGY = -77.0404 RDTITL> * VAN DER WAALS = -26.7618 ELECTROSTATIC = -50.2786 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7026" Parameter: CONF_N -> "8002" Comparing "7026" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7027" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753021 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41143 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30165 from a total of 750118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7027 -77.14569 0.10528 0.66549 INTE EXTERN> -29.87583 -47.26986 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1457" Parameter: A <- "-77.1457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8758" Parameter: B <- "-29.8758" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2699" Parameter: C <- "-47.2699" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7027 TOTAL ENERGY = -77.1457 RDTITL> * VAN DER WAALS = -29.8758 ELECTROSTATIC = -47.2699 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7027" Parameter: CONF_N -> "8002" Comparing "7027" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7028" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747709 ATOM PAIRS WERE FOUND FOR ATOM LIST 41056 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29634 from a total of 747709 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7028 -79.28458 2.13888 0.65985 INTE EXTERN> -30.06316 -49.22142 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2846" Parameter: A <- "-79.2846" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0632" Parameter: B <- "-30.0632" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2214" Parameter: C <- "-49.2214" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7028 TOTAL ENERGY = -79.2846 RDTITL> * VAN DER WAALS = -30.0632 ELECTROSTATIC = -49.2214 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7028" Parameter: CONF_N -> "8002" Comparing "7028" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7029" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747709 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757220 ATOM PAIRS WERE FOUND FOR ATOM LIST 41611 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30233 from a total of 757220 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7029 -78.69440 -0.59018 0.68186 INTE EXTERN> -31.86683 -46.82757 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6944" Parameter: A <- "-78.6944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8668" Parameter: B <- "-31.8668" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8276" Parameter: C <- "-46.8276" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7029 TOTAL ENERGY = -78.6944 RDTITL> * VAN DER WAALS = -31.8668 ELECTROSTATIC = -46.8276 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7029" Parameter: CONF_N -> "8002" Comparing "7029" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7030" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757220 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754636 ATOM PAIRS WERE FOUND FOR ATOM LIST 41318 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30326 from a total of 754636 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7030 -72.55328 -6.14111 0.66980 INTE EXTERN> -29.66031 -42.89298 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5533" Parameter: A <- "-72.5533" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6603" Parameter: B <- "-29.6603" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.893" Parameter: C <- "-42.893" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7030 TOTAL ENERGY = -72.5533 RDTITL> * VAN DER WAALS = -29.6603 ELECTROSTATIC = -42.893 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7030" Parameter: CONF_N -> "8002" Comparing "7030" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7031" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754636 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750914 ATOM PAIRS WERE FOUND FOR ATOM LIST 40971 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29533 from a total of 750914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7031 -76.63010 4.07682 0.62951 INTE EXTERN> -32.13551 -44.49459 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6301" Parameter: A <- "-76.6301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1355" Parameter: B <- "-32.1355" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4946" Parameter: C <- "-44.4946" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7031 TOTAL ENERGY = -76.6301 RDTITL> * VAN DER WAALS = -32.1355 ELECTROSTATIC = -44.4946 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7031" Parameter: CONF_N -> "8002" Comparing "7031" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7032" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748384 ATOM PAIRS WERE FOUND FOR ATOM LIST 41054 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29494 from a total of 748384 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7032 -73.82340 -2.80671 0.70036 INTE EXTERN> -29.71214 -44.11125 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8234" Parameter: A <- "-73.8234" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7121" Parameter: B <- "-29.7121" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1113" Parameter: C <- "-44.1113" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7032 TOTAL ENERGY = -73.8234 RDTITL> * VAN DER WAALS = -29.7121 ELECTROSTATIC = -44.1113 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7032" Parameter: CONF_N -> "8002" Comparing "7032" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7033" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748384 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748497 ATOM PAIRS WERE FOUND FOR ATOM LIST 41094 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29788 from a total of 748497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7033 -77.03013 3.20673 0.63791 INTE EXTERN> -31.05260 -45.97753 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0301" Parameter: A <- "-77.0301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0526" Parameter: B <- "-31.0526" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9775" Parameter: C <- "-45.9775" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7033 TOTAL ENERGY = -77.0301 RDTITL> * VAN DER WAALS = -31.0526 ELECTROSTATIC = -45.9775 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7033" Parameter: CONF_N -> "8002" Comparing "7033" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7034" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 741222 ATOM PAIRS WERE FOUND FOR ATOM LIST 40735 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29243 from a total of 741222 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7034 -75.12861 -1.90152 0.78744 INTE EXTERN> -26.55540 -48.57321 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1286" Parameter: A <- "-75.1286" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5554" Parameter: B <- "-26.5554" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5732" Parameter: C <- "-48.5732" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7034 TOTAL ENERGY = -75.1286 RDTITL> * VAN DER WAALS = -26.5554 ELECTROSTATIC = -48.5732 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7034" Parameter: CONF_N -> "8002" Comparing "7034" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7035" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 741222 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747171 ATOM PAIRS WERE FOUND FOR ATOM LIST 41156 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29322 from a total of 747171 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7035 -69.06236 -6.06625 0.66785 INTE EXTERN> -28.25421 -40.80814 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0624" Parameter: A <- "-69.0624" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2542" Parameter: B <- "-28.2542" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8081" Parameter: C <- "-40.8081" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7035 TOTAL ENERGY = -69.0624 RDTITL> * VAN DER WAALS = -28.2542 ELECTROSTATIC = -40.8081 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7035" Parameter: CONF_N -> "8002" Comparing "7035" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7036" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747171 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748883 ATOM PAIRS WERE FOUND FOR ATOM LIST 41093 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29748 from a total of 748883 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7036 -73.46974 4.40739 0.65529 INTE EXTERN> -28.96211 -44.50763 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4697" Parameter: A <- "-73.4697" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9621" Parameter: B <- "-28.9621" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5076" Parameter: C <- "-44.5076" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7036 TOTAL ENERGY = -73.4697 RDTITL> * VAN DER WAALS = -28.9621 ELECTROSTATIC = -44.5076 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7036" Parameter: CONF_N -> "8002" Comparing "7036" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7037" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748883 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753113 ATOM PAIRS WERE FOUND FOR ATOM LIST 41298 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29652 from a total of 753113 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7037 -80.18456 6.71482 0.61063 INTE EXTERN> -33.42393 -46.76063 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1846" Parameter: A <- "-80.1846" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4239" Parameter: B <- "-33.4239" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7606" Parameter: C <- "-46.7606" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7037 TOTAL ENERGY = -80.1846 RDTITL> * VAN DER WAALS = -33.4239 ELECTROSTATIC = -46.7606 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7037" Parameter: CONF_N -> "8002" Comparing "7037" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7038" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753113 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746699 ATOM PAIRS WERE FOUND FOR ATOM LIST 41119 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28481 from a total of 746699 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7038 -72.76657 -7.41799 0.73078 INTE EXTERN> -26.21239 -46.55418 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7666" Parameter: A <- "-72.7666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2124" Parameter: B <- "-26.2124" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5542" Parameter: C <- "-46.5542" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7038 TOTAL ENERGY = -72.7666 RDTITL> * VAN DER WAALS = -26.2124 ELECTROSTATIC = -46.5542 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7038" Parameter: CONF_N -> "8002" Comparing "7038" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7039" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746699 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744392 ATOM PAIRS WERE FOUND FOR ATOM LIST 41271 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29003 from a total of 744392 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7039 -73.50830 0.74173 0.70676 INTE EXTERN> -26.46191 -47.04639 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5083" Parameter: A <- "-73.5083" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4619" Parameter: B <- "-26.4619" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0464" Parameter: C <- "-47.0464" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7039 TOTAL ENERGY = -73.5083 RDTITL> * VAN DER WAALS = -26.4619 ELECTROSTATIC = -47.0464 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7039" Parameter: CONF_N -> "8002" Comparing "7039" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7040" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744392 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747922 ATOM PAIRS WERE FOUND FOR ATOM LIST 40957 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29256 from a total of 747922 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7040 -72.99444 -0.51386 0.70648 INTE EXTERN> -29.14632 -43.84813 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9944" Parameter: A <- "-72.9944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1463" Parameter: B <- "-29.1463" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8481" Parameter: C <- "-43.8481" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7040 TOTAL ENERGY = -72.9944 RDTITL> * VAN DER WAALS = -29.1463 ELECTROSTATIC = -43.8481 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7040" Parameter: CONF_N -> "8002" Comparing "7040" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7041" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747922 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746088 ATOM PAIRS WERE FOUND FOR ATOM LIST 40935 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29361 from a total of 746088 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7041 -79.64888 6.65444 0.90491 INTE EXTERN> -22.52640 -57.12249 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6489" Parameter: A <- "-79.6489" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.5264" Parameter: B <- "-22.5264" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.1225" Parameter: C <- "-57.1225" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7041 TOTAL ENERGY = -79.6489 RDTITL> * VAN DER WAALS = -22.5264 ELECTROSTATIC = -57.1225 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7041" Parameter: CONF_N -> "8002" Comparing "7041" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7042" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746088 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747692 ATOM PAIRS WERE FOUND FOR ATOM LIST 41231 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29331 from a total of 747692 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7042 -81.79576 2.14688 0.77218 INTE EXTERN> -26.31032 -55.48544 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.7958" Parameter: A <- "-81.7958" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3103" Parameter: B <- "-26.3103" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.4854" Parameter: C <- "-55.4854" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7042 TOTAL ENERGY = -81.7958 RDTITL> * VAN DER WAALS = -26.3103 ELECTROSTATIC = -55.4854 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7042" Parameter: CONF_N -> "8002" Comparing "7042" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7043" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747692 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747624 ATOM PAIRS WERE FOUND FOR ATOM LIST 41201 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28836 from a total of 747624 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7043 -71.36990 -10.42586 0.59557 INTE EXTERN> -29.48873 -41.88117 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3699" Parameter: A <- "-71.3699" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4887" Parameter: B <- "-29.4887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8812" Parameter: C <- "-41.8812" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7043 TOTAL ENERGY = -71.3699 RDTITL> * VAN DER WAALS = -29.4887 ELECTROSTATIC = -41.8812 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7043" Parameter: CONF_N -> "8002" Comparing "7043" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7044" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747624 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747683 ATOM PAIRS WERE FOUND FOR ATOM LIST 41205 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29391 from a total of 747683 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7044 -74.08796 2.71806 0.73742 INTE EXTERN> -23.77806 -50.30990 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.088" Parameter: A <- "-74.088" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7781" Parameter: B <- "-23.7781" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3099" Parameter: C <- "-50.3099" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7044 TOTAL ENERGY = -74.088 RDTITL> * VAN DER WAALS = -23.7781 ELECTROSTATIC = -50.3099 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7044" Parameter: CONF_N -> "8002" Comparing "7044" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7045" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747683 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 743786 ATOM PAIRS WERE FOUND FOR ATOM LIST 41119 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29179 from a total of 743786 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7045 -77.31976 3.23180 0.75718 INTE EXTERN> -25.77814 -51.54162 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3198" Parameter: A <- "-77.3198" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7781" Parameter: B <- "-25.7781" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5416" Parameter: C <- "-51.5416" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7045 TOTAL ENERGY = -77.3198 RDTITL> * VAN DER WAALS = -25.7781 ELECTROSTATIC = -51.5416 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7045" Parameter: CONF_N -> "8002" Comparing "7045" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7046" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 743786 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750830 ATOM PAIRS WERE FOUND FOR ATOM LIST 41223 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29369 from a total of 750830 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7046 -79.53083 2.21107 0.65310 INTE EXTERN> -30.46103 -49.06980 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5308" Parameter: A <- "-79.5308" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.461" Parameter: B <- "-30.461" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0698" Parameter: C <- "-49.0698" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7046 TOTAL ENERGY = -79.5308 RDTITL> * VAN DER WAALS = -30.461 ELECTROSTATIC = -49.0698 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7046" Parameter: CONF_N -> "8002" Comparing "7046" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7047" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750830 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744147 ATOM PAIRS WERE FOUND FOR ATOM LIST 40991 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29424 from a total of 744147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7047 -79.80480 0.27397 0.77518 INTE EXTERN> -25.77833 -54.02648 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8048" Parameter: A <- "-79.8048" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7783" Parameter: B <- "-25.7783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0265" Parameter: C <- "-54.0265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7047 TOTAL ENERGY = -79.8048 RDTITL> * VAN DER WAALS = -25.7783 ELECTROSTATIC = -54.0265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7047" Parameter: CONF_N -> "8002" Comparing "7047" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7048" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747209 ATOM PAIRS WERE FOUND FOR ATOM LIST 41003 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29527 from a total of 747209 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7048 -82.40546 2.60066 0.79986 INTE EXTERN> -26.84387 -55.56159 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.4055" Parameter: A <- "-82.4055" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8439" Parameter: B <- "-26.8439" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.5616" Parameter: C <- "-55.5616" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7048 TOTAL ENERGY = -82.4055 RDTITL> * VAN DER WAALS = -26.8439 ELECTROSTATIC = -55.5616 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7048" Parameter: CONF_N -> "8002" Comparing "7048" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7049" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747209 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747841 ATOM PAIRS WERE FOUND FOR ATOM LIST 41121 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29842 from a total of 747841 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7049 -77.22030 -5.18516 0.70181 INTE EXTERN> -31.37590 -45.84440 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2203" Parameter: A <- "-77.2203" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3759" Parameter: B <- "-31.3759" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8444" Parameter: C <- "-45.8444" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7049 TOTAL ENERGY = -77.2203 RDTITL> * VAN DER WAALS = -31.3759 ELECTROSTATIC = -45.8444 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7049" Parameter: CONF_N -> "8002" Comparing "7049" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7050" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747841 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747661 ATOM PAIRS WERE FOUND FOR ATOM LIST 41121 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29927 from a total of 747661 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7050 -78.03236 0.81206 0.67967 INTE EXTERN> -31.35378 -46.67859 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0324" Parameter: A <- "-78.0324" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3538" Parameter: B <- "-31.3538" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6786" Parameter: C <- "-46.6786" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7050 TOTAL ENERGY = -78.0324 RDTITL> * VAN DER WAALS = -31.3538 ELECTROSTATIC = -46.6786 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7050" Parameter: CONF_N -> "8002" Comparing "7050" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7051" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747661 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751787 ATOM PAIRS WERE FOUND FOR ATOM LIST 41434 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29987 from a total of 751787 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7051 -75.24694 -2.78542 0.58385 INTE EXTERN> -34.81681 -40.43013 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2469" Parameter: A <- "-75.2469" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-34.8168" Parameter: B <- "-34.8168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4301" Parameter: C <- "-40.4301" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7051 TOTAL ENERGY = -75.2469 RDTITL> * VAN DER WAALS = -34.8168 ELECTROSTATIC = -40.4301 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7051" Parameter: CONF_N -> "8002" Comparing "7051" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7052" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751787 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753133 ATOM PAIRS WERE FOUND FOR ATOM LIST 41331 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29739 from a total of 753133 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7052 -75.15114 -0.09580 0.71130 INTE EXTERN> -28.00543 -47.14571 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1511" Parameter: A <- "-75.1511" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0054" Parameter: B <- "-28.0054" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1457" Parameter: C <- "-47.1457" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7052 TOTAL ENERGY = -75.1511 RDTITL> * VAN DER WAALS = -28.0054 ELECTROSTATIC = -47.1457 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7052" Parameter: CONF_N -> "8002" Comparing "7052" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7053" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753133 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753387 ATOM PAIRS WERE FOUND FOR ATOM LIST 41494 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29890 from a total of 753387 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7053 -73.84112 -1.31002 0.74130 INTE EXTERN> -27.09599 -46.74513 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8411" Parameter: A <- "-73.8411" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.096" Parameter: B <- "-27.096" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7451" Parameter: C <- "-46.7451" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7053 TOTAL ENERGY = -73.8411 RDTITL> * VAN DER WAALS = -27.096 ELECTROSTATIC = -46.7451 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7053" Parameter: CONF_N -> "8002" Comparing "7053" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7054" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753387 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747599 ATOM PAIRS WERE FOUND FOR ATOM LIST 41226 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29818 from a total of 747599 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7054 -76.15096 2.30984 0.63778 INTE EXTERN> -32.02061 -44.13035 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.151" Parameter: A <- "-76.151" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0206" Parameter: B <- "-32.0206" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1303" Parameter: C <- "-44.1303" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7054 TOTAL ENERGY = -76.151 RDTITL> * VAN DER WAALS = -32.0206 ELECTROSTATIC = -44.1303 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7054" Parameter: CONF_N -> "8002" Comparing "7054" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7055" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747599 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754383 ATOM PAIRS WERE FOUND FOR ATOM LIST 41247 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29723 from a total of 754383 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7055 -70.96847 -5.18249 0.76199 INTE EXTERN> -22.24763 -48.72084 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9685" Parameter: A <- "-70.9685" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.2476" Parameter: B <- "-22.2476" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7208" Parameter: C <- "-48.7208" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7055 TOTAL ENERGY = -70.9685 RDTITL> * VAN DER WAALS = -22.2476 ELECTROSTATIC = -48.7208 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7055" Parameter: CONF_N -> "8002" Comparing "7055" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7056" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754383 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753534 ATOM PAIRS WERE FOUND FOR ATOM LIST 41487 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30046 from a total of 753534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7056 -82.17237 11.20391 0.85424 INTE EXTERN> -24.43886 -57.73352 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.1724" Parameter: A <- "-82.1724" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4389" Parameter: B <- "-24.4389" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.7335" Parameter: C <- "-57.7335" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7056 TOTAL ENERGY = -82.1724 RDTITL> * VAN DER WAALS = -24.4389 ELECTROSTATIC = -57.7335 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7056" Parameter: CONF_N -> "8002" Comparing "7056" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7057" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748633 ATOM PAIRS WERE FOUND FOR ATOM LIST 41151 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29692 from a total of 748633 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7057 -72.62425 -9.54812 0.67245 INTE EXTERN> -30.53498 -42.08928 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6243" Parameter: A <- "-72.6243" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.535" Parameter: B <- "-30.535" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0893" Parameter: C <- "-42.0893" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7057 TOTAL ENERGY = -72.6243 RDTITL> * VAN DER WAALS = -30.535 ELECTROSTATIC = -42.0893 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7057" Parameter: CONF_N -> "8002" Comparing "7057" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7058" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748633 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749055 ATOM PAIRS WERE FOUND FOR ATOM LIST 41069 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29651 from a total of 749055 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7058 -75.91748 3.29323 0.57056 INTE EXTERN> -32.08221 -43.83528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9175" Parameter: A <- "-75.9175" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0822" Parameter: B <- "-32.0822" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8353" Parameter: C <- "-43.8353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7058 TOTAL ENERGY = -75.9175 RDTITL> * VAN DER WAALS = -32.0822 ELECTROSTATIC = -43.8353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7058" Parameter: CONF_N -> "8002" Comparing "7058" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7059" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749055 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746691 ATOM PAIRS WERE FOUND FOR ATOM LIST 40862 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29694 from a total of 746691 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7059 -74.50452 -1.41297 0.66234 INTE EXTERN> -29.01986 -45.48466 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5045" Parameter: A <- "-74.5045" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0199" Parameter: B <- "-29.0199" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4847" Parameter: C <- "-45.4847" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7059 TOTAL ENERGY = -74.5045 RDTITL> * VAN DER WAALS = -29.0199 ELECTROSTATIC = -45.4847 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7059" Parameter: CONF_N -> "8002" Comparing "7059" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7060" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746691 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751810 ATOM PAIRS WERE FOUND FOR ATOM LIST 41211 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29556 from a total of 751810 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7060 -82.16114 7.65663 0.65026 INTE EXTERN> -32.11927 -50.04188 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.1611" Parameter: A <- "-82.1611" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1193" Parameter: B <- "-32.1193" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0419" Parameter: C <- "-50.0419" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7060 TOTAL ENERGY = -82.1611 RDTITL> * VAN DER WAALS = -32.1193 ELECTROSTATIC = -50.0419 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7060" Parameter: CONF_N -> "8002" Comparing "7060" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7061" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751810 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751746 ATOM PAIRS WERE FOUND FOR ATOM LIST 41299 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29327 from a total of 751746 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7061 -77.78966 -4.37149 0.66132 INTE EXTERN> -27.48252 -50.30714 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7897" Parameter: A <- "-77.7897" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4825" Parameter: B <- "-27.4825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3071" Parameter: C <- "-50.3071" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7061 TOTAL ENERGY = -77.7897 RDTITL> * VAN DER WAALS = -27.4825 ELECTROSTATIC = -50.3071 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7061" Parameter: CONF_N -> "8002" Comparing "7061" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7062" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751746 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748956 ATOM PAIRS WERE FOUND FOR ATOM LIST 41354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29151 from a total of 748956 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7062 -74.91195 -2.87771 0.60320 INTE EXTERN> -30.75346 -44.15849 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9119" Parameter: A <- "-74.9119" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7535" Parameter: B <- "-30.7535" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1585" Parameter: C <- "-44.1585" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7062 TOTAL ENERGY = -74.9119 RDTITL> * VAN DER WAALS = -30.7535 ELECTROSTATIC = -44.1585 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7062" Parameter: CONF_N -> "8002" Comparing "7062" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7063" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748956 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751725 ATOM PAIRS WERE FOUND FOR ATOM LIST 41270 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28864 from a total of 751725 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7063 -72.49607 -2.41588 0.52698 INTE EXTERN> -32.37737 -40.11870 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4961" Parameter: A <- "-72.4961" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3774" Parameter: B <- "-32.3774" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1187" Parameter: C <- "-40.1187" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7063 TOTAL ENERGY = -72.4961 RDTITL> * VAN DER WAALS = -32.3774 ELECTROSTATIC = -40.1187 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7063" Parameter: CONF_N -> "8002" Comparing "7063" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7064" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751725 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755345 ATOM PAIRS WERE FOUND FOR ATOM LIST 41560 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29142 from a total of 755345 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7064 -72.99330 0.49723 0.64391 INTE EXTERN> -29.39377 -43.59953 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9933" Parameter: A <- "-72.9933" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3938" Parameter: B <- "-29.3938" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5995" Parameter: C <- "-43.5995" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7064 TOTAL ENERGY = -72.9933 RDTITL> * VAN DER WAALS = -29.3938 ELECTROSTATIC = -43.5995 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7064" Parameter: CONF_N -> "8002" Comparing "7064" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7065" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755345 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755398 ATOM PAIRS WERE FOUND FOR ATOM LIST 41523 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28991 from a total of 755398 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7065 -69.82244 -3.17085 0.79838 INTE EXTERN> -23.16925 -46.65319 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8224" Parameter: A <- "-69.8224" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.1693" Parameter: B <- "-23.1693" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6532" Parameter: C <- "-46.6532" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7065 TOTAL ENERGY = -69.8224 RDTITL> * VAN DER WAALS = -23.1693 ELECTROSTATIC = -46.6532 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7065" Parameter: CONF_N -> "8002" Comparing "7065" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7066" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755398 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749753 ATOM PAIRS WERE FOUND FOR ATOM LIST 41238 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28978 from a total of 749753 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7066 -70.96501 1.14257 0.84824 INTE EXTERN> -22.13949 -48.82552 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.965" Parameter: A <- "-70.965" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.1395" Parameter: B <- "-22.1395" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8255" Parameter: C <- "-48.8255" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7066 TOTAL ENERGY = -70.965 RDTITL> * VAN DER WAALS = -22.1395 ELECTROSTATIC = -48.8255 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7066" Parameter: CONF_N -> "8002" Comparing "7066" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7067" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749753 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754826 ATOM PAIRS WERE FOUND FOR ATOM LIST 41396 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29525 from a total of 754826 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7067 -72.39876 1.43375 0.63152 INTE EXTERN> -29.33485 -43.06391 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3988" Parameter: A <- "-72.3988" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3348" Parameter: B <- "-29.3348" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0639" Parameter: C <- "-43.0639" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7067 TOTAL ENERGY = -72.3988 RDTITL> * VAN DER WAALS = -29.3348 ELECTROSTATIC = -43.0639 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7067" Parameter: CONF_N -> "8002" Comparing "7067" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7068" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754826 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755606 ATOM PAIRS WERE FOUND FOR ATOM LIST 41492 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28981 from a total of 755606 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7068 -78.01602 5.61726 0.53651 INTE EXTERN> -32.26635 -45.74967 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.016" Parameter: A <- "-78.016" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2664" Parameter: B <- "-32.2664" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7497" Parameter: C <- "-45.7497" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7068 TOTAL ENERGY = -78.016 RDTITL> * VAN DER WAALS = -32.2664 ELECTROSTATIC = -45.7497 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7068" Parameter: CONF_N -> "8002" Comparing "7068" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7069" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755606 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749188 ATOM PAIRS WERE FOUND FOR ATOM LIST 41198 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28974 from a total of 749188 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7069 -79.66282 1.64680 0.67913 INTE EXTERN> -30.10550 -49.55732 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6628" Parameter: A <- "-79.6628" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1055" Parameter: B <- "-30.1055" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5573" Parameter: C <- "-49.5573" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7069 TOTAL ENERGY = -79.6628 RDTITL> * VAN DER WAALS = -30.1055 ELECTROSTATIC = -49.5573 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7069" Parameter: CONF_N -> "8002" Comparing "7069" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7070" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749188 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751334 ATOM PAIRS WERE FOUND FOR ATOM LIST 41232 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29268 from a total of 751334 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7070 -84.00222 4.33940 0.78670 INTE EXTERN> -26.79181 -57.21041 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.0022" Parameter: A <- "-84.0022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7918" Parameter: B <- "-26.7918" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.2104" Parameter: C <- "-57.2104" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7070 TOTAL ENERGY = -84.0022 RDTITL> * VAN DER WAALS = -26.7918 ELECTROSTATIC = -57.2104 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7070" Parameter: CONF_N -> "8002" Comparing "7070" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7071" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751334 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749228 ATOM PAIRS WERE FOUND FOR ATOM LIST 41302 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28665 from a total of 749228 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7071 -79.44351 -4.55872 0.55061 INTE EXTERN> -32.97811 -46.46540 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4435" Parameter: A <- "-79.4435" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.9781" Parameter: B <- "-32.9781" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4654" Parameter: C <- "-46.4654" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7071 TOTAL ENERGY = -79.4435 RDTITL> * VAN DER WAALS = -32.9781 ELECTROSTATIC = -46.4654 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7071" Parameter: CONF_N -> "8002" Comparing "7071" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7072" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749228 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749771 ATOM PAIRS WERE FOUND FOR ATOM LIST 41271 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28990 from a total of 749771 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7072 -81.29362 1.85011 0.58973 INTE EXTERN> -33.22960 -48.06401 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.2936" Parameter: A <- "-81.2936" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2296" Parameter: B <- "-33.2296" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.064" Parameter: C <- "-48.064" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7072 TOTAL ENERGY = -81.2936 RDTITL> * VAN DER WAALS = -33.2296 ELECTROSTATIC = -48.064 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7072" Parameter: CONF_N -> "8002" Comparing "7072" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7073" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749771 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750815 ATOM PAIRS WERE FOUND FOR ATOM LIST 41156 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29087 from a total of 750815 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7073 -76.52991 -4.76370 0.77651 INTE EXTERN> -27.18047 -49.34945 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5299" Parameter: A <- "-76.5299" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1805" Parameter: B <- "-27.1805" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3494" Parameter: C <- "-49.3494" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7073 TOTAL ENERGY = -76.5299 RDTITL> * VAN DER WAALS = -27.1805 ELECTROSTATIC = -49.3494 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7073" Parameter: CONF_N -> "8002" Comparing "7073" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7074" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750815 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752488 ATOM PAIRS WERE FOUND FOR ATOM LIST 41272 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28816 from a total of 752488 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7074 -77.40887 0.87896 0.70313 INTE EXTERN> -26.61706 -50.79181 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4089" Parameter: A <- "-77.4089" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6171" Parameter: B <- "-26.6171" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7918" Parameter: C <- "-50.7918" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7074 TOTAL ENERGY = -77.4089 RDTITL> * VAN DER WAALS = -26.6171 ELECTROSTATIC = -50.7918 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7074" Parameter: CONF_N -> "8002" Comparing "7074" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7075" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752488 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749411 ATOM PAIRS WERE FOUND FOR ATOM LIST 41414 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29177 from a total of 749411 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7075 -76.04631 -1.36256 0.56674 INTE EXTERN> -31.63862 -44.40769 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0463" Parameter: A <- "-76.0463" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6386" Parameter: B <- "-31.6386" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4077" Parameter: C <- "-44.4077" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7075 TOTAL ENERGY = -76.0463 RDTITL> * VAN DER WAALS = -31.6386 ELECTROSTATIC = -44.4077 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7075" Parameter: CONF_N -> "8002" Comparing "7075" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7076" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749411 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744899 ATOM PAIRS WERE FOUND FOR ATOM LIST 40862 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29678 from a total of 744899 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7076 -76.12354 0.07722 0.73165 INTE EXTERN> -25.62808 -50.49546 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1235" Parameter: A <- "-76.1235" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6281" Parameter: B <- "-25.6281" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4955" Parameter: C <- "-50.4955" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7076 TOTAL ENERGY = -76.1235 RDTITL> * VAN DER WAALS = -25.6281 ELECTROSTATIC = -50.4955 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7076" Parameter: CONF_N -> "8002" Comparing "7076" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7077" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744899 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749803 ATOM PAIRS WERE FOUND FOR ATOM LIST 41225 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29240 from a total of 749803 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7077 -69.42029 -6.70324 0.59422 INTE EXTERN> -31.40351 -38.01678 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4203" Parameter: A <- "-69.4203" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4035" Parameter: B <- "-31.4035" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0168" Parameter: C <- "-38.0168" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7077 TOTAL ENERGY = -69.4203 RDTITL> * VAN DER WAALS = -31.4035 ELECTROSTATIC = -38.0168 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7077" Parameter: CONF_N -> "8002" Comparing "7077" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7078" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749803 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750419 ATOM PAIRS WERE FOUND FOR ATOM LIST 41245 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29319 from a total of 750419 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7078 -80.52787 11.10758 0.79719 INTE EXTERN> -25.38848 -55.13940 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5279" Parameter: A <- "-80.5279" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3885" Parameter: B <- "-25.3885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.1394" Parameter: C <- "-55.1394" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7078 TOTAL ENERGY = -80.5279 RDTITL> * VAN DER WAALS = -25.3885 ELECTROSTATIC = -55.1394 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7078" Parameter: CONF_N -> "8002" Comparing "7078" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7079" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750419 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747621 ATOM PAIRS WERE FOUND FOR ATOM LIST 41107 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28768 from a total of 747621 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7079 -70.67350 -9.85438 0.65145 INTE EXTERN> -27.91272 -42.76077 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6735" Parameter: A <- "-70.6735" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9127" Parameter: B <- "-27.9127" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7608" Parameter: C <- "-42.7608" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7079 TOTAL ENERGY = -70.6735 RDTITL> * VAN DER WAALS = -27.9127 ELECTROSTATIC = -42.7608 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7079" Parameter: CONF_N -> "8002" Comparing "7079" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7080" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747621 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754041 ATOM PAIRS WERE FOUND FOR ATOM LIST 41487 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29111 from a total of 754041 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7080 -76.29559 5.62209 0.75949 INTE EXTERN> -25.06635 -51.22924 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2956" Parameter: A <- "-76.2956" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0663" Parameter: B <- "-25.0663" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2292" Parameter: C <- "-51.2292" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7080 TOTAL ENERGY = -76.2956 RDTITL> * VAN DER WAALS = -25.0663 ELECTROSTATIC = -51.2292 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7080" Parameter: CONF_N -> "8002" Comparing "7080" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7081" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754041 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750776 ATOM PAIRS WERE FOUND FOR ATOM LIST 41297 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28936 from a total of 750776 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7081 -73.42893 -2.86665 0.56878 INTE EXTERN> -31.87175 -41.55718 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4289" Parameter: A <- "-73.4289" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8717" Parameter: B <- "-31.8717" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5572" Parameter: C <- "-41.5572" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7081 TOTAL ENERGY = -73.4289 RDTITL> * VAN DER WAALS = -31.8717 ELECTROSTATIC = -41.5572 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7081" Parameter: CONF_N -> "8002" Comparing "7081" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7082" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750776 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744130 ATOM PAIRS WERE FOUND FOR ATOM LIST 40919 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29321 from a total of 744130 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7082 -83.04692 9.61799 0.68537 INTE EXTERN> -29.03403 -54.01289 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.0469" Parameter: A <- "-83.0469" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.034" Parameter: B <- "-29.034" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0129" Parameter: C <- "-54.0129" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7082 TOTAL ENERGY = -83.0469 RDTITL> * VAN DER WAALS = -29.034 ELECTROSTATIC = -54.0129 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7082" Parameter: CONF_N -> "8002" Comparing "7082" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7083" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744130 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 743183 ATOM PAIRS WERE FOUND FOR ATOM LIST 41033 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29868 from a total of 743183 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7083 -74.11612 -8.93079 0.70936 INTE EXTERN> -26.76937 -47.34676 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1161" Parameter: A <- "-74.1161" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7694" Parameter: B <- "-26.7694" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3468" Parameter: C <- "-47.3468" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7083 TOTAL ENERGY = -74.1161 RDTITL> * VAN DER WAALS = -26.7694 ELECTROSTATIC = -47.3468 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7083" Parameter: CONF_N -> "8002" Comparing "7083" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7084" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 743183 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 742279 ATOM PAIRS WERE FOUND FOR ATOM LIST 40982 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29481 from a total of 742279 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7084 -76.11277 1.99664 0.61876 INTE EXTERN> -30.10891 -46.00385 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1128" Parameter: A <- "-76.1128" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1089" Parameter: B <- "-30.1089" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0039" Parameter: C <- "-46.0039" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7084 TOTAL ENERGY = -76.1128 RDTITL> * VAN DER WAALS = -30.1089 ELECTROSTATIC = -46.0039 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7084" Parameter: CONF_N -> "8002" Comparing "7084" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7085" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 742279 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 742890 ATOM PAIRS WERE FOUND FOR ATOM LIST 41031 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29463 from a total of 742890 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7085 -74.31286 -1.79990 0.67177 INTE EXTERN> -27.87307 -46.43979 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3129" Parameter: A <- "-74.3129" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8731" Parameter: B <- "-27.8731" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4398" Parameter: C <- "-46.4398" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7085 TOTAL ENERGY = -74.3129 RDTITL> * VAN DER WAALS = -27.8731 ELECTROSTATIC = -46.4398 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7085" Parameter: CONF_N -> "8002" Comparing "7085" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7086" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 742890 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750188 ATOM PAIRS WERE FOUND FOR ATOM LIST 41352 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29405 from a total of 750188 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7086 -77.18437 2.87151 0.57150 INTE EXTERN> -30.84186 -46.34252 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1844" Parameter: A <- "-77.1844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8419" Parameter: B <- "-30.8419" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3425" Parameter: C <- "-46.3425" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7086 TOTAL ENERGY = -77.1844 RDTITL> * VAN DER WAALS = -30.8419 ELECTROSTATIC = -46.3425 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7086" Parameter: CONF_N -> "8002" Comparing "7086" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7087" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750188 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754423 ATOM PAIRS WERE FOUND FOR ATOM LIST 41326 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29827 from a total of 754423 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7087 -73.09261 -4.09176 0.72865 INTE EXTERN> -25.88239 -47.21022 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0926" Parameter: A <- "-73.0926" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8824" Parameter: B <- "-25.8824" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2102" Parameter: C <- "-47.2102" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7087 TOTAL ENERGY = -73.0926 RDTITL> * VAN DER WAALS = -25.8824 ELECTROSTATIC = -47.2102 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7087" Parameter: CONF_N -> "8002" Comparing "7087" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7088" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754423 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753215 ATOM PAIRS WERE FOUND FOR ATOM LIST 41393 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29476 from a total of 753215 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7088 -75.86872 2.77610 0.79000 INTE EXTERN> -23.05979 -52.80893 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8687" Parameter: A <- "-75.8687" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.0598" Parameter: B <- "-23.0598" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8089" Parameter: C <- "-52.8089" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7088 TOTAL ENERGY = -75.8687 RDTITL> * VAN DER WAALS = -23.0598 ELECTROSTATIC = -52.8089 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7088" Parameter: CONF_N -> "8002" Comparing "7088" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7089" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753215 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 742889 ATOM PAIRS WERE FOUND FOR ATOM LIST 40819 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29562 from a total of 742889 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7089 -75.11792 -0.75079 0.60065 INTE EXTERN> -29.47980 -45.63812 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1179" Parameter: A <- "-75.1179" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4798" Parameter: B <- "-29.4798" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6381" Parameter: C <- "-45.6381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7089 TOTAL ENERGY = -75.1179 RDTITL> * VAN DER WAALS = -29.4798 ELECTROSTATIC = -45.6381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7089" Parameter: CONF_N -> "8002" Comparing "7089" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7090" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 742889 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747741 ATOM PAIRS WERE FOUND FOR ATOM LIST 41138 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29408 from a total of 747741 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7090 -72.26469 -2.85324 0.49286 INTE EXTERN> -33.30829 -38.95640 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2647" Parameter: A <- "-72.2647" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3083" Parameter: B <- "-33.3083" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.9564" Parameter: C <- "-38.9564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7090 TOTAL ENERGY = -72.2647 RDTITL> * VAN DER WAALS = -33.3083 ELECTROSTATIC = -38.9564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7090" Parameter: CONF_N -> "8002" Comparing "7090" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7091" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747741 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749162 ATOM PAIRS WERE FOUND FOR ATOM LIST 41034 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29570 from a total of 749162 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7091 -81.80039 9.53570 0.72739 INTE EXTERN> -26.89323 -54.90717 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8004" Parameter: A <- "-81.8004" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8932" Parameter: B <- "-26.8932" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.9072" Parameter: C <- "-54.9072" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7091 TOTAL ENERGY = -81.8004 RDTITL> * VAN DER WAALS = -26.8932 ELECTROSTATIC = -54.9072 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7091" Parameter: CONF_N -> "8002" Comparing "7091" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7092" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749162 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752378 ATOM PAIRS WERE FOUND FOR ATOM LIST 41338 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29967 from a total of 752378 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7092 -79.70563 -2.09476 0.74081 INTE EXTERN> -25.84945 -53.85619 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7056" Parameter: A <- "-79.7056" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8494" Parameter: B <- "-25.8494" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8562" Parameter: C <- "-53.8562" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7092 TOTAL ENERGY = -79.7056 RDTITL> * VAN DER WAALS = -25.8494 ELECTROSTATIC = -53.8562 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7092" Parameter: CONF_N -> "8002" Comparing "7092" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7093" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752378 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746147 ATOM PAIRS WERE FOUND FOR ATOM LIST 41136 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29732 from a total of 746147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7093 -74.03551 -5.67013 0.65334 INTE EXTERN> -30.86531 -43.17020 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0355" Parameter: A <- "-74.0355" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8653" Parameter: B <- "-30.8653" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1702" Parameter: C <- "-43.1702" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7093 TOTAL ENERGY = -74.0355 RDTITL> * VAN DER WAALS = -30.8653 ELECTROSTATIC = -43.1702 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7093" Parameter: CONF_N -> "8002" Comparing "7093" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7094" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748767 ATOM PAIRS WERE FOUND FOR ATOM LIST 41192 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29878 from a total of 748767 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7094 -74.04444 0.00893 0.69151 INTE EXTERN> -26.42501 -47.61943 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0444" Parameter: A <- "-74.0444" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.425" Parameter: B <- "-26.425" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6194" Parameter: C <- "-47.6194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7094 TOTAL ENERGY = -74.0444 RDTITL> * VAN DER WAALS = -26.425 ELECTROSTATIC = -47.6194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7094" Parameter: CONF_N -> "8002" Comparing "7094" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7095" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748767 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744841 ATOM PAIRS WERE FOUND FOR ATOM LIST 40852 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29321 from a total of 744841 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7095 -76.11700 2.07256 0.64816 INTE EXTERN> -28.88359 -47.23341 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.117" Parameter: A <- "-76.117" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8836" Parameter: B <- "-28.8836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2334" Parameter: C <- "-47.2334" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7095 TOTAL ENERGY = -76.117 RDTITL> * VAN DER WAALS = -28.8836 ELECTROSTATIC = -47.2334 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7095" Parameter: CONF_N -> "8002" Comparing "7095" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7096" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744841 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754159 ATOM PAIRS WERE FOUND FOR ATOM LIST 41415 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29540 from a total of 754159 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7096 -73.23644 -2.88056 0.61548 INTE EXTERN> -29.18365 -44.05279 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2364" Parameter: A <- "-73.2364" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1837" Parameter: B <- "-29.1837" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0528" Parameter: C <- "-44.0528" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7096 TOTAL ENERGY = -73.2364 RDTITL> * VAN DER WAALS = -29.1837 ELECTROSTATIC = -44.0528 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7096" Parameter: CONF_N -> "8002" Comparing "7096" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7097" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754159 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754184 ATOM PAIRS WERE FOUND FOR ATOM LIST 41465 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29453 from a total of 754184 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7097 -71.63142 -1.60502 0.93319 INTE EXTERN> -18.03102 -53.60040 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6314" Parameter: A <- "-71.6314" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-18.031" Parameter: B <- "-18.031" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6004" Parameter: C <- "-53.6004" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7097 TOTAL ENERGY = -71.6314 RDTITL> * VAN DER WAALS = -18.031 ELECTROSTATIC = -53.6004 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7097" Parameter: CONF_N -> "8002" Comparing "7097" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7098" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754184 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747177 ATOM PAIRS WERE FOUND FOR ATOM LIST 41129 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29557 from a total of 747177 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7098 -70.30952 -1.32190 0.57568 INTE EXTERN> -27.24292 -43.06660 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3095" Parameter: A <- "-70.3095" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2429" Parameter: B <- "-27.2429" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0666" Parameter: C <- "-43.0666" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7098 TOTAL ENERGY = -70.3095 RDTITL> * VAN DER WAALS = -27.2429 ELECTROSTATIC = -43.0666 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7098" Parameter: CONF_N -> "8002" Comparing "7098" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7099" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747177 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747932 ATOM PAIRS WERE FOUND FOR ATOM LIST 41081 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29558 from a total of 747932 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7099 -82.26720 11.95768 0.75659 INTE EXTERN> -24.80845 -57.45876 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.2672" Parameter: A <- "-82.2672" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8084" Parameter: B <- "-24.8084" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.4588" Parameter: C <- "-57.4588" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7099 TOTAL ENERGY = -82.2672 RDTITL> * VAN DER WAALS = -24.8084 ELECTROSTATIC = -57.4588 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7099" Parameter: CONF_N -> "8002" Comparing "7099" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7100" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747932 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750942 ATOM PAIRS WERE FOUND FOR ATOM LIST 41190 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29110 from a total of 750942 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7100 -76.22469 -6.04252 0.59954 INTE EXTERN> -29.40735 -46.81733 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2247" Parameter: A <- "-76.2247" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4074" Parameter: B <- "-29.4074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8173" Parameter: C <- "-46.8173" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7100 TOTAL ENERGY = -76.2247 RDTITL> * VAN DER WAALS = -29.4074 ELECTROSTATIC = -46.8173 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7100" Parameter: CONF_N -> "8002" Comparing "7100" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7101" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750942 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749777 ATOM PAIRS WERE FOUND FOR ATOM LIST 41059 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29201 from a total of 749777 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7101 -68.58796 -7.63673 0.78471 INTE EXTERN> -22.02116 -46.56680 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.588" Parameter: A <- "-68.588" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.0212" Parameter: B <- "-22.0212" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5668" Parameter: C <- "-46.5668" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7101 TOTAL ENERGY = -68.588 RDTITL> * VAN DER WAALS = -22.0212 ELECTROSTATIC = -46.5668 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7101" Parameter: CONF_N -> "8002" Comparing "7101" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7102" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749777 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751688 ATOM PAIRS WERE FOUND FOR ATOM LIST 41204 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30160 from a total of 751688 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7102 -73.88498 5.29702 0.62362 INTE EXTERN> -31.08767 -42.79731 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.885" Parameter: A <- "-73.885" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0877" Parameter: B <- "-31.0877" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7973" Parameter: C <- "-42.7973" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7102 TOTAL ENERGY = -73.885 RDTITL> * VAN DER WAALS = -31.0877 ELECTROSTATIC = -42.7973 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7102" Parameter: CONF_N -> "8002" Comparing "7102" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7103" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751688 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754328 ATOM PAIRS WERE FOUND FOR ATOM LIST 41407 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30285 from a total of 754328 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7103 -78.86115 4.97617 0.63608 INTE EXTERN> -31.52010 -47.34105 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8611" Parameter: A <- "-78.8611" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5201" Parameter: B <- "-31.5201" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3411" Parameter: C <- "-47.3411" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7103 TOTAL ENERGY = -78.8611 RDTITL> * VAN DER WAALS = -31.5201 ELECTROSTATIC = -47.3411 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7103" Parameter: CONF_N -> "8002" Comparing "7103" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7104" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754328 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750379 ATOM PAIRS WERE FOUND FOR ATOM LIST 41379 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29685 from a total of 750379 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7104 -75.84315 -3.01800 0.69107 INTE EXTERN> -28.78851 -47.05464 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8431" Parameter: A <- "-75.8431" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7885" Parameter: B <- "-28.7885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0546" Parameter: C <- "-47.0546" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7104 TOTAL ENERGY = -75.8431 RDTITL> * VAN DER WAALS = -28.7885 ELECTROSTATIC = -47.0546 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7104" Parameter: CONF_N -> "8002" Comparing "7104" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7105" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750379 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758977 ATOM PAIRS WERE FOUND FOR ATOM LIST 41704 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30027 from a total of 758977 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7105 -78.38207 2.53893 0.73286 INTE EXTERN> -29.44978 -48.93229 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3821" Parameter: A <- "-78.3821" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4498" Parameter: B <- "-29.4498" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9323" Parameter: C <- "-48.9323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7105 TOTAL ENERGY = -78.3821 RDTITL> * VAN DER WAALS = -29.4498 ELECTROSTATIC = -48.9323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7105" Parameter: CONF_N -> "8002" Comparing "7105" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7106" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758977 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758646 ATOM PAIRS WERE FOUND FOR ATOM LIST 41745 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29506 from a total of 758646 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7106 -73.82691 -4.55516 0.69426 INTE EXTERN> -29.38406 -44.44286 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8269" Parameter: A <- "-73.8269" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3841" Parameter: B <- "-29.3841" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4429" Parameter: C <- "-44.4429" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7106 TOTAL ENERGY = -73.8269 RDTITL> * VAN DER WAALS = -29.3841 ELECTROSTATIC = -44.4429 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7106" Parameter: CONF_N -> "8002" Comparing "7106" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7107" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758646 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756232 ATOM PAIRS WERE FOUND FOR ATOM LIST 41433 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29812 from a total of 756232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7107 -76.73283 2.90591 0.78801 INTE EXTERN> -24.66922 -52.06361 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7328" Parameter: A <- "-76.7328" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6692" Parameter: B <- "-24.6692" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0636" Parameter: C <- "-52.0636" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7107 TOTAL ENERGY = -76.7328 RDTITL> * VAN DER WAALS = -24.6692 ELECTROSTATIC = -52.0636 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7107" Parameter: CONF_N -> "8002" Comparing "7107" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7108" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757184 ATOM PAIRS WERE FOUND FOR ATOM LIST 41735 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29525 from a total of 757184 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7108 -75.98304 -0.74979 0.57495 INTE EXTERN> -33.11446 -42.86858 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.983" Parameter: A <- "-75.983" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1145" Parameter: B <- "-33.1145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8686" Parameter: C <- "-42.8686" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7108 TOTAL ENERGY = -75.983 RDTITL> * VAN DER WAALS = -33.1145 ELECTROSTATIC = -42.8686 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7108" Parameter: CONF_N -> "8002" Comparing "7108" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7109" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757184 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756326 ATOM PAIRS WERE FOUND FOR ATOM LIST 41449 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29303 from a total of 756326 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7109 -72.19892 -3.78412 0.71575 INTE EXTERN> -26.55974 -45.63919 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1989" Parameter: A <- "-72.1989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5597" Parameter: B <- "-26.5597" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6392" Parameter: C <- "-45.6392" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7109 TOTAL ENERGY = -72.1989 RDTITL> * VAN DER WAALS = -26.5597 ELECTROSTATIC = -45.6392 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7109" Parameter: CONF_N -> "8002" Comparing "7109" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7110" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756326 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759596 ATOM PAIRS WERE FOUND FOR ATOM LIST 41710 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29109 from a total of 759596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7110 -78.54896 6.35003 0.67940 INTE EXTERN> -30.21919 -48.32977 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.549" Parameter: A <- "-78.549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2192" Parameter: B <- "-30.2192" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3298" Parameter: C <- "-48.3298" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7110 TOTAL ENERGY = -78.549 RDTITL> * VAN DER WAALS = -30.2192 ELECTROSTATIC = -48.3298 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7110" Parameter: CONF_N -> "8002" Comparing "7110" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7111" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762219 ATOM PAIRS WERE FOUND FOR ATOM LIST 41721 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29720 from a total of 762219 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7111 -74.06642 -4.48254 0.68109 INTE EXTERN> -29.14495 -44.92146 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0664" Parameter: A <- "-74.0664" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.145" Parameter: B <- "-29.145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9215" Parameter: C <- "-44.9215" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7111 TOTAL ENERGY = -74.0664 RDTITL> * VAN DER WAALS = -29.145 ELECTROSTATIC = -44.9215 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7111" Parameter: CONF_N -> "8002" Comparing "7111" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7112" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762219 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758569 ATOM PAIRS WERE FOUND FOR ATOM LIST 41656 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28979 from a total of 758569 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7112 -83.27977 9.21336 0.67605 INTE EXTERN> -29.66874 -53.61104 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.2798" Parameter: A <- "-83.2798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6687" Parameter: B <- "-29.6687" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.611" Parameter: C <- "-53.611" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7112 TOTAL ENERGY = -83.2798 RDTITL> * VAN DER WAALS = -29.6687 ELECTROSTATIC = -53.611 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7112" Parameter: CONF_N -> "8002" Comparing "7112" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7113" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758569 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758430 ATOM PAIRS WERE FOUND FOR ATOM LIST 41426 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28918 from a total of 758430 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7113 -79.20838 -4.07139 0.70986 INTE EXTERN> -27.56273 -51.64565 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2084" Parameter: A <- "-79.2084" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5627" Parameter: B <- "-27.5627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6456" Parameter: C <- "-51.6456" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7113 TOTAL ENERGY = -79.2084 RDTITL> * VAN DER WAALS = -27.5627 ELECTROSTATIC = -51.6456 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7113" Parameter: CONF_N -> "8002" Comparing "7113" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7114" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758430 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762572 ATOM PAIRS WERE FOUND FOR ATOM LIST 41816 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29766 from a total of 762572 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7114 -80.64367 1.43529 0.65386 INTE EXTERN> -30.01727 -50.62640 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6437" Parameter: A <- "-80.6437" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0173" Parameter: B <- "-30.0173" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6264" Parameter: C <- "-50.6264" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7114 TOTAL ENERGY = -80.6437 RDTITL> * VAN DER WAALS = -30.0173 ELECTROSTATIC = -50.6264 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7114" Parameter: CONF_N -> "8002" Comparing "7114" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7115" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762572 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762206 ATOM PAIRS WERE FOUND FOR ATOM LIST 41884 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28394 from a total of 762206 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7115 -89.73622 9.09255 0.73852 INTE EXTERN> -28.27879 -61.45743 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-89.7362" Parameter: A <- "-89.7362" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2788" Parameter: B <- "-28.2788" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-61.4574" Parameter: C <- "-61.4574" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7115 TOTAL ENERGY = -89.7362 RDTITL> * VAN DER WAALS = -28.2788 ELECTROSTATIC = -61.4574 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7115" Parameter: CONF_N -> "8002" Comparing "7115" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7116" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762206 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756635 ATOM PAIRS WERE FOUND FOR ATOM LIST 41389 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28752 from a total of 756635 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7116 -79.67471 -10.06151 0.60926 INTE EXTERN> -30.24620 -49.42851 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6747" Parameter: A <- "-79.6747" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2462" Parameter: B <- "-30.2462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4285" Parameter: C <- "-49.4285" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7116 TOTAL ENERGY = -79.6747 RDTITL> * VAN DER WAALS = -30.2462 ELECTROSTATIC = -49.4285 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7116" Parameter: CONF_N -> "8002" Comparing "7116" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7117" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756635 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758610 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29567 from a total of 758610 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7117 -79.79461 0.11990 0.66219 INTE EXTERN> -29.28973 -50.50488 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7946" Parameter: A <- "-79.7946" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2897" Parameter: B <- "-29.2897" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5049" Parameter: C <- "-50.5049" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7117 TOTAL ENERGY = -79.7946 RDTITL> * VAN DER WAALS = -29.2897 ELECTROSTATIC = -50.5049 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7117" Parameter: CONF_N -> "8002" Comparing "7117" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7118" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758610 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41769 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29953 from a total of 757958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7118 -77.25258 -2.54204 0.70586 INTE EXTERN> -26.43705 -50.81552 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2526" Parameter: A <- "-77.2526" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4371" Parameter: B <- "-26.4371" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8155" Parameter: C <- "-50.8155" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7118 TOTAL ENERGY = -77.2526 RDTITL> * VAN DER WAALS = -26.4371 ELECTROSTATIC = -50.8155 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7118" Parameter: CONF_N -> "8002" Comparing "7118" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7119" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751317 ATOM PAIRS WERE FOUND FOR ATOM LIST 41227 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29827 from a total of 751317 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7119 -76.69841 -0.55417 0.62428 INTE EXTERN> -30.33336 -46.36505 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6984" Parameter: A <- "-76.6984" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3334" Parameter: B <- "-30.3334" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.365" Parameter: C <- "-46.365" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7119 TOTAL ENERGY = -76.6984 RDTITL> * VAN DER WAALS = -30.3334 ELECTROSTATIC = -46.365 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7119" Parameter: CONF_N -> "8002" Comparing "7119" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7120" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751317 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 743437 ATOM PAIRS WERE FOUND FOR ATOM LIST 40717 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28871 from a total of 743437 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7120 -82.69647 5.99805 0.63759 INTE EXTERN> -31.24156 -51.45490 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.6965" Parameter: A <- "-82.6965" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2416" Parameter: B <- "-31.2416" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4549" Parameter: C <- "-51.4549" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7120 TOTAL ENERGY = -82.6965 RDTITL> * VAN DER WAALS = -31.2416 ELECTROSTATIC = -51.4549 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7120" Parameter: CONF_N -> "8002" Comparing "7120" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7121" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 743437 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749798 ATOM PAIRS WERE FOUND FOR ATOM LIST 41401 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29373 from a total of 749798 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7121 -80.75811 -1.93835 0.65010 INTE EXTERN> -29.54119 -51.21693 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7581" Parameter: A <- "-80.7581" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5412" Parameter: B <- "-29.5412" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2169" Parameter: C <- "-51.2169" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7121 TOTAL ENERGY = -80.7581 RDTITL> * VAN DER WAALS = -29.5412 ELECTROSTATIC = -51.2169 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7121" Parameter: CONF_N -> "8002" Comparing "7121" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7122" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749798 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749972 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29485 from a total of 749972 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7122 -84.40705 3.64894 0.73861 INTE EXTERN> -27.13416 -57.27289 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.4071" Parameter: A <- "-84.4071" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1342" Parameter: B <- "-27.1342" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.2729" Parameter: C <- "-57.2729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7122 TOTAL ENERGY = -84.4071 RDTITL> * VAN DER WAALS = -27.1342 ELECTROSTATIC = -57.2729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7122" Parameter: CONF_N -> "8002" Comparing "7122" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7123" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749972 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752183 ATOM PAIRS WERE FOUND FOR ATOM LIST 41327 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30068 from a total of 752183 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7123 -79.27115 -5.13590 0.81000 INTE EXTERN> -24.64448 -54.62667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2712" Parameter: A <- "-79.2712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6445" Parameter: B <- "-24.6445" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.6267" Parameter: C <- "-54.6267" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7123 TOTAL ENERGY = -79.2712 RDTITL> * VAN DER WAALS = -24.6445 ELECTROSTATIC = -54.6267 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7123" Parameter: CONF_N -> "8002" Comparing "7123" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7124" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752183 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755409 ATOM PAIRS WERE FOUND FOR ATOM LIST 41511 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29898 from a total of 755409 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7124 -81.86258 2.59143 0.73049 INTE EXTERN> -26.70403 -55.15855 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8626" Parameter: A <- "-81.8626" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.704" Parameter: B <- "-26.704" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.1586" Parameter: C <- "-55.1586" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7124 TOTAL ENERGY = -81.8626 RDTITL> * VAN DER WAALS = -26.704 ELECTROSTATIC = -55.1586 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7124" Parameter: CONF_N -> "8002" Comparing "7124" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7125" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755409 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754755 ATOM PAIRS WERE FOUND FOR ATOM LIST 41272 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29612 from a total of 754755 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7125 -77.14300 -4.71958 0.65895 INTE EXTERN> -29.88412 -47.25888 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.143" Parameter: A <- "-77.143" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8841" Parameter: B <- "-29.8841" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2589" Parameter: C <- "-47.2589" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7125 TOTAL ENERGY = -77.143 RDTITL> * VAN DER WAALS = -29.8841 ELECTROSTATIC = -47.2589 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7125" Parameter: CONF_N -> "8002" Comparing "7125" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7126" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754755 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750545 ATOM PAIRS WERE FOUND FOR ATOM LIST 41182 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29729 from a total of 750545 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7126 -82.76280 5.61980 0.64253 INTE EXTERN> -31.81672 -50.94608 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7628" Parameter: A <- "-82.7628" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8167" Parameter: B <- "-31.8167" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9461" Parameter: C <- "-50.9461" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7126 TOTAL ENERGY = -82.7628 RDTITL> * VAN DER WAALS = -31.8167 ELECTROSTATIC = -50.9461 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7126" Parameter: CONF_N -> "8002" Comparing "7126" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7127" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750545 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753057 ATOM PAIRS WERE FOUND FOR ATOM LIST 41516 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29823 from a total of 753057 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7127 -84.61063 1.84783 0.70010 INTE EXTERN> -30.62753 -53.98309 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.6106" Parameter: A <- "-84.6106" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6275" Parameter: B <- "-30.6275" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.9831" Parameter: C <- "-53.9831" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7127 TOTAL ENERGY = -84.6106 RDTITL> * VAN DER WAALS = -30.6275 ELECTROSTATIC = -53.9831 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7127" Parameter: CONF_N -> "8002" Comparing "7127" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7128" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753057 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751187 ATOM PAIRS WERE FOUND FOR ATOM LIST 41154 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29444 from a total of 751187 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7128 -82.71724 -1.89338 0.75050 INTE EXTERN> -26.61531 -56.10194 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7172" Parameter: A <- "-82.7172" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6153" Parameter: B <- "-26.6153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.1019" Parameter: C <- "-56.1019" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7128 TOTAL ENERGY = -82.7172 RDTITL> * VAN DER WAALS = -26.6153 ELECTROSTATIC = -56.1019 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7128" Parameter: CONF_N -> "8002" Comparing "7128" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7129" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751187 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754600 ATOM PAIRS WERE FOUND FOR ATOM LIST 41528 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30224 from a total of 754600 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7129 -82.28747 -0.42978 0.67477 INTE EXTERN> -29.73397 -52.55350 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.2875" Parameter: A <- "-82.2875" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.734" Parameter: B <- "-29.734" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5535" Parameter: C <- "-52.5535" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7129 TOTAL ENERGY = -82.2875 RDTITL> * VAN DER WAALS = -29.734 ELECTROSTATIC = -52.5535 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7129" Parameter: CONF_N -> "8002" Comparing "7129" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7130" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754600 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751070 ATOM PAIRS WERE FOUND FOR ATOM LIST 41327 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29150 from a total of 751070 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7130 -74.12144 -8.16602 0.62444 INTE EXTERN> -31.68942 -42.43203 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1214" Parameter: A <- "-74.1214" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6894" Parameter: B <- "-31.6894" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.432" Parameter: C <- "-42.432" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7130 TOTAL ENERGY = -74.1214 RDTITL> * VAN DER WAALS = -31.6894 ELECTROSTATIC = -42.432 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7130" Parameter: CONF_N -> "8002" Comparing "7130" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7131" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751070 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755646 ATOM PAIRS WERE FOUND FOR ATOM LIST 41401 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29370 from a total of 755646 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7131 -76.48160 2.36015 0.64405 INTE EXTERN> -29.83231 -46.64929 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4816" Parameter: A <- "-76.4816" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8323" Parameter: B <- "-29.8323" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6493" Parameter: C <- "-46.6493" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7131 TOTAL ENERGY = -76.4816 RDTITL> * VAN DER WAALS = -29.8323 ELECTROSTATIC = -46.6493 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7131" Parameter: CONF_N -> "8002" Comparing "7131" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7132" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755646 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752534 ATOM PAIRS WERE FOUND FOR ATOM LIST 41490 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28893 from a total of 752534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7132 -81.81518 5.33358 0.73430 INTE EXTERN> -26.04488 -55.77030 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8152" Parameter: A <- "-81.8152" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0449" Parameter: B <- "-26.0449" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.7703" Parameter: C <- "-55.7703" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7132 TOTAL ENERGY = -81.8152 RDTITL> * VAN DER WAALS = -26.0449 ELECTROSTATIC = -55.7703 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7132" Parameter: CONF_N -> "8002" Comparing "7132" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7133" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753853 ATOM PAIRS WERE FOUND FOR ATOM LIST 41338 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29147 from a total of 753853 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7133 -86.54231 4.72713 0.73995 INTE EXTERN> -28.26811 -58.27420 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.5423" Parameter: A <- "-86.5423" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2681" Parameter: B <- "-28.2681" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.2742" Parameter: C <- "-58.2742" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7133 TOTAL ENERGY = -86.5423 RDTITL> * VAN DER WAALS = -28.2681 ELECTROSTATIC = -58.2742 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7133" Parameter: CONF_N -> "8002" Comparing "7133" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7134" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753853 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753430 ATOM PAIRS WERE FOUND FOR ATOM LIST 41461 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29463 from a total of 753430 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7134 -84.91209 -1.63022 0.75288 INTE EXTERN> -28.47702 -56.43507 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.9121" Parameter: A <- "-84.9121" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.477" Parameter: B <- "-28.477" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.4351" Parameter: C <- "-56.4351" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7134 TOTAL ENERGY = -84.9121 RDTITL> * VAN DER WAALS = -28.477 ELECTROSTATIC = -56.4351 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7134" Parameter: CONF_N -> "8002" Comparing "7134" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7135" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753430 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753396 ATOM PAIRS WERE FOUND FOR ATOM LIST 41537 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29253 from a total of 753396 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7135 -78.12010 -6.79199 0.76042 INTE EXTERN> -28.26115 -49.85895 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1201" Parameter: A <- "-78.1201" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2612" Parameter: B <- "-28.2612" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8589" Parameter: C <- "-49.8589" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7135 TOTAL ENERGY = -78.1201 RDTITL> * VAN DER WAALS = -28.2612 ELECTROSTATIC = -49.8589 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7135" Parameter: CONF_N -> "8002" Comparing "7135" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7136" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753396 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755157 ATOM PAIRS WERE FOUND FOR ATOM LIST 41439 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29500 from a total of 755157 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7136 -74.42576 -3.69434 0.78478 INTE EXTERN> -25.34096 -49.08480 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4258" Parameter: A <- "-74.4258" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.341" Parameter: B <- "-25.341" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0848" Parameter: C <- "-49.0848" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7136 TOTAL ENERGY = -74.4258 RDTITL> * VAN DER WAALS = -25.341 ELECTROSTATIC = -49.0848 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7136" Parameter: CONF_N -> "8002" Comparing "7136" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7137" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755157 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748908 ATOM PAIRS WERE FOUND FOR ATOM LIST 41043 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29046 from a total of 748908 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7137 -83.97258 9.54682 0.71157 INTE EXTERN> -30.02261 -53.94996 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.9726" Parameter: A <- "-83.9726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0226" Parameter: B <- "-30.0226" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.95" Parameter: C <- "-53.95" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7137 TOTAL ENERGY = -83.9726 RDTITL> * VAN DER WAALS = -30.0226 ELECTROSTATIC = -53.95 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7137" Parameter: CONF_N -> "8002" Comparing "7137" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7138" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748908 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749329 ATOM PAIRS WERE FOUND FOR ATOM LIST 41291 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29635 from a total of 749329 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7138 -78.30166 -5.67092 0.63079 INTE EXTERN> -30.52799 -47.77366 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3017" Parameter: A <- "-78.3017" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.528" Parameter: B <- "-30.528" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7737" Parameter: C <- "-47.7737" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7138 TOTAL ENERGY = -78.3017 RDTITL> * VAN DER WAALS = -30.528 ELECTROSTATIC = -47.7737 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7138" Parameter: CONF_N -> "8002" Comparing "7138" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7139" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749329 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747051 ATOM PAIRS WERE FOUND FOR ATOM LIST 41031 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28398 from a total of 747051 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7139 -78.29240 -0.00926 0.64797 INTE EXTERN> -31.05408 -47.23832 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2924" Parameter: A <- "-78.2924" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0541" Parameter: B <- "-31.0541" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2383" Parameter: C <- "-47.2383" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7139 TOTAL ENERGY = -78.2924 RDTITL> * VAN DER WAALS = -31.0541 ELECTROSTATIC = -47.2383 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7139" Parameter: CONF_N -> "8002" Comparing "7139" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7140" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747051 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754638 ATOM PAIRS WERE FOUND FOR ATOM LIST 41385 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29167 from a total of 754638 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7140 -76.80582 -1.48658 0.68218 INTE EXTERN> -29.29026 -47.51556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8058" Parameter: A <- "-76.8058" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2903" Parameter: B <- "-29.2903" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5156" Parameter: C <- "-47.5156" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7140 TOTAL ENERGY = -76.8058 RDTITL> * VAN DER WAALS = -29.2903 ELECTROSTATIC = -47.5156 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7140" Parameter: CONF_N -> "8002" Comparing "7140" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7141" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754638 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753277 ATOM PAIRS WERE FOUND FOR ATOM LIST 41395 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29711 from a total of 753277 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7141 -80.37319 3.56737 0.62880 INTE EXTERN> -33.17348 -47.19971 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3732" Parameter: A <- "-80.3732" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.1735" Parameter: B <- "-33.1735" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1997" Parameter: C <- "-47.1997" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7141 TOTAL ENERGY = -80.3732 RDTITL> * VAN DER WAALS = -33.1735 ELECTROSTATIC = -47.1997 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7141" Parameter: CONF_N -> "8002" Comparing "7141" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7142" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753277 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750059 ATOM PAIRS WERE FOUND FOR ATOM LIST 41282 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28933 from a total of 750059 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7142 -75.76773 -4.60546 0.57374 INTE EXTERN> -31.75251 -44.01522 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7677" Parameter: A <- "-75.7677" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7525" Parameter: B <- "-31.7525" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0152" Parameter: C <- "-44.0152" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7142 TOTAL ENERGY = -75.7677 RDTITL> * VAN DER WAALS = -31.7525 ELECTROSTATIC = -44.0152 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7142" Parameter: CONF_N -> "8002" Comparing "7142" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7143" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750059 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751203 ATOM PAIRS WERE FOUND FOR ATOM LIST 41287 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29631 from a total of 751203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7143 -76.91093 1.14320 0.73921 INTE EXTERN> -27.92362 -48.98731 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9109" Parameter: A <- "-76.9109" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9236" Parameter: B <- "-27.9236" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9873" Parameter: C <- "-48.9873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7143 TOTAL ENERGY = -76.9109 RDTITL> * VAN DER WAALS = -27.9236 ELECTROSTATIC = -48.9873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7143" Parameter: CONF_N -> "8002" Comparing "7143" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7144" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762132 ATOM PAIRS WERE FOUND FOR ATOM LIST 41863 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30191 from a total of 762132 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7144 -82.91657 6.00564 0.73874 INTE EXTERN> -29.07639 -53.84018 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9166" Parameter: A <- "-82.9166" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0764" Parameter: B <- "-29.0764" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8402" Parameter: C <- "-53.8402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7144 TOTAL ENERGY = -82.9166 RDTITL> * VAN DER WAALS = -29.0764 ELECTROSTATIC = -53.8402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7144" Parameter: CONF_N -> "8002" Comparing "7144" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7145" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762132 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752093 ATOM PAIRS WERE FOUND FOR ATOM LIST 41508 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29761 from a total of 752093 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7145 -81.15852 -1.75805 0.63820 INTE EXTERN> -32.81539 -48.34313 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1585" Parameter: A <- "-81.1585" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.8154" Parameter: B <- "-32.8154" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3431" Parameter: C <- "-48.3431" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7145 TOTAL ENERGY = -81.1585 RDTITL> * VAN DER WAALS = -32.8154 ELECTROSTATIC = -48.3431 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7145" Parameter: CONF_N -> "8002" Comparing "7145" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7146" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752093 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 743645 ATOM PAIRS WERE FOUND FOR ATOM LIST 40897 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29377 from a total of 743645 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7146 -82.53939 1.38087 0.69572 INTE EXTERN> -31.58291 -50.95649 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5394" Parameter: A <- "-82.5394" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5829" Parameter: B <- "-31.5829" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9565" Parameter: C <- "-50.9565" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7146 TOTAL ENERGY = -82.5394 RDTITL> * VAN DER WAALS = -31.5829 ELECTROSTATIC = -50.9565 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7146" Parameter: CONF_N -> "8002" Comparing "7146" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7147" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 743645 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749518 ATOM PAIRS WERE FOUND FOR ATOM LIST 41329 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29460 from a total of 749518 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7147 -81.67156 -0.86783 0.73502 INTE EXTERN> -30.28098 -51.39058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6716" Parameter: A <- "-81.6716" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.281" Parameter: B <- "-30.281" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3906" Parameter: C <- "-51.3906" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7147 TOTAL ENERGY = -81.6716 RDTITL> * VAN DER WAALS = -30.281 ELECTROSTATIC = -51.3906 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7147" Parameter: CONF_N -> "8002" Comparing "7147" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7148" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749518 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753780 ATOM PAIRS WERE FOUND FOR ATOM LIST 41358 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29063 from a total of 753780 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7148 -79.93724 -1.73432 0.66009 INTE EXTERN> -28.65851 -51.27874 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9372" Parameter: A <- "-79.9372" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6585" Parameter: B <- "-28.6585" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2787" Parameter: C <- "-51.2787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7148 TOTAL ENERGY = -79.9372 RDTITL> * VAN DER WAALS = -28.6585 ELECTROSTATIC = -51.2787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7148" Parameter: CONF_N -> "8002" Comparing "7148" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7149" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753780 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753672 ATOM PAIRS WERE FOUND FOR ATOM LIST 41620 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29380 from a total of 753672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7149 -79.62395 -0.31330 0.71085 INTE EXTERN> -28.98922 -50.63472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6239" Parameter: A <- "-79.6239" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9892" Parameter: B <- "-28.9892" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6347" Parameter: C <- "-50.6347" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7149 TOTAL ENERGY = -79.6239 RDTITL> * VAN DER WAALS = -28.9892 ELECTROSTATIC = -50.6347 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7149" Parameter: CONF_N -> "8002" Comparing "7149" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7150" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759828 ATOM PAIRS WERE FOUND FOR ATOM LIST 41681 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29528 from a total of 759828 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7150 -79.13011 -0.49383 0.67985 INTE EXTERN> -28.44718 -50.68293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1301" Parameter: A <- "-79.1301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4472" Parameter: B <- "-28.4472" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6829" Parameter: C <- "-50.6829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7150 TOTAL ENERGY = -79.1301 RDTITL> * VAN DER WAALS = -28.4472 ELECTROSTATIC = -50.6829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7150" Parameter: CONF_N -> "8002" Comparing "7150" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7151" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759828 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752474 ATOM PAIRS WERE FOUND FOR ATOM LIST 41500 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29774 from a total of 752474 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7151 -85.02695 5.89683 0.71884 INTE EXTERN> -29.66525 -55.36170 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.0269" Parameter: A <- "-85.0269" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6653" Parameter: B <- "-29.6653" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.3617" Parameter: C <- "-55.3617" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7151 TOTAL ENERGY = -85.0269 RDTITL> * VAN DER WAALS = -29.6653 ELECTROSTATIC = -55.3617 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7151" Parameter: CONF_N -> "8002" Comparing "7151" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7152" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752474 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753406 ATOM PAIRS WERE FOUND FOR ATOM LIST 41423 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29406 from a total of 753406 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7152 -76.44592 -8.58103 0.65066 INTE EXTERN> -29.91937 -46.52655 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4459" Parameter: A <- "-76.4459" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9194" Parameter: B <- "-29.9194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5266" Parameter: C <- "-46.5266" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7152 TOTAL ENERGY = -76.4459 RDTITL> * VAN DER WAALS = -29.9194 ELECTROSTATIC = -46.5266 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7152" Parameter: CONF_N -> "8002" Comparing "7152" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7153" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753406 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754125 ATOM PAIRS WERE FOUND FOR ATOM LIST 41540 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29315 from a total of 754125 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7153 -76.36142 -0.08450 0.62807 INTE EXTERN> -30.69004 -45.67138 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3614" Parameter: A <- "-76.3614" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.69" Parameter: B <- "-30.69" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6714" Parameter: C <- "-45.6714" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7153 TOTAL ENERGY = -76.3614 RDTITL> * VAN DER WAALS = -30.69 ELECTROSTATIC = -45.6714 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7153" Parameter: CONF_N -> "8002" Comparing "7153" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7154" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754125 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756668 ATOM PAIRS WERE FOUND FOR ATOM LIST 41508 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29281 from a total of 756668 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7154 -80.21695 3.85553 0.70628 INTE EXTERN> -29.31435 -50.90259 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2169" Parameter: A <- "-80.2169" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3144" Parameter: B <- "-29.3144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.9026" Parameter: C <- "-50.9026" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7154 TOTAL ENERGY = -80.2169 RDTITL> * VAN DER WAALS = -29.3144 ELECTROSTATIC = -50.9026 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7154" Parameter: CONF_N -> "8002" Comparing "7154" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7155" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756668 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751849 ATOM PAIRS WERE FOUND FOR ATOM LIST 41422 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29296 from a total of 751849 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7155 -74.81975 -5.39720 0.63753 INTE EXTERN> -31.02750 -43.79224 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8197" Parameter: A <- "-74.8197" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0275" Parameter: B <- "-31.0275" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7922" Parameter: C <- "-43.7922" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7155 TOTAL ENERGY = -74.8197 RDTITL> * VAN DER WAALS = -31.0275 ELECTROSTATIC = -43.7922 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7155" Parameter: CONF_N -> "8002" Comparing "7155" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7156" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751849 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750560 ATOM PAIRS WERE FOUND FOR ATOM LIST 41364 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29637 from a total of 750560 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7156 -76.33667 1.51693 0.65387 INTE EXTERN> -29.10936 -47.22731 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3367" Parameter: A <- "-76.3367" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1094" Parameter: B <- "-29.1094" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2273" Parameter: C <- "-47.2273" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7156 TOTAL ENERGY = -76.3367 RDTITL> * VAN DER WAALS = -29.1094 ELECTROSTATIC = -47.2273 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7156" Parameter: CONF_N -> "8002" Comparing "7156" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7157" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750560 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755073 ATOM PAIRS WERE FOUND FOR ATOM LIST 41616 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29425 from a total of 755073 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7157 -84.40431 8.06763 0.83468 INTE EXTERN> -26.26841 -58.13590 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.4043" Parameter: A <- "-84.4043" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2684" Parameter: B <- "-26.2684" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.1359" Parameter: C <- "-58.1359" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7157 TOTAL ENERGY = -84.4043 RDTITL> * VAN DER WAALS = -26.2684 ELECTROSTATIC = -58.1359 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7157" Parameter: CONF_N -> "8002" Comparing "7157" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7158" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755073 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751618 ATOM PAIRS WERE FOUND FOR ATOM LIST 41341 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29503 from a total of 751618 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7158 -78.26781 -6.13650 0.70190 INTE EXTERN> -30.11139 -48.15643 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2678" Parameter: A <- "-78.2678" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1114" Parameter: B <- "-30.1114" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1564" Parameter: C <- "-48.1564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7158 TOTAL ENERGY = -78.2678 RDTITL> * VAN DER WAALS = -30.1114 ELECTROSTATIC = -48.1564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7158" Parameter: CONF_N -> "8002" Comparing "7158" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7159" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751618 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751969 ATOM PAIRS WERE FOUND FOR ATOM LIST 41391 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29521 from a total of 751969 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7159 -81.11692 2.84910 0.64051 INTE EXTERN> -30.77198 -50.34494 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1169" Parameter: A <- "-81.1169" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.772" Parameter: B <- "-30.772" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3449" Parameter: C <- "-50.3449" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7159 TOTAL ENERGY = -81.1169 RDTITL> * VAN DER WAALS = -30.772 ELECTROSTATIC = -50.3449 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7159" Parameter: CONF_N -> "8002" Comparing "7159" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7160" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751969 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753351 ATOM PAIRS WERE FOUND FOR ATOM LIST 41382 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29075 from a total of 753351 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7160 -80.78119 -0.33573 0.68970 INTE EXTERN> -28.81530 -51.96588 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7812" Parameter: A <- "-80.7812" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8153" Parameter: B <- "-28.8153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.9659" Parameter: C <- "-51.9659" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7160 TOTAL ENERGY = -80.7812 RDTITL> * VAN DER WAALS = -28.8153 ELECTROSTATIC = -51.9659 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7160" Parameter: CONF_N -> "8002" Comparing "7160" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7161" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753351 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753286 ATOM PAIRS WERE FOUND FOR ATOM LIST 41342 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29674 from a total of 753286 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7161 -84.35215 3.57096 0.66933 INTE EXTERN> -31.62483 -52.72732 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.3522" Parameter: A <- "-84.3522" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6248" Parameter: B <- "-31.6248" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.7273" Parameter: C <- "-52.7273" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7161 TOTAL ENERGY = -84.3522 RDTITL> * VAN DER WAALS = -31.6248 ELECTROSTATIC = -52.7273 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7161" Parameter: CONF_N -> "8002" Comparing "7161" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7162" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753286 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757492 ATOM PAIRS WERE FOUND FOR ATOM LIST 41727 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29704 from a total of 757492 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7162 -87.70375 3.35160 0.71901 INTE EXTERN> -30.79138 -56.91236 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.7037" Parameter: A <- "-87.7037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7914" Parameter: B <- "-30.7914" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.9124" Parameter: C <- "-56.9124" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7162 TOTAL ENERGY = -87.7037 RDTITL> * VAN DER WAALS = -30.7914 ELECTROSTATIC = -56.9124 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7162" Parameter: CONF_N -> "8002" Comparing "7162" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7163" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757492 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753073 ATOM PAIRS WERE FOUND FOR ATOM LIST 41446 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29121 from a total of 753073 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7163 -86.52626 -1.17748 0.67667 INTE EXTERN> -29.32486 -57.20140 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.5263" Parameter: A <- "-86.5263" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3249" Parameter: B <- "-29.3249" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.2014" Parameter: C <- "-57.2014" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7163 TOTAL ENERGY = -86.5263 RDTITL> * VAN DER WAALS = -29.3249 ELECTROSTATIC = -57.2014 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7163" Parameter: CONF_N -> "8002" Comparing "7163" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7164" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753073 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757824 ATOM PAIRS WERE FOUND FOR ATOM LIST 41486 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29596 from a total of 757824 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7164 -82.31585 -4.21041 0.75019 INTE EXTERN> -28.24596 -54.06989 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3159" Parameter: A <- "-82.3159" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.246" Parameter: B <- "-28.246" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0699" Parameter: C <- "-54.0699" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7164 TOTAL ENERGY = -82.3159 RDTITL> * VAN DER WAALS = -28.246 ELECTROSTATIC = -54.0699 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7164" Parameter: CONF_N -> "8002" Comparing "7164" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7165" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757824 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757294 ATOM PAIRS WERE FOUND FOR ATOM LIST 41342 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29785 from a total of 757294 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7165 -82.26891 -0.04694 0.66878 INTE EXTERN> -31.03168 -51.23724 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.2689" Parameter: A <- "-82.2689" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0317" Parameter: B <- "-31.0317" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2372" Parameter: C <- "-51.2372" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7165 TOTAL ENERGY = -82.2689 RDTITL> * VAN DER WAALS = -31.0317 ELECTROSTATIC = -51.2372 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7165" Parameter: CONF_N -> "8002" Comparing "7165" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7166" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757294 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757687 ATOM PAIRS WERE FOUND FOR ATOM LIST 41580 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29790 from a total of 757687 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7166 -86.12627 3.85735 0.66902 INTE EXTERN> -31.38204 -54.74423 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.1263" Parameter: A <- "-86.1263" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.382" Parameter: B <- "-31.382" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.7442" Parameter: C <- "-54.7442" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7166 TOTAL ENERGY = -86.1263 RDTITL> * VAN DER WAALS = -31.382 ELECTROSTATIC = -54.7442 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7166" Parameter: CONF_N -> "8002" Comparing "7166" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7167" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757687 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761128 ATOM PAIRS WERE FOUND FOR ATOM LIST 41665 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29547 from a total of 761128 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7167 -77.22389 -8.90238 0.69968 INTE EXTERN> -27.56783 -49.65605 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2239" Parameter: A <- "-77.2239" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5678" Parameter: B <- "-27.5678" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6561" Parameter: C <- "-49.6561" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7167 TOTAL ENERGY = -77.2239 RDTITL> * VAN DER WAALS = -27.5678 ELECTROSTATIC = -49.6561 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7167" Parameter: CONF_N -> "8002" Comparing "7167" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7168" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761128 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757355 ATOM PAIRS WERE FOUND FOR ATOM LIST 41549 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30028 from a total of 757355 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7168 -75.58004 -1.64384 0.66309 INTE EXTERN> -30.67810 -44.90195 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.58" Parameter: A <- "-75.58" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6781" Parameter: B <- "-30.6781" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9019" Parameter: C <- "-44.9019" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7168 TOTAL ENERGY = -75.58 RDTITL> * VAN DER WAALS = -30.6781 ELECTROSTATIC = -44.9019 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7168" Parameter: CONF_N -> "8002" Comparing "7168" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7169" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757355 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760406 ATOM PAIRS WERE FOUND FOR ATOM LIST 41835 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30221 from a total of 760406 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7169 -78.84158 3.26153 0.68832 INTE EXTERN> -28.50854 -50.33303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8416" Parameter: A <- "-78.8416" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5085" Parameter: B <- "-28.5085" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.333" Parameter: C <- "-50.333" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7169 TOTAL ENERGY = -78.8416 RDTITL> * VAN DER WAALS = -28.5085 ELECTROSTATIC = -50.333 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7169" Parameter: CONF_N -> "8002" Comparing "7169" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7170" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760406 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753191 ATOM PAIRS WERE FOUND FOR ATOM LIST 41487 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29416 from a total of 753191 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7170 -80.62139 1.77981 0.65625 INTE EXTERN> -27.31369 -53.30770 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6214" Parameter: A <- "-80.6214" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3137" Parameter: B <- "-27.3137" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3077" Parameter: C <- "-53.3077" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7170 TOTAL ENERGY = -80.6214 RDTITL> * VAN DER WAALS = -27.3137 ELECTROSTATIC = -53.3077 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7170" Parameter: CONF_N -> "8002" Comparing "7170" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7171" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753191 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749863 ATOM PAIRS WERE FOUND FOR ATOM LIST 41348 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29866 from a total of 749863 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7171 -78.63837 -1.98302 0.58191 INTE EXTERN> -33.27660 -45.36177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6384" Parameter: A <- "-78.6384" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2766" Parameter: B <- "-33.2766" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3618" Parameter: C <- "-45.3618" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7171 TOTAL ENERGY = -78.6384 RDTITL> * VAN DER WAALS = -33.2766 ELECTROSTATIC = -45.3618 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7171" Parameter: CONF_N -> "8002" Comparing "7171" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7172" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749863 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753124 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29456 from a total of 753124 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7172 -77.58685 -1.05152 0.56805 INTE EXTERN> -32.49536 -45.09150 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5869" Parameter: A <- "-77.5869" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4954" Parameter: B <- "-32.4954" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0915" Parameter: C <- "-45.0915" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7172 TOTAL ENERGY = -77.5869 RDTITL> * VAN DER WAALS = -32.4954 ELECTROSTATIC = -45.0915 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7172" Parameter: CONF_N -> "8002" Comparing "7172" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7173" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753124 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761068 ATOM PAIRS WERE FOUND FOR ATOM LIST 41809 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29728 from a total of 761068 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7173 -82.96446 5.37761 0.74134 INTE EXTERN> -25.98521 -56.97925 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9645" Parameter: A <- "-82.9645" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9852" Parameter: B <- "-25.9852" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.9792" Parameter: C <- "-56.9792" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7173 TOTAL ENERGY = -82.9645 RDTITL> * VAN DER WAALS = -25.9852 ELECTROSTATIC = -56.9792 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7173" Parameter: CONF_N -> "8002" Comparing "7173" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7174" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761068 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752129 ATOM PAIRS WERE FOUND FOR ATOM LIST 41672 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29273 from a total of 752129 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7174 -80.67585 -2.28861 0.90660 INTE EXTERN> -24.72069 -55.95516 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6759" Parameter: A <- "-80.6759" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7207" Parameter: B <- "-24.7207" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.9552" Parameter: C <- "-55.9552" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7174 TOTAL ENERGY = -80.6759 RDTITL> * VAN DER WAALS = -24.7207 ELECTROSTATIC = -55.9552 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7174" Parameter: CONF_N -> "8002" Comparing "7174" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7175" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752129 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757036 ATOM PAIRS WERE FOUND FOR ATOM LIST 41610 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29948 from a total of 757036 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7175 -81.69039 1.01454 0.69656 INTE EXTERN> -30.38588 -51.30451 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6904" Parameter: A <- "-81.6904" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3859" Parameter: B <- "-30.3859" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3045" Parameter: C <- "-51.3045" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7175 TOTAL ENERGY = -81.6904 RDTITL> * VAN DER WAALS = -30.3859 ELECTROSTATIC = -51.3045 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7175" Parameter: CONF_N -> "8002" Comparing "7175" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7176" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757036 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756323 ATOM PAIRS WERE FOUND FOR ATOM LIST 41587 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29793 from a total of 756323 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7176 -73.91947 -7.77092 0.67721 INTE EXTERN> -29.93450 -43.98498 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9195" Parameter: A <- "-73.9195" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9345" Parameter: B <- "-29.9345" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.985" Parameter: C <- "-43.985" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7176 TOTAL ENERGY = -73.9195 RDTITL> * VAN DER WAALS = -29.9345 ELECTROSTATIC = -43.985 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7176" Parameter: CONF_N -> "8002" Comparing "7176" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7177" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756323 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754530 ATOM PAIRS WERE FOUND FOR ATOM LIST 41458 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29216 from a total of 754530 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7177 -75.06311 1.14364 0.67850 INTE EXTERN> -28.25963 -46.80348 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0631" Parameter: A <- "-75.0631" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2596" Parameter: B <- "-28.2596" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8035" Parameter: C <- "-46.8035" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7177 TOTAL ENERGY = -75.0631 RDTITL> * VAN DER WAALS = -28.2596 ELECTROSTATIC = -46.8035 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7177" Parameter: CONF_N -> "8002" Comparing "7177" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7178" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754530 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754436 ATOM PAIRS WERE FOUND FOR ATOM LIST 41571 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28895 from a total of 754436 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7178 -80.99076 5.92765 0.60044 INTE EXTERN> -32.05896 -48.93180 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9908" Parameter: A <- "-80.9908" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.059" Parameter: B <- "-32.059" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9318" Parameter: C <- "-48.9318" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7178 TOTAL ENERGY = -80.9908 RDTITL> * VAN DER WAALS = -32.059 ELECTROSTATIC = -48.9318 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7178" Parameter: CONF_N -> "8002" Comparing "7178" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7179" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754436 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757736 ATOM PAIRS WERE FOUND FOR ATOM LIST 41752 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29690 from a total of 757736 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7179 -79.57739 -1.41336 0.62669 INTE EXTERN> -31.48482 -48.09257 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5774" Parameter: A <- "-79.5774" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4848" Parameter: B <- "-31.4848" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0926" Parameter: C <- "-48.0926" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7179 TOTAL ENERGY = -79.5774 RDTITL> * VAN DER WAALS = -31.4848 ELECTROSTATIC = -48.0926 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7179" Parameter: CONF_N -> "8002" Comparing "7179" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7180" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757736 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761215 ATOM PAIRS WERE FOUND FOR ATOM LIST 41771 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30099 from a total of 761215 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7180 -74.11375 -5.46364 0.73194 INTE EXTERN> -26.84003 -47.27373 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1138" Parameter: A <- "-74.1138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.84" Parameter: B <- "-26.84" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2737" Parameter: C <- "-47.2737" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7180 TOTAL ENERGY = -74.1138 RDTITL> * VAN DER WAALS = -26.84 ELECTROSTATIC = -47.2737 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7180" Parameter: CONF_N -> "8002" Comparing "7180" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7181" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761215 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760352 ATOM PAIRS WERE FOUND FOR ATOM LIST 41915 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30082 from a total of 760352 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7181 -72.06352 -2.05024 0.79865 INTE EXTERN> -26.02824 -46.03527 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0635" Parameter: A <- "-72.0635" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0282" Parameter: B <- "-26.0282" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0353" Parameter: C <- "-46.0353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7181 TOTAL ENERGY = -72.0635 RDTITL> * VAN DER WAALS = -26.0282 ELECTROSTATIC = -46.0353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7181" Parameter: CONF_N -> "8002" Comparing "7181" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7182" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760352 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762254 ATOM PAIRS WERE FOUND FOR ATOM LIST 41901 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29547 from a total of 762254 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7182 -77.47921 5.41569 0.62584 INTE EXTERN> -33.00155 -44.47766 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4792" Parameter: A <- "-77.4792" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.0015" Parameter: B <- "-33.0015" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4777" Parameter: C <- "-44.4777" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7182 TOTAL ENERGY = -77.4792 RDTITL> * VAN DER WAALS = -33.0015 ELECTROSTATIC = -44.4777 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7182" Parameter: CONF_N -> "8002" Comparing "7182" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7183" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762254 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757845 ATOM PAIRS WERE FOUND FOR ATOM LIST 41712 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29979 from a total of 757845 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7183 -76.85269 -0.62651 0.89524 INTE EXTERN> -23.37116 -53.48153 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8527" Parameter: A <- "-76.8527" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.3712" Parameter: B <- "-23.3712" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4815" Parameter: C <- "-53.4815" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7183 TOTAL ENERGY = -76.8527 RDTITL> * VAN DER WAALS = -23.3712 ELECTROSTATIC = -53.4815 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7183" Parameter: CONF_N -> "8002" Comparing "7183" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7184" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757845 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760691 ATOM PAIRS WERE FOUND FOR ATOM LIST 41766 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29715 from a total of 760691 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7184 -81.33422 4.48153 0.60848 INTE EXTERN> -33.75145 -47.58277 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.3342" Parameter: A <- "-81.3342" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.7514" Parameter: B <- "-33.7514" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5828" Parameter: C <- "-47.5828" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7184 TOTAL ENERGY = -81.3342 RDTITL> * VAN DER WAALS = -33.7514 ELECTROSTATIC = -47.5828 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7184" Parameter: CONF_N -> "8002" Comparing "7184" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7185" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760691 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764302 ATOM PAIRS WERE FOUND FOR ATOM LIST 41872 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29611 from a total of 764302 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7185 -84.81884 3.48462 0.79953 INTE EXTERN> -27.59588 -57.22296 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.8188" Parameter: A <- "-84.8188" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5959" Parameter: B <- "-27.5959" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.223" Parameter: C <- "-57.223" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7185 TOTAL ENERGY = -84.8188 RDTITL> * VAN DER WAALS = -27.5959 ELECTROSTATIC = -57.223 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7185" Parameter: CONF_N -> "8002" Comparing "7185" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7186" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764302 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756104 ATOM PAIRS WERE FOUND FOR ATOM LIST 41637 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29946 from a total of 756104 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7186 -80.68108 -4.13776 0.74376 INTE EXTERN> -28.45678 -52.22431 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6811" Parameter: A <- "-80.6811" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4568" Parameter: B <- "-28.4568" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2243" Parameter: C <- "-52.2243" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7186 TOTAL ENERGY = -80.6811 RDTITL> * VAN DER WAALS = -28.4568 ELECTROSTATIC = -52.2243 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7186" Parameter: CONF_N -> "8002" Comparing "7186" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7187" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756104 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763000 ATOM PAIRS WERE FOUND FOR ATOM LIST 41890 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30014 from a total of 763000 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7187 -74.80122 -5.87986 0.61058 INTE EXTERN> -32.36913 -42.43209 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8012" Parameter: A <- "-74.8012" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3691" Parameter: B <- "-32.3691" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4321" Parameter: C <- "-42.4321" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7187 TOTAL ENERGY = -74.8012 RDTITL> * VAN DER WAALS = -32.3691 ELECTROSTATIC = -42.4321 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7187" Parameter: CONF_N -> "8002" Comparing "7187" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7188" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763000 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762108 ATOM PAIRS WERE FOUND FOR ATOM LIST 41817 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30067 from a total of 762108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7188 -82.15008 7.34886 0.66411 INTE EXTERN> -31.25828 -50.89179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.1501" Parameter: A <- "-82.1501" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2583" Parameter: B <- "-31.2583" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8918" Parameter: C <- "-50.8918" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7188 TOTAL ENERGY = -82.1501 RDTITL> * VAN DER WAALS = -31.2583 ELECTROSTATIC = -50.8918 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7188" Parameter: CONF_N -> "8002" Comparing "7188" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7189" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758192 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29988 from a total of 758192 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7189 -77.74711 -4.40297 0.65556 INTE EXTERN> -31.55676 -46.19035 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7471" Parameter: A <- "-77.7471" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5568" Parameter: B <- "-31.5568" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1903" Parameter: C <- "-46.1903" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7189 TOTAL ENERGY = -77.7471 RDTITL> * VAN DER WAALS = -31.5568 ELECTROSTATIC = -46.1903 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7189" Parameter: CONF_N -> "8002" Comparing "7189" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7190" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758192 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 769168 ATOM PAIRS WERE FOUND FOR ATOM LIST 42231 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30280 from a total of 769168 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7190 -76.16459 -1.58251 0.67929 INTE EXTERN> -28.16961 -47.99499 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1646" Parameter: A <- "-76.1646" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1696" Parameter: B <- "-28.1696" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.995" Parameter: C <- "-47.995" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7190 TOTAL ENERGY = -76.1646 RDTITL> * VAN DER WAALS = -28.1696 ELECTROSTATIC = -47.995 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7190" Parameter: CONF_N -> "8002" Comparing "7190" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7191" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 769168 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762991 ATOM PAIRS WERE FOUND FOR ATOM LIST 41864 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30035 from a total of 762991 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7191 -84.60881 8.44422 0.75656 INTE EXTERN> -25.92734 -58.68148 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.6088" Parameter: A <- "-84.6088" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9273" Parameter: B <- "-25.9273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.6815" Parameter: C <- "-58.6815" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7191 TOTAL ENERGY = -84.6088 RDTITL> * VAN DER WAALS = -25.9273 ELECTROSTATIC = -58.6815 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7191" Parameter: CONF_N -> "8002" Comparing "7191" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7192" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762991 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760197 ATOM PAIRS WERE FOUND FOR ATOM LIST 41658 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30348 from a total of 760197 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7192 -81.15885 -3.44996 0.72170 INTE EXTERN> -28.57923 -52.57962 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.1589" Parameter: A <- "-81.1589" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5792" Parameter: B <- "-28.5792" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5796" Parameter: C <- "-52.5796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7192 TOTAL ENERGY = -81.1589 RDTITL> * VAN DER WAALS = -28.5792 ELECTROSTATIC = -52.5796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7192" Parameter: CONF_N -> "8002" Comparing "7192" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7193" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760197 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754281 ATOM PAIRS WERE FOUND FOR ATOM LIST 41586 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30271 from a total of 754281 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7193 -83.06859 1.90974 0.69110 INTE EXTERN> -30.14801 -52.92058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.0686" Parameter: A <- "-83.0686" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.148" Parameter: B <- "-30.148" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9206" Parameter: C <- "-52.9206" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7193 TOTAL ENERGY = -83.0686 RDTITL> * VAN DER WAALS = -30.148 ELECTROSTATIC = -52.9206 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7193" Parameter: CONF_N -> "8002" Comparing "7193" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7194" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754281 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757153 ATOM PAIRS WERE FOUND FOR ATOM LIST 41712 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30040 from a total of 757153 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7194 -82.37913 -0.68945 0.63895 INTE EXTERN> -30.68062 -51.69851 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3791" Parameter: A <- "-82.3791" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6806" Parameter: B <- "-30.6806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6985" Parameter: C <- "-51.6985" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7194 TOTAL ENERGY = -82.3791 RDTITL> * VAN DER WAALS = -30.6806 ELECTROSTATIC = -51.6985 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7194" Parameter: CONF_N -> "8002" Comparing "7194" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7195" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757153 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758249 ATOM PAIRS WERE FOUND FOR ATOM LIST 41798 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29155 from a total of 758249 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7195 -73.28815 -9.09099 0.53717 INTE EXTERN> -31.29594 -41.99221 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2881" Parameter: A <- "-73.2881" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2959" Parameter: B <- "-31.2959" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9922" Parameter: C <- "-41.9922" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7195 TOTAL ENERGY = -73.2881 RDTITL> * VAN DER WAALS = -31.2959 ELECTROSTATIC = -41.9922 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7195" Parameter: CONF_N -> "8002" Comparing "7195" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7196" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758249 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758230 ATOM PAIRS WERE FOUND FOR ATOM LIST 41658 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29689 from a total of 758230 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7196 -89.12394 15.83579 0.77188 INTE EXTERN> -30.31390 -58.81003 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-89.1239" Parameter: A <- "-89.1239" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3139" Parameter: B <- "-30.3139" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.81" Parameter: C <- "-58.81" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7196 TOTAL ENERGY = -89.1239 RDTITL> * VAN DER WAALS = -30.3139 ELECTROSTATIC = -58.81 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7196" Parameter: CONF_N -> "8002" Comparing "7196" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7197" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758230 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760629 ATOM PAIRS WERE FOUND FOR ATOM LIST 41742 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29539 from a total of 760629 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7197 -76.77858 -12.34536 0.67841 INTE EXTERN> -30.33496 -46.44361 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7786" Parameter: A <- "-76.7786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.335" Parameter: B <- "-30.335" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4436" Parameter: C <- "-46.4436" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7197 TOTAL ENERGY = -76.7786 RDTITL> * VAN DER WAALS = -30.335 ELECTROSTATIC = -46.4436 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7197" Parameter: CONF_N -> "8002" Comparing "7197" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7198" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760629 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757606 ATOM PAIRS WERE FOUND FOR ATOM LIST 41577 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29685 from a total of 757606 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7198 -82.53631 5.75773 0.70078 INTE EXTERN> -30.57183 -51.96448 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.5363" Parameter: A <- "-82.5363" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5718" Parameter: B <- "-30.5718" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.9645" Parameter: C <- "-51.9645" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7198 TOTAL ENERGY = -82.5363 RDTITL> * VAN DER WAALS = -30.5718 ELECTROSTATIC = -51.9645 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7198" Parameter: CONF_N -> "8002" Comparing "7198" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7199" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757606 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749654 ATOM PAIRS WERE FOUND FOR ATOM LIST 41350 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29552 from a total of 749654 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7199 -78.71813 -3.81818 0.71693 INTE EXTERN> -27.81878 -50.89935 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7181" Parameter: A <- "-78.7181" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8188" Parameter: B <- "-27.8188" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8993" Parameter: C <- "-50.8993" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7199 TOTAL ENERGY = -78.7181 RDTITL> * VAN DER WAALS = -27.8188 ELECTROSTATIC = -50.8993 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7199" Parameter: CONF_N -> "8002" Comparing "7199" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7200" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749654 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756650 ATOM PAIRS WERE FOUND FOR ATOM LIST 41473 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29906 from a total of 756650 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7200 -79.25315 0.53502 0.76495 INTE EXTERN> -26.04237 -53.21078 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2532" Parameter: A <- "-79.2532" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0424" Parameter: B <- "-26.0424" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.2108" Parameter: C <- "-53.2108" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7200 TOTAL ENERGY = -79.2532 RDTITL> * VAN DER WAALS = -26.0424 ELECTROSTATIC = -53.2108 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7200" Parameter: CONF_N -> "8002" Comparing "7200" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7201" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756650 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757979 ATOM PAIRS WERE FOUND FOR ATOM LIST 41691 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30003 from a total of 757979 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7201 -82.61850 3.36535 0.82715 INTE EXTERN> -28.06511 -54.55339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.6185" Parameter: A <- "-82.6185" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0651" Parameter: B <- "-28.0651" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.5534" Parameter: C <- "-54.5534" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7201 TOTAL ENERGY = -82.6185 RDTITL> * VAN DER WAALS = -28.0651 ELECTROSTATIC = -54.5534 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7201" Parameter: CONF_N -> "8002" Comparing "7201" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7202" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757979 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751529 ATOM PAIRS WERE FOUND FOR ATOM LIST 41435 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29291 from a total of 751529 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7202 -80.59972 -2.01879 0.73941 INTE EXTERN> -28.63223 -51.96748 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5997" Parameter: A <- "-80.5997" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6322" Parameter: B <- "-28.6322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.9675" Parameter: C <- "-51.9675" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7202 TOTAL ENERGY = -80.5997 RDTITL> * VAN DER WAALS = -28.6322 ELECTROSTATIC = -51.9675 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7202" Parameter: CONF_N -> "8002" Comparing "7202" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7203" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751529 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747165 ATOM PAIRS WERE FOUND FOR ATOM LIST 41218 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29203 from a total of 747165 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7203 -72.10833 -8.49139 0.59633 INTE EXTERN> -27.71815 -44.39017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1083" Parameter: A <- "-72.1083" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7182" Parameter: B <- "-27.7182" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3902" Parameter: C <- "-44.3902" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7203 TOTAL ENERGY = -72.1083 RDTITL> * VAN DER WAALS = -27.7182 ELECTROSTATIC = -44.3902 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7203" Parameter: CONF_N -> "8002" Comparing "7203" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7204" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747165 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755566 ATOM PAIRS WERE FOUND FOR ATOM LIST 41471 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29418 from a total of 755566 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7204 -81.49229 9.38397 0.68117 INTE EXTERN> -30.31831 -51.17398 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4923" Parameter: A <- "-81.4923" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3183" Parameter: B <- "-30.3183" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.174" Parameter: C <- "-51.174" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7204 TOTAL ENERGY = -81.4923 RDTITL> * VAN DER WAALS = -30.3183 ELECTROSTATIC = -51.174 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7204" Parameter: CONF_N -> "8002" Comparing "7204" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7205" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755566 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756933 ATOM PAIRS WERE FOUND FOR ATOM LIST 41476 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29789 from a total of 756933 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7205 -83.97083 2.47854 0.63800 INTE EXTERN> -30.52610 -53.44473 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.9708" Parameter: A <- "-83.9708" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5261" Parameter: B <- "-30.5261" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4447" Parameter: C <- "-53.4447" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7205 TOTAL ENERGY = -83.9708 RDTITL> * VAN DER WAALS = -30.5261 ELECTROSTATIC = -53.4447 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7205" Parameter: CONF_N -> "8002" Comparing "7205" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7206" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756933 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756309 ATOM PAIRS WERE FOUND FOR ATOM LIST 41664 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29133 from a total of 756309 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7206 -74.07118 -9.89965 0.60949 INTE EXTERN> -29.03214 -45.03904 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0712" Parameter: A <- "-74.0712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0321" Parameter: B <- "-29.0321" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.039" Parameter: C <- "-45.039" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7206 TOTAL ENERGY = -74.0712 RDTITL> * VAN DER WAALS = -29.0321 ELECTROSTATIC = -45.039 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7206" Parameter: CONF_N -> "8002" Comparing "7206" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7207" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756309 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748735 ATOM PAIRS WERE FOUND FOR ATOM LIST 41208 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28928 from a total of 748735 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7207 -67.84572 -6.22546 0.66978 INTE EXTERN> -26.66347 -41.18226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8457" Parameter: A <- "-67.8457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6635" Parameter: B <- "-26.6635" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1823" Parameter: C <- "-41.1823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7207 TOTAL ENERGY = -67.8457 RDTITL> * VAN DER WAALS = -26.6635 ELECTROSTATIC = -41.1823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7207" Parameter: CONF_N -> "8002" Comparing "7207" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7208" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748735 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751521 ATOM PAIRS WERE FOUND FOR ATOM LIST 41366 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29630 from a total of 751521 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7208 -81.74551 13.89979 0.62351 INTE EXTERN> -32.25273 -49.49278 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.7455" Parameter: A <- "-81.7455" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2527" Parameter: B <- "-32.2527" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4928" Parameter: C <- "-49.4928" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7208 TOTAL ENERGY = -81.7455 RDTITL> * VAN DER WAALS = -32.2527 ELECTROSTATIC = -49.4928 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7208" Parameter: CONF_N -> "8002" Comparing "7208" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7209" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751521 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758534 ATOM PAIRS WERE FOUND FOR ATOM LIST 41759 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29768 from a total of 758534 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7209 -80.57010 -1.17541 0.69736 INTE EXTERN> -30.78190 -49.78821 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5701" Parameter: A <- "-80.5701" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7819" Parameter: B <- "-30.7819" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7882" Parameter: C <- "-49.7882" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7209 TOTAL ENERGY = -80.5701 RDTITL> * VAN DER WAALS = -30.7819 ELECTROSTATIC = -49.7882 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7209" Parameter: CONF_N -> "8002" Comparing "7209" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7210" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758534 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751727 ATOM PAIRS WERE FOUND FOR ATOM LIST 41431 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29681 from a total of 751727 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7210 -74.90850 -5.66161 0.63571 INTE EXTERN> -29.87077 -45.03773 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9085" Parameter: A <- "-74.9085" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8708" Parameter: B <- "-29.8708" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0377" Parameter: C <- "-45.0377" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7210 TOTAL ENERGY = -74.9085 RDTITL> * VAN DER WAALS = -29.8708 ELECTROSTATIC = -45.0377 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7210" Parameter: CONF_N -> "8002" Comparing "7210" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7211" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751727 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753873 ATOM PAIRS WERE FOUND FOR ATOM LIST 41692 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28918 from a total of 753873 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7211 -82.40352 7.49503 0.66270 INTE EXTERN> -29.78739 -52.61614 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.4035" Parameter: A <- "-82.4035" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7874" Parameter: B <- "-29.7874" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6161" Parameter: C <- "-52.6161" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7211 TOTAL ENERGY = -82.4035 RDTITL> * VAN DER WAALS = -29.7874 ELECTROSTATIC = -52.6161 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7211" Parameter: CONF_N -> "8002" Comparing "7211" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7212" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753873 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751859 ATOM PAIRS WERE FOUND FOR ATOM LIST 41248 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29532 from a total of 751859 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7212 -71.97859 -10.42493 0.66291 INTE EXTERN> -26.74026 -45.23833 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9786" Parameter: A <- "-71.9786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7403" Parameter: B <- "-26.7403" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2383" Parameter: C <- "-45.2383" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7212 TOTAL ENERGY = -71.9786 RDTITL> * VAN DER WAALS = -26.7403 ELECTROSTATIC = -45.2383 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7212" Parameter: CONF_N -> "8002" Comparing "7212" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7213" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751859 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749967 ATOM PAIRS WERE FOUND FOR ATOM LIST 41441 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29497 from a total of 749967 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7213 -77.19259 5.21400 0.63545 INTE EXTERN> -30.49779 -46.69480 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1926" Parameter: A <- "-77.1926" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4978" Parameter: B <- "-30.4978" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6948" Parameter: C <- "-46.6948" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7213 TOTAL ENERGY = -77.1926 RDTITL> * VAN DER WAALS = -30.4978 ELECTROSTATIC = -46.6948 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7213" Parameter: CONF_N -> "8002" Comparing "7213" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7214" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749967 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761736 ATOM PAIRS WERE FOUND FOR ATOM LIST 41913 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30174 from a total of 761736 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7214 -85.66824 8.47565 0.70499 INTE EXTERN> -29.47370 -56.19454 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.6682" Parameter: A <- "-85.6682" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4737" Parameter: B <- "-29.4737" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.1945" Parameter: C <- "-56.1945" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7214 TOTAL ENERGY = -85.6682 RDTITL> * VAN DER WAALS = -29.4737 ELECTROSTATIC = -56.1945 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7214" Parameter: CONF_N -> "8002" Comparing "7214" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7215" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761736 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753014 ATOM PAIRS WERE FOUND FOR ATOM LIST 41404 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30271 from a total of 753014 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7215 -80.44627 -5.22197 0.68409 INTE EXTERN> -28.99016 -51.45611 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4463" Parameter: A <- "-80.4463" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9902" Parameter: B <- "-28.9902" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4561" Parameter: C <- "-51.4561" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7215 TOTAL ENERGY = -80.4463 RDTITL> * VAN DER WAALS = -28.9902 ELECTROSTATIC = -51.4561 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7215" Parameter: CONF_N -> "8002" Comparing "7215" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7216" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753014 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752775 ATOM PAIRS WERE FOUND FOR ATOM LIST 41339 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30123 from a total of 752775 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7216 -84.12745 3.68117 0.57068 INTE EXTERN> -33.65510 -50.47235 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.1274" Parameter: A <- "-84.1274" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.6551" Parameter: B <- "-33.6551" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4723" Parameter: C <- "-50.4723" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7216 TOTAL ENERGY = -84.1274 RDTITL> * VAN DER WAALS = -33.6551 ELECTROSTATIC = -50.4723 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7216" Parameter: CONF_N -> "8002" Comparing "7216" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7217" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752775 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755801 ATOM PAIRS WERE FOUND FOR ATOM LIST 41374 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30322 from a total of 755801 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7217 -83.68486 -0.44259 0.65267 INTE EXTERN> -29.01896 -54.66590 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.6849" Parameter: A <- "-83.6849" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.019" Parameter: B <- "-29.019" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.6659" Parameter: C <- "-54.6659" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7217 TOTAL ENERGY = -83.6849 RDTITL> * VAN DER WAALS = -29.019 ELECTROSTATIC = -54.6659 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7217" Parameter: CONF_N -> "8002" Comparing "7217" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7218" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755801 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752915 ATOM PAIRS WERE FOUND FOR ATOM LIST 41449 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30250 from a total of 752915 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7218 -77.08263 -6.60223 0.63532 INTE EXTERN> -30.69567 -46.38696 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0826" Parameter: A <- "-77.0826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6957" Parameter: B <- "-30.6957" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.387" Parameter: C <- "-46.387" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7218 TOTAL ENERGY = -77.0826 RDTITL> * VAN DER WAALS = -30.6957 ELECTROSTATIC = -46.387 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7218" Parameter: CONF_N -> "8002" Comparing "7218" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7219" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752915 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754412 ATOM PAIRS WERE FOUND FOR ATOM LIST 41418 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30180 from a total of 754412 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7219 -86.40140 9.31876 0.65536 INTE EXTERN> -31.89061 -54.51079 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.4014" Parameter: A <- "-86.4014" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8906" Parameter: B <- "-31.8906" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.5108" Parameter: C <- "-54.5108" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7219 TOTAL ENERGY = -86.4014 RDTITL> * VAN DER WAALS = -31.8906 ELECTROSTATIC = -54.5108 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7219" Parameter: CONF_N -> "8002" Comparing "7219" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7220" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754412 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755891 ATOM PAIRS WERE FOUND FOR ATOM LIST 41427 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30815 from a total of 755891 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7220 -67.89338 -18.50802 0.64625 INTE EXTERN> -31.75480 -36.13858 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8934" Parameter: A <- "-67.8934" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7548" Parameter: B <- "-31.7548" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1386" Parameter: C <- "-36.1386" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7220 TOTAL ENERGY = -67.8934 RDTITL> * VAN DER WAALS = -31.7548 ELECTROSTATIC = -36.1386 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7220" Parameter: CONF_N -> "8002" Comparing "7220" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7221" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755891 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754566 ATOM PAIRS WERE FOUND FOR ATOM LIST 41294 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30351 from a total of 754566 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7221 -78.73354 10.84016 0.74244 INTE EXTERN> -25.70446 -53.02908 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7335" Parameter: A <- "-78.7335" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7045" Parameter: B <- "-25.7045" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0291" Parameter: C <- "-53.0291" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7221 TOTAL ENERGY = -78.7335 RDTITL> * VAN DER WAALS = -25.7045 ELECTROSTATIC = -53.0291 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7221" Parameter: CONF_N -> "8002" Comparing "7221" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7222" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754566 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753412 ATOM PAIRS WERE FOUND FOR ATOM LIST 41498 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30222 from a total of 753412 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7222 -77.91758 -0.81596 0.68634 INTE EXTERN> -28.83575 -49.08183 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9176" Parameter: A <- "-77.9176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8357" Parameter: B <- "-28.8357" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0818" Parameter: C <- "-49.0818" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7222 TOTAL ENERGY = -77.9176 RDTITL> * VAN DER WAALS = -28.8357 ELECTROSTATIC = -49.0818 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7222" Parameter: CONF_N -> "8002" Comparing "7222" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7223" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753412 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41219 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29989 from a total of 753586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7223 -79.83432 1.91674 0.78880 INTE EXTERN> -26.70254 -53.13179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8343" Parameter: A <- "-79.8343" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7025" Parameter: B <- "-26.7025" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.1318" Parameter: C <- "-53.1318" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7223 TOTAL ENERGY = -79.8343 RDTITL> * VAN DER WAALS = -26.7025 ELECTROSTATIC = -53.1318 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7223" Parameter: CONF_N -> "8002" Comparing "7223" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7224" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754861 ATOM PAIRS WERE FOUND FOR ATOM LIST 41396 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29759 from a total of 754861 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7224 -75.16085 -4.67348 0.61567 INTE EXTERN> -29.14328 -46.01756 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1608" Parameter: A <- "-75.1608" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1433" Parameter: B <- "-29.1433" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0176" Parameter: C <- "-46.0176" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7224 TOTAL ENERGY = -75.1608 RDTITL> * VAN DER WAALS = -29.1433 ELECTROSTATIC = -46.0176 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7224" Parameter: CONF_N -> "8002" Comparing "7224" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7225" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754861 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759425 ATOM PAIRS WERE FOUND FOR ATOM LIST 41872 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30037 from a total of 759425 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7225 -81.48622 6.32537 0.88267 INTE EXTERN> -21.61812 -59.86810 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.4862" Parameter: A <- "-81.4862" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.6181" Parameter: B <- "-21.6181" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.8681" Parameter: C <- "-59.8681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7225 TOTAL ENERGY = -81.4862 RDTITL> * VAN DER WAALS = -21.6181 ELECTROSTATIC = -59.8681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7225" Parameter: CONF_N -> "8002" Comparing "7225" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7226" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759425 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760611 ATOM PAIRS WERE FOUND FOR ATOM LIST 41661 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30221 from a total of 760611 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7226 -80.06494 -1.42128 0.79589 INTE EXTERN> -26.09869 -53.96625 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0649" Parameter: A <- "-80.0649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0987" Parameter: B <- "-26.0987" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.9662" Parameter: C <- "-53.9662" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7226 TOTAL ENERGY = -80.0649 RDTITL> * VAN DER WAALS = -26.0987 ELECTROSTATIC = -53.9662 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7226" Parameter: CONF_N -> "8002" Comparing "7226" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7227" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760611 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757103 ATOM PAIRS WERE FOUND FOR ATOM LIST 41421 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29811 from a total of 757103 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7227 -79.14233 -0.92261 0.72723 INTE EXTERN> -27.81579 -51.32654 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1423" Parameter: A <- "-79.1423" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8158" Parameter: B <- "-27.8158" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3265" Parameter: C <- "-51.3265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7227 TOTAL ENERGY = -79.1423 RDTITL> * VAN DER WAALS = -27.8158 ELECTROSTATIC = -51.3265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7227" Parameter: CONF_N -> "8002" Comparing "7227" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7228" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757103 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757158 ATOM PAIRS WERE FOUND FOR ATOM LIST 41677 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29379 from a total of 757158 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7228 -75.93145 -3.21088 0.62483 INTE EXTERN> -32.81203 -43.11942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9314" Parameter: A <- "-75.9314" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.812" Parameter: B <- "-32.812" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1194" Parameter: C <- "-43.1194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7228 TOTAL ENERGY = -75.9314 RDTITL> * VAN DER WAALS = -32.812 ELECTROSTATIC = -43.1194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7228" Parameter: CONF_N -> "8002" Comparing "7228" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7229" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757158 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757115 ATOM PAIRS WERE FOUND FOR ATOM LIST 41730 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29543 from a total of 757115 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7229 -82.30901 6.37756 0.89656 INTE EXTERN> -24.11499 -58.19402 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.309" Parameter: A <- "-82.309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.115" Parameter: B <- "-24.115" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.194" Parameter: C <- "-58.194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7229 TOTAL ENERGY = -82.309 RDTITL> * VAN DER WAALS = -24.115 ELECTROSTATIC = -58.194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7229" Parameter: CONF_N -> "8002" Comparing "7229" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7230" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757115 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757437 ATOM PAIRS WERE FOUND FOR ATOM LIST 41531 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29845 from a total of 757437 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7230 -78.22026 -4.08875 0.69961 INTE EXTERN> -29.30747 -48.91279 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.2203" Parameter: A <- "-78.2203" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3075" Parameter: B <- "-29.3075" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9128" Parameter: C <- "-48.9128" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7230 TOTAL ENERGY = -78.2203 RDTITL> * VAN DER WAALS = -29.3075 ELECTROSTATIC = -48.9128 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7230" Parameter: CONF_N -> "8002" Comparing "7230" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7231" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757437 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760642 ATOM PAIRS WERE FOUND FOR ATOM LIST 41809 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29523 from a total of 760642 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7231 -85.96671 7.74645 0.73443 INTE EXTERN> -27.32898 -58.63773 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.9667" Parameter: A <- "-85.9667" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.329" Parameter: B <- "-27.329" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.6377" Parameter: C <- "-58.6377" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7231 TOTAL ENERGY = -85.9667 RDTITL> * VAN DER WAALS = -27.329 ELECTROSTATIC = -58.6377 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7231" Parameter: CONF_N -> "8002" Comparing "7231" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7232" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760642 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758193 ATOM PAIRS WERE FOUND FOR ATOM LIST 41671 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30107 from a total of 758193 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7232 -80.18905 -5.77766 0.67246 INTE EXTERN> -30.76189 -49.42716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1891" Parameter: A <- "-80.1891" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7619" Parameter: B <- "-30.7619" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4272" Parameter: C <- "-49.4272" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7232 TOTAL ENERGY = -80.1891 RDTITL> * VAN DER WAALS = -30.7619 ELECTROSTATIC = -49.4272 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7232" Parameter: CONF_N -> "8002" Comparing "7232" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7233" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758193 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758859 ATOM PAIRS WERE FOUND FOR ATOM LIST 41576 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29797 from a total of 758859 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7233 -84.65285 4.46380 0.74446 INTE EXTERN> -26.92356 -57.72929 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.6529" Parameter: A <- "-84.6529" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9236" Parameter: B <- "-26.9236" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.7293" Parameter: C <- "-57.7293" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7233 TOTAL ENERGY = -84.6529 RDTITL> * VAN DER WAALS = -26.9236 ELECTROSTATIC = -57.7293 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7233" Parameter: CONF_N -> "8002" Comparing "7233" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7234" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758859 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760308 ATOM PAIRS WERE FOUND FOR ATOM LIST 41757 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29086 from a total of 760308 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7234 -69.17507 -15.47778 0.69751 INTE EXTERN> -28.77116 -40.40390 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1751" Parameter: A <- "-69.1751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7712" Parameter: B <- "-28.7712" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4039" Parameter: C <- "-40.4039" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7234 TOTAL ENERGY = -69.1751 RDTITL> * VAN DER WAALS = -28.7712 ELECTROSTATIC = -40.4039 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7234" Parameter: CONF_N -> "8002" Comparing "7234" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7235" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760308 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761818 ATOM PAIRS WERE FOUND FOR ATOM LIST 41661 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29486 from a total of 761818 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7235 -78.01259 8.83752 0.69703 INTE EXTERN> -25.31018 -52.70241 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0126" Parameter: A <- "-78.0126" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3102" Parameter: B <- "-25.3102" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.7024" Parameter: C <- "-52.7024" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7235 TOTAL ENERGY = -78.0126 RDTITL> * VAN DER WAALS = -25.3102 ELECTROSTATIC = -52.7024 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7235" Parameter: CONF_N -> "8002" Comparing "7235" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7236" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761818 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754440 ATOM PAIRS WERE FOUND FOR ATOM LIST 41587 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29473 from a total of 754440 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7236 -88.69973 10.68714 0.74412 INTE EXTERN> -28.34965 -60.35008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.6997" Parameter: A <- "-88.6997" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3496" Parameter: B <- "-28.3496" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-60.3501" Parameter: C <- "-60.3501" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7236 TOTAL ENERGY = -88.6997 RDTITL> * VAN DER WAALS = -28.3496 ELECTROSTATIC = -60.3501 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7236" Parameter: CONF_N -> "8002" Comparing "7236" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7237" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754440 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747367 ATOM PAIRS WERE FOUND FOR ATOM LIST 40902 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29116 from a total of 747367 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7237 -81.08283 -7.61690 0.65985 INTE EXTERN> -25.59032 -55.49251 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.0828" Parameter: A <- "-81.0828" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5903" Parameter: B <- "-25.5903" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.4925" Parameter: C <- "-55.4925" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7237 TOTAL ENERGY = -81.0828 RDTITL> * VAN DER WAALS = -25.5903 ELECTROSTATIC = -55.4925 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7237" Parameter: CONF_N -> "8002" Comparing "7237" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7238" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747367 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757326 ATOM PAIRS WERE FOUND FOR ATOM LIST 41504 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30032 from a total of 757326 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7238 -76.54338 -4.53945 0.70721 INTE EXTERN> -26.82574 -49.71764 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5434" Parameter: A <- "-76.5434" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8257" Parameter: B <- "-26.8257" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7176" Parameter: C <- "-49.7176" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7238 TOTAL ENERGY = -76.5434 RDTITL> * VAN DER WAALS = -26.8257 ELECTROSTATIC = -49.7176 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7238" Parameter: CONF_N -> "8002" Comparing "7238" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7239" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757326 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754396 ATOM PAIRS WERE FOUND FOR ATOM LIST 41443 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29028 from a total of 754396 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7239 -80.44462 3.90124 0.61456 INTE EXTERN> -31.54815 -48.89647 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4446" Parameter: A <- "-80.4446" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5482" Parameter: B <- "-31.5482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8965" Parameter: C <- "-48.8965" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7239 TOTAL ENERGY = -80.4446 RDTITL> * VAN DER WAALS = -31.5482 ELECTROSTATIC = -48.8965 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7239" Parameter: CONF_N -> "8002" Comparing "7239" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7240" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754396 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757053 ATOM PAIRS WERE FOUND FOR ATOM LIST 41336 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29991 from a total of 757053 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7240 -91.32098 10.87636 0.80116 INTE EXTERN> -25.32905 -65.99193 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-91.321" Parameter: A <- "-91.321" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.329" Parameter: B <- "-25.329" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-65.9919" Parameter: C <- "-65.9919" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7240 TOTAL ENERGY = -91.321 RDTITL> * VAN DER WAALS = -25.329 ELECTROSTATIC = -65.9919 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7240" Parameter: CONF_N -> "8002" Comparing "7240" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7241" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757053 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758883 ATOM PAIRS WERE FOUND FOR ATOM LIST 41552 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29557 from a total of 758883 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7241 -89.34282 -1.97816 0.67589 INTE EXTERN> -31.60995 -57.73286 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-89.3428" Parameter: A <- "-89.3428" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.61" Parameter: B <- "-31.61" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.7329" Parameter: C <- "-57.7329" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7241 TOTAL ENERGY = -89.3428 RDTITL> * VAN DER WAALS = -31.61 ELECTROSTATIC = -57.7329 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7241" Parameter: CONF_N -> "8002" Comparing "7241" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7242" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758883 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758794 ATOM PAIRS WERE FOUND FOR ATOM LIST 41537 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29341 from a total of 758794 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7242 -83.07856 -6.26426 0.70991 INTE EXTERN> -28.71861 -54.35995 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.0786" Parameter: A <- "-83.0786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7186" Parameter: B <- "-28.7186" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.3599" Parameter: C <- "-54.3599" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7242 TOTAL ENERGY = -83.0786 RDTITL> * VAN DER WAALS = -28.7186 ELECTROSTATIC = -54.3599 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7242" Parameter: CONF_N -> "8002" Comparing "7242" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7243" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758794 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757299 ATOM PAIRS WERE FOUND FOR ATOM LIST 41543 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29811 from a total of 757299 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7243 -69.91021 -13.16835 0.60421 INTE EXTERN> -31.01576 -38.89445 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.9102" Parameter: A <- "-69.9102" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0158" Parameter: B <- "-31.0158" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8944" Parameter: C <- "-38.8944" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7243 TOTAL ENERGY = -69.9102 RDTITL> * VAN DER WAALS = -31.0158 ELECTROSTATIC = -38.8944 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7243" Parameter: CONF_N -> "8002" Comparing "7243" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7244" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757299 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753176 ATOM PAIRS WERE FOUND FOR ATOM LIST 41368 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29462 from a total of 753176 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7244 -76.56203 6.65182 0.70977 INTE EXTERN> -28.01367 -48.54836 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.562" Parameter: A <- "-76.562" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0137" Parameter: B <- "-28.0137" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5484" Parameter: C <- "-48.5484" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7244 TOTAL ENERGY = -76.562 RDTITL> * VAN DER WAALS = -28.0137 ELECTROSTATIC = -48.5484 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7244" Parameter: CONF_N -> "8002" Comparing "7244" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7245" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753176 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756520 ATOM PAIRS WERE FOUND FOR ATOM LIST 41461 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29941 from a total of 756520 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7245 -78.02334 1.46130 0.75001 INTE EXTERN> -25.57306 -52.45028 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0233" Parameter: A <- "-78.0233" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5731" Parameter: B <- "-25.5731" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.4503" Parameter: C <- "-52.4503" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7245 TOTAL ENERGY = -78.0233 RDTITL> * VAN DER WAALS = -25.5731 ELECTROSTATIC = -52.4503 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7245" Parameter: CONF_N -> "8002" Comparing "7245" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7246" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756520 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755560 ATOM PAIRS WERE FOUND FOR ATOM LIST 41158 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29680 from a total of 755560 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7246 -81.81563 3.79229 0.70113 INTE EXTERN> -27.91531 -53.90032 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8156" Parameter: A <- "-81.8156" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9153" Parameter: B <- "-27.9153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.9003" Parameter: C <- "-53.9003" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7246 TOTAL ENERGY = -81.8156 RDTITL> * VAN DER WAALS = -27.9153 ELECTROSTATIC = -53.9003 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7246" Parameter: CONF_N -> "8002" Comparing "7246" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7247" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755560 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764195 ATOM PAIRS WERE FOUND FOR ATOM LIST 41999 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30529 from a total of 764195 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7247 -82.30430 0.48867 0.71581 INTE EXTERN> -27.26276 -55.04153 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.3043" Parameter: A <- "-82.3043" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2628" Parameter: B <- "-27.2628" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.0415" Parameter: C <- "-55.0415" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7247 TOTAL ENERGY = -82.3043 RDTITL> * VAN DER WAALS = -27.2628 ELECTROSTATIC = -55.0415 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7247" Parameter: CONF_N -> "8002" Comparing "7247" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7248" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764195 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761566 ATOM PAIRS WERE FOUND FOR ATOM LIST 41666 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30334 from a total of 761566 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7248 -75.68991 -6.61438 0.69547 INTE EXTERN> -24.09001 -51.59990 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6899" Parameter: A <- "-75.6899" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.09" Parameter: B <- "-24.09" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5999" Parameter: C <- "-51.5999" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7248 TOTAL ENERGY = -75.6899 RDTITL> * VAN DER WAALS = -24.09 ELECTROSTATIC = -51.5999 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7248" Parameter: CONF_N -> "8002" Comparing "7248" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7249" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761566 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759321 ATOM PAIRS WERE FOUND FOR ATOM LIST 41628 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29714 from a total of 759321 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7249 -87.72235 12.03243 0.70202 INTE EXTERN> -27.06008 -60.66227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.7223" Parameter: A <- "-87.7223" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0601" Parameter: B <- "-27.0601" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-60.6623" Parameter: C <- "-60.6623" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7249 TOTAL ENERGY = -87.7223 RDTITL> * VAN DER WAALS = -27.0601 ELECTROSTATIC = -60.6623 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7249" Parameter: CONF_N -> "8002" Comparing "7249" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7250" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759321 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756593 ATOM PAIRS WERE FOUND FOR ATOM LIST 41737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29960 from a total of 756593 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7250 -85.89874 -1.82361 0.71043 INTE EXTERN> -27.53144 -58.36730 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.8987" Parameter: A <- "-85.8987" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5314" Parameter: B <- "-27.5314" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.3673" Parameter: C <- "-58.3673" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7250 TOTAL ENERGY = -85.8987 RDTITL> * VAN DER WAALS = -27.5314 ELECTROSTATIC = -58.3673 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7250" Parameter: CONF_N -> "8002" Comparing "7250" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7251" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756593 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758505 ATOM PAIRS WERE FOUND FOR ATOM LIST 41688 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29851 from a total of 758505 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7251 -80.86487 -5.03387 0.79186 INTE EXTERN> -26.21998 -54.64489 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.8649" Parameter: A <- "-80.8649" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.22" Parameter: B <- "-26.22" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.6449" Parameter: C <- "-54.6449" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7251 TOTAL ENERGY = -80.8649 RDTITL> * VAN DER WAALS = -26.22 ELECTROSTATIC = -54.6449 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7251" Parameter: CONF_N -> "8002" Comparing "7251" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7252" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758505 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759033 ATOM PAIRS WERE FOUND FOR ATOM LIST 41763 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29670 from a total of 759033 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7252 -85.58599 4.72112 0.84095 INTE EXTERN> -25.49944 -60.08655 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.586" Parameter: A <- "-85.586" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4994" Parameter: B <- "-25.4994" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-60.0865" Parameter: C <- "-60.0865" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7252 TOTAL ENERGY = -85.586 RDTITL> * VAN DER WAALS = -25.4994 ELECTROSTATIC = -60.0865 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7252" Parameter: CONF_N -> "8002" Comparing "7252" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7253" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759033 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760932 ATOM PAIRS WERE FOUND FOR ATOM LIST 41800 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30444 from a total of 760932 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7253 -79.75834 -5.82765 0.69450 INTE EXTERN> -30.10021 -49.65813 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7583" Parameter: A <- "-79.7583" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1002" Parameter: B <- "-30.1002" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6581" Parameter: C <- "-49.6581" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7253 TOTAL ENERGY = -79.7583 RDTITL> * VAN DER WAALS = -30.1002 ELECTROSTATIC = -49.6581 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7253" Parameter: CONF_N -> "8002" Comparing "7253" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7254" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760932 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758414 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29720 from a total of 758414 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7254 -89.01415 9.25581 0.69536 INTE EXTERN> -30.23529 -58.77886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-89.0141" Parameter: A <- "-89.0141" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2353" Parameter: B <- "-30.2353" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.7789" Parameter: C <- "-58.7789" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7254 TOTAL ENERGY = -89.0141 RDTITL> * VAN DER WAALS = -30.2353 ELECTROSTATIC = -58.7789 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7254" Parameter: CONF_N -> "8002" Comparing "7254" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7255" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758414 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752350 ATOM PAIRS WERE FOUND FOR ATOM LIST 41153 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29260 from a total of 752350 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7255 -80.29644 -8.71771 0.65222 INTE EXTERN> -29.27826 -51.01818 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2964" Parameter: A <- "-80.2964" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2783" Parameter: B <- "-29.2783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0182" Parameter: C <- "-51.0182" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7255 TOTAL ENERGY = -80.2964 RDTITL> * VAN DER WAALS = -29.2783 ELECTROSTATIC = -51.0182 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7255" Parameter: CONF_N -> "8002" Comparing "7255" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7256" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752350 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763543 ATOM PAIRS WERE FOUND FOR ATOM LIST 41964 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29914 from a total of 763543 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7256 -86.10299 5.80655 0.70933 INTE EXTERN> -30.83009 -55.27290 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.103" Parameter: A <- "-86.103" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8301" Parameter: B <- "-30.8301" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.2729" Parameter: C <- "-55.2729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7256 TOTAL ENERGY = -86.103 RDTITL> * VAN DER WAALS = -30.8301 ELECTROSTATIC = -55.2729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7256" Parameter: CONF_N -> "8002" Comparing "7256" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7257" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763543 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759746 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29613 from a total of 759746 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7257 -75.38235 -10.72064 0.63082 INTE EXTERN> -31.33309 -44.04926 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3823" Parameter: A <- "-75.3823" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.3331" Parameter: B <- "-31.3331" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0493" Parameter: C <- "-44.0493" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7257 TOTAL ENERGY = -75.3823 RDTITL> * VAN DER WAALS = -31.3331 ELECTROSTATIC = -44.0493 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7257" Parameter: CONF_N -> "8002" Comparing "7257" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7258" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759746 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753116 ATOM PAIRS WERE FOUND FOR ATOM LIST 41455 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29295 from a total of 753116 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7258 -87.84302 12.46067 0.76868 INTE EXTERN> -27.70597 -60.13705 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.843" Parameter: A <- "-87.843" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.706" Parameter: B <- "-27.706" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-60.137" Parameter: C <- "-60.137" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7258 TOTAL ENERGY = -87.843 RDTITL> * VAN DER WAALS = -27.706 ELECTROSTATIC = -60.137 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7258" Parameter: CONF_N -> "8002" Comparing "7258" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7259" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753116 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754848 ATOM PAIRS WERE FOUND FOR ATOM LIST 41380 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29948 from a total of 754848 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7259 -84.03933 -3.80369 0.85446 INTE EXTERN> -24.80628 -59.23305 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.0393" Parameter: A <- "-84.0393" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8063" Parameter: B <- "-24.8063" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.233" Parameter: C <- "-59.233" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7259 TOTAL ENERGY = -84.0393 RDTITL> * VAN DER WAALS = -24.8063 ELECTROSTATIC = -59.233 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7259" Parameter: CONF_N -> "8002" Comparing "7259" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7260" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754848 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751818 ATOM PAIRS WERE FOUND FOR ATOM LIST 41076 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29410 from a total of 751818 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7260 -83.71587 -0.32346 0.64414 INTE EXTERN> -31.41680 -52.29908 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.7159" Parameter: A <- "-83.7159" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4168" Parameter: B <- "-31.4168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2991" Parameter: C <- "-52.2991" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7260 TOTAL ENERGY = -83.7159 RDTITL> * VAN DER WAALS = -31.4168 ELECTROSTATIC = -52.2991 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7260" Parameter: CONF_N -> "8002" Comparing "7260" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7261" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751818 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759921 ATOM PAIRS WERE FOUND FOR ATOM LIST 41719 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30038 from a total of 759921 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7261 -90.85240 7.13653 0.78248 INTE EXTERN> -29.07688 -61.77552 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-90.8524" Parameter: A <- "-90.8524" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0769" Parameter: B <- "-29.0769" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-61.7755" Parameter: C <- "-61.7755" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7261 TOTAL ENERGY = -90.8524 RDTITL> * VAN DER WAALS = -29.0769 ELECTROSTATIC = -61.7755 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7261" Parameter: CONF_N -> "8002" Comparing "7261" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7262" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759921 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754346 ATOM PAIRS WERE FOUND FOR ATOM LIST 41380 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29490 from a total of 754346 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7262 -77.02891 -13.82349 0.69485 INTE EXTERN> -28.78866 -48.24024 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0289" Parameter: A <- "-77.0289" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7887" Parameter: B <- "-28.7887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2402" Parameter: C <- "-48.2402" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7262 TOTAL ENERGY = -77.0289 RDTITL> * VAN DER WAALS = -28.7887 ELECTROSTATIC = -48.2402 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7262" Parameter: CONF_N -> "8002" Comparing "7262" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7263" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754346 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752832 ATOM PAIRS WERE FOUND FOR ATOM LIST 41415 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29577 from a total of 752832 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7263 -89.20000 12.17110 0.80885 INTE EXTERN> -25.61597 -63.58403 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-89.2" Parameter: A <- "-89.2" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.616" Parameter: B <- "-25.616" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-63.584" Parameter: C <- "-63.584" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7263 TOTAL ENERGY = -89.2 RDTITL> * VAN DER WAALS = -25.616 ELECTROSTATIC = -63.584 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7263" Parameter: CONF_N -> "8002" Comparing "7263" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7264" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752832 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758469 ATOM PAIRS WERE FOUND FOR ATOM LIST 41464 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30234 from a total of 758469 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7264 -77.01803 -12.18197 0.69127 INTE EXTERN> -28.89758 -48.12045 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.018" Parameter: A <- "-77.018" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8976" Parameter: B <- "-28.8976" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1205" Parameter: C <- "-48.1205" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7264 TOTAL ENERGY = -77.018 RDTITL> * VAN DER WAALS = -28.8976 ELECTROSTATIC = -48.1205 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7264" Parameter: CONF_N -> "8002" Comparing "7264" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7265" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758469 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752818 ATOM PAIRS WERE FOUND FOR ATOM LIST 41546 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29764 from a total of 752818 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7265 -80.54488 3.52685 0.63577 INTE EXTERN> -31.80307 -48.74181 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5449" Parameter: A <- "-80.5449" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8031" Parameter: B <- "-31.8031" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7418" Parameter: C <- "-48.7418" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7265 TOTAL ENERGY = -80.5449 RDTITL> * VAN DER WAALS = -31.8031 ELECTROSTATIC = -48.7418 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7265" Parameter: CONF_N -> "8002" Comparing "7265" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7266" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752818 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753620 ATOM PAIRS WERE FOUND FOR ATOM LIST 41465 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30196 from a total of 753620 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7266 -78.02397 -2.52091 0.85796 INTE EXTERN> -21.21333 -56.81064 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.024" Parameter: A <- "-78.024" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.2133" Parameter: B <- "-21.2133" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.8106" Parameter: C <- "-56.8106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7266 TOTAL ENERGY = -78.024 RDTITL> * VAN DER WAALS = -21.2133 ELECTROSTATIC = -56.8106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7266" Parameter: CONF_N -> "8002" Comparing "7266" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7267" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753620 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41827 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30247 from a total of 763526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7267 -80.65633 2.63235 0.72326 INTE EXTERN> -29.81552 -50.84080 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6563" Parameter: A <- "-80.6563" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8155" Parameter: B <- "-29.8155" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8408" Parameter: C <- "-50.8408" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7267 TOTAL ENERGY = -80.6563 RDTITL> * VAN DER WAALS = -29.8155 ELECTROSTATIC = -50.8408 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7267" Parameter: CONF_N -> "8002" Comparing "7267" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7268" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756756 ATOM PAIRS WERE FOUND FOR ATOM LIST 41477 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29920 from a total of 756756 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7268 -79.16709 -1.48923 0.68519 INTE EXTERN> -30.14380 -49.02329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1671" Parameter: A <- "-79.1671" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1438" Parameter: B <- "-30.1438" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0233" Parameter: C <- "-49.0233" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7268 TOTAL ENERGY = -79.1671 RDTITL> * VAN DER WAALS = -30.1438 ELECTROSTATIC = -49.0233 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7268" Parameter: CONF_N -> "8002" Comparing "7268" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7269" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756756 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758726 ATOM PAIRS WERE FOUND FOR ATOM LIST 41825 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30286 from a total of 758726 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7269 -74.41708 -4.75002 0.68733 INTE EXTERN> -27.64686 -46.77022 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4171" Parameter: A <- "-74.4171" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6469" Parameter: B <- "-27.6469" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7702" Parameter: C <- "-46.7702" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7269 TOTAL ENERGY = -74.4171 RDTITL> * VAN DER WAALS = -27.6469 ELECTROSTATIC = -46.7702 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7269" Parameter: CONF_N -> "8002" Comparing "7269" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7270" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758726 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756640 ATOM PAIRS WERE FOUND FOR ATOM LIST 41613 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30387 from a total of 756640 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7270 -83.15310 8.73603 0.64343 INTE EXTERN> -28.82302 -54.33008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.1531" Parameter: A <- "-83.1531" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.823" Parameter: B <- "-28.823" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.3301" Parameter: C <- "-54.3301" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7270 TOTAL ENERGY = -83.1531 RDTITL> * VAN DER WAALS = -28.823 ELECTROSTATIC = -54.3301 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7270" Parameter: CONF_N -> "8002" Comparing "7270" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7271" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756640 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760057 ATOM PAIRS WERE FOUND FOR ATOM LIST 41901 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30619 from a total of 760057 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7271 -76.46817 -6.68493 0.69235 INTE EXTERN> -28.53088 -47.93730 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4682" Parameter: A <- "-76.4682" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5309" Parameter: B <- "-28.5309" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9373" Parameter: C <- "-47.9373" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7271 TOTAL ENERGY = -76.4682 RDTITL> * VAN DER WAALS = -28.5309 ELECTROSTATIC = -47.9373 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7271" Parameter: CONF_N -> "8002" Comparing "7271" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7272" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760057 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757026 ATOM PAIRS WERE FOUND FOR ATOM LIST 41529 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29894 from a total of 757026 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7272 -86.04976 9.58158 0.62009 INTE EXTERN> -31.09333 -54.95642 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.0498" Parameter: A <- "-86.0498" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0933" Parameter: B <- "-31.0933" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.9564" Parameter: C <- "-54.9564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7272 TOTAL ENERGY = -86.0498 RDTITL> * VAN DER WAALS = -31.0933 ELECTROSTATIC = -54.9564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7272" Parameter: CONF_N -> "8002" Comparing "7272" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7273" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757026 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754938 ATOM PAIRS WERE FOUND FOR ATOM LIST 41394 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30022 from a total of 754938 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7273 -81.91536 -4.13439 0.65847 INTE EXTERN> -29.30695 -52.60841 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9154" Parameter: A <- "-81.9154" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.307" Parameter: B <- "-29.307" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6084" Parameter: C <- "-52.6084" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7273 TOTAL ENERGY = -81.9154 RDTITL> * VAN DER WAALS = -29.307 ELECTROSTATIC = -52.6084 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7273" Parameter: CONF_N -> "8002" Comparing "7273" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7274" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754938 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758378 ATOM PAIRS WERE FOUND FOR ATOM LIST 41691 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30149 from a total of 758378 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7274 -81.65541 -0.25995 0.62968 INTE EXTERN> -31.15886 -50.49655 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6554" Parameter: A <- "-81.6554" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1589" Parameter: B <- "-31.1589" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4966" Parameter: C <- "-50.4966" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7274 TOTAL ENERGY = -81.6554 RDTITL> * VAN DER WAALS = -31.1589 ELECTROSTATIC = -50.4966 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7274" Parameter: CONF_N -> "8002" Comparing "7274" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7275" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758378 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756737 ATOM PAIRS WERE FOUND FOR ATOM LIST 41582 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29759 from a total of 756737 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7275 -78.04258 -3.61283 0.60972 INTE EXTERN> -30.07490 -47.96768 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.0426" Parameter: A <- "-78.0426" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0749" Parameter: B <- "-30.0749" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9677" Parameter: C <- "-47.9677" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7275 TOTAL ENERGY = -78.0426 RDTITL> * VAN DER WAALS = -30.0749 ELECTROSTATIC = -47.9677 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7275" Parameter: CONF_N -> "8002" Comparing "7275" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7276" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756737 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755203 ATOM PAIRS WERE FOUND FOR ATOM LIST 41546 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30518 from a total of 755203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7276 -76.53875 -1.50383 0.74273 INTE EXTERN> -25.78395 -50.75481 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5388" Parameter: A <- "-76.5388" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7839" Parameter: B <- "-25.7839" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7548" Parameter: C <- "-50.7548" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7276 TOTAL ENERGY = -76.5388 RDTITL> * VAN DER WAALS = -25.7839 ELECTROSTATIC = -50.7548 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7276" Parameter: CONF_N -> "8002" Comparing "7276" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7277" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756076 ATOM PAIRS WERE FOUND FOR ATOM LIST 41581 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29538 from a total of 756076 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7277 -75.70117 -0.83759 0.65942 INTE EXTERN> -27.10113 -48.60004 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7012" Parameter: A <- "-75.7012" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1011" Parameter: B <- "-27.1011" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6" Parameter: C <- "-48.6" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7277 TOTAL ENERGY = -75.7012 RDTITL> * VAN DER WAALS = -27.1011 ELECTROSTATIC = -48.6 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7277" Parameter: CONF_N -> "8002" Comparing "7277" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7278" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756076 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753605 ATOM PAIRS WERE FOUND FOR ATOM LIST 41555 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29832 from a total of 753605 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7278 -74.22862 -1.47255 0.68851 INTE EXTERN> -27.90546 -46.32316 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2286" Parameter: A <- "-74.2286" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9055" Parameter: B <- "-27.9055" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3232" Parameter: C <- "-46.3232" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7278 TOTAL ENERGY = -74.2286 RDTITL> * VAN DER WAALS = -27.9055 ELECTROSTATIC = -46.3232 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7278" Parameter: CONF_N -> "8002" Comparing "7278" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7279" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753605 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754509 ATOM PAIRS WERE FOUND FOR ATOM LIST 41493 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29665 from a total of 754509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7279 -78.58531 4.35669 0.74503 INTE EXTERN> -24.95700 -53.62830 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5853" Parameter: A <- "-78.5853" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.957" Parameter: B <- "-24.957" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6283" Parameter: C <- "-53.6283" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7279 TOTAL ENERGY = -78.5853 RDTITL> * VAN DER WAALS = -24.957 ELECTROSTATIC = -53.6283 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7279" Parameter: CONF_N -> "8002" Comparing "7279" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7280" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757370 ATOM PAIRS WERE FOUND FOR ATOM LIST 41633 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29857 from a total of 757370 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7280 -84.47996 5.89465 0.73550 INTE EXTERN> -27.51912 -56.96084 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.48" Parameter: A <- "-84.48" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5191" Parameter: B <- "-27.5191" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.9608" Parameter: C <- "-56.9608" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7280 TOTAL ENERGY = -84.48 RDTITL> * VAN DER WAALS = -27.5191 ELECTROSTATIC = -56.9608 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7280" Parameter: CONF_N -> "8002" Comparing "7280" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7281" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757370 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758890 ATOM PAIRS WERE FOUND FOR ATOM LIST 41662 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29717 from a total of 758890 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7281 -75.68201 -8.79794 0.72921 INTE EXTERN> -28.46167 -47.22034 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.682" Parameter: A <- "-75.682" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4617" Parameter: B <- "-28.4617" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2203" Parameter: C <- "-47.2203" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7281 TOTAL ENERGY = -75.682 RDTITL> * VAN DER WAALS = -28.4617 ELECTROSTATIC = -47.2203 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7281" Parameter: CONF_N -> "8002" Comparing "7281" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7282" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758890 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757921 ATOM PAIRS WERE FOUND FOR ATOM LIST 41720 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29871 from a total of 757921 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7282 -74.07720 -1.60481 0.72906 INTE EXTERN> -28.80638 -45.27082 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.0772" Parameter: A <- "-74.0772" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8064" Parameter: B <- "-28.8064" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2708" Parameter: C <- "-45.2708" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7282 TOTAL ENERGY = -74.0772 RDTITL> * VAN DER WAALS = -28.8064 ELECTROSTATIC = -45.2708 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7282" Parameter: CONF_N -> "8002" Comparing "7282" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7283" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757921 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753953 ATOM PAIRS WERE FOUND FOR ATOM LIST 41289 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30657 from a total of 753953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7283 -72.70489 -1.37232 0.70667 INTE EXTERN> -28.94568 -43.75920 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7049" Parameter: A <- "-72.7049" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9457" Parameter: B <- "-28.9457" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7592" Parameter: C <- "-43.7592" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7283 TOTAL ENERGY = -72.7049 RDTITL> * VAN DER WAALS = -28.9457 ELECTROSTATIC = -43.7592 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7283" Parameter: CONF_N -> "8002" Comparing "7283" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7284" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756415 ATOM PAIRS WERE FOUND FOR ATOM LIST 41451 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30267 from a total of 756415 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7284 -76.43066 3.72577 0.59601 INTE EXTERN> -31.52669 -44.90397 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4307" Parameter: A <- "-76.4307" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5267" Parameter: B <- "-31.5267" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.904" Parameter: C <- "-44.904" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7284 TOTAL ENERGY = -76.4307 RDTITL> * VAN DER WAALS = -31.5267 ELECTROSTATIC = -44.904 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7284" Parameter: CONF_N -> "8002" Comparing "7284" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7285" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756415 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755001 ATOM PAIRS WERE FOUND FOR ATOM LIST 41525 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29984 from a total of 755001 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7285 -70.12239 -6.30827 0.65417 INTE EXTERN> -32.04684 -38.07555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1224" Parameter: A <- "-70.1224" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0468" Parameter: B <- "-32.0468" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0755" Parameter: C <- "-38.0755" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7285 TOTAL ENERGY = -70.1224 RDTITL> * VAN DER WAALS = -32.0468 ELECTROSTATIC = -38.0755 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7285" Parameter: CONF_N -> "8002" Comparing "7285" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7286" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755001 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761398 ATOM PAIRS WERE FOUND FOR ATOM LIST 41741 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29757 from a total of 761398 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7286 -80.66110 10.53871 0.62855 INTE EXTERN> -30.82622 -49.83488 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6611" Parameter: A <- "-80.6611" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8262" Parameter: B <- "-30.8262" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8349" Parameter: C <- "-49.8349" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7286 TOTAL ENERGY = -80.6611 RDTITL> * VAN DER WAALS = -30.8262 ELECTROSTATIC = -49.8349 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7286" Parameter: CONF_N -> "8002" Comparing "7286" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7287" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761398 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757247 ATOM PAIRS WERE FOUND FOR ATOM LIST 41627 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29659 from a total of 757247 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7287 -73.07308 -7.58803 0.68617 INTE EXTERN> -24.75661 -48.31647 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0731" Parameter: A <- "-73.0731" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7566" Parameter: B <- "-24.7566" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3165" Parameter: C <- "-48.3165" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7287 TOTAL ENERGY = -73.0731 RDTITL> * VAN DER WAALS = -24.7566 ELECTROSTATIC = -48.3165 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7287" Parameter: CONF_N -> "8002" Comparing "7287" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7288" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757247 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750882 ATOM PAIRS WERE FOUND FOR ATOM LIST 41341 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29835 from a total of 750882 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7288 -73.53817 0.46509 0.66759 INTE EXTERN> -26.80498 -46.73319 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5382" Parameter: A <- "-73.5382" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.805" Parameter: B <- "-26.805" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7332" Parameter: C <- "-46.7332" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7288 TOTAL ENERGY = -73.5382 RDTITL> * VAN DER WAALS = -26.805 ELECTROSTATIC = -46.7332 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7288" Parameter: CONF_N -> "8002" Comparing "7288" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7289" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750882 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751124 ATOM PAIRS WERE FOUND FOR ATOM LIST 41366 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29341 from a total of 751124 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7289 -78.64110 5.10293 0.69869 INTE EXTERN> -27.56621 -51.07489 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6411" Parameter: A <- "-78.6411" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5662" Parameter: B <- "-27.5662" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0749" Parameter: C <- "-51.0749" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7289 TOTAL ENERGY = -78.6411 RDTITL> * VAN DER WAALS = -27.5662 ELECTROSTATIC = -51.0749 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7289" Parameter: CONF_N -> "8002" Comparing "7289" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7290" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751124 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751565 ATOM PAIRS WERE FOUND FOR ATOM LIST 41455 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29932 from a total of 751565 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7290 -71.35458 -7.28652 0.58913 INTE EXTERN> -31.07246 -40.28212 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3546" Parameter: A <- "-71.3546" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0725" Parameter: B <- "-31.0725" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2821" Parameter: C <- "-40.2821" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7290 TOTAL ENERGY = -71.3546 RDTITL> * VAN DER WAALS = -31.0725 ELECTROSTATIC = -40.2821 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7290" Parameter: CONF_N -> "8002" Comparing "7290" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7291" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751565 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756390 ATOM PAIRS WERE FOUND FOR ATOM LIST 41571 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30550 from a total of 756390 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7291 -78.56321 7.20864 0.72337 INTE EXTERN> -28.15598 -50.40723 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5632" Parameter: A <- "-78.5632" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.156" Parameter: B <- "-28.156" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4072" Parameter: C <- "-50.4072" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7291 TOTAL ENERGY = -78.5632 RDTITL> * VAN DER WAALS = -28.156 ELECTROSTATIC = -50.4072 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7291" Parameter: CONF_N -> "8002" Comparing "7291" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7292" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756390 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753678 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29742 from a total of 753678 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7292 -75.05799 -3.50522 0.58828 INTE EXTERN> -30.15260 -44.90539 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.058" Parameter: A <- "-75.058" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1526" Parameter: B <- "-30.1526" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9054" Parameter: C <- "-44.9054" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7292 TOTAL ENERGY = -75.058 RDTITL> * VAN DER WAALS = -30.1526 ELECTROSTATIC = -44.9054 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7292" Parameter: CONF_N -> "8002" Comparing "7292" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7293" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753678 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757457 ATOM PAIRS WERE FOUND FOR ATOM LIST 41738 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30385 from a total of 757457 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7293 -78.75051 3.69252 0.63987 INTE EXTERN> -30.78475 -47.96576 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7505" Parameter: A <- "-78.7505" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7847" Parameter: B <- "-30.7847" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9658" Parameter: C <- "-47.9658" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7293 TOTAL ENERGY = -78.7505 RDTITL> * VAN DER WAALS = -30.7847 ELECTROSTATIC = -47.9658 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7293" Parameter: CONF_N -> "8002" Comparing "7293" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7294" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757457 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754363 ATOM PAIRS WERE FOUND FOR ATOM LIST 41477 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30622 from a total of 754363 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7294 -74.59751 -4.15300 0.58051 INTE EXTERN> -31.43847 -43.15904 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5975" Parameter: A <- "-74.5975" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4385" Parameter: B <- "-31.4385" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.159" Parameter: C <- "-43.159" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7294 TOTAL ENERGY = -74.5975 RDTITL> * VAN DER WAALS = -31.4385 ELECTROSTATIC = -43.159 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7294" Parameter: CONF_N -> "8002" Comparing "7294" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7295" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754363 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753043 ATOM PAIRS WERE FOUND FOR ATOM LIST 41581 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29484 from a total of 753043 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7295 -68.45212 -6.14539 0.67155 INTE EXTERN> -25.70016 -42.75197 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4521" Parameter: A <- "-68.4521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7002" Parameter: B <- "-25.7002" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.752" Parameter: C <- "-42.752" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7295 TOTAL ENERGY = -68.4521 RDTITL> * VAN DER WAALS = -25.7002 ELECTROSTATIC = -42.752 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7295" Parameter: CONF_N -> "8002" Comparing "7295" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7296" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753043 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755909 ATOM PAIRS WERE FOUND FOR ATOM LIST 41409 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29844 from a total of 755909 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7296 -73.22209 4.76997 0.64398 INTE EXTERN> -28.55122 -44.67087 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2221" Parameter: A <- "-73.2221" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5512" Parameter: B <- "-28.5512" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6709" Parameter: C <- "-44.6709" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7296 TOTAL ENERGY = -73.2221 RDTITL> * VAN DER WAALS = -28.5512 ELECTROSTATIC = -44.6709 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7296" Parameter: CONF_N -> "8002" Comparing "7296" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7297" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755909 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755903 ATOM PAIRS WERE FOUND FOR ATOM LIST 41477 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29642 from a total of 755903 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7297 -66.65675 -6.56534 0.78988 INTE EXTERN> -23.49005 -43.16670 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.6568" Parameter: A <- "-66.6568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.49" Parameter: B <- "-23.49" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1667" Parameter: C <- "-43.1667" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7297 TOTAL ENERGY = -66.6568 RDTITL> * VAN DER WAALS = -23.49 ELECTROSTATIC = -43.1667 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7297" Parameter: CONF_N -> "8002" Comparing "7297" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7298" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755903 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753170 ATOM PAIRS WERE FOUND FOR ATOM LIST 41267 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29631 from a total of 753170 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7298 -73.82367 7.16692 0.63800 INTE EXTERN> -29.55999 -44.26368 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8237" Parameter: A <- "-73.8237" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.56" Parameter: B <- "-29.56" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2637" Parameter: C <- "-44.2637" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7298 TOTAL ENERGY = -73.8237 RDTITL> * VAN DER WAALS = -29.56 ELECTROSTATIC = -44.2637 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7298" Parameter: CONF_N -> "8002" Comparing "7298" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7299" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753170 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749786 ATOM PAIRS WERE FOUND FOR ATOM LIST 41103 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29461 from a total of 749786 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7299 -76.37655 2.55288 0.75635 INTE EXTERN> -24.78543 -51.59112 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3766" Parameter: A <- "-76.3766" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7854" Parameter: B <- "-24.7854" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5911" Parameter: C <- "-51.5911" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7299 TOTAL ENERGY = -76.3766 RDTITL> * VAN DER WAALS = -24.7854 ELECTROSTATIC = -51.5911 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7299" Parameter: CONF_N -> "8002" Comparing "7299" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7300" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749786 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753501 ATOM PAIRS WERE FOUND FOR ATOM LIST 41253 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29476 from a total of 753501 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7300 -68.43248 -7.94407 0.62937 INTE EXTERN> -28.13611 -40.29637 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4325" Parameter: A <- "-68.4325" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1361" Parameter: B <- "-28.1361" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2964" Parameter: C <- "-40.2964" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7300 TOTAL ENERGY = -68.4325 RDTITL> * VAN DER WAALS = -28.1361 ELECTROSTATIC = -40.2964 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7300" Parameter: CONF_N -> "8002" Comparing "7300" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7301" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753501 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749044 ATOM PAIRS WERE FOUND FOR ATOM LIST 40976 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29326 from a total of 749044 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7301 -71.76529 3.33281 0.66903 INTE EXTERN> -25.69003 -46.07526 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7653" Parameter: A <- "-71.7653" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.69" Parameter: B <- "-25.69" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0753" Parameter: C <- "-46.0753" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7301 TOTAL ENERGY = -71.7653 RDTITL> * VAN DER WAALS = -25.69 ELECTROSTATIC = -46.0753 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7301" Parameter: CONF_N -> "8002" Comparing "7301" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7302" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749044 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754267 ATOM PAIRS WERE FOUND FOR ATOM LIST 41386 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29719 from a total of 754267 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7302 -76.94519 5.17990 0.59897 INTE EXTERN> -29.88967 -47.05552 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9452" Parameter: A <- "-76.9452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8897" Parameter: B <- "-29.8897" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0555" Parameter: C <- "-47.0555" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7302 TOTAL ENERGY = -76.9452 RDTITL> * VAN DER WAALS = -29.8897 ELECTROSTATIC = -47.0555 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7302" Parameter: CONF_N -> "8002" Comparing "7302" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7303" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754267 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753758 ATOM PAIRS WERE FOUND FOR ATOM LIST 41409 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29219 from a total of 753758 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7303 -68.07116 -8.87403 0.69826 INTE EXTERN> -25.34332 -42.72784 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.0712" Parameter: A <- "-68.0712" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3433" Parameter: B <- "-25.3433" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7278" Parameter: C <- "-42.7278" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7303 TOTAL ENERGY = -68.0712 RDTITL> * VAN DER WAALS = -25.3433 ELECTROSTATIC = -42.7278 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7303" Parameter: CONF_N -> "8002" Comparing "7303" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7304" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753758 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746172 ATOM PAIRS WERE FOUND FOR ATOM LIST 40862 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29627 from a total of 746172 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7304 -78.56410 10.49294 0.73095 INTE EXTERN> -25.64247 -52.92163 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5641" Parameter: A <- "-78.5641" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6425" Parameter: B <- "-25.6425" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9216" Parameter: C <- "-52.9216" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7304 TOTAL ENERGY = -78.5641 RDTITL> * VAN DER WAALS = -25.6425 ELECTROSTATIC = -52.9216 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7304" Parameter: CONF_N -> "8002" Comparing "7304" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7305" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746172 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757016 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29729 from a total of 757016 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7305 -69.44041 -9.12370 0.54686 INTE EXTERN> -30.88445 -38.55595 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4404" Parameter: A <- "-69.4404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8845" Parameter: B <- "-30.8845" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.556" Parameter: C <- "-38.556" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7305 TOTAL ENERGY = -69.4404 RDTITL> * VAN DER WAALS = -30.8845 ELECTROSTATIC = -38.556 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7305" Parameter: CONF_N -> "8002" Comparing "7305" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7306" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757016 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756425 ATOM PAIRS WERE FOUND FOR ATOM LIST 41471 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29698 from a total of 756425 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7306 -71.55118 2.11077 0.55558 INTE EXTERN> -32.27445 -39.27673 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5512" Parameter: A <- "-71.5512" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2745" Parameter: B <- "-32.2745" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2767" Parameter: C <- "-39.2767" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7306 TOTAL ENERGY = -71.5512 RDTITL> * VAN DER WAALS = -32.2745 ELECTROSTATIC = -39.2767 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7306" Parameter: CONF_N -> "8002" Comparing "7306" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7307" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756425 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752511 ATOM PAIRS WERE FOUND FOR ATOM LIST 41377 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30282 from a total of 752511 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7307 -70.11905 -1.43213 0.60622 INTE EXTERN> -29.71901 -40.40004 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1191" Parameter: A <- "-70.1191" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.719" Parameter: B <- "-29.719" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4" Parameter: C <- "-40.4" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7307 TOTAL ENERGY = -70.1191 RDTITL> * VAN DER WAALS = -29.719 ELECTROSTATIC = -40.4 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7307" Parameter: CONF_N -> "8002" Comparing "7307" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7308" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752511 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751058 ATOM PAIRS WERE FOUND FOR ATOM LIST 41236 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29706 from a total of 751058 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7308 -72.13114 2.01209 0.59619 INTE EXTERN> -28.47977 -43.65138 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1311" Parameter: A <- "-72.1311" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4798" Parameter: B <- "-28.4798" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6514" Parameter: C <- "-43.6514" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7308 TOTAL ENERGY = -72.1311 RDTITL> * VAN DER WAALS = -28.4798 ELECTROSTATIC = -43.6514 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7308" Parameter: CONF_N -> "8002" Comparing "7308" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7309" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751058 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748506 ATOM PAIRS WERE FOUND FOR ATOM LIST 41130 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28567 from a total of 748506 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7309 -73.92541 1.79427 0.58795 INTE EXTERN> -29.83434 -44.09107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9254" Parameter: A <- "-73.9254" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8343" Parameter: B <- "-29.8343" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0911" Parameter: C <- "-44.0911" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7309 TOTAL ENERGY = -73.9254 RDTITL> * VAN DER WAALS = -29.8343 ELECTROSTATIC = -44.0911 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7309" Parameter: CONF_N -> "8002" Comparing "7309" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7310" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748506 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755257 ATOM PAIRS WERE FOUND FOR ATOM LIST 41526 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29428 from a total of 755257 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7310 -72.85884 -1.06658 0.69558 INTE EXTERN> -24.92787 -47.93097 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8588" Parameter: A <- "-72.8588" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9279" Parameter: B <- "-24.9279" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.931" Parameter: C <- "-47.931" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7310 TOTAL ENERGY = -72.8588 RDTITL> * VAN DER WAALS = -24.9279 ELECTROSTATIC = -47.931 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7310" Parameter: CONF_N -> "8002" Comparing "7310" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7311" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755257 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755255 ATOM PAIRS WERE FOUND FOR ATOM LIST 41475 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29568 from a total of 755255 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7311 -72.66160 -0.19724 0.76807 INTE EXTERN> -22.52817 -50.13343 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6616" Parameter: A <- "-72.6616" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.5282" Parameter: B <- "-22.5282" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1334" Parameter: C <- "-50.1334" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7311 TOTAL ENERGY = -72.6616 RDTITL> * VAN DER WAALS = -22.5282 ELECTROSTATIC = -50.1334 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7311" Parameter: CONF_N -> "8002" Comparing "7311" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7312" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755255 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753851 ATOM PAIRS WERE FOUND FOR ATOM LIST 41401 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29575 from a total of 753851 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7312 -74.93968 2.27809 0.58466 INTE EXTERN> -30.69819 -44.24150 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9397" Parameter: A <- "-74.9397" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6982" Parameter: B <- "-30.6982" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2415" Parameter: C <- "-44.2415" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7312 TOTAL ENERGY = -74.9397 RDTITL> * VAN DER WAALS = -30.6982 ELECTROSTATIC = -44.2415 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7312" Parameter: CONF_N -> "8002" Comparing "7312" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7313" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753851 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755497 ATOM PAIRS WERE FOUND FOR ATOM LIST 41504 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30101 from a total of 755497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7313 -75.16656 0.22688 0.82745 INTE EXTERN> -24.16102 -51.00554 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1666" Parameter: A <- "-75.1666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.161" Parameter: B <- "-24.161" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0055" Parameter: C <- "-51.0055" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7313 TOTAL ENERGY = -75.1666 RDTITL> * VAN DER WAALS = -24.161 ELECTROSTATIC = -51.0055 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7313" Parameter: CONF_N -> "8002" Comparing "7313" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7314" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751335 ATOM PAIRS WERE FOUND FOR ATOM LIST 41259 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28773 from a total of 751335 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7314 -71.81667 -3.34989 0.55450 INTE EXTERN> -31.49390 -40.32276 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8167" Parameter: A <- "-71.8167" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4939" Parameter: B <- "-31.4939" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3228" Parameter: C <- "-40.3228" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7314 TOTAL ENERGY = -71.8167 RDTITL> * VAN DER WAALS = -31.4939 ELECTROSTATIC = -40.3228 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7314" Parameter: CONF_N -> "8002" Comparing "7314" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7315" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751335 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751367 ATOM PAIRS WERE FOUND FOR ATOM LIST 41290 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29562 from a total of 751367 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7315 -72.12006 0.30339 0.68715 INTE EXTERN> -26.87371 -45.24635 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1201" Parameter: A <- "-72.1201" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8737" Parameter: B <- "-26.8737" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2463" Parameter: C <- "-45.2463" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7315 TOTAL ENERGY = -72.1201 RDTITL> * VAN DER WAALS = -26.8737 ELECTROSTATIC = -45.2463 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7315" Parameter: CONF_N -> "8002" Comparing "7315" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7316" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751367 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747112 ATOM PAIRS WERE FOUND FOR ATOM LIST 41147 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29134 from a total of 747112 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7316 -70.22066 -1.89939 0.67731 INTE EXTERN> -27.91092 -42.30975 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2207" Parameter: A <- "-70.2207" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9109" Parameter: B <- "-27.9109" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3097" Parameter: C <- "-42.3097" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7316 TOTAL ENERGY = -70.2207 RDTITL> * VAN DER WAALS = -27.9109 ELECTROSTATIC = -42.3097 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7316" Parameter: CONF_N -> "8002" Comparing "7316" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7317" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747112 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753224 ATOM PAIRS WERE FOUND FOR ATOM LIST 41350 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30147 from a total of 753224 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7317 -76.98977 6.76910 0.62194 INTE EXTERN> -28.20744 -48.78232 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9898" Parameter: A <- "-76.9898" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2074" Parameter: B <- "-28.2074" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7823" Parameter: C <- "-48.7823" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7317 TOTAL ENERGY = -76.9898 RDTITL> * VAN DER WAALS = -28.2074 ELECTROSTATIC = -48.7823 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7317" Parameter: CONF_N -> "8002" Comparing "7317" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7318" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753224 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757739 ATOM PAIRS WERE FOUND FOR ATOM LIST 41567 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30414 from a total of 757739 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7318 -71.54699 -5.44277 0.63631 INTE EXTERN> -28.32600 -43.22099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.547" Parameter: A <- "-71.547" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.326" Parameter: B <- "-28.326" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.221" Parameter: C <- "-43.221" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7318 TOTAL ENERGY = -71.547 RDTITL> * VAN DER WAALS = -28.326 ELECTROSTATIC = -43.221 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7318" Parameter: CONF_N -> "8002" Comparing "7318" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7319" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757739 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756268 ATOM PAIRS WERE FOUND FOR ATOM LIST 41710 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29256 from a total of 756268 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7319 -73.15602 1.60903 0.69392 INTE EXTERN> -28.99672 -44.15930 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.156" Parameter: A <- "-73.156" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9967" Parameter: B <- "-28.9967" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1593" Parameter: C <- "-44.1593" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7319 TOTAL ENERGY = -73.156 RDTITL> * VAN DER WAALS = -28.9967 ELECTROSTATIC = -44.1593 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7319" Parameter: CONF_N -> "8002" Comparing "7319" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7320" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756268 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752706 ATOM PAIRS WERE FOUND FOR ATOM LIST 41286 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29283 from a total of 752706 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7320 -67.77309 -5.38293 0.49081 INTE EXTERN> -29.67653 -38.09656 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7731" Parameter: A <- "-67.7731" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6765" Parameter: B <- "-29.6765" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.0966" Parameter: C <- "-38.0966" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7320 TOTAL ENERGY = -67.7731 RDTITL> * VAN DER WAALS = -29.6765 ELECTROSTATIC = -38.0966 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7320" Parameter: CONF_N -> "8002" Comparing "7320" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7321" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752706 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756657 ATOM PAIRS WERE FOUND FOR ATOM LIST 41510 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30153 from a total of 756657 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7321 -75.96307 8.18998 0.66579 INTE EXTERN> -28.88340 -47.07967 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9631" Parameter: A <- "-75.9631" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8834" Parameter: B <- "-28.8834" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0797" Parameter: C <- "-47.0797" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7321 TOTAL ENERGY = -75.9631 RDTITL> * VAN DER WAALS = -28.8834 ELECTROSTATIC = -47.0797 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7321" Parameter: CONF_N -> "8002" Comparing "7321" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7322" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756657 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752778 ATOM PAIRS WERE FOUND FOR ATOM LIST 41423 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30164 from a total of 752778 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7322 -73.06978 -2.89329 0.65909 INTE EXTERN> -28.13582 -44.93396 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0698" Parameter: A <- "-73.0698" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1358" Parameter: B <- "-28.1358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.934" Parameter: C <- "-44.934" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7322 TOTAL ENERGY = -73.0698 RDTITL> * VAN DER WAALS = -28.1358 ELECTROSTATIC = -44.934 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7322" Parameter: CONF_N -> "8002" Comparing "7322" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7323" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752778 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755596 ATOM PAIRS WERE FOUND FOR ATOM LIST 41480 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29584 from a total of 755596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7323 -68.79332 -4.27646 0.57566 INTE EXTERN> -31.98209 -36.81122 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7933" Parameter: A <- "-68.7933" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9821" Parameter: B <- "-31.9821" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.8112" Parameter: C <- "-36.8112" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7323 TOTAL ENERGY = -68.7933 RDTITL> * VAN DER WAALS = -31.9821 ELECTROSTATIC = -36.8112 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7323" Parameter: CONF_N -> "8002" Comparing "7323" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7324" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760791 ATOM PAIRS WERE FOUND FOR ATOM LIST 41560 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29754 from a total of 760791 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7324 -71.21315 2.41983 0.71640 INTE EXTERN> -24.13573 -47.07742 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2131" Parameter: A <- "-71.2131" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1357" Parameter: B <- "-24.1357" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0774" Parameter: C <- "-47.0774" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7324 TOTAL ENERGY = -71.2131 RDTITL> * VAN DER WAALS = -24.1357 ELECTROSTATIC = -47.0774 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7324" Parameter: CONF_N -> "8002" Comparing "7324" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7325" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760791 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755374 ATOM PAIRS WERE FOUND FOR ATOM LIST 41546 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29838 from a total of 755374 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7325 -74.87516 3.66202 0.65135 INTE EXTERN> -28.06595 -46.80922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8752" Parameter: A <- "-74.8752" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0659" Parameter: B <- "-28.0659" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8092" Parameter: C <- "-46.8092" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7325 TOTAL ENERGY = -74.8752 RDTITL> * VAN DER WAALS = -28.0659 ELECTROSTATIC = -46.8092 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7325" Parameter: CONF_N -> "8002" Comparing "7325" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7326" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755374 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754726 ATOM PAIRS WERE FOUND FOR ATOM LIST 41240 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30094 from a total of 754726 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7326 -74.40926 -0.46590 0.63216 INTE EXTERN> -29.05559 -45.35367 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4093" Parameter: A <- "-74.4093" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0556" Parameter: B <- "-29.0556" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3537" Parameter: C <- "-45.3537" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7326 TOTAL ENERGY = -74.4093 RDTITL> * VAN DER WAALS = -29.0556 ELECTROSTATIC = -45.3537 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7326" Parameter: CONF_N -> "8002" Comparing "7326" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7327" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754726 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761496 ATOM PAIRS WERE FOUND FOR ATOM LIST 41525 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29748 from a total of 761496 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7327 -71.51566 -2.89360 0.51858 INTE EXTERN> -32.63922 -38.87644 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5157" Parameter: A <- "-71.5157" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6392" Parameter: B <- "-32.6392" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8764" Parameter: C <- "-38.8764" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7327 TOTAL ENERGY = -71.5157 RDTITL> * VAN DER WAALS = -32.6392 ELECTROSTATIC = -38.8764 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7327" Parameter: CONF_N -> "8002" Comparing "7327" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7328" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761496 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752258 ATOM PAIRS WERE FOUND FOR ATOM LIST 41098 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29781 from a total of 752258 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7328 -73.14075 1.62509 0.61838 INTE EXTERN> -28.66909 -44.47167 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1408" Parameter: A <- "-73.1408" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6691" Parameter: B <- "-28.6691" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4717" Parameter: C <- "-44.4717" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7328 TOTAL ENERGY = -73.1408 RDTITL> * VAN DER WAALS = -28.6691 ELECTROSTATIC = -44.4717 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7328" Parameter: CONF_N -> "8002" Comparing "7328" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7329" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752258 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756036 ATOM PAIRS WERE FOUND FOR ATOM LIST 41268 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29184 from a total of 756036 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7329 -74.01195 0.87120 0.70527 INTE EXTERN> -25.80299 -48.20896 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.012" Parameter: A <- "-74.012" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.803" Parameter: B <- "-25.803" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.209" Parameter: C <- "-48.209" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7329 TOTAL ENERGY = -74.012 RDTITL> * VAN DER WAALS = -25.803 ELECTROSTATIC = -48.209 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7329" Parameter: CONF_N -> "8002" Comparing "7329" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7330" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756036 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756097 ATOM PAIRS WERE FOUND FOR ATOM LIST 41419 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30207 from a total of 756097 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7330 -75.21316 1.20121 0.63897 INTE EXTERN> -29.47147 -45.74170 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2132" Parameter: A <- "-75.2132" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4715" Parameter: B <- "-29.4715" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7417" Parameter: C <- "-45.7417" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7330 TOTAL ENERGY = -75.2132 RDTITL> * VAN DER WAALS = -29.4715 ELECTROSTATIC = -45.7417 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7330" Parameter: CONF_N -> "8002" Comparing "7330" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7331" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756097 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753664 ATOM PAIRS WERE FOUND FOR ATOM LIST 41113 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29476 from a total of 753664 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7331 -65.62548 -9.58768 0.68279 INTE EXTERN> -24.66557 -40.95991 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6255" Parameter: A <- "-65.6255" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6656" Parameter: B <- "-24.6656" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9599" Parameter: C <- "-40.9599" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7331 TOTAL ENERGY = -65.6255 RDTITL> * VAN DER WAALS = -24.6656 ELECTROSTATIC = -40.9599 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7331" Parameter: CONF_N -> "8002" Comparing "7331" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7332" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753664 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751660 ATOM PAIRS WERE FOUND FOR ATOM LIST 41151 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28863 from a total of 751660 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7332 -63.07815 -2.54733 0.54155 INTE EXTERN> -29.79063 -33.28752 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.0782" Parameter: A <- "-63.0782" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7906" Parameter: B <- "-29.7906" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.2875" Parameter: C <- "-33.2875" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7332 TOTAL ENERGY = -63.0782 RDTITL> * VAN DER WAALS = -29.7906 ELECTROSTATIC = -33.2875 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7332" Parameter: CONF_N -> "8002" Comparing "7332" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7333" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751660 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750082 ATOM PAIRS WERE FOUND FOR ATOM LIST 41128 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29627 from a total of 750082 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7333 -71.32305 8.24490 0.74268 INTE EXTERN> -26.01573 -45.30732 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3231" Parameter: A <- "-71.3231" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0157" Parameter: B <- "-26.0157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3073" Parameter: C <- "-45.3073" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7333 TOTAL ENERGY = -71.3231 RDTITL> * VAN DER WAALS = -26.0157 ELECTROSTATIC = -45.3073 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7333" Parameter: CONF_N -> "8002" Comparing "7333" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7334" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750082 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754141 ATOM PAIRS WERE FOUND FOR ATOM LIST 41225 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29452 from a total of 754141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7334 -71.35165 0.02860 0.61593 INTE EXTERN> -29.50671 -41.84494 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3516" Parameter: A <- "-71.3516" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5067" Parameter: B <- "-29.5067" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8449" Parameter: C <- "-41.8449" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7334 TOTAL ENERGY = -71.3516 RDTITL> * VAN DER WAALS = -29.5067 ELECTROSTATIC = -41.8449 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7334" Parameter: CONF_N -> "8002" Comparing "7334" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7335" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755216 ATOM PAIRS WERE FOUND FOR ATOM LIST 41308 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29547 from a total of 755216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7335 -69.15813 -2.19352 0.71012 INTE EXTERN> -26.92336 -42.23477 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1581" Parameter: A <- "-69.1581" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9234" Parameter: B <- "-26.9234" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2348" Parameter: C <- "-42.2348" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7335 TOTAL ENERGY = -69.1581 RDTITL> * VAN DER WAALS = -26.9234 ELECTROSTATIC = -42.2348 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7335" Parameter: CONF_N -> "8002" Comparing "7335" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7336" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753244 ATOM PAIRS WERE FOUND FOR ATOM LIST 41393 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30035 from a total of 753244 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7336 -67.92613 -1.23201 0.65548 INTE EXTERN> -26.66263 -41.26350 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9261" Parameter: A <- "-67.9261" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6626" Parameter: B <- "-26.6626" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2635" Parameter: C <- "-41.2635" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7336 TOTAL ENERGY = -67.9261 RDTITL> * VAN DER WAALS = -26.6626 ELECTROSTATIC = -41.2635 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7336" Parameter: CONF_N -> "8002" Comparing "7336" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7337" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753244 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754599 ATOM PAIRS WERE FOUND FOR ATOM LIST 41501 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29172 from a total of 754599 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7337 -72.79446 4.86833 0.62171 INTE EXTERN> -30.07832 -42.71614 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7945" Parameter: A <- "-72.7945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0783" Parameter: B <- "-30.0783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7161" Parameter: C <- "-42.7161" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7337 TOTAL ENERGY = -72.7945 RDTITL> * VAN DER WAALS = -30.0783 ELECTROSTATIC = -42.7161 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7337" Parameter: CONF_N -> "8002" Comparing "7337" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7338" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754599 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752203 ATOM PAIRS WERE FOUND FOR ATOM LIST 41332 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29486 from a total of 752203 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7338 -69.40185 -3.39261 0.63062 INTE EXTERN> -29.60451 -39.79734 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4018" Parameter: A <- "-69.4018" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6045" Parameter: B <- "-29.6045" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7973" Parameter: C <- "-39.7973" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7338 TOTAL ENERGY = -69.4018 RDTITL> * VAN DER WAALS = -29.6045 ELECTROSTATIC = -39.7973 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7338" Parameter: CONF_N -> "8002" Comparing "7338" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7339" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752203 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749137 ATOM PAIRS WERE FOUND FOR ATOM LIST 41342 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29264 from a total of 749137 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7339 -60.35551 -9.04634 0.69452 INTE EXTERN> -24.57295 -35.78255 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.3555" Parameter: A <- "-60.3555" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.573" Parameter: B <- "-24.573" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7826" Parameter: C <- "-35.7826" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7339 TOTAL ENERGY = -60.3555 RDTITL> * VAN DER WAALS = -24.573 ELECTROSTATIC = -35.7826 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7339" Parameter: CONF_N -> "8002" Comparing "7339" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7340" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749137 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751992 ATOM PAIRS WERE FOUND FOR ATOM LIST 41264 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29975 from a total of 751992 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7340 -66.48261 6.12710 0.76653 INTE EXTERN> -24.35516 -42.12745 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4826" Parameter: A <- "-66.4826" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3552" Parameter: B <- "-24.3552" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1275" Parameter: C <- "-42.1275" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7340 TOTAL ENERGY = -66.4826 RDTITL> * VAN DER WAALS = -24.3552 ELECTROSTATIC = -42.1275 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7340" Parameter: CONF_N -> "8002" Comparing "7340" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7341" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751992 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755180 ATOM PAIRS WERE FOUND FOR ATOM LIST 41571 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29924 from a total of 755180 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7341 -75.54883 9.06622 0.62102 INTE EXTERN> -29.89624 -45.65259 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5488" Parameter: A <- "-75.5488" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8962" Parameter: B <- "-29.8962" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6526" Parameter: C <- "-45.6526" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7341 TOTAL ENERGY = -75.5488 RDTITL> * VAN DER WAALS = -29.8962 ELECTROSTATIC = -45.6526 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7341" Parameter: CONF_N -> "8002" Comparing "7341" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7342" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755180 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752819 ATOM PAIRS WERE FOUND FOR ATOM LIST 41459 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29546 from a total of 752819 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7342 -71.00214 -4.54669 0.69131 INTE EXTERN> -25.96789 -45.03425 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0021" Parameter: A <- "-71.0021" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9679" Parameter: B <- "-25.9679" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0342" Parameter: C <- "-45.0342" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7342 TOTAL ENERGY = -71.0021 RDTITL> * VAN DER WAALS = -25.9679 ELECTROSTATIC = -45.0342 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7342" Parameter: CONF_N -> "8002" Comparing "7342" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7343" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752819 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747747 ATOM PAIRS WERE FOUND FOR ATOM LIST 41192 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29420 from a total of 747747 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7343 -72.19193 1.18979 0.60656 INTE EXTERN> -28.04867 -44.14327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1919" Parameter: A <- "-72.1919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0487" Parameter: B <- "-28.0487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1433" Parameter: C <- "-44.1433" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7343 TOTAL ENERGY = -72.1919 RDTITL> * VAN DER WAALS = -28.0487 ELECTROSTATIC = -44.1433 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7343" Parameter: CONF_N -> "8002" Comparing "7343" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7344" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747747 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753507 ATOM PAIRS WERE FOUND FOR ATOM LIST 41227 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29943 from a total of 753507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7344 -71.80083 -0.39111 0.69044 INTE EXTERN> -28.17978 -43.62104 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8008" Parameter: A <- "-71.8008" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1798" Parameter: B <- "-28.1798" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.621" Parameter: C <- "-43.621" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7344 TOTAL ENERGY = -71.8008 RDTITL> * VAN DER WAALS = -28.1798 ELECTROSTATIC = -43.621 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7344" Parameter: CONF_N -> "8002" Comparing "7344" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7345" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757350 ATOM PAIRS WERE FOUND FOR ATOM LIST 41587 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29817 from a total of 757350 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7345 -83.33362 11.53279 0.66122 INTE EXTERN> -30.72359 -52.61003 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.3336" Parameter: A <- "-83.3336" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7236" Parameter: B <- "-30.7236" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.61" Parameter: C <- "-52.61" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7345 TOTAL ENERGY = -83.3336 RDTITL> * VAN DER WAALS = -30.7236 ELECTROSTATIC = -52.61 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7345" Parameter: CONF_N -> "8002" Comparing "7345" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7346" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757350 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758936 ATOM PAIRS WERE FOUND FOR ATOM LIST 41647 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29966 from a total of 758936 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7346 -70.88941 -12.44421 0.74549 INTE EXTERN> -24.43602 -46.45339 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8894" Parameter: A <- "-70.8894" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.436" Parameter: B <- "-24.436" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4534" Parameter: C <- "-46.4534" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7346 TOTAL ENERGY = -70.8894 RDTITL> * VAN DER WAALS = -24.436 ELECTROSTATIC = -46.4534 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7346" Parameter: CONF_N -> "8002" Comparing "7346" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7347" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758936 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755831 ATOM PAIRS WERE FOUND FOR ATOM LIST 41446 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30093 from a total of 755831 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7347 -73.26319 2.37377 0.54716 INTE EXTERN> -33.38249 -39.88069 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2632" Parameter: A <- "-73.2632" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3825" Parameter: B <- "-33.3825" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8807" Parameter: C <- "-39.8807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7347 TOTAL ENERGY = -73.2632 RDTITL> * VAN DER WAALS = -33.3825 ELECTROSTATIC = -39.8807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7347" Parameter: CONF_N -> "8002" Comparing "7347" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7348" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755831 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749656 ATOM PAIRS WERE FOUND FOR ATOM LIST 41340 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29432 from a total of 749656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7348 -71.02889 -2.23429 0.61476 INTE EXTERN> -29.66677 -41.36213 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0289" Parameter: A <- "-71.0289" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6668" Parameter: B <- "-29.6668" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3621" Parameter: C <- "-41.3621" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7348 TOTAL ENERGY = -71.0289 RDTITL> * VAN DER WAALS = -29.6668 ELECTROSTATIC = -41.3621 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7348" Parameter: CONF_N -> "8002" Comparing "7348" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7349" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754451 ATOM PAIRS WERE FOUND FOR ATOM LIST 41266 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29275 from a total of 754451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7349 -72.25728 1.22838 0.56796 INTE EXTERN> -33.38089 -38.87638 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2573" Parameter: A <- "-72.2573" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3809" Parameter: B <- "-33.3809" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8764" Parameter: C <- "-38.8764" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7349 TOTAL ENERGY = -72.2573 RDTITL> * VAN DER WAALS = -33.3809 ELECTROSTATIC = -38.8764 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7349" Parameter: CONF_N -> "8002" Comparing "7349" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7350" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756826 ATOM PAIRS WERE FOUND FOR ATOM LIST 41236 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29674 from a total of 756826 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7350 -72.61882 0.36154 0.70488 INTE EXTERN> -25.08580 -47.53301 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6188" Parameter: A <- "-72.6188" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0858" Parameter: B <- "-25.0858" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.533" Parameter: C <- "-47.533" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7350 TOTAL ENERGY = -72.6188 RDTITL> * VAN DER WAALS = -25.0858 ELECTROSTATIC = -47.533 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7350" Parameter: CONF_N -> "8002" Comparing "7350" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7351" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756826 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756893 ATOM PAIRS WERE FOUND FOR ATOM LIST 41520 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29907 from a total of 756893 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7351 -68.73328 -3.88553 0.71994 INTE EXTERN> -26.45081 -42.28247 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7333" Parameter: A <- "-68.7333" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4508" Parameter: B <- "-26.4508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2825" Parameter: C <- "-42.2825" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7351 TOTAL ENERGY = -68.7333 RDTITL> * VAN DER WAALS = -26.4508 ELECTROSTATIC = -42.2825 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7351" Parameter: CONF_N -> "8002" Comparing "7351" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7352" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756893 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763595 ATOM PAIRS WERE FOUND FOR ATOM LIST 41886 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30377 from a total of 763595 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7352 -66.26159 -2.47169 0.61312 INTE EXTERN> -29.57598 -36.68561 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2616" Parameter: A <- "-66.2616" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.576" Parameter: B <- "-29.576" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6856" Parameter: C <- "-36.6856" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7352 TOTAL ENERGY = -66.2616 RDTITL> * VAN DER WAALS = -29.576 ELECTROSTATIC = -36.6856 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7352" Parameter: CONF_N -> "8002" Comparing "7352" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7353" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763595 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759719 ATOM PAIRS WERE FOUND FOR ATOM LIST 41636 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30189 from a total of 759719 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7353 -64.10570 -2.15589 0.68049 INTE EXTERN> -25.68666 -38.41904 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.1057" Parameter: A <- "-64.1057" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6867" Parameter: B <- "-25.6867" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.419" Parameter: C <- "-38.419" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7353 TOTAL ENERGY = -64.1057 RDTITL> * VAN DER WAALS = -25.6867 ELECTROSTATIC = -38.419 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7353" Parameter: CONF_N -> "8002" Comparing "7353" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7354" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759719 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749042 ATOM PAIRS WERE FOUND FOR ATOM LIST 41067 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29991 from a total of 749042 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7354 -68.22114 4.11544 0.58299 INTE EXTERN> -30.24906 -37.97208 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2211" Parameter: A <- "-68.2211" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2491" Parameter: B <- "-30.2491" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9721" Parameter: C <- "-37.9721" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7354 TOTAL ENERGY = -68.2211 RDTITL> * VAN DER WAALS = -30.2491 ELECTROSTATIC = -37.9721 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7354" Parameter: CONF_N -> "8002" Comparing "7354" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7355" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749042 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755298 ATOM PAIRS WERE FOUND FOR ATOM LIST 41462 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30276 from a total of 755298 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7355 -64.47016 -3.75098 0.74104 INTE EXTERN> -23.88802 -40.58213 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.4702" Parameter: A <- "-64.4702" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.888" Parameter: B <- "-23.888" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5821" Parameter: C <- "-40.5821" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7355 TOTAL ENERGY = -64.4702 RDTITL> * VAN DER WAALS = -23.888 ELECTROSTATIC = -40.5821 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7355" Parameter: CONF_N -> "8002" Comparing "7355" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7356" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755298 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753603 ATOM PAIRS WERE FOUND FOR ATOM LIST 41389 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29973 from a total of 753603 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7356 -68.33083 3.86067 0.53790 INTE EXTERN> -32.15450 -36.17633 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3308" Parameter: A <- "-68.3308" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1545" Parameter: B <- "-32.1545" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1763" Parameter: C <- "-36.1763" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7356 TOTAL ENERGY = -68.3308 RDTITL> * VAN DER WAALS = -32.1545 ELECTROSTATIC = -36.1763 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7356" Parameter: CONF_N -> "8002" Comparing "7356" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7357" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753603 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754465 ATOM PAIRS WERE FOUND FOR ATOM LIST 41512 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30145 from a total of 754465 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7357 -68.65430 0.32348 0.51986 INTE EXTERN> -31.89953 -36.75478 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6543" Parameter: A <- "-68.6543" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8995" Parameter: B <- "-31.8995" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.7548" Parameter: C <- "-36.7548" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7357 TOTAL ENERGY = -68.6543 RDTITL> * VAN DER WAALS = -31.8995 ELECTROSTATIC = -36.7548 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7357" Parameter: CONF_N -> "8002" Comparing "7357" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7358" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754465 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755500 ATOM PAIRS WERE FOUND FOR ATOM LIST 41248 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29957 from a total of 755500 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7358 -65.04451 -3.60980 0.50413 INTE EXTERN> -30.29268 -34.75183 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0445" Parameter: A <- "-65.0445" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2927" Parameter: B <- "-30.2927" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7518" Parameter: C <- "-34.7518" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7358 TOTAL ENERGY = -65.0445 RDTITL> * VAN DER WAALS = -30.2927 ELECTROSTATIC = -34.7518 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7358" Parameter: CONF_N -> "8002" Comparing "7358" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7359" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755500 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758789 ATOM PAIRS WERE FOUND FOR ATOM LIST 41458 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29857 from a total of 758789 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7359 -72.80375 7.75924 0.60326 INTE EXTERN> -30.46835 -42.33539 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8037" Parameter: A <- "-72.8037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4684" Parameter: B <- "-30.4684" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3354" Parameter: C <- "-42.3354" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7359 TOTAL ENERGY = -72.8037 RDTITL> * VAN DER WAALS = -30.4684 ELECTROSTATIC = -42.3354 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7359" Parameter: CONF_N -> "8002" Comparing "7359" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7360" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758789 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759331 ATOM PAIRS WERE FOUND FOR ATOM LIST 41579 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29820 from a total of 759331 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7360 -70.83503 -1.96872 0.71150 INTE EXTERN> -25.44612 -45.38890 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.835" Parameter: A <- "-70.835" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4461" Parameter: B <- "-25.4461" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3889" Parameter: C <- "-45.3889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7360 TOTAL ENERGY = -70.835 RDTITL> * VAN DER WAALS = -25.4461 ELECTROSTATIC = -45.3889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7360" Parameter: CONF_N -> "8002" Comparing "7360" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7361" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759331 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755648 ATOM PAIRS WERE FOUND FOR ATOM LIST 41269 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30067 from a total of 755648 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7361 -72.90387 2.06884 0.66553 INTE EXTERN> -26.88168 -46.02218 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9039" Parameter: A <- "-72.9039" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8817" Parameter: B <- "-26.8817" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0222" Parameter: C <- "-46.0222" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7361 TOTAL ENERGY = -72.9039 RDTITL> * VAN DER WAALS = -26.8817 ELECTROSTATIC = -46.0222 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7361" Parameter: CONF_N -> "8002" Comparing "7361" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7362" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755648 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757974 ATOM PAIRS WERE FOUND FOR ATOM LIST 41374 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29921 from a total of 757974 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7362 -66.41062 -6.49325 0.63833 INTE EXTERN> -25.39502 -41.01560 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4106" Parameter: A <- "-66.4106" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.395" Parameter: B <- "-25.395" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0156" Parameter: C <- "-41.0156" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7362 TOTAL ENERGY = -66.4106 RDTITL> * VAN DER WAALS = -25.395 ELECTROSTATIC = -41.0156 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7362" Parameter: CONF_N -> "8002" Comparing "7362" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7363" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757974 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752619 ATOM PAIRS WERE FOUND FOR ATOM LIST 41217 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29746 from a total of 752619 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7363 -69.50353 3.09291 0.71078 INTE EXTERN> -25.25042 -44.25311 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5035" Parameter: A <- "-69.5035" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2504" Parameter: B <- "-25.2504" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2531" Parameter: C <- "-44.2531" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7363 TOTAL ENERGY = -69.5035 RDTITL> * VAN DER WAALS = -25.2504 ELECTROSTATIC = -44.2531 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7363" Parameter: CONF_N -> "8002" Comparing "7363" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7364" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752619 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750382 ATOM PAIRS WERE FOUND FOR ATOM LIST 41279 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29245 from a total of 750382 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7364 -59.96760 -9.53594 0.62571 INTE EXTERN> -23.85712 -36.11047 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.9676" Parameter: A <- "-59.9676" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8571" Parameter: B <- "-23.8571" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1105" Parameter: C <- "-36.1105" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7364 TOTAL ENERGY = -59.9676 RDTITL> * VAN DER WAALS = -23.8571 ELECTROSTATIC = -36.1105 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7364" Parameter: CONF_N -> "8002" Comparing "7364" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7365" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750382 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750417 ATOM PAIRS WERE FOUND FOR ATOM LIST 41062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29120 from a total of 750417 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7365 -63.31852 3.35093 0.56251 INTE EXTERN> -27.05881 -36.25972 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3185" Parameter: A <- "-63.3185" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0588" Parameter: B <- "-27.0588" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.2597" Parameter: C <- "-36.2597" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7365 TOTAL ENERGY = -63.3185 RDTITL> * VAN DER WAALS = -27.0588 ELECTROSTATIC = -36.2597 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7365" Parameter: CONF_N -> "8002" Comparing "7365" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7366" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750417 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748130 ATOM PAIRS WERE FOUND FOR ATOM LIST 41068 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28537 from a total of 748130 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7366 -67.90868 4.59015 0.52613 INTE EXTERN> -29.36339 -38.54529 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9087" Parameter: A <- "-67.9087" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3634" Parameter: B <- "-29.3634" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5453" Parameter: C <- "-38.5453" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7366 TOTAL ENERGY = -67.9087 RDTITL> * VAN DER WAALS = -29.3634 ELECTROSTATIC = -38.5453 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7366" Parameter: CONF_N -> "8002" Comparing "7366" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7367" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748130 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758955 ATOM PAIRS WERE FOUND FOR ATOM LIST 41526 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29377 from a total of 758955 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7367 -70.64843 2.73976 0.59180 INTE EXTERN> -28.55331 -42.09513 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6484" Parameter: A <- "-70.6484" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5533" Parameter: B <- "-28.5533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0951" Parameter: C <- "-42.0951" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7367 TOTAL ENERGY = -70.6484 RDTITL> * VAN DER WAALS = -28.5533 ELECTROSTATIC = -42.0951 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7367" Parameter: CONF_N -> "8002" Comparing "7367" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7368" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758955 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752139 ATOM PAIRS WERE FOUND FOR ATOM LIST 41256 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29078 from a total of 752139 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7368 -71.20753 0.55910 0.54342 INTE EXTERN> -28.53114 -42.67639 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2075" Parameter: A <- "-71.2075" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5311" Parameter: B <- "-28.5311" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6764" Parameter: C <- "-42.6764" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7368 TOTAL ENERGY = -71.2075 RDTITL> * VAN DER WAALS = -28.5311 ELECTROSTATIC = -42.6764 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7368" Parameter: CONF_N -> "8002" Comparing "7368" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7369" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752139 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753703 ATOM PAIRS WERE FOUND FOR ATOM LIST 41134 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28954 from a total of 753703 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7369 -69.83456 -1.37297 0.55389 INTE EXTERN> -28.48500 -41.34956 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.8346" Parameter: A <- "-69.8346" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.485" Parameter: B <- "-28.485" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3496" Parameter: C <- "-41.3496" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7369 TOTAL ENERGY = -69.8346 RDTITL> * VAN DER WAALS = -28.485 ELECTROSTATIC = -41.3496 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7369" Parameter: CONF_N -> "8002" Comparing "7369" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7370" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753703 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752614 ATOM PAIRS WERE FOUND FOR ATOM LIST 41181 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28812 from a total of 752614 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7370 -63.44950 -6.38506 0.52420 INTE EXTERN> -28.42589 -35.02361 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4495" Parameter: A <- "-63.4495" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4259" Parameter: B <- "-28.4259" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.0236" Parameter: C <- "-35.0236" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7370 TOTAL ENERGY = -63.4495 RDTITL> * VAN DER WAALS = -28.4259 ELECTROSTATIC = -35.0236 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7370" Parameter: CONF_N -> "8002" Comparing "7370" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7371" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752614 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752663 ATOM PAIRS WERE FOUND FOR ATOM LIST 41102 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29716 from a total of 752663 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7371 -75.75282 12.30331 0.64474 INTE EXTERN> -29.63740 -46.11541 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7528" Parameter: A <- "-75.7528" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6374" Parameter: B <- "-29.6374" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1154" Parameter: C <- "-46.1154" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7371 TOTAL ENERGY = -75.7528 RDTITL> * VAN DER WAALS = -29.6374 ELECTROSTATIC = -46.1154 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7371" Parameter: CONF_N -> "8002" Comparing "7371" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7372" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752663 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756847 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29989 from a total of 756847 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7372 -75.34360 -0.40922 0.61519 INTE EXTERN> -30.96668 -44.37691 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.3436" Parameter: A <- "-75.3436" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9667" Parameter: B <- "-30.9667" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3769" Parameter: C <- "-44.3769" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7372 TOTAL ENERGY = -75.3436 RDTITL> * VAN DER WAALS = -30.9667 ELECTROSTATIC = -44.3769 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7372" Parameter: CONF_N -> "8002" Comparing "7372" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7373" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756847 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755569 ATOM PAIRS WERE FOUND FOR ATOM LIST 41360 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29372 from a total of 755569 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7373 -67.73801 -7.60558 0.57373 INTE EXTERN> -29.56008 -38.17793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.738" Parameter: A <- "-67.738" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5601" Parameter: B <- "-29.5601" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.1779" Parameter: C <- "-38.1779" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7373 TOTAL ENERGY = -67.738 RDTITL> * VAN DER WAALS = -29.5601 ELECTROSTATIC = -38.1779 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7373" Parameter: CONF_N -> "8002" Comparing "7373" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7374" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755569 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757672 ATOM PAIRS WERE FOUND FOR ATOM LIST 41534 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29912 from a total of 757672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7374 -66.39623 -1.34179 0.59039 INTE EXTERN> -29.77471 -36.62152 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3962" Parameter: A <- "-66.3962" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7747" Parameter: B <- "-29.7747" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6215" Parameter: C <- "-36.6215" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7374 TOTAL ENERGY = -66.3962 RDTITL> * VAN DER WAALS = -29.7747 ELECTROSTATIC = -36.6215 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7374" Parameter: CONF_N -> "8002" Comparing "7374" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7375" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752966 ATOM PAIRS WERE FOUND FOR ATOM LIST 41264 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29198 from a total of 752966 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7375 -67.06663 0.67040 0.57997 INTE EXTERN> -28.64283 -38.42380 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0666" Parameter: A <- "-67.0666" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6428" Parameter: B <- "-28.6428" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4238" Parameter: C <- "-38.4238" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7375 TOTAL ENERGY = -67.0666 RDTITL> * VAN DER WAALS = -28.6428 ELECTROSTATIC = -38.4238 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7375" Parameter: CONF_N -> "8002" Comparing "7375" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7376" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752966 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757094 ATOM PAIRS WERE FOUND FOR ATOM LIST 41490 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29359 from a total of 757094 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7376 -71.03556 3.96893 0.49242 INTE EXTERN> -32.75227 -38.28329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0356" Parameter: A <- "-71.0356" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7523" Parameter: B <- "-32.7523" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2833" Parameter: C <- "-38.2833" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7376 TOTAL ENERGY = -71.0356 RDTITL> * VAN DER WAALS = -32.7523 ELECTROSTATIC = -38.2833 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7376" Parameter: CONF_N -> "8002" Comparing "7376" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7377" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757094 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750477 ATOM PAIRS WERE FOUND FOR ATOM LIST 41278 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29033 from a total of 750477 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7377 -64.68350 -6.35206 0.52761 INTE EXTERN> -30.55076 -34.13274 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.6835" Parameter: A <- "-64.6835" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5508" Parameter: B <- "-30.5508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1327" Parameter: C <- "-34.1327" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7377 TOTAL ENERGY = -64.6835 RDTITL> * VAN DER WAALS = -30.5508 ELECTROSTATIC = -34.1327 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7377" Parameter: CONF_N -> "8002" Comparing "7377" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7378" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750477 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755983 ATOM PAIRS WERE FOUND FOR ATOM LIST 41433 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30235 from a total of 755983 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7378 -69.12415 4.44065 0.59890 INTE EXTERN> -29.68967 -39.43448 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1242" Parameter: A <- "-69.1242" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6897" Parameter: B <- "-29.6897" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4345" Parameter: C <- "-39.4345" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7378 TOTAL ENERGY = -69.1242 RDTITL> * VAN DER WAALS = -29.6897 ELECTROSTATIC = -39.4345 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7378" Parameter: CONF_N -> "8002" Comparing "7378" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7379" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755983 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756638 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29465 from a total of 756638 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7379 -67.91111 -1.21305 0.62179 INTE EXTERN> -28.90938 -39.00173 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9111" Parameter: A <- "-67.9111" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9094" Parameter: B <- "-28.9094" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0017" Parameter: C <- "-39.0017" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7379 TOTAL ENERGY = -67.9111 RDTITL> * VAN DER WAALS = -28.9094 ELECTROSTATIC = -39.0017 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7379" Parameter: CONF_N -> "8002" Comparing "7379" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7380" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756638 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751212 ATOM PAIRS WERE FOUND FOR ATOM LIST 41270 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29257 from a total of 751212 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7380 -67.74793 -0.16317 0.55081 INTE EXTERN> -28.87480 -38.87313 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7479" Parameter: A <- "-67.7479" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8748" Parameter: B <- "-28.8748" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8731" Parameter: C <- "-38.8731" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7380 TOTAL ENERGY = -67.7479 RDTITL> * VAN DER WAALS = -28.8748 ELECTROSTATIC = -38.8731 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7380" Parameter: CONF_N -> "8002" Comparing "7380" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7381" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751212 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753017 ATOM PAIRS WERE FOUND FOR ATOM LIST 41375 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29295 from a total of 753017 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7381 -69.35357 1.60564 0.60446 INTE EXTERN> -29.06253 -40.29104 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3536" Parameter: A <- "-69.3536" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0625" Parameter: B <- "-29.0625" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.291" Parameter: C <- "-40.291" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7381 TOTAL ENERGY = -69.3536 RDTITL> * VAN DER WAALS = -29.0625 ELECTROSTATIC = -40.291 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7381" Parameter: CONF_N -> "8002" Comparing "7381" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7382" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753017 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748848 ATOM PAIRS WERE FOUND FOR ATOM LIST 40979 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29225 from a total of 748848 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7382 -58.67800 -10.67558 0.47841 INTE EXTERN> -27.96998 -30.70802 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-58.678" Parameter: A <- "-58.678" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.97" Parameter: B <- "-27.97" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.708" Parameter: C <- "-30.708" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7382 TOTAL ENERGY = -58.678 RDTITL> * VAN DER WAALS = -27.97 ELECTROSTATIC = -30.708 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7382" Parameter: CONF_N -> "8002" Comparing "7382" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7383" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748848 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759419 ATOM PAIRS WERE FOUND FOR ATOM LIST 41654 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30353 from a total of 759419 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7383 -63.37859 4.70059 0.55848 INTE EXTERN> -31.08120 -32.29739 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.3786" Parameter: A <- "-63.3786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0812" Parameter: B <- "-31.0812" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-32.2974" Parameter: C <- "-32.2974" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7383 TOTAL ENERGY = -63.3786 RDTITL> * VAN DER WAALS = -31.0812 ELECTROSTATIC = -32.2974 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7383" Parameter: CONF_N -> "8002" Comparing "7383" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7384" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759419 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754451 ATOM PAIRS WERE FOUND FOR ATOM LIST 41335 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30122 from a total of 754451 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7384 -73.97350 10.59490 0.57023 INTE EXTERN> -31.85275 -42.12074 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9735" Parameter: A <- "-73.9735" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8528" Parameter: B <- "-31.8528" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1207" Parameter: C <- "-42.1207" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7384 TOTAL ENERGY = -73.9735 RDTITL> * VAN DER WAALS = -31.8528 ELECTROSTATIC = -42.1207 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7384" Parameter: CONF_N -> "8002" Comparing "7384" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7385" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754451 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749520 ATOM PAIRS WERE FOUND FOR ATOM LIST 41120 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29848 from a total of 749520 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7385 -74.39208 0.41858 0.62313 INTE EXTERN> -29.27626 -45.11582 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3921" Parameter: A <- "-74.3921" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2763" Parameter: B <- "-29.2763" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1158" Parameter: C <- "-45.1158" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7385 TOTAL ENERGY = -74.3921 RDTITL> * VAN DER WAALS = -29.2763 ELECTROSTATIC = -45.1158 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7385" Parameter: CONF_N -> "8002" Comparing "7385" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7386" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749520 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755835 ATOM PAIRS WERE FOUND FOR ATOM LIST 41449 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29593 from a total of 755835 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7386 -69.97595 -4.41613 0.61144 INTE EXTERN> -30.36850 -39.60745 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.976" Parameter: A <- "-69.976" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3685" Parameter: B <- "-30.3685" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.6074" Parameter: C <- "-39.6074" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7386 TOTAL ENERGY = -69.976 RDTITL> * VAN DER WAALS = -30.3685 ELECTROSTATIC = -39.6074 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7386" Parameter: CONF_N -> "8002" Comparing "7386" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7387" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755835 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758770 ATOM PAIRS WERE FOUND FOR ATOM LIST 41575 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29907 from a total of 758770 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7387 -76.10477 6.12881 0.63818 INTE EXTERN> -28.40452 -47.70025 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1048" Parameter: A <- "-76.1048" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4045" Parameter: B <- "-28.4045" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7002" Parameter: C <- "-47.7002" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7387 TOTAL ENERGY = -76.1048 RDTITL> * VAN DER WAALS = -28.4045 ELECTROSTATIC = -47.7002 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7387" Parameter: CONF_N -> "8002" Comparing "7387" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7388" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758770 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750394 ATOM PAIRS WERE FOUND FOR ATOM LIST 41245 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29698 from a total of 750394 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7388 -66.79871 -9.30606 0.52591 INTE EXTERN> -29.31031 -37.48840 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7987" Parameter: A <- "-66.7987" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3103" Parameter: B <- "-29.3103" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4884" Parameter: C <- "-37.4884" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7388 TOTAL ENERGY = -66.7987 RDTITL> * VAN DER WAALS = -29.3103 ELECTROSTATIC = -37.4884 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7388" Parameter: CONF_N -> "8002" Comparing "7388" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7389" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750394 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756643 ATOM PAIRS WERE FOUND FOR ATOM LIST 41491 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30109 from a total of 756643 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7389 -72.29692 5.49821 0.79721 INTE EXTERN> -22.91543 -49.38148 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2969" Parameter: A <- "-72.2969" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.9154" Parameter: B <- "-22.9154" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3815" Parameter: C <- "-49.3815" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7389 TOTAL ENERGY = -72.2969 RDTITL> * VAN DER WAALS = -22.9154 ELECTROSTATIC = -49.3815 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7389" Parameter: CONF_N -> "8002" Comparing "7389" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7390" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756643 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754002 ATOM PAIRS WERE FOUND FOR ATOM LIST 41350 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29985 from a total of 754002 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7390 -67.85845 -4.43847 0.61066 INTE EXTERN> -26.92733 -40.93111 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8584" Parameter: A <- "-67.8584" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9273" Parameter: B <- "-26.9273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9311" Parameter: C <- "-40.9311" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7390 TOTAL ENERGY = -67.8584 RDTITL> * VAN DER WAALS = -26.9273 ELECTROSTATIC = -40.9311 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7390" Parameter: CONF_N -> "8002" Comparing "7390" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7391" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754002 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750972 ATOM PAIRS WERE FOUND FOR ATOM LIST 41091 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30093 from a total of 750972 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7391 -80.00846 12.15001 0.66955 INTE EXTERN> -28.31833 -51.69013 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.0085" Parameter: A <- "-80.0085" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3183" Parameter: B <- "-28.3183" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6901" Parameter: C <- "-51.6901" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7391 TOTAL ENERGY = -80.0085 RDTITL> * VAN DER WAALS = -28.3183 ELECTROSTATIC = -51.6901 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7391" Parameter: CONF_N -> "8002" Comparing "7391" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7392" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750972 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751379 ATOM PAIRS WERE FOUND FOR ATOM LIST 41022 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29642 from a total of 751379 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7392 -72.67759 -7.33087 0.55862 INTE EXTERN> -28.71416 -43.96343 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6776" Parameter: A <- "-72.6776" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7142" Parameter: B <- "-28.7142" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9634" Parameter: C <- "-43.9634" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7392 TOTAL ENERGY = -72.6776 RDTITL> * VAN DER WAALS = -28.7142 ELECTROSTATIC = -43.9634 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7392" Parameter: CONF_N -> "8002" Comparing "7392" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7393" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751379 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750825 ATOM PAIRS WERE FOUND FOR ATOM LIST 41211 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29430 from a total of 750825 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7393 -72.02830 -0.64929 0.61468 INTE EXTERN> -27.88041 -44.14788 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0283" Parameter: A <- "-72.0283" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8804" Parameter: B <- "-27.8804" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1479" Parameter: C <- "-44.1479" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7393 TOTAL ENERGY = -72.0283 RDTITL> * VAN DER WAALS = -27.8804 ELECTROSTATIC = -44.1479 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7393" Parameter: CONF_N -> "8002" Comparing "7393" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7394" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750825 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749867 ATOM PAIRS WERE FOUND FOR ATOM LIST 41061 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29268 from a total of 749867 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7394 -71.69646 -0.33184 0.54510 INTE EXTERN> -32.23963 -39.45683 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6965" Parameter: A <- "-71.6965" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2396" Parameter: B <- "-32.2396" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4568" Parameter: C <- "-39.4568" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7394 TOTAL ENERGY = -71.6965 RDTITL> * VAN DER WAALS = -32.2396 ELECTROSTATIC = -39.4568 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7394" Parameter: CONF_N -> "8002" Comparing "7394" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7395" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749867 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754298 ATOM PAIRS WERE FOUND FOR ATOM LIST 41362 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29403 from a total of 754298 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7395 -73.08571 1.38925 0.63802 INTE EXTERN> -26.49927 -46.58644 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0857" Parameter: A <- "-73.0857" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4993" Parameter: B <- "-26.4993" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5864" Parameter: C <- "-46.5864" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7395 TOTAL ENERGY = -73.0857 RDTITL> * VAN DER WAALS = -26.4993 ELECTROSTATIC = -46.5864 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7395" Parameter: CONF_N -> "8002" Comparing "7395" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7396" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754298 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752761 ATOM PAIRS WERE FOUND FOR ATOM LIST 41240 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29855 from a total of 752761 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7396 -76.45490 3.36919 0.68712 INTE EXTERN> -27.40209 -49.05281 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4549" Parameter: A <- "-76.4549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4021" Parameter: B <- "-27.4021" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0528" Parameter: C <- "-49.0528" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7396 TOTAL ENERGY = -76.4549 RDTITL> * VAN DER WAALS = -27.4021 ELECTROSTATIC = -49.0528 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7396" Parameter: CONF_N -> "8002" Comparing "7396" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7397" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752761 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746954 ATOM PAIRS WERE FOUND FOR ATOM LIST 41062 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29172 from a total of 746954 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7397 -69.74841 -6.70649 0.60086 INTE EXTERN> -27.61501 -42.13340 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7484" Parameter: A <- "-69.7484" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.615" Parameter: B <- "-27.615" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1334" Parameter: C <- "-42.1334" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7397 TOTAL ENERGY = -69.7484 RDTITL> * VAN DER WAALS = -27.615 ELECTROSTATIC = -42.1334 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7397" Parameter: CONF_N -> "8002" Comparing "7397" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7398" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746954 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 742863 ATOM PAIRS WERE FOUND FOR ATOM LIST 40737 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29252 from a total of 742863 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7398 -73.67780 3.92939 0.73452 INTE EXTERN> -26.06782 -47.60998 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6778" Parameter: A <- "-73.6778" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0678" Parameter: B <- "-26.0678" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.61" Parameter: C <- "-47.61" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7398 TOTAL ENERGY = -73.6778 RDTITL> * VAN DER WAALS = -26.0678 ELECTROSTATIC = -47.61 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7398" Parameter: CONF_N -> "8002" Comparing "7398" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7399" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 742863 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41042 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28934 from a total of 747110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7399 -69.29603 -4.38177 0.58531 INTE EXTERN> -29.67205 -39.62398 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.296" Parameter: A <- "-69.296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.672" Parameter: B <- "-29.672" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.624" Parameter: C <- "-39.624" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7399 TOTAL ENERGY = -69.296 RDTITL> * VAN DER WAALS = -29.672 ELECTROSTATIC = -39.624 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7399" Parameter: CONF_N -> "8002" Comparing "7399" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7400" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749999 ATOM PAIRS WERE FOUND FOR ATOM LIST 41114 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29144 from a total of 749999 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7400 -69.14346 -0.15256 0.64058 INTE EXTERN> -26.89776 -42.24570 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1435" Parameter: A <- "-69.1435" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8978" Parameter: B <- "-26.8978" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2457" Parameter: C <- "-42.2457" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7400 TOTAL ENERGY = -69.1435 RDTITL> * VAN DER WAALS = -26.8978 ELECTROSTATIC = -42.2457 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7400" Parameter: CONF_N -> "8002" Comparing "7400" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7401" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749999 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750392 ATOM PAIRS WERE FOUND FOR ATOM LIST 40848 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29277 from a total of 750392 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7401 -77.20483 8.06137 0.58241 INTE EXTERN> -29.89414 -47.31069 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2048" Parameter: A <- "-77.2048" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8941" Parameter: B <- "-29.8941" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3107" Parameter: C <- "-47.3107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7401 TOTAL ENERGY = -77.2048 RDTITL> * VAN DER WAALS = -29.8941 ELECTROSTATIC = -47.3107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7401" Parameter: CONF_N -> "8002" Comparing "7401" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7402" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750392 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41082 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29634 from a total of 748586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7402 -74.63702 -2.56781 0.57678 INTE EXTERN> -30.66170 -43.97532 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.637" Parameter: A <- "-74.637" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6617" Parameter: B <- "-30.6617" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9753" Parameter: C <- "-43.9753" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7402 TOTAL ENERGY = -74.637 RDTITL> * VAN DER WAALS = -30.6617 ELECTROSTATIC = -43.9753 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7402" Parameter: CONF_N -> "8002" Comparing "7402" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7403" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748315 ATOM PAIRS WERE FOUND FOR ATOM LIST 41042 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28892 from a total of 748315 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7403 -71.68928 -2.94774 0.64584 INTE EXTERN> -24.52799 -47.16130 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6893" Parameter: A <- "-71.6893" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.528" Parameter: B <- "-24.528" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1613" Parameter: C <- "-47.1613" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7403 TOTAL ENERGY = -71.6893 RDTITL> * VAN DER WAALS = -24.528 ELECTROSTATIC = -47.1613 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7403" Parameter: CONF_N -> "8002" Comparing "7403" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7404" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748315 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747111 ATOM PAIRS WERE FOUND FOR ATOM LIST 40884 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29629 from a total of 747111 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7404 -68.85423 -2.83505 0.57821 INTE EXTERN> -29.33066 -39.52357 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8542" Parameter: A <- "-68.8542" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3307" Parameter: B <- "-29.3307" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.5236" Parameter: C <- "-39.5236" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7404 TOTAL ENERGY = -68.8542 RDTITL> * VAN DER WAALS = -29.3307 ELECTROSTATIC = -39.5236 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7404" Parameter: CONF_N -> "8002" Comparing "7404" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7405" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747111 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756488 ATOM PAIRS WERE FOUND FOR ATOM LIST 41337 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29831 from a total of 756488 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7405 -74.74757 5.89334 0.58910 INTE EXTERN> -29.79469 -44.95288 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7476" Parameter: A <- "-74.7476" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7947" Parameter: B <- "-29.7947" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9529" Parameter: C <- "-44.9529" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7405 TOTAL ENERGY = -74.7476 RDTITL> * VAN DER WAALS = -29.7947 ELECTROSTATIC = -44.9529 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7405" Parameter: CONF_N -> "8002" Comparing "7405" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7406" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756488 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750117 ATOM PAIRS WERE FOUND FOR ATOM LIST 41053 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29496 from a total of 750117 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7406 -78.71596 3.96840 0.79715 INTE EXTERN> -24.69064 -54.02532 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.716" Parameter: A <- "-78.716" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6906" Parameter: B <- "-24.6906" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0253" Parameter: C <- "-54.0253" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7406 TOTAL ENERGY = -78.716 RDTITL> * VAN DER WAALS = -24.6906 ELECTROSTATIC = -54.0253 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7406" Parameter: CONF_N -> "8002" Comparing "7406" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7407" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750117 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756468 ATOM PAIRS WERE FOUND FOR ATOM LIST 41434 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29809 from a total of 756468 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7407 -68.53729 -10.17867 0.59008 INTE EXTERN> -30.30821 -38.22908 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5373" Parameter: A <- "-68.5373" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3082" Parameter: B <- "-30.3082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.2291" Parameter: C <- "-38.2291" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7407 TOTAL ENERGY = -68.5373 RDTITL> * VAN DER WAALS = -30.3082 ELECTROSTATIC = -38.2291 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7407" Parameter: CONF_N -> "8002" Comparing "7407" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7408" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756468 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754380 ATOM PAIRS WERE FOUND FOR ATOM LIST 41415 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30103 from a total of 754380 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7408 -72.51225 3.97496 0.66798 INTE EXTERN> -27.93009 -44.58216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5123" Parameter: A <- "-72.5123" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9301" Parameter: B <- "-27.9301" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5822" Parameter: C <- "-44.5822" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7408 TOTAL ENERGY = -72.5123 RDTITL> * VAN DER WAALS = -27.9301 ELECTROSTATIC = -44.5822 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7408" Parameter: CONF_N -> "8002" Comparing "7408" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7409" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754380 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758252 ATOM PAIRS WERE FOUND FOR ATOM LIST 41537 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30431 from a total of 758252 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7409 -73.43773 0.92548 0.65272 INTE EXTERN> -29.45633 -43.98140 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4377" Parameter: A <- "-73.4377" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4563" Parameter: B <- "-29.4563" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9814" Parameter: C <- "-43.9814" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7409 TOTAL ENERGY = -73.4377 RDTITL> * VAN DER WAALS = -29.4563 ELECTROSTATIC = -43.9814 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7409" Parameter: CONF_N -> "8002" Comparing "7409" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7410" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758252 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746357 ATOM PAIRS WERE FOUND FOR ATOM LIST 40978 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29122 from a total of 746357 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7410 -71.74108 -1.69665 0.63548 INTE EXTERN> -27.42070 -44.32039 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7411" Parameter: A <- "-71.7411" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4207" Parameter: B <- "-27.4207" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3204" Parameter: C <- "-44.3204" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7410 TOTAL ENERGY = -71.7411 RDTITL> * VAN DER WAALS = -27.4207 ELECTROSTATIC = -44.3204 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7410" Parameter: CONF_N -> "8002" Comparing "7410" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7411" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746357 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750083 ATOM PAIRS WERE FOUND FOR ATOM LIST 41070 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29980 from a total of 750083 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7411 -67.98646 -3.75463 0.48669 INTE EXTERN> -33.26837 -34.71809 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9865" Parameter: A <- "-67.9865" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.2684" Parameter: B <- "-33.2684" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7181" Parameter: C <- "-34.7181" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7411 TOTAL ENERGY = -67.9865 RDTITL> * VAN DER WAALS = -33.2684 ELECTROSTATIC = -34.7181 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7411" Parameter: CONF_N -> "8002" Comparing "7411" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7412" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750083 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754539 ATOM PAIRS WERE FOUND FOR ATOM LIST 41300 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29643 from a total of 754539 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7412 -78.41076 10.42430 0.69754 INTE EXTERN> -26.60757 -51.80319 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4108" Parameter: A <- "-78.4108" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6076" Parameter: B <- "-26.6076" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8032" Parameter: C <- "-51.8032" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7412 TOTAL ENERGY = -78.4108 RDTITL> * VAN DER WAALS = -26.6076 ELECTROSTATIC = -51.8032 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7412" Parameter: CONF_N -> "8002" Comparing "7412" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7413" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754539 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748033 ATOM PAIRS WERE FOUND FOR ATOM LIST 40956 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29404 from a total of 748033 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7413 -72.87652 -5.53424 0.69391 INTE EXTERN> -24.26269 -48.61383 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8765" Parameter: A <- "-72.8765" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2627" Parameter: B <- "-24.2627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6138" Parameter: C <- "-48.6138" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7413 TOTAL ENERGY = -72.8765 RDTITL> * VAN DER WAALS = -24.2627 ELECTROSTATIC = -48.6138 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7413" Parameter: CONF_N -> "8002" Comparing "7413" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7414" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748033 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756556 ATOM PAIRS WERE FOUND FOR ATOM LIST 41585 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29103 from a total of 756556 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7414 -76.00813 3.13160 0.74135 INTE EXTERN> -23.02987 -52.97826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0081" Parameter: A <- "-76.0081" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.0299" Parameter: B <- "-23.0299" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9783" Parameter: C <- "-52.9783" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7414 TOTAL ENERGY = -76.0081 RDTITL> * VAN DER WAALS = -23.0299 ELECTROSTATIC = -52.9783 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7414" Parameter: CONF_N -> "8002" Comparing "7414" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7415" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756556 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757054 ATOM PAIRS WERE FOUND FOR ATOM LIST 41483 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29755 from a total of 757054 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7415 -72.07535 -3.93278 0.75011 INTE EXTERN> -24.56732 -47.50803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0753" Parameter: A <- "-72.0753" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5673" Parameter: B <- "-24.5673" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.508" Parameter: C <- "-47.508" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7415 TOTAL ENERGY = -72.0753 RDTITL> * VAN DER WAALS = -24.5673 ELECTROSTATIC = -47.508 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7415" Parameter: CONF_N -> "8002" Comparing "7415" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7416" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757054 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41346 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29889 from a total of 753009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7416 -74.89022 2.81487 0.68186 INTE EXTERN> -26.33140 -48.55882 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8902" Parameter: A <- "-74.8902" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3314" Parameter: B <- "-26.3314" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5588" Parameter: C <- "-48.5588" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7416 TOTAL ENERGY = -74.8902 RDTITL> * VAN DER WAALS = -26.3314 ELECTROSTATIC = -48.5588 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7416" Parameter: CONF_N -> "8002" Comparing "7416" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7417" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755562 ATOM PAIRS WERE FOUND FOR ATOM LIST 41529 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29893 from a total of 755562 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7417 -75.27260 0.38239 0.66079 INTE EXTERN> -26.82391 -48.44869 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2726" Parameter: A <- "-75.2726" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8239" Parameter: B <- "-26.8239" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.4487" Parameter: C <- "-48.4487" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7417 TOTAL ENERGY = -75.2726 RDTITL> * VAN DER WAALS = -26.8239 ELECTROSTATIC = -48.4487 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7417" Parameter: CONF_N -> "8002" Comparing "7417" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7418" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755562 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41421 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30248 from a total of 757110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7418 -70.20136 -5.07124 0.70098 INTE EXTERN> -23.08257 -47.11879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2014" Parameter: A <- "-70.2014" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.0826" Parameter: B <- "-23.0826" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1188" Parameter: C <- "-47.1188" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7418 TOTAL ENERGY = -70.2014 RDTITL> * VAN DER WAALS = -23.0826 ELECTROSTATIC = -47.1188 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7418" Parameter: CONF_N -> "8002" Comparing "7418" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7419" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755176 ATOM PAIRS WERE FOUND FOR ATOM LIST 41235 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30225 from a total of 755176 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7419 -68.88655 -1.31481 0.55616 INTE EXTERN> -30.45237 -38.43418 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8865" Parameter: A <- "-68.8865" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4524" Parameter: B <- "-30.4524" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4342" Parameter: C <- "-38.4342" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7419 TOTAL ENERGY = -68.8865 RDTITL> * VAN DER WAALS = -30.4524 ELECTROSTATIC = -38.4342 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7419" Parameter: CONF_N -> "8002" Comparing "7419" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7420" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755176 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751776 ATOM PAIRS WERE FOUND FOR ATOM LIST 41220 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30008 from a total of 751776 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7420 -71.44569 2.55914 0.57238 INTE EXTERN> -30.23584 -41.20986 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4457" Parameter: A <- "-71.4457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2358" Parameter: B <- "-30.2358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.2099" Parameter: C <- "-41.2099" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7420 TOTAL ENERGY = -71.4457 RDTITL> * VAN DER WAALS = -30.2358 ELECTROSTATIC = -41.2099 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7420" Parameter: CONF_N -> "8002" Comparing "7420" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7421" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751776 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749363 ATOM PAIRS WERE FOUND FOR ATOM LIST 41115 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29353 from a total of 749363 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7421 -66.88792 -4.55777 0.61455 INTE EXTERN> -27.16346 -39.72446 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8879" Parameter: A <- "-66.8879" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1635" Parameter: B <- "-27.1635" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7245" Parameter: C <- "-39.7245" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7421 TOTAL ENERGY = -66.8879 RDTITL> * VAN DER WAALS = -27.1635 ELECTROSTATIC = -39.7245 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7421" Parameter: CONF_N -> "8002" Comparing "7421" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7422" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749363 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753379 ATOM PAIRS WERE FOUND FOR ATOM LIST 41439 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29942 from a total of 753379 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7422 -70.07270 3.18479 0.58808 INTE EXTERN> -25.71589 -44.35682 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0727" Parameter: A <- "-70.0727" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7159" Parameter: B <- "-25.7159" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3568" Parameter: C <- "-44.3568" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7422 TOTAL ENERGY = -70.0727 RDTITL> * VAN DER WAALS = -25.7159 ELECTROSTATIC = -44.3568 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7422" Parameter: CONF_N -> "8002" Comparing "7422" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7423" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753379 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750414 ATOM PAIRS WERE FOUND FOR ATOM LIST 41342 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30063 from a total of 750414 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7423 -70.24038 0.16767 0.62325 INTE EXTERN> -26.99647 -43.24391 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2404" Parameter: A <- "-70.2404" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9965" Parameter: B <- "-26.9965" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2439" Parameter: C <- "-43.2439" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7423 TOTAL ENERGY = -70.2404 RDTITL> * VAN DER WAALS = -26.9965 ELECTROSTATIC = -43.2439 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7423" Parameter: CONF_N -> "8002" Comparing "7423" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7424" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750414 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753958 ATOM PAIRS WERE FOUND FOR ATOM LIST 41361 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29731 from a total of 753958 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7424 -76.95982 6.71944 0.69788 INTE EXTERN> -28.45887 -48.50095 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9598" Parameter: A <- "-76.9598" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4589" Parameter: B <- "-28.4589" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5009" Parameter: C <- "-48.5009" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7424 TOTAL ENERGY = -76.9598 RDTITL> * VAN DER WAALS = -28.4589 ELECTROSTATIC = -48.5009 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7424" Parameter: CONF_N -> "8002" Comparing "7424" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7425" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753958 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757507 ATOM PAIRS WERE FOUND FOR ATOM LIST 41691 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30285 from a total of 757507 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7425 -63.40370 -13.55613 0.77738 INTE EXTERN> -20.85787 -42.54583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.4037" Parameter: A <- "-63.4037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.8579" Parameter: B <- "-20.8579" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5458" Parameter: C <- "-42.5458" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7425 TOTAL ENERGY = -63.4037 RDTITL> * VAN DER WAALS = -20.8579 ELECTROSTATIC = -42.5458 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7425" Parameter: CONF_N -> "8002" Comparing "7425" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7426" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757507 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751407 ATOM PAIRS WERE FOUND FOR ATOM LIST 41177 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29269 from a total of 751407 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7426 -74.99143 11.58773 0.62614 INTE EXTERN> -28.42352 -46.56791 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9914" Parameter: A <- "-74.9914" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4235" Parameter: B <- "-28.4235" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5679" Parameter: C <- "-46.5679" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7426 TOTAL ENERGY = -74.9914 RDTITL> * VAN DER WAALS = -28.4235 ELECTROSTATIC = -46.5679 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7426" Parameter: CONF_N -> "8002" Comparing "7426" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7427" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751407 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757529 ATOM PAIRS WERE FOUND FOR ATOM LIST 41476 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30052 from a total of 757529 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7427 -67.31481 -7.67662 0.60353 INTE EXTERN> -27.33285 -39.98196 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3148" Parameter: A <- "-67.3148" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3328" Parameter: B <- "-27.3328" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.982" Parameter: C <- "-39.982" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7427 TOTAL ENERGY = -67.3148 RDTITL> * VAN DER WAALS = -27.3328 ELECTROSTATIC = -39.982 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7427" Parameter: CONF_N -> "8002" Comparing "7427" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7428" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757529 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754044 ATOM PAIRS WERE FOUND FOR ATOM LIST 41423 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29868 from a total of 754044 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7428 -80.44966 13.13485 0.59269 INTE EXTERN> -32.11964 -48.33002 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4497" Parameter: A <- "-80.4497" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1196" Parameter: B <- "-32.1196" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.33" Parameter: C <- "-48.33" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7428 TOTAL ENERGY = -80.4497 RDTITL> * VAN DER WAALS = -32.1196 ELECTROSTATIC = -48.33 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7428" Parameter: CONF_N -> "8002" Comparing "7428" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7429" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754044 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755003 ATOM PAIRS WERE FOUND FOR ATOM LIST 41534 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29383 from a total of 755003 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7429 -76.94481 -3.50485 0.54193 INTE EXTERN> -30.98261 -45.96220 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9448" Parameter: A <- "-76.9448" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9826" Parameter: B <- "-30.9826" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9622" Parameter: C <- "-45.9622" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7429 TOTAL ENERGY = -76.9448 RDTITL> * VAN DER WAALS = -30.9826 ELECTROSTATIC = -45.9622 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7429" Parameter: CONF_N -> "8002" Comparing "7429" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7430" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755003 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755864 ATOM PAIRS WERE FOUND FOR ATOM LIST 41266 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30115 from a total of 755864 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7430 -66.76074 -10.18406 0.66117 INTE EXTERN> -25.01903 -41.74171 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7607" Parameter: A <- "-66.7607" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.019" Parameter: B <- "-25.019" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7417" Parameter: C <- "-41.7417" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7430 TOTAL ENERGY = -66.7607 RDTITL> * VAN DER WAALS = -25.019 ELECTROSTATIC = -41.7417 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7430" Parameter: CONF_N -> "8002" Comparing "7430" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7431" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755864 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755088 ATOM PAIRS WERE FOUND FOR ATOM LIST 41278 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30087 from a total of 755088 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7431 -72.18593 5.42519 0.51585 INTE EXTERN> -31.69400 -40.49193 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1859" Parameter: A <- "-72.1859" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.694" Parameter: B <- "-31.694" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4919" Parameter: C <- "-40.4919" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7431 TOTAL ENERGY = -72.1859 RDTITL> * VAN DER WAALS = -31.694 ELECTROSTATIC = -40.4919 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7431" Parameter: CONF_N -> "8002" Comparing "7431" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7432" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755088 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752217 ATOM PAIRS WERE FOUND FOR ATOM LIST 41347 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30047 from a total of 752217 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7432 -65.55482 -6.63112 0.55222 INTE EXTERN> -29.81745 -35.73737 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5548" Parameter: A <- "-65.5548" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8174" Parameter: B <- "-29.8174" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.7374" Parameter: C <- "-35.7374" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7432 TOTAL ENERGY = -65.5548 RDTITL> * VAN DER WAALS = -29.8174 ELECTROSTATIC = -35.7374 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7432" Parameter: CONF_N -> "8002" Comparing "7432" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7433" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752217 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749873 ATOM PAIRS WERE FOUND FOR ATOM LIST 41116 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30373 from a total of 749873 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7433 -69.12477 3.56996 0.71203 INTE EXTERN> -25.19404 -43.93074 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1248" Parameter: A <- "-69.1248" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.194" Parameter: B <- "-25.194" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9307" Parameter: C <- "-43.9307" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7433 TOTAL ENERGY = -69.1248 RDTITL> * VAN DER WAALS = -25.194 ELECTROSTATIC = -43.9307 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7433" Parameter: CONF_N -> "8002" Comparing "7433" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7434" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749873 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755224 ATOM PAIRS WERE FOUND FOR ATOM LIST 41271 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29634 from a total of 755224 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7434 -72.84154 3.71677 0.54446 INTE EXTERN> -30.14732 -42.69422 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8415" Parameter: A <- "-72.8415" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1473" Parameter: B <- "-30.1473" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6942" Parameter: C <- "-42.6942" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7434 TOTAL ENERGY = -72.8415 RDTITL> * VAN DER WAALS = -30.1473 ELECTROSTATIC = -42.6942 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7434" Parameter: CONF_N -> "8002" Comparing "7434" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7435" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755224 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754227 ATOM PAIRS WERE FOUND FOR ATOM LIST 41228 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30313 from a total of 754227 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7435 -70.61647 -2.22507 0.65844 INTE EXTERN> -25.94910 -44.66736 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6165" Parameter: A <- "-70.6165" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9491" Parameter: B <- "-25.9491" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6674" Parameter: C <- "-44.6674" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7435 TOTAL ENERGY = -70.6165 RDTITL> * VAN DER WAALS = -25.9491 ELECTROSTATIC = -44.6674 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7435" Parameter: CONF_N -> "8002" Comparing "7435" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7436" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754227 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751622 ATOM PAIRS WERE FOUND FOR ATOM LIST 41311 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29936 from a total of 751622 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7436 -72.43711 1.82064 0.66629 INTE EXTERN> -25.63294 -46.80417 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4371" Parameter: A <- "-72.4371" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6329" Parameter: B <- "-25.6329" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8042" Parameter: C <- "-46.8042" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7436 TOTAL ENERGY = -72.4371 RDTITL> * VAN DER WAALS = -25.6329 ELECTROSTATIC = -46.8042 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7436" Parameter: CONF_N -> "8002" Comparing "7436" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7437" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751622 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755775 ATOM PAIRS WERE FOUND FOR ATOM LIST 41513 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30634 from a total of 755775 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7437 -74.80193 2.36482 0.67265 INTE EXTERN> -27.39838 -47.40354 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8019" Parameter: A <- "-74.8019" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3984" Parameter: B <- "-27.3984" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4035" Parameter: C <- "-47.4035" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7437 TOTAL ENERGY = -74.8019 RDTITL> * VAN DER WAALS = -27.3984 ELECTROSTATIC = -47.4035 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7437" Parameter: CONF_N -> "8002" Comparing "7437" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7438" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755775 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751027 ATOM PAIRS WERE FOUND FOR ATOM LIST 41049 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29892 from a total of 751027 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7438 -74.31195 -0.48998 0.66032 INTE EXTERN> -28.26167 -46.05028 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3119" Parameter: A <- "-74.3119" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2617" Parameter: B <- "-28.2617" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0503" Parameter: C <- "-46.0503" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7438 TOTAL ENERGY = -74.3119 RDTITL> * VAN DER WAALS = -28.2617 ELECTROSTATIC = -46.0503 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7438" Parameter: CONF_N -> "8002" Comparing "7438" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7439" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751027 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755153 ATOM PAIRS WERE FOUND FOR ATOM LIST 41428 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29923 from a total of 755153 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7439 -72.94253 -1.36942 0.63962 INTE EXTERN> -27.86314 -45.07939 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9425" Parameter: A <- "-72.9425" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8631" Parameter: B <- "-27.8631" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0794" Parameter: C <- "-45.0794" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7439 TOTAL ENERGY = -72.9425 RDTITL> * VAN DER WAALS = -27.8631 ELECTROSTATIC = -45.0794 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7439" Parameter: CONF_N -> "8002" Comparing "7439" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7440" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755153 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760004 ATOM PAIRS WERE FOUND FOR ATOM LIST 41573 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30213 from a total of 760004 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7440 -70.69818 -2.24434 0.65920 INTE EXTERN> -28.17283 -42.52535 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6982" Parameter: A <- "-70.6982" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1728" Parameter: B <- "-28.1728" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5254" Parameter: C <- "-42.5254" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7440 TOTAL ENERGY = -70.6982 RDTITL> * VAN DER WAALS = -28.1728 ELECTROSTATIC = -42.5254 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7440" Parameter: CONF_N -> "8002" Comparing "7440" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7441" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760004 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759494 ATOM PAIRS WERE FOUND FOR ATOM LIST 41550 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30118 from a total of 759494 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7441 -72.37513 1.67695 0.61643 INTE EXTERN> -28.73371 -43.64142 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3751" Parameter: A <- "-72.3751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7337" Parameter: B <- "-28.7337" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6414" Parameter: C <- "-43.6414" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7441 TOTAL ENERGY = -72.3751 RDTITL> * VAN DER WAALS = -28.7337 ELECTROSTATIC = -43.6414 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7441" Parameter: CONF_N -> "8002" Comparing "7441" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7442" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759494 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750327 ATOM PAIRS WERE FOUND FOR ATOM LIST 41120 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30091 from a total of 750327 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7442 -68.96814 -3.40700 0.62031 INTE EXTERN> -29.48273 -39.48541 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.9681" Parameter: A <- "-68.9681" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4827" Parameter: B <- "-29.4827" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4854" Parameter: C <- "-39.4854" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7442 TOTAL ENERGY = -68.9681 RDTITL> * VAN DER WAALS = -29.4827 ELECTROSTATIC = -39.4854 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7442" Parameter: CONF_N -> "8002" Comparing "7442" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7443" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750327 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753815 ATOM PAIRS WERE FOUND FOR ATOM LIST 41347 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30127 from a total of 753815 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7443 -75.57621 6.60808 0.64045 INTE EXTERN> -27.45205 -48.12417 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5762" Parameter: A <- "-75.5762" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.452" Parameter: B <- "-27.452" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1242" Parameter: C <- "-48.1242" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7443 TOTAL ENERGY = -75.5762 RDTITL> * VAN DER WAALS = -27.452 ELECTROSTATIC = -48.1242 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7443" Parameter: CONF_N -> "8002" Comparing "7443" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7444" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753815 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762002 ATOM PAIRS WERE FOUND FOR ATOM LIST 41742 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30124 from a total of 762002 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7444 -74.66694 -0.90927 0.63498 INTE EXTERN> -32.00964 -42.65730 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6669" Parameter: A <- "-74.6669" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0096" Parameter: B <- "-32.0096" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6573" Parameter: C <- "-42.6573" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7444 TOTAL ENERGY = -74.6669 RDTITL> * VAN DER WAALS = -32.0096 ELECTROSTATIC = -42.6573 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7444" Parameter: CONF_N -> "8002" Comparing "7444" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7445" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762002 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755612 ATOM PAIRS WERE FOUND FOR ATOM LIST 41303 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29832 from a total of 755612 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7445 -74.37188 -0.29506 0.52359 INTE EXTERN> -31.57865 -42.79323 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3719" Parameter: A <- "-74.3719" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5787" Parameter: B <- "-31.5787" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7932" Parameter: C <- "-42.7932" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7445 TOTAL ENERGY = -74.3719 RDTITL> * VAN DER WAALS = -31.5787 ELECTROSTATIC = -42.7932 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7445" Parameter: CONF_N -> "8002" Comparing "7445" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7446" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755612 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750007 ATOM PAIRS WERE FOUND FOR ATOM LIST 41183 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29289 from a total of 750007 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7446 -64.51201 -9.85987 0.61743 INTE EXTERN> -24.75975 -39.75227 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.512" Parameter: A <- "-64.512" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7597" Parameter: B <- "-24.7597" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7523" Parameter: C <- "-39.7523" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7446 TOTAL ENERGY = -64.512 RDTITL> * VAN DER WAALS = -24.7597 ELECTROSTATIC = -39.7523 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7446" Parameter: CONF_N -> "8002" Comparing "7446" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7447" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750007 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757405 ATOM PAIRS WERE FOUND FOR ATOM LIST 41361 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29931 from a total of 757405 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7447 -71.36549 6.85348 0.51897 INTE EXTERN> -32.77192 -38.59357 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3655" Parameter: A <- "-71.3655" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.7719" Parameter: B <- "-32.7719" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5936" Parameter: C <- "-38.5936" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7447 TOTAL ENERGY = -71.3655 RDTITL> * VAN DER WAALS = -32.7719 ELECTROSTATIC = -38.5936 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7447" Parameter: CONF_N -> "8002" Comparing "7447" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7448" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757405 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757131 ATOM PAIRS WERE FOUND FOR ATOM LIST 41645 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30810 from a total of 757131 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7448 -73.00334 1.63786 0.71286 INTE EXTERN> -24.71682 -48.28653 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0033" Parameter: A <- "-73.0033" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7168" Parameter: B <- "-24.7168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2865" Parameter: C <- "-48.2865" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7448 TOTAL ENERGY = -73.0033 RDTITL> * VAN DER WAALS = -24.7168 ELECTROSTATIC = -48.2865 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7448" Parameter: CONF_N -> "8002" Comparing "7448" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7449" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757131 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757542 ATOM PAIRS WERE FOUND FOR ATOM LIST 41516 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30089 from a total of 757542 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7449 -73.38393 0.38059 0.63149 INTE EXTERN> -26.41359 -46.97034 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3839" Parameter: A <- "-73.3839" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4136" Parameter: B <- "-26.4136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9703" Parameter: C <- "-46.9703" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7449 TOTAL ENERGY = -73.3839 RDTITL> * VAN DER WAALS = -26.4136 ELECTROSTATIC = -46.9703 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7449" Parameter: CONF_N -> "8002" Comparing "7449" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7450" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757542 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760860 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29768 from a total of 760860 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7450 -76.69238 3.30845 0.68062 INTE EXTERN> -29.06882 -47.62355 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6924" Parameter: A <- "-76.6924" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0688" Parameter: B <- "-29.0688" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6236" Parameter: C <- "-47.6236" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7450 TOTAL ENERGY = -76.6924 RDTITL> * VAN DER WAALS = -29.0688 ELECTROSTATIC = -47.6236 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7450" Parameter: CONF_N -> "8002" Comparing "7450" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7451" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760860 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757172 ATOM PAIRS WERE FOUND FOR ATOM LIST 41468 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29373 from a total of 757172 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7451 -69.00777 -7.68461 0.73359 INTE EXTERN> -23.63222 -45.37555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0078" Parameter: A <- "-69.0078" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6322" Parameter: B <- "-23.6322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3755" Parameter: C <- "-45.3755" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7451 TOTAL ENERGY = -69.0078 RDTITL> * VAN DER WAALS = -23.6322 ELECTROSTATIC = -45.3755 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7451" Parameter: CONF_N -> "8002" Comparing "7451" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7452" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757172 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755886 ATOM PAIRS WERE FOUND FOR ATOM LIST 41259 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29967 from a total of 755886 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7452 -71.64303 2.63526 0.61915 INTE EXTERN> -28.80335 -42.83967 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.643" Parameter: A <- "-71.643" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8034" Parameter: B <- "-28.8034" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8397" Parameter: C <- "-42.8397" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7452 TOTAL ENERGY = -71.643 RDTITL> * VAN DER WAALS = -28.8034 ELECTROSTATIC = -42.8397 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7452" Parameter: CONF_N -> "8002" Comparing "7452" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7453" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755886 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756042 ATOM PAIRS WERE FOUND FOR ATOM LIST 41543 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30064 from a total of 756042 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7453 -75.03757 3.39454 0.62261 INTE EXTERN> -28.11186 -46.92571 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0376" Parameter: A <- "-75.0376" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1119" Parameter: B <- "-28.1119" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9257" Parameter: C <- "-46.9257" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7453 TOTAL ENERGY = -75.0376 RDTITL> * VAN DER WAALS = -28.1119 ELECTROSTATIC = -46.9257 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7453" Parameter: CONF_N -> "8002" Comparing "7453" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7454" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756042 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755509 ATOM PAIRS WERE FOUND FOR ATOM LIST 41364 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29742 from a total of 755509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7454 -70.63952 -4.39804 0.66327 INTE EXTERN> -28.84397 -41.79555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6395" Parameter: A <- "-70.6395" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.844" Parameter: B <- "-28.844" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7956" Parameter: C <- "-41.7956" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7454 TOTAL ENERGY = -70.6395 RDTITL> * VAN DER WAALS = -28.844 ELECTROSTATIC = -41.7956 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7454" Parameter: CONF_N -> "8002" Comparing "7454" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7455" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753154 ATOM PAIRS WERE FOUND FOR ATOM LIST 41176 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29464 from a total of 753154 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7455 -79.49136 8.85184 0.65343 INTE EXTERN> -28.56339 -50.92797 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.4914" Parameter: A <- "-79.4914" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5634" Parameter: B <- "-28.5634" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.928" Parameter: C <- "-50.928" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7455 TOTAL ENERGY = -79.4914 RDTITL> * VAN DER WAALS = -28.5634 ELECTROSTATIC = -50.928 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7455" Parameter: CONF_N -> "8002" Comparing "7455" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7456" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753154 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754690 ATOM PAIRS WERE FOUND FOR ATOM LIST 41487 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29753 from a total of 754690 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7456 -67.61764 -11.87373 0.58367 INTE EXTERN> -29.76508 -37.85256 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.6176" Parameter: A <- "-67.6176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7651" Parameter: B <- "-29.7651" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8526" Parameter: C <- "-37.8526" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7456 TOTAL ENERGY = -67.6176 RDTITL> * VAN DER WAALS = -29.7651 ELECTROSTATIC = -37.8526 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7456" Parameter: CONF_N -> "8002" Comparing "7456" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7457" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754690 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756259 ATOM PAIRS WERE FOUND FOR ATOM LIST 41451 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30034 from a total of 756259 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7457 -73.46937 5.85173 0.60116 INTE EXTERN> -30.23677 -43.23259 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4694" Parameter: A <- "-73.4694" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2368" Parameter: B <- "-30.2368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2326" Parameter: C <- "-43.2326" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7457 TOTAL ENERGY = -73.4694 RDTITL> * VAN DER WAALS = -30.2368 ELECTROSTATIC = -43.2326 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7457" Parameter: CONF_N -> "8002" Comparing "7457" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7458" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756259 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756679 ATOM PAIRS WERE FOUND FOR ATOM LIST 41281 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29524 from a total of 756679 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7458 -70.76911 -2.70026 0.61502 INTE EXTERN> -29.26766 -41.50145 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7691" Parameter: A <- "-70.7691" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2677" Parameter: B <- "-29.2677" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5014" Parameter: C <- "-41.5014" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7458 TOTAL ENERGY = -70.7691 RDTITL> * VAN DER WAALS = -29.2677 ELECTROSTATIC = -41.5014 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7458" Parameter: CONF_N -> "8002" Comparing "7458" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7459" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756679 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753319 ATOM PAIRS WERE FOUND FOR ATOM LIST 41287 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29372 from a total of 753319 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7459 -69.43515 -1.33396 0.70468 INTE EXTERN> -23.18059 -46.25456 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4352" Parameter: A <- "-69.4352" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.1806" Parameter: B <- "-23.1806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2546" Parameter: C <- "-46.2546" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7459 TOTAL ENERGY = -69.4352 RDTITL> * VAN DER WAALS = -23.1806 ELECTROSTATIC = -46.2546 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7459" Parameter: CONF_N -> "8002" Comparing "7459" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7460" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753319 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755145 ATOM PAIRS WERE FOUND FOR ATOM LIST 41228 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29723 from a total of 755145 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7460 -71.35722 1.92207 0.63656 INTE EXTERN> -28.57118 -42.78605 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3572" Parameter: A <- "-71.3572" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5712" Parameter: B <- "-28.5712" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.786" Parameter: C <- "-42.786" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7460 TOTAL ENERGY = -71.3572 RDTITL> * VAN DER WAALS = -28.5712 ELECTROSTATIC = -42.786 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7460" Parameter: CONF_N -> "8002" Comparing "7460" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7461" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755145 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757026 ATOM PAIRS WERE FOUND FOR ATOM LIST 41680 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29289 from a total of 757026 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7461 -70.78523 -0.57199 0.66620 INTE EXTERN> -25.77081 -45.01442 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7852" Parameter: A <- "-70.7852" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7708" Parameter: B <- "-25.7708" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0144" Parameter: C <- "-45.0144" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7461 TOTAL ENERGY = -70.7852 RDTITL> * VAN DER WAALS = -25.7708 ELECTROSTATIC = -45.0144 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7461" Parameter: CONF_N -> "8002" Comparing "7461" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7462" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757026 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761299 ATOM PAIRS WERE FOUND FOR ATOM LIST 41709 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29715 from a total of 761299 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7462 -79.75201 8.96678 0.70881 INTE EXTERN> -25.72372 -54.02829 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.752" Parameter: A <- "-79.752" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7237" Parameter: B <- "-25.7237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0283" Parameter: C <- "-54.0283" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7462 TOTAL ENERGY = -79.752 RDTITL> * VAN DER WAALS = -25.7237 ELECTROSTATIC = -54.0283 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7462" Parameter: CONF_N -> "8002" Comparing "7462" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7463" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761299 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758024 ATOM PAIRS WERE FOUND FOR ATOM LIST 41652 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29726 from a total of 758024 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7463 -63.79786 -15.95416 0.64619 INTE EXTERN> -23.14403 -40.65383 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.7979" Parameter: A <- "-63.7979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.144" Parameter: B <- "-23.144" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6538" Parameter: C <- "-40.6538" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7463 TOTAL ENERGY = -63.7979 RDTITL> * VAN DER WAALS = -23.144 ELECTROSTATIC = -40.6538 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7463" Parameter: CONF_N -> "8002" Comparing "7463" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7464" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758024 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755224 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30180 from a total of 755224 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7464 -72.01097 8.21311 0.67584 INTE EXTERN> -25.67054 -46.34043 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.011" Parameter: A <- "-72.011" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6705" Parameter: B <- "-25.6705" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3404" Parameter: C <- "-46.3404" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7464 TOTAL ENERGY = -72.011 RDTITL> * VAN DER WAALS = -25.6705 ELECTROSTATIC = -46.3404 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7464" Parameter: CONF_N -> "8002" Comparing "7464" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7465" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755224 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753946 ATOM PAIRS WERE FOUND FOR ATOM LIST 41249 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29719 from a total of 753946 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7465 -62.28860 -9.72237 0.58849 INTE EXTERN> -26.18814 -36.10046 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.2886" Parameter: A <- "-62.2886" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1881" Parameter: B <- "-26.1881" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1005" Parameter: C <- "-36.1005" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7465 TOTAL ENERGY = -62.2886 RDTITL> * VAN DER WAALS = -26.1881 ELECTROSTATIC = -36.1005 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7465" Parameter: CONF_N -> "8002" Comparing "7465" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7466" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753946 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755913 ATOM PAIRS WERE FOUND FOR ATOM LIST 41162 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29692 from a total of 755913 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7466 -68.41640 6.12780 0.68663 INTE EXTERN> -25.85868 -42.55772 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4164" Parameter: A <- "-68.4164" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8587" Parameter: B <- "-25.8587" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5577" Parameter: C <- "-42.5577" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7466 TOTAL ENERGY = -68.4164 RDTITL> * VAN DER WAALS = -25.8587 ELECTROSTATIC = -42.5577 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7466" Parameter: CONF_N -> "8002" Comparing "7466" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7467" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755913 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751443 ATOM PAIRS WERE FOUND FOR ATOM LIST 41110 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29770 from a total of 751443 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7467 -64.96250 -3.45391 0.74255 INTE EXTERN> -23.48787 -41.47462 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9625" Parameter: A <- "-64.9625" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4879" Parameter: B <- "-23.4879" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4746" Parameter: C <- "-41.4746" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7467 TOTAL ENERGY = -64.9625 RDTITL> * VAN DER WAALS = -23.4879 ELECTROSTATIC = -41.4746 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7467" Parameter: CONF_N -> "8002" Comparing "7467" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7468" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751443 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748673 ATOM PAIRS WERE FOUND FOR ATOM LIST 40932 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29398 from a total of 748673 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7468 -68.84756 3.88506 0.63019 INTE EXTERN> -27.20771 -41.63985 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8476" Parameter: A <- "-68.8476" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2077" Parameter: B <- "-27.2077" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6398" Parameter: C <- "-41.6398" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7468 TOTAL ENERGY = -68.8476 RDTITL> * VAN DER WAALS = -27.2077 ELECTROSTATIC = -41.6398 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7468" Parameter: CONF_N -> "8002" Comparing "7468" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7469" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748673 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750959 ATOM PAIRS WERE FOUND FOR ATOM LIST 41122 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29895 from a total of 750959 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7469 -67.16632 -1.68123 0.67187 INTE EXTERN> -25.43340 -41.73292 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1663" Parameter: A <- "-67.1663" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4334" Parameter: B <- "-25.4334" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7329" Parameter: C <- "-41.7329" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7469 TOTAL ENERGY = -67.1663 RDTITL> * VAN DER WAALS = -25.4334 ELECTROSTATIC = -41.7329 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7469" Parameter: CONF_N -> "8002" Comparing "7469" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7470" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750959 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751060 ATOM PAIRS WERE FOUND FOR ATOM LIST 41079 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29539 from a total of 751060 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7470 -66.98374 -0.18258 0.72997 INTE EXTERN> -24.52413 -42.45961 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9837" Parameter: A <- "-66.9837" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5241" Parameter: B <- "-24.5241" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4596" Parameter: C <- "-42.4596" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7470 TOTAL ENERGY = -66.9837 RDTITL> * VAN DER WAALS = -24.5241 ELECTROSTATIC = -42.4596 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7470" Parameter: CONF_N -> "8002" Comparing "7470" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7471" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751060 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751650 ATOM PAIRS WERE FOUND FOR ATOM LIST 41078 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29995 from a total of 751650 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7471 -74.51566 7.53192 0.67020 INTE EXTERN> -26.70715 -47.80851 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5157" Parameter: A <- "-74.5157" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7072" Parameter: B <- "-26.7072" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8085" Parameter: C <- "-47.8085" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7471 TOTAL ENERGY = -74.5157 RDTITL> * VAN DER WAALS = -26.7072 ELECTROSTATIC = -47.8085 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7471" Parameter: CONF_N -> "8002" Comparing "7471" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7472" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751650 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749656 ATOM PAIRS WERE FOUND FOR ATOM LIST 41012 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29868 from a total of 749656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7472 -75.84299 1.32733 0.70063 INTE EXTERN> -26.56676 -49.27624 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.843" Parameter: A <- "-75.843" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5668" Parameter: B <- "-26.5668" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2762" Parameter: C <- "-49.2762" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7472 TOTAL ENERGY = -75.843 RDTITL> * VAN DER WAALS = -26.5668 ELECTROSTATIC = -49.2762 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7472" Parameter: CONF_N -> "8002" Comparing "7472" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7473" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748007 ATOM PAIRS WERE FOUND FOR ATOM LIST 41192 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29672 from a total of 748007 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7473 -66.93468 -8.90832 0.70425 INTE EXTERN> -25.91572 -41.01895 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9347" Parameter: A <- "-66.9347" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9157" Parameter: B <- "-25.9157" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.019" Parameter: C <- "-41.019" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7473 TOTAL ENERGY = -66.9347 RDTITL> * VAN DER WAALS = -25.9157 ELECTROSTATIC = -41.019 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7473" Parameter: CONF_N -> "8002" Comparing "7473" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7474" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748007 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752501 ATOM PAIRS WERE FOUND FOR ATOM LIST 41146 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29598 from a total of 752501 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7474 -71.45614 4.52146 0.70121 INTE EXTERN> -24.57547 -46.88067 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4561" Parameter: A <- "-71.4561" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5755" Parameter: B <- "-24.5755" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8807" Parameter: C <- "-46.8807" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7474 TOTAL ENERGY = -71.4561 RDTITL> * VAN DER WAALS = -24.5755 ELECTROSTATIC = -46.8807 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7474" Parameter: CONF_N -> "8002" Comparing "7474" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7475" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752501 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754489 ATOM PAIRS WERE FOUND FOR ATOM LIST 41160 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29651 from a total of 754489 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7475 -68.93997 -2.51617 0.63752 INTE EXTERN> -25.47128 -43.46869 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.94" Parameter: A <- "-68.94" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4713" Parameter: B <- "-25.4713" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4687" Parameter: C <- "-43.4687" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7475 TOTAL ENERGY = -68.94 RDTITL> * VAN DER WAALS = -25.4713 ELECTROSTATIC = -43.4687 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7475" Parameter: CONF_N -> "8002" Comparing "7475" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7476" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754489 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747283 ATOM PAIRS WERE FOUND FOR ATOM LIST 40925 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29682 from a total of 747283 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7476 -68.61338 -0.32659 0.64011 INTE EXTERN> -27.22449 -41.38889 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6134" Parameter: A <- "-68.6134" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2245" Parameter: B <- "-27.2245" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3889" Parameter: C <- "-41.3889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7476 TOTAL ENERGY = -68.6134 RDTITL> * VAN DER WAALS = -27.2245 ELECTROSTATIC = -41.3889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7476" Parameter: CONF_N -> "8002" Comparing "7476" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7477" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747283 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749777 ATOM PAIRS WERE FOUND FOR ATOM LIST 41120 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29180 from a total of 749777 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7477 -61.49603 -7.11735 0.53729 INTE EXTERN> -29.78357 -31.71246 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.496" Parameter: A <- "-61.496" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7836" Parameter: B <- "-29.7836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.7125" Parameter: C <- "-31.7125" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7477 TOTAL ENERGY = -61.496 RDTITL> * VAN DER WAALS = -29.7836 ELECTROSTATIC = -31.7125 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7477" Parameter: CONF_N -> "8002" Comparing "7477" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7478" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749777 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753439 ATOM PAIRS WERE FOUND FOR ATOM LIST 41261 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29290 from a total of 753439 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7478 -65.57176 4.07573 0.67836 INTE EXTERN> -25.73130 -39.84047 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.5718" Parameter: A <- "-65.5718" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7313" Parameter: B <- "-25.7313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8405" Parameter: C <- "-39.8405" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7478 TOTAL ENERGY = -65.5718 RDTITL> * VAN DER WAALS = -25.7313 ELECTROSTATIC = -39.8405 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7478" Parameter: CONF_N -> "8002" Comparing "7478" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7479" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753439 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753516 ATOM PAIRS WERE FOUND FOR ATOM LIST 41380 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29961 from a total of 753516 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7479 -70.75049 5.17873 0.58316 INTE EXTERN> -28.83623 -41.91426 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7505" Parameter: A <- "-70.7505" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8362" Parameter: B <- "-28.8362" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9143" Parameter: C <- "-41.9143" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7479 TOTAL ENERGY = -70.7505 RDTITL> * VAN DER WAALS = -28.8362 ELECTROSTATIC = -41.9143 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7479" Parameter: CONF_N -> "8002" Comparing "7479" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7480" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753516 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746732 ATOM PAIRS WERE FOUND FOR ATOM LIST 41076 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29722 from a total of 746732 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7480 -64.23258 -6.51791 0.60346 INTE EXTERN> -28.13259 -36.09999 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2326" Parameter: A <- "-64.2326" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1326" Parameter: B <- "-28.1326" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.1" Parameter: C <- "-36.1" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7480 TOTAL ENERGY = -64.2326 RDTITL> * VAN DER WAALS = -28.1326 ELECTROSTATIC = -36.1 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7480" Parameter: CONF_N -> "8002" Comparing "7480" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7481" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746732 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754334 ATOM PAIRS WERE FOUND FOR ATOM LIST 41626 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29849 from a total of 754334 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7481 -67.09767 2.86509 0.63719 INTE EXTERN> -27.38196 -39.71571 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0977" Parameter: A <- "-67.0977" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.382" Parameter: B <- "-27.382" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7157" Parameter: C <- "-39.7157" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7481 TOTAL ENERGY = -67.0977 RDTITL> * VAN DER WAALS = -27.382 ELECTROSTATIC = -39.7157 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7481" Parameter: CONF_N -> "8002" Comparing "7481" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7482" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754334 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747390 ATOM PAIRS WERE FOUND FOR ATOM LIST 41021 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29474 from a total of 747390 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7482 -67.35205 0.25438 0.77683 INTE EXTERN> -22.74424 -44.60781 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.3521" Parameter: A <- "-67.3521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.7442" Parameter: B <- "-22.7442" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6078" Parameter: C <- "-44.6078" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7482 TOTAL ENERGY = -67.3521 RDTITL> * VAN DER WAALS = -22.7442 ELECTROSTATIC = -44.6078 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7482" Parameter: CONF_N -> "8002" Comparing "7482" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7483" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747390 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748583 ATOM PAIRS WERE FOUND FOR ATOM LIST 41141 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30116 from a total of 748583 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7483 -59.40963 -7.94242 0.61441 INTE EXTERN> -29.08753 -30.32210 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-59.4096" Parameter: A <- "-59.4096" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0875" Parameter: B <- "-29.0875" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-30.3221" Parameter: C <- "-30.3221" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7483 TOTAL ENERGY = -59.4096 RDTITL> * VAN DER WAALS = -29.0875 ELECTROSTATIC = -30.3221 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7483" Parameter: CONF_N -> "8002" Comparing "7483" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7484" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748583 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754416 ATOM PAIRS WERE FOUND FOR ATOM LIST 41222 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30139 from a total of 754416 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7484 -62.90086 3.49123 0.58986 INTE EXTERN> -29.76649 -33.13436 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-62.9009" Parameter: A <- "-62.9009" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7665" Parameter: B <- "-29.7665" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-33.1344" Parameter: C <- "-33.1344" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7484 TOTAL ENERGY = -62.9009 RDTITL> * VAN DER WAALS = -29.7665 ELECTROSTATIC = -33.1344 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7484" Parameter: CONF_N -> "8002" Comparing "7484" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7485" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754416 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752066 ATOM PAIRS WERE FOUND FOR ATOM LIST 41082 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29838 from a total of 752066 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7485 -66.76094 3.86008 0.70315 INTE EXTERN> -25.23421 -41.52673 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7609" Parameter: A <- "-66.7609" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2342" Parameter: B <- "-25.2342" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5267" Parameter: C <- "-41.5267" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7485 TOTAL ENERGY = -66.7609 RDTITL> * VAN DER WAALS = -25.2342 ELECTROSTATIC = -41.5267 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7485" Parameter: CONF_N -> "8002" Comparing "7485" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7486" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752066 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753045 ATOM PAIRS WERE FOUND FOR ATOM LIST 41218 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29782 from a total of 753045 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7486 -67.94428 1.18334 0.54044 INTE EXTERN> -30.83872 -37.10556 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.9443" Parameter: A <- "-67.9443" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8387" Parameter: B <- "-30.8387" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.1056" Parameter: C <- "-37.1056" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7486 TOTAL ENERGY = -67.9443 RDTITL> * VAN DER WAALS = -30.8387 ELECTROSTATIC = -37.1056 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7486" Parameter: CONF_N -> "8002" Comparing "7486" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7487" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753045 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748971 ATOM PAIRS WERE FOUND FOR ATOM LIST 40952 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29986 from a total of 748971 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7487 -69.19531 1.25104 0.70932 INTE EXTERN> -25.61477 -43.58054 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1953" Parameter: A <- "-69.1953" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6148" Parameter: B <- "-25.6148" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5805" Parameter: C <- "-43.5805" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7487 TOTAL ENERGY = -69.1953 RDTITL> * VAN DER WAALS = -25.6148 ELECTROSTATIC = -43.5805 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7487" Parameter: CONF_N -> "8002" Comparing "7487" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7488" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748971 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753174 ATOM PAIRS WERE FOUND FOR ATOM LIST 41158 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29835 from a total of 753174 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7488 -66.25365 -2.94167 0.64335 INTE EXTERN> -27.88961 -38.36403 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2536" Parameter: A <- "-66.2536" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8896" Parameter: B <- "-27.8896" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.364" Parameter: C <- "-38.364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7488 TOTAL ENERGY = -66.2536 RDTITL> * VAN DER WAALS = -27.8896 ELECTROSTATIC = -38.364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7488" Parameter: CONF_N -> "8002" Comparing "7488" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7489" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753174 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757350 ATOM PAIRS WERE FOUND FOR ATOM LIST 41454 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30139 from a total of 757350 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7489 -66.05205 -0.20159 0.64592 INTE EXTERN> -25.48792 -40.56413 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0521" Parameter: A <- "-66.0521" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4879" Parameter: B <- "-25.4879" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5641" Parameter: C <- "-40.5641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7489 TOTAL ENERGY = -66.0521 RDTITL> * VAN DER WAALS = -25.4879 ELECTROSTATIC = -40.5641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7489" Parameter: CONF_N -> "8002" Comparing "7489" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7490" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757350 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752374 ATOM PAIRS WERE FOUND FOR ATOM LIST 41074 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29707 from a total of 752374 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7490 -71.27537 5.22332 0.86754 INTE EXTERN> -21.37496 -49.90042 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2754" Parameter: A <- "-71.2754" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.375" Parameter: B <- "-21.375" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9004" Parameter: C <- "-49.9004" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7490 TOTAL ENERGY = -71.2754 RDTITL> * VAN DER WAALS = -21.375 ELECTROSTATIC = -49.9004 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7490" Parameter: CONF_N -> "8002" Comparing "7490" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7491" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752374 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752550 ATOM PAIRS WERE FOUND FOR ATOM LIST 41054 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29364 from a total of 752550 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7491 -61.84338 -9.43200 0.58171 INTE EXTERN> -26.75337 -35.09000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-61.8434" Parameter: A <- "-61.8434" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7534" Parameter: B <- "-26.7534" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.09" Parameter: C <- "-35.09" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7491 TOTAL ENERGY = -61.8434 RDTITL> * VAN DER WAALS = -26.7534 ELECTROSTATIC = -35.09 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7491" Parameter: CONF_N -> "8002" Comparing "7491" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7492" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752550 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753462 ATOM PAIRS WERE FOUND FOR ATOM LIST 41137 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29504 from a total of 753462 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7492 -71.52397 9.68059 0.72599 INTE EXTERN> -23.54957 -47.97440 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.524" Parameter: A <- "-71.524" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.5496" Parameter: B <- "-23.5496" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9744" Parameter: C <- "-47.9744" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7492 TOTAL ENERGY = -71.524 RDTITL> * VAN DER WAALS = -23.5496 ELECTROSTATIC = -47.9744 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7492" Parameter: CONF_N -> "8002" Comparing "7492" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7493" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753462 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747179 ATOM PAIRS WERE FOUND FOR ATOM LIST 40869 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28849 from a total of 747179 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7493 -68.27237 -3.25160 0.68760 INTE EXTERN> -24.53316 -43.73921 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2724" Parameter: A <- "-68.2724" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5332" Parameter: B <- "-24.5332" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7392" Parameter: C <- "-43.7392" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7493 TOTAL ENERGY = -68.2724 RDTITL> * VAN DER WAALS = -24.5332 ELECTROSTATIC = -43.7392 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7493" Parameter: CONF_N -> "8002" Comparing "7493" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7494" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747179 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751817 ATOM PAIRS WERE FOUND FOR ATOM LIST 41006 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29835 from a total of 751817 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7494 -74.93000 6.65763 0.77571 INTE EXTERN> -24.77532 -50.15468 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.93" Parameter: A <- "-74.93" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7753" Parameter: B <- "-24.7753" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1547" Parameter: C <- "-50.1547" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7494 TOTAL ENERGY = -74.93 RDTITL> * VAN DER WAALS = -24.7753 ELECTROSTATIC = -50.1547 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7494" Parameter: CONF_N -> "8002" Comparing "7494" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7495" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751817 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751581 ATOM PAIRS WERE FOUND FOR ATOM LIST 41011 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29760 from a total of 751581 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7495 -73.06115 -1.86885 0.75119 INTE EXTERN> -24.15636 -48.90479 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0612" Parameter: A <- "-73.0612" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1564" Parameter: B <- "-24.1564" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9048" Parameter: C <- "-48.9048" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7495 TOTAL ENERGY = -73.0612 RDTITL> * VAN DER WAALS = -24.1564 ELECTROSTATIC = -48.9048 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7495" Parameter: CONF_N -> "8002" Comparing "7495" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7496" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751581 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752640 ATOM PAIRS WERE FOUND FOR ATOM LIST 41272 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30057 from a total of 752640 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7496 -80.10725 7.04610 0.72969 INTE EXTERN> -26.73616 -53.37109 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1073" Parameter: A <- "-80.1073" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7362" Parameter: B <- "-26.7362" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.3711" Parameter: C <- "-53.3711" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7496 TOTAL ENERGY = -80.1073 RDTITL> * VAN DER WAALS = -26.7362 ELECTROSTATIC = -53.3711 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7496" Parameter: CONF_N -> "8002" Comparing "7496" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7497" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752640 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750891 ATOM PAIRS WERE FOUND FOR ATOM LIST 41035 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30160 from a total of 750891 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7497 -72.02563 -8.08162 0.71442 INTE EXTERN> -23.32435 -48.70128 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0256" Parameter: A <- "-72.0256" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.3244" Parameter: B <- "-23.3244" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7013" Parameter: C <- "-48.7013" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7497 TOTAL ENERGY = -72.0256 RDTITL> * VAN DER WAALS = -23.3244 ELECTROSTATIC = -48.7013 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7497" Parameter: CONF_N -> "8002" Comparing "7497" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7498" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750891 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749669 ATOM PAIRS WERE FOUND FOR ATOM LIST 41009 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29651 from a total of 749669 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7498 -74.68354 2.65791 0.70772 INTE EXTERN> -25.84488 -48.83866 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6835" Parameter: A <- "-74.6835" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8449" Parameter: B <- "-25.8449" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8387" Parameter: C <- "-48.8387" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7498 TOTAL ENERGY = -74.6835 RDTITL> * VAN DER WAALS = -25.8449 ELECTROSTATIC = -48.8387 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7498" Parameter: CONF_N -> "8002" Comparing "7498" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7499" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749669 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755384 ATOM PAIRS WERE FOUND FOR ATOM LIST 41197 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29679 from a total of 755384 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7499 -69.55348 -5.13006 0.80786 INTE EXTERN> -21.76440 -47.78908 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.5535" Parameter: A <- "-69.5535" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.7644" Parameter: B <- "-21.7644" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7891" Parameter: C <- "-47.7891" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7499 TOTAL ENERGY = -69.5535 RDTITL> * VAN DER WAALS = -21.7644 ELECTROSTATIC = -47.7891 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7499" Parameter: CONF_N -> "8002" Comparing "7499" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7500" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755384 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752910 ATOM PAIRS WERE FOUND FOR ATOM LIST 41267 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30151 from a total of 752910 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7500 -71.00830 1.45483 0.59397 INTE EXTERN> -30.02863 -40.97967 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0083" Parameter: A <- "-71.0083" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0286" Parameter: B <- "-30.0286" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9797" Parameter: C <- "-40.9797" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7500 TOTAL ENERGY = -71.0083 RDTITL> * VAN DER WAALS = -30.0286 ELECTROSTATIC = -40.9797 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7500" Parameter: CONF_N -> "8002" Comparing "7500" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7501" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752910 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41132 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29248 from a total of 751422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7501 -73.87984 2.87154 0.61026 INTE EXTERN> -27.47396 -46.40588 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8798" Parameter: A <- "-73.8798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.474" Parameter: B <- "-27.474" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4059" Parameter: C <- "-46.4059" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7501 TOTAL ENERGY = -73.8798 RDTITL> * VAN DER WAALS = -27.474 ELECTROSTATIC = -46.4059 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7501" Parameter: CONF_N -> "8002" Comparing "7501" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7502" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750195 ATOM PAIRS WERE FOUND FOR ATOM LIST 40888 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29695 from a total of 750195 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7502 -74.59309 0.71324 0.68940 INTE EXTERN> -26.50964 -48.08345 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5931" Parameter: A <- "-74.5931" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5096" Parameter: B <- "-26.5096" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0834" Parameter: C <- "-48.0834" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7502 TOTAL ENERGY = -74.5931 RDTITL> * VAN DER WAALS = -26.5096 ELECTROSTATIC = -48.0834 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7502" Parameter: CONF_N -> "8002" Comparing "7502" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7503" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750195 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753130 ATOM PAIRS WERE FOUND FOR ATOM LIST 41110 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30026 from a total of 753130 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7503 -75.40148 0.80839 0.64428 INTE EXTERN> -28.36458 -47.03690 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4015" Parameter: A <- "-75.4015" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3646" Parameter: B <- "-28.3646" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0369" Parameter: C <- "-47.0369" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7503 TOTAL ENERGY = -75.4015 RDTITL> * VAN DER WAALS = -28.3646 ELECTROSTATIC = -47.0369 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7503" Parameter: CONF_N -> "8002" Comparing "7503" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7504" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753130 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753358 ATOM PAIRS WERE FOUND FOR ATOM LIST 41252 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29978 from a total of 753358 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7504 -73.06876 -2.33272 0.57725 INTE EXTERN> -30.60658 -42.46218 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0688" Parameter: A <- "-73.0688" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6066" Parameter: B <- "-30.6066" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4622" Parameter: C <- "-42.4622" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7504 TOTAL ENERGY = -73.0688 RDTITL> * VAN DER WAALS = -30.6066 ELECTROSTATIC = -42.4622 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7504" Parameter: CONF_N -> "8002" Comparing "7504" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7505" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753358 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750698 ATOM PAIRS WERE FOUND FOR ATOM LIST 41132 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29841 from a total of 750698 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7505 -70.27494 -2.79382 0.70073 INTE EXTERN> -24.78600 -45.48893 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2749" Parameter: A <- "-70.2749" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.786" Parameter: B <- "-24.786" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4889" Parameter: C <- "-45.4889" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7505 TOTAL ENERGY = -70.2749 RDTITL> * VAN DER WAALS = -24.786 ELECTROSTATIC = -45.4889 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7505" Parameter: CONF_N -> "8002" Comparing "7505" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7506" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750698 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754052 ATOM PAIRS WERE FOUND FOR ATOM LIST 41335 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29665 from a total of 754052 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7506 -63.94824 -6.32670 0.57075 INTE EXTERN> -29.63329 -34.31494 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.9482" Parameter: A <- "-63.9482" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6333" Parameter: B <- "-29.6333" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.3149" Parameter: C <- "-34.3149" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7506 TOTAL ENERGY = -63.9482 RDTITL> * VAN DER WAALS = -29.6333 ELECTROSTATIC = -34.3149 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7506" Parameter: CONF_N -> "8002" Comparing "7506" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7507" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754052 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760776 ATOM PAIRS WERE FOUND FOR ATOM LIST 41475 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30823 from a total of 760776 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7507 -71.34195 7.39372 0.74043 INTE EXTERN> -24.65858 -46.68337 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.342" Parameter: A <- "-71.342" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6586" Parameter: B <- "-24.6586" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6834" Parameter: C <- "-46.6834" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7507 TOTAL ENERGY = -71.342 RDTITL> * VAN DER WAALS = -24.6586 ELECTROSTATIC = -46.6834 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7507" Parameter: CONF_N -> "8002" Comparing "7507" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7508" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760776 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753509 ATOM PAIRS WERE FOUND FOR ATOM LIST 41208 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29921 from a total of 753509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7508 -71.87744 0.53549 0.68845 INTE EXTERN> -26.62860 -45.24884 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8774" Parameter: A <- "-71.8774" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6286" Parameter: B <- "-26.6286" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2488" Parameter: C <- "-45.2488" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7508 TOTAL ENERGY = -71.8774 RDTITL> * VAN DER WAALS = -26.6286 ELECTROSTATIC = -45.2488 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7508" Parameter: CONF_N -> "8002" Comparing "7508" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7509" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753773 ATOM PAIRS WERE FOUND FOR ATOM LIST 41276 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30516 from a total of 753773 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7509 -73.34182 1.46438 0.77901 INTE EXTERN> -23.73114 -49.61068 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3418" Parameter: A <- "-73.3418" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7311" Parameter: B <- "-23.7311" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6107" Parameter: C <- "-49.6107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7509 TOTAL ENERGY = -73.3418 RDTITL> * VAN DER WAALS = -23.7311 ELECTROSTATIC = -49.6107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7509" Parameter: CONF_N -> "8002" Comparing "7509" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7510" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753773 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756899 ATOM PAIRS WERE FOUND FOR ATOM LIST 41315 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30517 from a total of 756899 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7510 -65.84096 -7.50086 0.60113 INTE EXTERN> -27.88691 -37.95405 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.841" Parameter: A <- "-65.841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8869" Parameter: B <- "-27.8869" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.9541" Parameter: C <- "-37.9541" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7510 TOTAL ENERGY = -65.841 RDTITL> * VAN DER WAALS = -27.8869 ELECTROSTATIC = -37.9541 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7510" Parameter: CONF_N -> "8002" Comparing "7510" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7511" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756899 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754520 ATOM PAIRS WERE FOUND FOR ATOM LIST 41324 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30504 from a total of 754520 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7511 -71.97268 6.13172 0.56389 INTE EXTERN> -32.65280 -39.31988 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.9727" Parameter: A <- "-71.9727" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6528" Parameter: B <- "-32.6528" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3199" Parameter: C <- "-39.3199" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7511 TOTAL ENERGY = -71.9727 RDTITL> * VAN DER WAALS = -32.6528 ELECTROSTATIC = -39.3199 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7511" Parameter: CONF_N -> "8002" Comparing "7511" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7512" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754520 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753273 ATOM PAIRS WERE FOUND FOR ATOM LIST 41296 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30345 from a total of 753273 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7512 -71.11583 -0.85685 0.64338 INTE EXTERN> -27.99184 -43.12399 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1158" Parameter: A <- "-71.1158" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9918" Parameter: B <- "-27.9918" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.124" Parameter: C <- "-43.124" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7512 TOTAL ENERGY = -71.1158 RDTITL> * VAN DER WAALS = -27.9918 ELECTROSTATIC = -43.124 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7512" Parameter: CONF_N -> "8002" Comparing "7512" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7513" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753273 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746526 ATOM PAIRS WERE FOUND FOR ATOM LIST 40834 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29904 from a total of 746526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7513 -73.72563 2.60979 0.61686 INTE EXTERN> -29.80827 -43.91736 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7256" Parameter: A <- "-73.7256" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8083" Parameter: B <- "-29.8083" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9174" Parameter: C <- "-43.9174" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7513 TOTAL ENERGY = -73.7256 RDTITL> * VAN DER WAALS = -29.8083 ELECTROSTATIC = -43.9174 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7513" Parameter: CONF_N -> "8002" Comparing "7513" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7514" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747076 ATOM PAIRS WERE FOUND FOR ATOM LIST 40917 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29393 from a total of 747076 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7514 -68.28411 -5.44151 0.52082 INTE EXTERN> -32.34796 -35.93615 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2841" Parameter: A <- "-68.2841" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.348" Parameter: B <- "-32.348" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.9362" Parameter: C <- "-35.9362" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7514 TOTAL ENERGY = -68.2841 RDTITL> * VAN DER WAALS = -32.348 ELECTROSTATIC = -35.9362 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7514" Parameter: CONF_N -> "8002" Comparing "7514" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7515" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747076 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755926 ATOM PAIRS WERE FOUND FOR ATOM LIST 41277 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30099 from a total of 755926 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7515 -69.61223 1.32811 0.70825 INTE EXTERN> -22.86797 -46.74426 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6122" Parameter: A <- "-69.6122" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.868" Parameter: B <- "-22.868" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7443" Parameter: C <- "-46.7443" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7515 TOTAL ENERGY = -69.6122 RDTITL> * VAN DER WAALS = -22.868 ELECTROSTATIC = -46.7443 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7515" Parameter: CONF_N -> "8002" Comparing "7515" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7516" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755926 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754011 ATOM PAIRS WERE FOUND FOR ATOM LIST 41187 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30552 from a total of 754011 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7516 -64.21051 -5.40172 0.72036 INTE EXTERN> -25.81849 -38.39202 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.2105" Parameter: A <- "-64.2105" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8185" Parameter: B <- "-25.8185" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.392" Parameter: C <- "-38.392" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7516 TOTAL ENERGY = -64.2105 RDTITL> * VAN DER WAALS = -25.8185 ELECTROSTATIC = -38.392 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7516" Parameter: CONF_N -> "8002" Comparing "7516" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7517" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754011 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751349 ATOM PAIRS WERE FOUND FOR ATOM LIST 41078 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29561 from a total of 751349 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7517 -64.57338 0.36287 0.59174 INTE EXTERN> -29.05608 -35.51730 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.5734" Parameter: A <- "-64.5734" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0561" Parameter: B <- "-29.0561" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5173" Parameter: C <- "-35.5173" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7517 TOTAL ENERGY = -64.5734 RDTITL> * VAN DER WAALS = -29.0561 ELECTROSTATIC = -35.5173 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7517" Parameter: CONF_N -> "8002" Comparing "7517" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7518" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751349 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755962 ATOM PAIRS WERE FOUND FOR ATOM LIST 41483 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30151 from a total of 755962 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7518 -71.21383 6.64045 0.71517 INTE EXTERN> -26.65541 -44.55842 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2138" Parameter: A <- "-71.2138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6554" Parameter: B <- "-26.6554" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5584" Parameter: C <- "-44.5584" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7518 TOTAL ENERGY = -71.2138 RDTITL> * VAN DER WAALS = -26.6554 ELECTROSTATIC = -44.5584 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7518" Parameter: CONF_N -> "8002" Comparing "7518" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7519" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755962 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754066 ATOM PAIRS WERE FOUND FOR ATOM LIST 41428 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30238 from a total of 754066 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7519 -71.24824 0.03441 0.67370 INTE EXTERN> -25.93088 -45.31736 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2482" Parameter: A <- "-71.2482" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9309" Parameter: B <- "-25.9309" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3174" Parameter: C <- "-45.3174" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7519 TOTAL ENERGY = -71.2482 RDTITL> * VAN DER WAALS = -25.9309 ELECTROSTATIC = -45.3174 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7519" Parameter: CONF_N -> "8002" Comparing "7519" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7520" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754066 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752483 ATOM PAIRS WERE FOUND FOR ATOM LIST 41310 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29616 from a total of 752483 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7520 -71.52482 0.27657 0.56152 INTE EXTERN> -29.56805 -41.95676 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5248" Parameter: A <- "-71.5248" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5681" Parameter: B <- "-29.5681" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.9568" Parameter: C <- "-41.9568" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7520 TOTAL ENERGY = -71.5248 RDTITL> * VAN DER WAALS = -29.5681 ELECTROSTATIC = -41.9568 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7520" Parameter: CONF_N -> "8002" Comparing "7520" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7521" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752483 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748577 ATOM PAIRS WERE FOUND FOR ATOM LIST 41025 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29848 from a total of 748577 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7521 -72.32608 0.80127 0.68004 INTE EXTERN> -28.57829 -43.74780 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3261" Parameter: A <- "-72.3261" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5783" Parameter: B <- "-28.5783" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7478" Parameter: C <- "-43.7478" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7521 TOTAL ENERGY = -72.3261 RDTITL> * VAN DER WAALS = -28.5783 ELECTROSTATIC = -43.7478 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7521" Parameter: CONF_N -> "8002" Comparing "7521" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7522" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748577 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752703 ATOM PAIRS WERE FOUND FOR ATOM LIST 41253 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29853 from a total of 752703 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7522 -73.88097 1.55489 0.71051 INTE EXTERN> -27.44458 -46.43639 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.881" Parameter: A <- "-73.881" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4446" Parameter: B <- "-27.4446" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4364" Parameter: C <- "-46.4364" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7522 TOTAL ENERGY = -73.881 RDTITL> * VAN DER WAALS = -27.4446 ELECTROSTATIC = -46.4364 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7522" Parameter: CONF_N -> "8002" Comparing "7522" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7523" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752703 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755880 ATOM PAIRS WERE FOUND FOR ATOM LIST 41189 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30014 from a total of 755880 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7523 -65.44374 -8.43724 0.61799 INTE EXTERN> -30.50646 -34.93727 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4437" Parameter: A <- "-65.4437" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5065" Parameter: B <- "-30.5065" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9373" Parameter: C <- "-34.9373" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7523 TOTAL ENERGY = -65.4437 RDTITL> * VAN DER WAALS = -30.5065 ELECTROSTATIC = -34.9373 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7523" Parameter: CONF_N -> "8002" Comparing "7523" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7524" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755880 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748547 ATOM PAIRS WERE FOUND FOR ATOM LIST 41028 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29497 from a total of 748547 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7524 -75.64009 10.19635 0.62662 INTE EXTERN> -29.86902 -45.77107 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6401" Parameter: A <- "-75.6401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.869" Parameter: B <- "-29.869" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7711" Parameter: C <- "-45.7711" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7524 TOTAL ENERGY = -75.6401 RDTITL> * VAN DER WAALS = -29.869 ELECTROSTATIC = -45.7711 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7524" Parameter: CONF_N -> "8002" Comparing "7524" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7525" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748547 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752600 ATOM PAIRS WERE FOUND FOR ATOM LIST 41215 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29906 from a total of 752600 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7525 -65.15170 -10.48839 0.63704 INTE EXTERN> -28.19351 -36.95819 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1517" Parameter: A <- "-65.1517" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1935" Parameter: B <- "-28.1935" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.9582" Parameter: C <- "-36.9582" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7525 TOTAL ENERGY = -65.1517 RDTITL> * VAN DER WAALS = -28.1935 ELECTROSTATIC = -36.9582 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7525" Parameter: CONF_N -> "8002" Comparing "7525" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7526" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752600 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755336 ATOM PAIRS WERE FOUND FOR ATOM LIST 41388 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30361 from a total of 755336 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7526 -65.16019 0.00848 0.64298 INTE EXTERN> -27.69051 -37.46967 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1602" Parameter: A <- "-65.1602" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6905" Parameter: B <- "-27.6905" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.4697" Parameter: C <- "-37.4697" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7526 TOTAL ENERGY = -65.1602 RDTITL> * VAN DER WAALS = -27.6905 ELECTROSTATIC = -37.4697 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7526" Parameter: CONF_N -> "8002" Comparing "7526" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7527" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755336 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757654 ATOM PAIRS WERE FOUND FOR ATOM LIST 41299 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30286 from a total of 757654 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7527 -71.43551 6.27533 0.60870 INTE EXTERN> -29.89614 -41.53937 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4355" Parameter: A <- "-71.4355" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8961" Parameter: B <- "-29.8961" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5394" Parameter: C <- "-41.5394" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7527 TOTAL ENERGY = -71.4355 RDTITL> * VAN DER WAALS = -29.8961 ELECTROSTATIC = -41.5394 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7527" Parameter: CONF_N -> "8002" Comparing "7527" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7528" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757654 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759189 ATOM PAIRS WERE FOUND FOR ATOM LIST 41530 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30009 from a total of 759189 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7528 -72.25096 0.81545 0.64769 INTE EXTERN> -30.17180 -42.07916 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.251" Parameter: A <- "-72.251" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1718" Parameter: B <- "-30.1718" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0792" Parameter: C <- "-42.0792" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7528 TOTAL ENERGY = -72.251 RDTITL> * VAN DER WAALS = -30.1718 ELECTROSTATIC = -42.0792 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7528" Parameter: CONF_N -> "8002" Comparing "7528" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7529" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759189 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759966 ATOM PAIRS WERE FOUND FOR ATOM LIST 41588 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30228 from a total of 759966 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7529 -65.86160 -6.38936 0.64534 INTE EXTERN> -29.26297 -36.59864 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8616" Parameter: A <- "-65.8616" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.263" Parameter: B <- "-29.263" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.5986" Parameter: C <- "-36.5986" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7529 TOTAL ENERGY = -65.8616 RDTITL> * VAN DER WAALS = -29.263 ELECTROSTATIC = -36.5986 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7529" Parameter: CONF_N -> "8002" Comparing "7529" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7530" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759966 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759409 ATOM PAIRS WERE FOUND FOR ATOM LIST 41469 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30429 from a total of 759409 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7530 -66.23807 0.37647 0.66847 INTE EXTERN> -25.25283 -40.98524 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.2381" Parameter: A <- "-66.2381" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2528" Parameter: B <- "-25.2528" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9852" Parameter: C <- "-40.9852" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7530 TOTAL ENERGY = -66.2381 RDTITL> * VAN DER WAALS = -25.2528 ELECTROSTATIC = -40.9852 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7530" Parameter: CONF_N -> "8002" Comparing "7530" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7531" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759409 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756692 ATOM PAIRS WERE FOUND FOR ATOM LIST 41470 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30094 from a total of 756692 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7531 -71.62343 5.38536 0.77358 INTE EXTERN> -24.02563 -47.59780 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6234" Parameter: A <- "-71.6234" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0256" Parameter: B <- "-24.0256" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5978" Parameter: C <- "-47.5978" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7531 TOTAL ENERGY = -71.6234 RDTITL> * VAN DER WAALS = -24.0256 ELECTROSTATIC = -47.5978 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7531" Parameter: CONF_N -> "8002" Comparing "7531" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7532" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756692 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758067 ATOM PAIRS WERE FOUND FOR ATOM LIST 41337 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30633 from a total of 758067 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7532 -72.34990 0.72648 0.66360 INTE EXTERN> -25.89953 -46.45037 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.3499" Parameter: A <- "-72.3499" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8995" Parameter: B <- "-25.8995" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4504" Parameter: C <- "-46.4504" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7532 TOTAL ENERGY = -72.3499 RDTITL> * VAN DER WAALS = -25.8995 ELECTROSTATIC = -46.4504 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7532" Parameter: CONF_N -> "8002" Comparing "7532" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7533" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758067 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756134 ATOM PAIRS WERE FOUND FOR ATOM LIST 41427 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30279 from a total of 756134 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7533 -73.05273 0.70283 0.69214 INTE EXTERN> -25.29631 -47.75642 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0527" Parameter: A <- "-73.0527" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2963" Parameter: B <- "-25.2963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7564" Parameter: C <- "-47.7564" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7533 TOTAL ENERGY = -73.0527 RDTITL> * VAN DER WAALS = -25.2963 ELECTROSTATIC = -47.7564 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7533" Parameter: CONF_N -> "8002" Comparing "7533" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7534" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756134 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756360 ATOM PAIRS WERE FOUND FOR ATOM LIST 41709 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29958 from a total of 756360 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7534 -74.63686 1.58413 0.71399 INTE EXTERN> -25.13208 -49.50478 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6369" Parameter: A <- "-74.6369" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1321" Parameter: B <- "-25.1321" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5048" Parameter: C <- "-49.5048" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7534 TOTAL ENERGY = -74.6369 RDTITL> * VAN DER WAALS = -25.1321 ELECTROSTATIC = -49.5048 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7534" Parameter: CONF_N -> "8002" Comparing "7534" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7535" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756360 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750619 ATOM PAIRS WERE FOUND FOR ATOM LIST 40985 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30442 from a total of 750619 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7535 -74.57061 -0.06625 0.62984 INTE EXTERN> -29.79078 -44.77983 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5706" Parameter: A <- "-74.5706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7908" Parameter: B <- "-29.7908" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7798" Parameter: C <- "-44.7798" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7535 TOTAL ENERGY = -74.5706 RDTITL> * VAN DER WAALS = -29.7908 ELECTROSTATIC = -44.7798 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7535" Parameter: CONF_N -> "8002" Comparing "7535" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7536" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750619 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756042 ATOM PAIRS WERE FOUND FOR ATOM LIST 41514 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30343 from a total of 756042 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7536 -75.24413 0.67352 0.63922 INTE EXTERN> -29.89120 -45.35293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2441" Parameter: A <- "-75.2441" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8912" Parameter: B <- "-29.8912" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3529" Parameter: C <- "-45.3529" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7536 TOTAL ENERGY = -75.2441 RDTITL> * VAN DER WAALS = -29.8912 ELECTROSTATIC = -45.3529 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7536" Parameter: CONF_N -> "8002" Comparing "7536" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7537" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756042 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758327 ATOM PAIRS WERE FOUND FOR ATOM LIST 41522 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30550 from a total of 758327 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7537 -69.36373 -5.88040 0.65598 INTE EXTERN> -26.74098 -42.62276 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.3637" Parameter: A <- "-69.3637" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.741" Parameter: B <- "-26.741" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.6228" Parameter: C <- "-42.6228" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7537 TOTAL ENERGY = -69.3637 RDTITL> * VAN DER WAALS = -26.741 ELECTROSTATIC = -42.6228 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7537" Parameter: CONF_N -> "8002" Comparing "7537" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7538" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758327 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758694 ATOM PAIRS WERE FOUND FOR ATOM LIST 41450 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30322 from a total of 758694 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7538 -75.71988 6.35614 0.76233 INTE EXTERN> -25.18359 -50.53629 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7199" Parameter: A <- "-75.7199" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1836" Parameter: B <- "-25.1836" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5363" Parameter: C <- "-50.5363" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7538 TOTAL ENERGY = -75.7199 RDTITL> * VAN DER WAALS = -25.1836 ELECTROSTATIC = -50.5363 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7538" Parameter: CONF_N -> "8002" Comparing "7538" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7539" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758694 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755676 ATOM PAIRS WERE FOUND FOR ATOM LIST 41376 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29642 from a total of 755676 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7539 -76.05274 0.33286 0.61944 INTE EXTERN> -29.49471 -46.55803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0527" Parameter: A <- "-76.0527" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4947" Parameter: B <- "-29.4947" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.558" Parameter: C <- "-46.558" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7539 TOTAL ENERGY = -76.0527 RDTITL> * VAN DER WAALS = -29.4947 ELECTROSTATIC = -46.558 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7539" Parameter: CONF_N -> "8002" Comparing "7539" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7540" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755676 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754445 ATOM PAIRS WERE FOUND FOR ATOM LIST 41329 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29513 from a total of 754445 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7540 -77.43036 1.37762 0.69083 INTE EXTERN> -27.43164 -49.99872 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4304" Parameter: A <- "-77.4304" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4316" Parameter: B <- "-27.4316" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9987" Parameter: C <- "-49.9987" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7540 TOTAL ENERGY = -77.4304 RDTITL> * VAN DER WAALS = -27.4316 ELECTROSTATIC = -49.9987 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7540" Parameter: CONF_N -> "8002" Comparing "7540" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7541" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754445 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756107 ATOM PAIRS WERE FOUND FOR ATOM LIST 41366 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30085 from a total of 756107 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7541 -72.54972 -4.88064 0.74619 INTE EXTERN> -22.79216 -49.75756 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5497" Parameter: A <- "-72.5497" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.7922" Parameter: B <- "-22.7922" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7576" Parameter: C <- "-49.7576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7541 TOTAL ENERGY = -72.5497 RDTITL> * VAN DER WAALS = -22.7922 ELECTROSTATIC = -49.7576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7541" Parameter: CONF_N -> "8002" Comparing "7541" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7542" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756107 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752675 ATOM PAIRS WERE FOUND FOR ATOM LIST 41242 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30071 from a total of 752675 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7542 -73.60391 1.05419 0.65556 INTE EXTERN> -28.46906 -45.13485 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6039" Parameter: A <- "-73.6039" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4691" Parameter: B <- "-28.4691" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.1349" Parameter: C <- "-45.1349" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7542 TOTAL ENERGY = -73.6039 RDTITL> * VAN DER WAALS = -28.4691 ELECTROSTATIC = -45.1349 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7542" Parameter: CONF_N -> "8002" Comparing "7542" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7543" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752675 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753207 ATOM PAIRS WERE FOUND FOR ATOM LIST 41354 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30051 from a total of 753207 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7543 -71.42030 -2.18361 0.73549 INTE EXTERN> -26.88046 -44.53983 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4203" Parameter: A <- "-71.4203" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8805" Parameter: B <- "-26.8805" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5398" Parameter: C <- "-44.5398" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7543 TOTAL ENERGY = -71.4203 RDTITL> * VAN DER WAALS = -26.8805 ELECTROSTATIC = -44.5398 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7543" Parameter: CONF_N -> "8002" Comparing "7543" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7544" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753207 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752596 ATOM PAIRS WERE FOUND FOR ATOM LIST 41157 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29327 from a total of 752596 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7544 -69.60826 -1.81203 0.68882 INTE EXTERN> -23.79795 -45.81032 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6083" Parameter: A <- "-69.6083" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7979" Parameter: B <- "-23.7979" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8103" Parameter: C <- "-45.8103" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7544 TOTAL ENERGY = -69.6083 RDTITL> * VAN DER WAALS = -23.7979 ELECTROSTATIC = -45.8103 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7544" Parameter: CONF_N -> "8002" Comparing "7544" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7545" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752596 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759232 ATOM PAIRS WERE FOUND FOR ATOM LIST 41527 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29720 from a total of 759232 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7545 -71.51876 1.91050 0.89918 INTE EXTERN> -19.46198 -52.05678 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5188" Parameter: A <- "-71.5188" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-19.462" Parameter: B <- "-19.462" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0568" Parameter: C <- "-52.0568" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7545 TOTAL ENERGY = -71.5188 RDTITL> * VAN DER WAALS = -19.462 ELECTROSTATIC = -52.0568 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7545" Parameter: CONF_N -> "8002" Comparing "7545" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7546" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759232 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752971 ATOM PAIRS WERE FOUND FOR ATOM LIST 41125 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29656 from a total of 752971 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7546 -76.93696 5.41820 0.81603 INTE EXTERN> -24.25482 -52.68215 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.937" Parameter: A <- "-76.937" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2548" Parameter: B <- "-24.2548" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6821" Parameter: C <- "-52.6821" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7546 TOTAL ENERGY = -76.937 RDTITL> * VAN DER WAALS = -24.2548 ELECTROSTATIC = -52.6821 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7546" Parameter: CONF_N -> "8002" Comparing "7546" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7547" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752971 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755567 ATOM PAIRS WERE FOUND FOR ATOM LIST 41396 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29604 from a total of 755567 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7547 -71.50086 -5.43610 0.62909 INTE EXTERN> -25.39488 -46.10598 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5009" Parameter: A <- "-71.5009" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3949" Parameter: B <- "-25.3949" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.106" Parameter: C <- "-46.106" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7547 TOTAL ENERGY = -71.5009 RDTITL> * VAN DER WAALS = -25.3949 ELECTROSTATIC = -46.106 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7547" Parameter: CONF_N -> "8002" Comparing "7547" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7548" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755567 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755454 ATOM PAIRS WERE FOUND FOR ATOM LIST 41425 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30199 from a total of 755454 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7548 -68.14016 -3.36070 0.62209 INTE EXTERN> -25.88140 -42.25875 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1402" Parameter: A <- "-68.1402" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8814" Parameter: B <- "-25.8814" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2588" Parameter: C <- "-42.2588" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7548 TOTAL ENERGY = -68.1402 RDTITL> * VAN DER WAALS = -25.8814 ELECTROSTATIC = -42.2588 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7548" Parameter: CONF_N -> "8002" Comparing "7548" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7549" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755454 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755630 ATOM PAIRS WERE FOUND FOR ATOM LIST 41398 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29832 from a total of 755630 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7549 -75.24403 7.10388 0.65530 INTE EXTERN> -29.21685 -46.02719 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.244" Parameter: A <- "-75.244" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2168" Parameter: B <- "-29.2168" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0272" Parameter: C <- "-46.0272" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7549 TOTAL ENERGY = -75.244 RDTITL> * VAN DER WAALS = -29.2168 ELECTROSTATIC = -46.0272 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7549" Parameter: CONF_N -> "8002" Comparing "7549" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7550" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755630 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754242 ATOM PAIRS WERE FOUND FOR ATOM LIST 41330 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29728 from a total of 754242 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7550 -76.46395 1.21991 0.66470 INTE EXTERN> -28.81446 -47.64948 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4639" Parameter: A <- "-76.4639" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8145" Parameter: B <- "-28.8145" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6495" Parameter: C <- "-47.6495" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7550 TOTAL ENERGY = -76.4639 RDTITL> * VAN DER WAALS = -28.8145 ELECTROSTATIC = -47.6495 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7550" Parameter: CONF_N -> "8002" Comparing "7550" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7551" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754242 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760254 ATOM PAIRS WERE FOUND FOR ATOM LIST 41689 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30033 from a total of 760254 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7551 -80.15397 3.69002 0.63752 INTE EXTERN> -30.32269 -49.83128 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.154" Parameter: A <- "-80.154" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3227" Parameter: B <- "-30.3227" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8313" Parameter: C <- "-49.8313" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7551 TOTAL ENERGY = -80.154 RDTITL> * VAN DER WAALS = -30.3227 ELECTROSTATIC = -49.8313 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7551" Parameter: CONF_N -> "8002" Comparing "7551" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7552" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760254 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760934 ATOM PAIRS WERE FOUND FOR ATOM LIST 41626 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29991 from a total of 760934 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7552 -78.30429 -1.84968 0.67636 INTE EXTERN> -27.66266 -50.64163 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3043" Parameter: A <- "-78.3043" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6627" Parameter: B <- "-27.6627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6416" Parameter: C <- "-50.6416" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7552 TOTAL ENERGY = -78.3043 RDTITL> * VAN DER WAALS = -27.6627 ELECTROSTATIC = -50.6416 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7552" Parameter: CONF_N -> "8002" Comparing "7552" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7553" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760934 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756569 ATOM PAIRS WERE FOUND FOR ATOM LIST 41494 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30374 from a total of 756569 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7553 -81.62871 3.32442 0.59773 INTE EXTERN> -31.99844 -49.63027 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6287" Parameter: A <- "-81.6287" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9984" Parameter: B <- "-31.9984" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6303" Parameter: C <- "-49.6303" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7553 TOTAL ENERGY = -81.6287 RDTITL> * VAN DER WAALS = -31.9984 ELECTROSTATIC = -49.6303 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7553" Parameter: CONF_N -> "8002" Comparing "7553" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7554" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756569 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757752 ATOM PAIRS WERE FOUND FOR ATOM LIST 41527 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30639 from a total of 757752 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7554 -76.65805 -4.97066 0.67129 INTE EXTERN> -28.05088 -48.60717 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6581" Parameter: A <- "-76.6581" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0509" Parameter: B <- "-28.0509" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6072" Parameter: C <- "-48.6072" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7554 TOTAL ENERGY = -76.6581 RDTITL> * VAN DER WAALS = -28.0509 ELECTROSTATIC = -48.6072 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7554" Parameter: CONF_N -> "8002" Comparing "7554" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7555" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757752 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755205 ATOM PAIRS WERE FOUND FOR ATOM LIST 41547 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29874 from a total of 755205 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7555 -78.63989 1.98183 0.60843 INTE EXTERN> -29.41509 -49.22480 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6399" Parameter: A <- "-78.6399" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4151" Parameter: B <- "-29.4151" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2248" Parameter: C <- "-49.2248" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7555 TOTAL ENERGY = -78.6399 RDTITL> * VAN DER WAALS = -29.4151 ELECTROSTATIC = -49.2248 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7555" Parameter: CONF_N -> "8002" Comparing "7555" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7556" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755205 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754573 ATOM PAIRS WERE FOUND FOR ATOM LIST 41457 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30165 from a total of 754573 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7556 -75.17434 -3.46554 0.59415 INTE EXTERN> -28.29585 -46.87849 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1743" Parameter: A <- "-75.1743" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2959" Parameter: B <- "-28.2959" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8785" Parameter: C <- "-46.8785" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7556 TOTAL ENERGY = -75.1743 RDTITL> * VAN DER WAALS = -28.2959 ELECTROSTATIC = -46.8785 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7556" Parameter: CONF_N -> "8002" Comparing "7556" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7557" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754573 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756002 ATOM PAIRS WERE FOUND FOR ATOM LIST 41427 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30216 from a total of 756002 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7557 -72.73086 -2.44349 0.64463 INTE EXTERN> -25.45794 -47.27292 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7309" Parameter: A <- "-72.7309" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4579" Parameter: B <- "-25.4579" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2729" Parameter: C <- "-47.2729" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7557 TOTAL ENERGY = -72.7309 RDTITL> * VAN DER WAALS = -25.4579 ELECTROSTATIC = -47.2729 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7557" Parameter: CONF_N -> "8002" Comparing "7557" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7558" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756002 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758470 ATOM PAIRS WERE FOUND FOR ATOM LIST 41507 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29457 from a total of 758470 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7558 -72.61571 -0.11515 0.60959 INTE EXTERN> -27.11389 -45.50182 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6157" Parameter: A <- "-72.6157" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1139" Parameter: B <- "-27.1139" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5018" Parameter: C <- "-45.5018" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7558 TOTAL ENERGY = -72.6157 RDTITL> * VAN DER WAALS = -27.1139 ELECTROSTATIC = -45.5018 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7558" Parameter: CONF_N -> "8002" Comparing "7558" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7559" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758470 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757441 ATOM PAIRS WERE FOUND FOR ATOM LIST 41479 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29690 from a total of 757441 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7559 -70.35120 -2.26452 0.62671 INTE EXTERN> -29.56565 -40.78555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3512" Parameter: A <- "-70.3512" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5656" Parameter: B <- "-29.5656" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.7856" Parameter: C <- "-40.7856" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7559 TOTAL ENERGY = -70.3512 RDTITL> * VAN DER WAALS = -29.5656 ELECTROSTATIC = -40.7856 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7559" Parameter: CONF_N -> "8002" Comparing "7559" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7560" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757441 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753680 ATOM PAIRS WERE FOUND FOR ATOM LIST 41342 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29808 from a total of 753680 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7560 -68.16199 -2.18921 0.71286 INTE EXTERN> -23.67188 -44.49011 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.162" Parameter: A <- "-68.162" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6719" Parameter: B <- "-23.6719" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4901" Parameter: C <- "-44.4901" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7560 TOTAL ENERGY = -68.162 RDTITL> * VAN DER WAALS = -23.6719 ELECTROSTATIC = -44.4901 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7560" Parameter: CONF_N -> "8002" Comparing "7560" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7561" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753680 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761618 ATOM PAIRS WERE FOUND FOR ATOM LIST 41796 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30190 from a total of 761618 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7561 -76.86686 8.70488 0.57282 INTE EXTERN> -31.54564 -45.32122 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8669" Parameter: A <- "-76.8669" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5456" Parameter: B <- "-31.5456" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3212" Parameter: C <- "-45.3212" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7561 TOTAL ENERGY = -76.8669 RDTITL> * VAN DER WAALS = -31.5456 ELECTROSTATIC = -45.3212 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7561" Parameter: CONF_N -> "8002" Comparing "7561" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7562" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761618 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758718 ATOM PAIRS WERE FOUND FOR ATOM LIST 41601 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30029 from a total of 758718 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7562 -75.59908 -1.26778 0.59242 INTE EXTERN> -29.21410 -46.38498 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.5991" Parameter: A <- "-75.5991" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2141" Parameter: B <- "-29.2141" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.385" Parameter: C <- "-46.385" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7562 TOTAL ENERGY = -75.5991 RDTITL> * VAN DER WAALS = -29.2141 ELECTROSTATIC = -46.385 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7562" Parameter: CONF_N -> "8002" Comparing "7562" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7563" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758718 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756959 ATOM PAIRS WERE FOUND FOR ATOM LIST 41428 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29613 from a total of 756959 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7563 -72.00501 -3.59407 0.56634 INTE EXTERN> -28.08463 -43.92038 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.005" Parameter: A <- "-72.005" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0846" Parameter: B <- "-28.0846" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9204" Parameter: C <- "-43.9204" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7563 TOTAL ENERGY = -72.005 RDTITL> * VAN DER WAALS = -28.0846 ELECTROSTATIC = -43.9204 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7563" Parameter: CONF_N -> "8002" Comparing "7563" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7564" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756959 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752517 ATOM PAIRS WERE FOUND FOR ATOM LIST 41222 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29669 from a total of 752517 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7564 -80.02196 8.01695 0.62476 INTE EXTERN> -28.75825 -51.26371 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.022" Parameter: A <- "-80.022" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7582" Parameter: B <- "-28.7582" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2637" Parameter: C <- "-51.2637" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7564 TOTAL ENERGY = -80.022 RDTITL> * VAN DER WAALS = -28.7582 ELECTROSTATIC = -51.2637 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7564" Parameter: CONF_N -> "8002" Comparing "7564" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7565" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752517 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751399 ATOM PAIRS WERE FOUND FOR ATOM LIST 41358 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29057 from a total of 751399 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7565 -79.74058 -0.28138 0.68795 INTE EXTERN> -26.06962 -53.67097 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7406" Parameter: A <- "-79.7406" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0696" Parameter: B <- "-26.0696" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.671" Parameter: C <- "-53.671" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7565 TOTAL ENERGY = -79.7406 RDTITL> * VAN DER WAALS = -26.0696 ELECTROSTATIC = -53.671 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7565" Parameter: CONF_N -> "8002" Comparing "7565" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7566" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751399 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757342 ATOM PAIRS WERE FOUND FOR ATOM LIST 41391 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29741 from a total of 757342 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7566 -74.34503 -5.39556 0.64364 INTE EXTERN> -27.52896 -46.81607 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.345" Parameter: A <- "-74.345" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.529" Parameter: B <- "-27.529" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8161" Parameter: C <- "-46.8161" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7566 TOTAL ENERGY = -74.345 RDTITL> * VAN DER WAALS = -27.529 ELECTROSTATIC = -46.8161 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7566" Parameter: CONF_N -> "8002" Comparing "7566" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7567" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757342 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757748 ATOM PAIRS WERE FOUND FOR ATOM LIST 41686 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29589 from a total of 757748 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7567 -74.28605 -0.05898 0.60577 INTE EXTERN> -28.29271 -45.99334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.286" Parameter: A <- "-74.286" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2927" Parameter: B <- "-28.2927" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9933" Parameter: C <- "-45.9933" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7567 TOTAL ENERGY = -74.286 RDTITL> * VAN DER WAALS = -28.2927 ELECTROSTATIC = -45.9933 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7567" Parameter: CONF_N -> "8002" Comparing "7567" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7568" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757748 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759480 ATOM PAIRS WERE FOUND FOR ATOM LIST 41596 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29935 from a total of 759480 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7568 -71.48432 -2.80173 0.53781 INTE EXTERN> -31.13788 -40.34644 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4843" Parameter: A <- "-71.4843" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1379" Parameter: B <- "-31.1379" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3464" Parameter: C <- "-40.3464" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7568 TOTAL ENERGY = -71.4843 RDTITL> * VAN DER WAALS = -31.1379 ELECTROSTATIC = -40.3464 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7568" Parameter: CONF_N -> "8002" Comparing "7568" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7569" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759480 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752332 ATOM PAIRS WERE FOUND FOR ATOM LIST 41241 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29720 from a total of 752332 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7569 -64.94424 -6.54008 0.53797 INTE EXTERN> -30.21267 -34.73157 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.9442" Parameter: A <- "-64.9442" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2127" Parameter: B <- "-30.2127" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.7316" Parameter: C <- "-34.7316" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7569 TOTAL ENERGY = -64.9442 RDTITL> * VAN DER WAALS = -30.2127 ELECTROSTATIC = -34.7316 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7569" Parameter: CONF_N -> "8002" Comparing "7569" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7570" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752332 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755586 ATOM PAIRS WERE FOUND FOR ATOM LIST 41462 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29406 from a total of 755586 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7570 -72.15074 7.20650 0.69639 INTE EXTERN> -26.41548 -45.73526 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1507" Parameter: A <- "-72.1507" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4155" Parameter: B <- "-26.4155" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7353" Parameter: C <- "-45.7353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7570 TOTAL ENERGY = -72.1507 RDTITL> * VAN DER WAALS = -26.4155 ELECTROSTATIC = -45.7353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7570" Parameter: CONF_N -> "8002" Comparing "7570" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7571" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755586 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753997 ATOM PAIRS WERE FOUND FOR ATOM LIST 41535 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29506 from a total of 753997 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7571 -73.42709 1.27636 0.60594 INTE EXTERN> -29.79325 -43.63384 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.4271" Parameter: A <- "-73.4271" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7933" Parameter: B <- "-29.7933" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6338" Parameter: C <- "-43.6338" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7571 TOTAL ENERGY = -73.4271 RDTITL> * VAN DER WAALS = -29.7933 ELECTROSTATIC = -43.6338 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7571" Parameter: CONF_N -> "8002" Comparing "7571" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7572" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753997 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753131 ATOM PAIRS WERE FOUND FOR ATOM LIST 41227 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29321 from a total of 753131 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7572 -63.89267 -9.53443 0.58576 INTE EXTERN> -26.07322 -37.81945 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.8927" Parameter: A <- "-63.8927" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0732" Parameter: B <- "-26.0732" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8194" Parameter: C <- "-37.8194" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7572 TOTAL ENERGY = -63.8927 RDTITL> * VAN DER WAALS = -26.0732 ELECTROSTATIC = -37.8194 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7572" Parameter: CONF_N -> "8002" Comparing "7572" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7573" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753131 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750892 ATOM PAIRS WERE FOUND FOR ATOM LIST 41401 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30077 from a total of 750892 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7573 -73.81593 9.92326 0.62992 INTE EXTERN> -27.71838 -46.09755 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8159" Parameter: A <- "-73.8159" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7184" Parameter: B <- "-27.7184" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0975" Parameter: C <- "-46.0975" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7573 TOTAL ENERGY = -73.8159 RDTITL> * VAN DER WAALS = -27.7184 ELECTROSTATIC = -46.0975 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7573" Parameter: CONF_N -> "8002" Comparing "7573" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7574" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750892 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752621 ATOM PAIRS WERE FOUND FOR ATOM LIST 41244 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29608 from a total of 752621 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7574 -74.19437 0.37844 0.57185 INTE EXTERN> -29.59500 -44.59937 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1944" Parameter: A <- "-74.1944" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.595" Parameter: B <- "-29.595" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5994" Parameter: C <- "-44.5994" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7574 TOTAL ENERGY = -74.1944 RDTITL> * VAN DER WAALS = -29.595 ELECTROSTATIC = -44.5994 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7574" Parameter: CONF_N -> "8002" Comparing "7574" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7575" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752621 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750795 ATOM PAIRS WERE FOUND FOR ATOM LIST 41139 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29394 from a total of 750795 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7575 -70.25928 -3.93509 0.53629 INTE EXTERN> -29.72158 -40.53769 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2593" Parameter: A <- "-70.2593" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7216" Parameter: B <- "-29.7216" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.5377" Parameter: C <- "-40.5377" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7575 TOTAL ENERGY = -70.2593 RDTITL> * VAN DER WAALS = -29.7216 ELECTROSTATIC = -40.5377 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7575" Parameter: CONF_N -> "8002" Comparing "7575" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7576" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750795 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749926 ATOM PAIRS WERE FOUND FOR ATOM LIST 41278 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29610 from a total of 749926 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7576 -65.84188 -4.41739 0.76617 INTE EXTERN> -21.11927 -44.72261 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8419" Parameter: A <- "-65.8419" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.1193" Parameter: B <- "-21.1193" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7226" Parameter: C <- "-44.7226" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7576 TOTAL ENERGY = -65.8419 RDTITL> * VAN DER WAALS = -21.1193 ELECTROSTATIC = -44.7226 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7576" Parameter: CONF_N -> "8002" Comparing "7576" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7577" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749926 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753588 ATOM PAIRS WERE FOUND FOR ATOM LIST 41319 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29984 from a total of 753588 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7577 -69.45129 3.60940 0.58230 INTE EXTERN> -30.26729 -39.18399 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4513" Parameter: A <- "-69.4513" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2673" Parameter: B <- "-30.2673" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.184" Parameter: C <- "-39.184" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7577 TOTAL ENERGY = -69.4513 RDTITL> * VAN DER WAALS = -30.2673 ELECTROSTATIC = -39.184 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7577" Parameter: CONF_N -> "8002" Comparing "7577" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7578" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753588 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753884 ATOM PAIRS WERE FOUND FOR ATOM LIST 41411 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29716 from a total of 753884 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7578 -70.51439 1.06311 0.60357 INTE EXTERN> -27.28105 -43.23334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5144" Parameter: A <- "-70.5144" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2811" Parameter: B <- "-27.2811" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.2333" Parameter: C <- "-43.2333" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7578 TOTAL ENERGY = -70.5144 RDTITL> * VAN DER WAALS = -27.2811 ELECTROSTATIC = -43.2333 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7578" Parameter: CONF_N -> "8002" Comparing "7578" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7579" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753884 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754829 ATOM PAIRS WERE FOUND FOR ATOM LIST 41416 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29859 from a total of 754829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7579 -69.10917 -1.40523 0.50666 INTE EXTERN> -29.00782 -40.10135 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1092" Parameter: A <- "-69.1092" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0078" Parameter: B <- "-29.0078" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.1013" Parameter: C <- "-40.1013" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7579 TOTAL ENERGY = -69.1092 RDTITL> * VAN DER WAALS = -29.0078 ELECTROSTATIC = -40.1013 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7579" Parameter: CONF_N -> "8002" Comparing "7579" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7580" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755852 ATOM PAIRS WERE FOUND FOR ATOM LIST 41577 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30106 from a total of 755852 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7580 -68.43581 -0.67336 0.67159 INTE EXTERN> -24.06350 -44.37231 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4358" Parameter: A <- "-68.4358" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0635" Parameter: B <- "-24.0635" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3723" Parameter: C <- "-44.3723" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7580 TOTAL ENERGY = -68.4358 RDTITL> * VAN DER WAALS = -24.0635 ELECTROSTATIC = -44.3723 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7580" Parameter: CONF_N -> "8002" Comparing "7580" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7581" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755852 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760348 ATOM PAIRS WERE FOUND FOR ATOM LIST 41899 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30146 from a total of 760348 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7581 -68.51374 0.07793 0.66162 INTE EXTERN> -24.37709 -44.13665 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.5137" Parameter: A <- "-68.5137" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3771" Parameter: B <- "-24.3771" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1367" Parameter: C <- "-44.1367" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7581 TOTAL ENERGY = -68.5137 RDTITL> * VAN DER WAALS = -24.3771 ELECTROSTATIC = -44.1367 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7581" Parameter: CONF_N -> "8002" Comparing "7581" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7582" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760348 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755340 ATOM PAIRS WERE FOUND FOR ATOM LIST 41548 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29802 from a total of 755340 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7582 -66.99395 -1.51979 0.59241 INTE EXTERN> -28.59169 -38.40226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9939" Parameter: A <- "-66.9939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5917" Parameter: B <- "-28.5917" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4023" Parameter: C <- "-38.4023" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7582 TOTAL ENERGY = -66.9939 RDTITL> * VAN DER WAALS = -28.5917 ELECTROSTATIC = -38.4023 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7582" Parameter: CONF_N -> "8002" Comparing "7582" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7583" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755340 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749963 ATOM PAIRS WERE FOUND FOR ATOM LIST 41441 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29687 from a total of 749963 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7583 -78.40004 11.40610 0.62704 INTE EXTERN> -29.83449 -48.56555 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4" Parameter: A <- "-78.4" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8345" Parameter: B <- "-29.8345" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5656" Parameter: C <- "-48.5656" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7583 TOTAL ENERGY = -78.4 RDTITL> * VAN DER WAALS = -29.8345 ELECTROSTATIC = -48.5656 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7583" Parameter: CONF_N -> "8002" Comparing "7583" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7584" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749963 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745593 ATOM PAIRS WERE FOUND FOR ATOM LIST 41099 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29563 from a total of 745593 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7584 -69.46422 -8.93583 0.66330 INTE EXTERN> -26.42071 -43.04351 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4642" Parameter: A <- "-69.4642" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4207" Parameter: B <- "-26.4207" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0435" Parameter: C <- "-43.0435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7584 TOTAL ENERGY = -69.4642 RDTITL> * VAN DER WAALS = -26.4207 ELECTROSTATIC = -43.0435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7584" Parameter: CONF_N -> "8002" Comparing "7584" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7585" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745593 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751914 ATOM PAIRS WERE FOUND FOR ATOM LIST 41314 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30009 from a total of 751914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7585 -70.02305 0.55883 0.72471 INTE EXTERN> -23.72297 -46.30008 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0231" Parameter: A <- "-70.0231" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.723" Parameter: B <- "-23.723" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3001" Parameter: C <- "-46.3001" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7585 TOTAL ENERGY = -70.0231 RDTITL> * VAN DER WAALS = -23.723 ELECTROSTATIC = -46.3001 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7585" Parameter: CONF_N -> "8002" Comparing "7585" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7586" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750462 ATOM PAIRS WERE FOUND FOR ATOM LIST 41097 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29569 from a total of 750462 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7586 -75.64177 5.61872 0.60840 INTE EXTERN> -28.49119 -47.15058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6418" Parameter: A <- "-75.6418" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4912" Parameter: B <- "-28.4912" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1506" Parameter: C <- "-47.1506" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7586 TOTAL ENERGY = -75.6418 RDTITL> * VAN DER WAALS = -28.4912 ELECTROSTATIC = -47.1506 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7586" Parameter: CONF_N -> "8002" Comparing "7586" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7587" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750462 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744269 ATOM PAIRS WERE FOUND FOR ATOM LIST 40897 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29227 from a total of 744269 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7587 -65.67821 -9.96356 0.58227 INTE EXTERN> -26.67290 -39.00531 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6782" Parameter: A <- "-65.6782" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6729" Parameter: B <- "-26.6729" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0053" Parameter: C <- "-39.0053" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7587 TOTAL ENERGY = -65.6782 RDTITL> * VAN DER WAALS = -26.6729 ELECTROSTATIC = -39.0053 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7587" Parameter: CONF_N -> "8002" Comparing "7587" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7588" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744269 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747594 ATOM PAIRS WERE FOUND FOR ATOM LIST 41065 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28926 from a total of 747594 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7588 -66.74823 1.07002 0.53825 INTE EXTERN> -29.24485 -37.50338 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.7482" Parameter: A <- "-66.7482" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2448" Parameter: B <- "-29.2448" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5034" Parameter: C <- "-37.5034" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7588 TOTAL ENERGY = -66.7482 RDTITL> * VAN DER WAALS = -29.2448 ELECTROSTATIC = -37.5034 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7588" Parameter: CONF_N -> "8002" Comparing "7588" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7589" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747594 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751718 ATOM PAIRS WERE FOUND FOR ATOM LIST 41294 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28957 from a total of 751718 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7589 -64.36382 -2.38441 0.60387 INTE EXTERN> -27.00085 -37.36297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3638" Parameter: A <- "-64.3638" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0008" Parameter: B <- "-27.0008" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.363" Parameter: C <- "-37.363" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7589 TOTAL ENERGY = -64.3638 RDTITL> * VAN DER WAALS = -27.0008 ELECTROSTATIC = -37.363 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7589" Parameter: CONF_N -> "8002" Comparing "7589" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7590" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751718 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752956 ATOM PAIRS WERE FOUND FOR ATOM LIST 41229 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29408 from a total of 752956 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7590 -65.81777 1.45395 0.67559 INTE EXTERN> -24.99187 -40.82590 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.8178" Parameter: A <- "-65.8178" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9919" Parameter: B <- "-24.9919" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8259" Parameter: C <- "-40.8259" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7590 TOTAL ENERGY = -65.8178 RDTITL> * VAN DER WAALS = -24.9919 ELECTROSTATIC = -40.8259 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7590" Parameter: CONF_N -> "8002" Comparing "7590" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7591" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752956 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749789 ATOM PAIRS WERE FOUND FOR ATOM LIST 41215 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29402 from a total of 749789 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7591 -71.60048 5.78271 0.70181 INTE EXTERN> -24.39257 -47.20791 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.6005" Parameter: A <- "-71.6005" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3926" Parameter: B <- "-24.3926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2079" Parameter: C <- "-47.2079" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7591 TOTAL ENERGY = -71.6005 RDTITL> * VAN DER WAALS = -24.3926 ELECTROSTATIC = -47.2079 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7591" Parameter: CONF_N -> "8002" Comparing "7591" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7592" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749789 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 744519 ATOM PAIRS WERE FOUND FOR ATOM LIST 40892 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28221 from a total of 744519 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7592 -74.19706 2.59658 0.58308 INTE EXTERN> -29.10966 -45.08741 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1971" Parameter: A <- "-74.1971" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1097" Parameter: B <- "-29.1097" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0874" Parameter: C <- "-45.0874" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7592 TOTAL ENERGY = -74.1971 RDTITL> * VAN DER WAALS = -29.1097 ELECTROSTATIC = -45.0874 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7592" Parameter: CONF_N -> "8002" Comparing "7592" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7593" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 744519 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754212 ATOM PAIRS WERE FOUND FOR ATOM LIST 41456 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29565 from a total of 754212 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7593 -70.06206 -4.13501 0.72115 INTE EXTERN> -24.59595 -45.46610 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0621" Parameter: A <- "-70.0621" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.596" Parameter: B <- "-24.596" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4661" Parameter: C <- "-45.4661" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7593 TOTAL ENERGY = -70.0621 RDTITL> * VAN DER WAALS = -24.596 ELECTROSTATIC = -45.4661 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7593" Parameter: CONF_N -> "8002" Comparing "7593" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7594" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754212 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749825 ATOM PAIRS WERE FOUND FOR ATOM LIST 41145 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28824 from a total of 749825 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7594 -68.65668 -1.40537 0.57571 INTE EXTERN> -29.62366 -39.03303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6567" Parameter: A <- "-68.6567" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6237" Parameter: B <- "-29.6237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.033" Parameter: C <- "-39.033" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7594 TOTAL ENERGY = -68.6567 RDTITL> * VAN DER WAALS = -29.6237 ELECTROSTATIC = -39.033 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7594" Parameter: CONF_N -> "8002" Comparing "7594" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7595" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749825 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754000 ATOM PAIRS WERE FOUND FOR ATOM LIST 41517 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29362 from a total of 754000 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7595 -71.72787 3.07118 0.66428 INTE EXTERN> -27.73828 -43.98958 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.7279" Parameter: A <- "-71.7279" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7383" Parameter: B <- "-27.7383" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9896" Parameter: C <- "-43.9896" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7595 TOTAL ENERGY = -71.7279 RDTITL> * VAN DER WAALS = -27.7383 ELECTROSTATIC = -43.9896 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7595" Parameter: CONF_N -> "8002" Comparing "7595" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7596" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754000 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747118 ATOM PAIRS WERE FOUND FOR ATOM LIST 41030 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29381 from a total of 747118 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7596 -76.19917 4.47130 0.64220 INTE EXTERN> -27.31258 -48.88659 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1992" Parameter: A <- "-76.1992" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3126" Parameter: B <- "-27.3126" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8866" Parameter: C <- "-48.8866" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7596 TOTAL ENERGY = -76.1992 RDTITL> * VAN DER WAALS = -27.3126 ELECTROSTATIC = -48.8866 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7596" Parameter: CONF_N -> "8002" Comparing "7596" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7597" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747118 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756197 ATOM PAIRS WERE FOUND FOR ATOM LIST 41551 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29470 from a total of 756197 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7597 -72.87176 -3.32742 0.62537 INTE EXTERN> -29.32848 -43.54328 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8718" Parameter: A <- "-72.8718" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3285" Parameter: B <- "-29.3285" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5433" Parameter: C <- "-43.5433" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7597 TOTAL ENERGY = -72.8718 RDTITL> * VAN DER WAALS = -29.3285 ELECTROSTATIC = -43.5433 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7597" Parameter: CONF_N -> "8002" Comparing "7597" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7598" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756197 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756823 ATOM PAIRS WERE FOUND FOR ATOM LIST 41424 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29228 from a total of 756823 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7598 -71.54920 -1.32256 0.70108 INTE EXTERN> -24.60468 -46.94452 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5492" Parameter: A <- "-71.5492" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6047" Parameter: B <- "-24.6047" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9445" Parameter: C <- "-46.9445" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7598 TOTAL ENERGY = -71.5492 RDTITL> * VAN DER WAALS = -24.6047 ELECTROSTATIC = -46.9445 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7598" Parameter: CONF_N -> "8002" Comparing "7598" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7599" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756823 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41315 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29255 from a total of 751526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7599 -68.33992 -3.20928 0.67176 INTE EXTERN> -26.20364 -42.13628 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3399" Parameter: A <- "-68.3399" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2036" Parameter: B <- "-26.2036" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1363" Parameter: C <- "-42.1363" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7599 TOTAL ENERGY = -68.3399 RDTITL> * VAN DER WAALS = -26.2036 ELECTROSTATIC = -42.1363 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7599" Parameter: CONF_N -> "8002" Comparing "7599" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7600" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757698 ATOM PAIRS WERE FOUND FOR ATOM LIST 41671 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29753 from a total of 757698 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7600 -77.39633 9.05641 0.67430 INTE EXTERN> -25.84086 -51.55546 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3963" Parameter: A <- "-77.3963" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8409" Parameter: B <- "-25.8409" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5555" Parameter: C <- "-51.5555" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7600 TOTAL ENERGY = -77.3963 RDTITL> * VAN DER WAALS = -25.8409 ELECTROSTATIC = -51.5555 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7600" Parameter: CONF_N -> "8002" Comparing "7600" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7601" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757698 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749252 ATOM PAIRS WERE FOUND FOR ATOM LIST 41039 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29172 from a total of 749252 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7601 -65.09508 -12.30125 0.63288 INTE EXTERN> -26.07154 -39.02353 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0951" Parameter: A <- "-65.0951" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0715" Parameter: B <- "-26.0715" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.0235" Parameter: C <- "-39.0235" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7601 TOTAL ENERGY = -65.0951 RDTITL> * VAN DER WAALS = -26.0715 ELECTROSTATIC = -39.0235 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7601" Parameter: CONF_N -> "8002" Comparing "7601" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7602" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749252 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754147 ATOM PAIRS WERE FOUND FOR ATOM LIST 41488 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29546 from a total of 754147 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7602 -66.14290 1.04783 0.59045 INTE EXTERN> -27.58533 -38.55758 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1429" Parameter: A <- "-66.1429" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5853" Parameter: B <- "-27.5853" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.5576" Parameter: C <- "-38.5576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7602 TOTAL ENERGY = -66.1429 RDTITL> * VAN DER WAALS = -27.5853 ELECTROSTATIC = -38.5576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7602" Parameter: CONF_N -> "8002" Comparing "7602" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7603" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754147 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753383 ATOM PAIRS WERE FOUND FOR ATOM LIST 41181 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29399 from a total of 753383 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7603 -65.38870 -0.75420 0.55987 INTE EXTERN> -31.19782 -34.19088 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.3887" Parameter: A <- "-65.3887" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1978" Parameter: B <- "-31.1978" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.1909" Parameter: C <- "-34.1909" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7603 TOTAL ENERGY = -65.3887 RDTITL> * VAN DER WAALS = -31.1978 ELECTROSTATIC = -34.1909 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7603" Parameter: CONF_N -> "8002" Comparing "7603" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7604" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753383 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760183 ATOM PAIRS WERE FOUND FOR ATOM LIST 41679 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29920 from a total of 760183 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7604 -63.61842 -1.77028 0.90311 INTE EXTERN> -14.77849 -48.83993 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6184" Parameter: A <- "-63.6184" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-14.7785" Parameter: B <- "-14.7785" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8399" Parameter: C <- "-48.8399" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7604 TOTAL ENERGY = -63.6184 RDTITL> * VAN DER WAALS = -14.7785 ELECTROSTATIC = -48.8399 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7604" Parameter: CONF_N -> "8002" Comparing "7604" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7605" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760183 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758273 ATOM PAIRS WERE FOUND FOR ATOM LIST 41599 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29797 from a total of 758273 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7605 -72.93934 9.32092 0.57392 INTE EXTERN> -32.25399 -40.68535 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9393" Parameter: A <- "-72.9393" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.254" Parameter: B <- "-32.254" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.6854" Parameter: C <- "-40.6854" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7605 TOTAL ENERGY = -72.9393 RDTITL> * VAN DER WAALS = -32.254 ELECTROSTATIC = -40.6854 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7605" Parameter: CONF_N -> "8002" Comparing "7605" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7606" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758273 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760288 ATOM PAIRS WERE FOUND FOR ATOM LIST 41736 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29879 from a total of 760288 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7606 -66.37154 -6.56780 0.65615 INTE EXTERN> -25.21157 -41.15997 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.3715" Parameter: A <- "-66.3715" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2116" Parameter: B <- "-25.2116" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.16" Parameter: C <- "-41.16" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7606 TOTAL ENERGY = -66.3715 RDTITL> * VAN DER WAALS = -25.2116 ELECTROSTATIC = -41.16 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7606" Parameter: CONF_N -> "8002" Comparing "7606" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7607" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760288 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750847 ATOM PAIRS WERE FOUND FOR ATOM LIST 41247 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29203 from a total of 750847 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7607 -68.42960 2.05806 0.65310 INTE EXTERN> -26.62218 -41.80742 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.4296" Parameter: A <- "-68.4296" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6222" Parameter: B <- "-26.6222" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.8074" Parameter: C <- "-41.8074" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7607 TOTAL ENERGY = -68.4296 RDTITL> * VAN DER WAALS = -26.6222 ELECTROSTATIC = -41.8074 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7607" Parameter: CONF_N -> "8002" Comparing "7607" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7608" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750847 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747123 ATOM PAIRS WERE FOUND FOR ATOM LIST 41184 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29024 from a total of 747123 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7608 -73.34887 4.91927 0.63937 INTE EXTERN> -27.62621 -45.72265 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3489" Parameter: A <- "-73.3489" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6262" Parameter: B <- "-27.6262" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7227" Parameter: C <- "-45.7227" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7608 TOTAL ENERGY = -73.3489 RDTITL> * VAN DER WAALS = -27.6262 ELECTROSTATIC = -45.7227 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7608" Parameter: CONF_N -> "8002" Comparing "7608" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7609" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747123 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754791 ATOM PAIRS WERE FOUND FOR ATOM LIST 41451 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29900 from a total of 754791 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7609 -67.85544 -5.49343 0.59691 INTE EXTERN> -27.75624 -40.09920 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.8554" Parameter: A <- "-67.8554" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7562" Parameter: B <- "-27.7562" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.0992" Parameter: C <- "-40.0992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7609 TOTAL ENERGY = -67.8554 RDTITL> * VAN DER WAALS = -27.7562 ELECTROSTATIC = -40.0992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7609" Parameter: CONF_N -> "8002" Comparing "7609" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7610" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754791 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751383 ATOM PAIRS WERE FOUND FOR ATOM LIST 41244 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29771 from a total of 751383 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7610 -66.98043 -0.87501 0.55465 INTE EXTERN> -31.50767 -35.47276 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9804" Parameter: A <- "-66.9804" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5077" Parameter: B <- "-31.5077" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4728" Parameter: C <- "-35.4728" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7610 TOTAL ENERGY = -66.9804 RDTITL> * VAN DER WAALS = -31.5077 ELECTROSTATIC = -35.4728 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7610" Parameter: CONF_N -> "8002" Comparing "7610" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7611" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751383 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749256 ATOM PAIRS WERE FOUND FOR ATOM LIST 41185 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29674 from a total of 749256 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7611 -73.87497 6.89454 0.75571 INTE EXTERN> -24.44325 -49.43171 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.875" Parameter: A <- "-73.875" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4433" Parameter: B <- "-24.4433" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4317" Parameter: C <- "-49.4317" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7611 TOTAL ENERGY = -73.875 RDTITL> * VAN DER WAALS = -24.4433 ELECTROSTATIC = -49.4317 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7611" Parameter: CONF_N -> "8002" Comparing "7611" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7612" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749256 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750833 ATOM PAIRS WERE FOUND FOR ATOM LIST 41163 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29882 from a total of 750833 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7612 -76.17440 2.29943 0.75135 INTE EXTERN> -26.14637 -50.02803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1744" Parameter: A <- "-76.1744" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1464" Parameter: B <- "-26.1464" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.028" Parameter: C <- "-50.028" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7612 TOTAL ENERGY = -76.1744 RDTITL> * VAN DER WAALS = -26.1464 ELECTROSTATIC = -50.028 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7612" Parameter: CONF_N -> "8002" Comparing "7612" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7613" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750833 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749292 ATOM PAIRS WERE FOUND FOR ATOM LIST 41068 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29736 from a total of 749292 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7613 -70.55607 -5.61833 0.74049 INTE EXTERN> -22.72886 -47.82721 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5561" Parameter: A <- "-70.5561" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.7289" Parameter: B <- "-22.7289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8272" Parameter: C <- "-47.8272" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7613 TOTAL ENERGY = -70.5561 RDTITL> * VAN DER WAALS = -22.7289 ELECTROSTATIC = -47.8272 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7613" Parameter: CONF_N -> "8002" Comparing "7613" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7614" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749292 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760158 ATOM PAIRS WERE FOUND FOR ATOM LIST 41563 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30245 from a total of 760158 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7614 -72.67709 2.12102 0.67442 INTE EXTERN> -26.43508 -46.24201 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6771" Parameter: A <- "-72.6771" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4351" Parameter: B <- "-26.4351" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.242" Parameter: C <- "-46.242" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7614 TOTAL ENERGY = -72.6771 RDTITL> * VAN DER WAALS = -26.4351 ELECTROSTATIC = -46.242 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7614" Parameter: CONF_N -> "8002" Comparing "7614" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7615" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760158 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755453 ATOM PAIRS WERE FOUND FOR ATOM LIST 41517 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 755453 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7615 -75.11356 2.43646 0.63272 INTE EXTERN> -28.30674 -46.80681 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1136" Parameter: A <- "-75.1136" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3067" Parameter: B <- "-28.3067" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8068" Parameter: C <- "-46.8068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7615 TOTAL ENERGY = -75.1136 RDTITL> * VAN DER WAALS = -28.3067 ELECTROSTATIC = -46.8068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7615" Parameter: CONF_N -> "8002" Comparing "7615" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7616" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755453 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749650 ATOM PAIRS WERE FOUND FOR ATOM LIST 41142 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29382 from a total of 749650 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7616 -80.08397 4.97041 0.61281 INTE EXTERN> -30.65078 -49.43319 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.084" Parameter: A <- "-80.084" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6508" Parameter: B <- "-30.6508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.4332" Parameter: C <- "-49.4332" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7616 TOTAL ENERGY = -80.084 RDTITL> * VAN DER WAALS = -30.6508 ELECTROSTATIC = -49.4332 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7616" Parameter: CONF_N -> "8002" Comparing "7616" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7617" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749650 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747847 ATOM PAIRS WERE FOUND FOR ATOM LIST 41174 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29352 from a total of 747847 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7617 -84.43485 4.35088 0.68661 INTE EXTERN> -27.71098 -56.72387 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.4348" Parameter: A <- "-84.4348" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.711" Parameter: B <- "-27.711" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.7239" Parameter: C <- "-56.7239" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7617 TOTAL ENERGY = -84.4348 RDTITL> * VAN DER WAALS = -27.711 ELECTROSTATIC = -56.7239 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7617" Parameter: CONF_N -> "8002" Comparing "7617" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7618" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747847 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750328 ATOM PAIRS WERE FOUND FOR ATOM LIST 41142 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29908 from a total of 750328 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7618 -76.06971 -8.36514 0.61858 INTE EXTERN> -28.06492 -48.00479 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0697" Parameter: A <- "-76.0697" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0649" Parameter: B <- "-28.0649" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0048" Parameter: C <- "-48.0048" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7618 TOTAL ENERGY = -76.0697 RDTITL> * VAN DER WAALS = -28.0649 ELECTROSTATIC = -48.0048 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7618" Parameter: CONF_N -> "8002" Comparing "7618" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7619" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750328 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756283 ATOM PAIRS WERE FOUND FOR ATOM LIST 41389 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29673 from a total of 756283 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7619 -81.24054 5.17083 0.71696 INTE EXTERN> -26.87614 -54.36440 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.2405" Parameter: A <- "-81.2405" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8761" Parameter: B <- "-26.8761" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.3644" Parameter: C <- "-54.3644" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7619 TOTAL ENERGY = -81.2405 RDTITL> * VAN DER WAALS = -26.8761 ELECTROSTATIC = -54.3644 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7619" Parameter: CONF_N -> "8002" Comparing "7619" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7620" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756283 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757337 ATOM PAIRS WERE FOUND FOR ATOM LIST 41466 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30174 from a total of 757337 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7620 -78.47638 -2.76416 0.71276 INTE EXTERN> -25.66622 -52.81017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4764" Parameter: A <- "-78.4764" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6662" Parameter: B <- "-25.6662" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8102" Parameter: C <- "-52.8102" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7620 TOTAL ENERGY = -78.4764 RDTITL> * VAN DER WAALS = -25.6662 ELECTROSTATIC = -52.8102 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7620" Parameter: CONF_N -> "8002" Comparing "7620" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7621" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757337 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753170 ATOM PAIRS WERE FOUND FOR ATOM LIST 41529 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30294 from a total of 753170 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7621 -78.81277 0.33639 0.69147 INTE EXTERN> -28.09317 -50.71960 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8128" Parameter: A <- "-78.8128" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0932" Parameter: B <- "-28.0932" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7196" Parameter: C <- "-50.7196" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7621 TOTAL ENERGY = -78.8128 RDTITL> * VAN DER WAALS = -28.0932 ELECTROSTATIC = -50.7196 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7621" Parameter: CONF_N -> "8002" Comparing "7621" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7622" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753170 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759917 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30844 from a total of 759917 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7622 -78.12514 -0.68763 0.77765 INTE EXTERN> -23.26569 -54.85945 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1251" Parameter: A <- "-78.1251" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.2657" Parameter: B <- "-23.2657" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8594" Parameter: C <- "-54.8594" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7622 TOTAL ENERGY = -78.1251 RDTITL> * VAN DER WAALS = -23.2657 ELECTROSTATIC = -54.8594 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7622" Parameter: CONF_N -> "8002" Comparing "7622" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7623" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759917 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761012 ATOM PAIRS WERE FOUND FOR ATOM LIST 41664 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30313 from a total of 761012 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7623 -78.91180 0.78666 0.78062 INTE EXTERN> -26.24076 -52.67104 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9118" Parameter: A <- "-78.9118" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2408" Parameter: B <- "-26.2408" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.671" Parameter: C <- "-52.671" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7623 TOTAL ENERGY = -78.9118 RDTITL> * VAN DER WAALS = -26.2408 ELECTROSTATIC = -52.671 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7623" Parameter: CONF_N -> "8002" Comparing "7623" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7624" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761012 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762414 ATOM PAIRS WERE FOUND FOR ATOM LIST 41629 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30193 from a total of 762414 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7624 -77.67007 -1.24173 0.64369 INTE EXTERN> -28.51864 -49.15143 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.6701" Parameter: A <- "-77.6701" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5186" Parameter: B <- "-28.5186" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1514" Parameter: C <- "-49.1514" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7624 TOTAL ENERGY = -77.6701 RDTITL> * VAN DER WAALS = -28.5186 ELECTROSTATIC = -49.1514 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7624" Parameter: CONF_N -> "8002" Comparing "7624" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7625" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762414 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762499 ATOM PAIRS WERE FOUND FOR ATOM LIST 41785 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30727 from a total of 762499 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7625 -76.67657 -0.99350 0.77181 INTE EXTERN> -24.93270 -51.74386 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6766" Parameter: A <- "-76.6766" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9327" Parameter: B <- "-24.9327" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7439" Parameter: C <- "-51.7439" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7625 TOTAL ENERGY = -76.6766 RDTITL> * VAN DER WAALS = -24.9327 ELECTROSTATIC = -51.7439 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7625" Parameter: CONF_N -> "8002" Comparing "7625" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7626" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762499 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754821 ATOM PAIRS WERE FOUND FOR ATOM LIST 41427 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30080 from a total of 754821 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7626 -78.89449 2.21792 0.75239 INTE EXTERN> -26.64383 -52.25066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8945" Parameter: A <- "-78.8945" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6438" Parameter: B <- "-26.6438" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.2507" Parameter: C <- "-52.2507" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7626 TOTAL ENERGY = -78.8945 RDTITL> * VAN DER WAALS = -26.6438 ELECTROSTATIC = -52.2507 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7626" Parameter: CONF_N -> "8002" Comparing "7626" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7627" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754821 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761419 ATOM PAIRS WERE FOUND FOR ATOM LIST 41768 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30132 from a total of 761419 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7627 -80.98428 2.08979 0.61423 INTE EXTERN> -27.98011 -53.00417 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9843" Parameter: A <- "-80.9843" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9801" Parameter: B <- "-27.9801" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0042" Parameter: C <- "-53.0042" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7627 TOTAL ENERGY = -80.9843 RDTITL> * VAN DER WAALS = -27.9801 ELECTROSTATIC = -53.0042 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7627" Parameter: CONF_N -> "8002" Comparing "7627" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7628" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761419 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755208 ATOM PAIRS WERE FOUND FOR ATOM LIST 41295 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30196 from a total of 755208 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7628 -85.67576 4.69148 0.70383 INTE EXTERN> -27.08434 -58.59142 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.6758" Parameter: A <- "-85.6758" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0843" Parameter: B <- "-27.0843" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.5914" Parameter: C <- "-58.5914" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7628 TOTAL ENERGY = -85.6758 RDTITL> * VAN DER WAALS = -27.0843 ELECTROSTATIC = -58.5914 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7628" Parameter: CONF_N -> "8002" Comparing "7628" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7629" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755208 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754408 ATOM PAIRS WERE FOUND FOR ATOM LIST 41282 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29863 from a total of 754408 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7629 -75.19382 -10.48194 0.59331 INTE EXTERN> -29.98703 -45.20679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1938" Parameter: A <- "-75.1938" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.987" Parameter: B <- "-29.987" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2068" Parameter: C <- "-45.2068" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7629 TOTAL ENERGY = -75.1938 RDTITL> * VAN DER WAALS = -29.987 ELECTROSTATIC = -45.2068 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7629" Parameter: CONF_N -> "8002" Comparing "7629" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7630" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754408 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756705 ATOM PAIRS WERE FOUND FOR ATOM LIST 41459 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30094 from a total of 756705 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7630 -76.96856 1.77473 0.65693 INTE EXTERN> -27.36548 -49.60308 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9686" Parameter: A <- "-76.9686" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3655" Parameter: B <- "-27.3655" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6031" Parameter: C <- "-49.6031" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7630 TOTAL ENERGY = -76.9686 RDTITL> * VAN DER WAALS = -27.3655 ELECTROSTATIC = -49.6031 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7630" Parameter: CONF_N -> "8002" Comparing "7630" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7631" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756705 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757641 ATOM PAIRS WERE FOUND FOR ATOM LIST 41683 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30298 from a total of 757641 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7631 -78.10104 1.13249 0.74788 INTE EXTERN> -24.95663 -53.14441 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.101" Parameter: A <- "-78.101" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9566" Parameter: B <- "-24.9566" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.1444" Parameter: C <- "-53.1444" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7631 TOTAL ENERGY = -78.101 RDTITL> * VAN DER WAALS = -24.9566 ELECTROSTATIC = -53.1444 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7631" Parameter: CONF_N -> "8002" Comparing "7631" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7632" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757641 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757798 ATOM PAIRS WERE FOUND FOR ATOM LIST 41615 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30236 from a total of 757798 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7632 -80.93084 2.82980 0.67912 INTE EXTERN> -28.35508 -52.57576 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9308" Parameter: A <- "-80.9308" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3551" Parameter: B <- "-28.3551" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5758" Parameter: C <- "-52.5758" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7632 TOTAL ENERGY = -80.9308 RDTITL> * VAN DER WAALS = -28.3551 ELECTROSTATIC = -52.5758 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7632" Parameter: CONF_N -> "8002" Comparing "7632" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7633" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757798 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758548 ATOM PAIRS WERE FOUND FOR ATOM LIST 41738 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29689 from a total of 758548 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7633 -76.30878 -4.62206 0.66539 INTE EXTERN> -28.36943 -47.93936 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3088" Parameter: A <- "-76.3088" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3694" Parameter: B <- "-28.3694" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9394" Parameter: C <- "-47.9394" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7633 TOTAL ENERGY = -76.3088 RDTITL> * VAN DER WAALS = -28.3694 ELECTROSTATIC = -47.9394 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7633" Parameter: CONF_N -> "8002" Comparing "7633" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7634" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758548 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747472 ATOM PAIRS WERE FOUND FOR ATOM LIST 40787 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29143 from a total of 747472 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7634 -74.84079 -1.46799 0.66231 INTE EXTERN> -27.44783 -47.39296 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8408" Parameter: A <- "-74.8408" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.4478" Parameter: B <- "-27.4478" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.393" Parameter: C <- "-47.393" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7634 TOTAL ENERGY = -74.8408 RDTITL> * VAN DER WAALS = -27.4478 ELECTROSTATIC = -47.393 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7634" Parameter: CONF_N -> "8002" Comparing "7634" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7635" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747472 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750248 ATOM PAIRS WERE FOUND FOR ATOM LIST 41056 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29298 from a total of 750248 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7635 -75.81226 0.97147 0.65440 INTE EXTERN> -27.65698 -48.15528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8123" Parameter: A <- "-75.8123" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.657" Parameter: B <- "-27.657" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1553" Parameter: C <- "-48.1553" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7635 TOTAL ENERGY = -75.8123 RDTITL> * VAN DER WAALS = -27.657 ELECTROSTATIC = -48.1553 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7635" Parameter: CONF_N -> "8002" Comparing "7635" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7636" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750248 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759706 ATOM PAIRS WERE FOUND FOR ATOM LIST 41838 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29814 from a total of 759706 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7636 -72.10577 -3.70649 0.67984 INTE EXTERN> -29.12876 -42.97701 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.1058" Parameter: A <- "-72.1058" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1288" Parameter: B <- "-29.1288" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.977" Parameter: C <- "-42.977" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7636 TOTAL ENERGY = -72.1058 RDTITL> * VAN DER WAALS = -29.1288 ELECTROSTATIC = -42.977 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7636" Parameter: CONF_N -> "8002" Comparing "7636" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7637" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759706 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759654 ATOM PAIRS WERE FOUND FOR ATOM LIST 41777 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29634 from a total of 759654 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7637 -73.23847 1.13270 0.57804 INTE EXTERN> -30.63966 -42.59881 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2385" Parameter: A <- "-73.2385" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6397" Parameter: B <- "-30.6397" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5988" Parameter: C <- "-42.5988" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7637 TOTAL ENERGY = -73.2385 RDTITL> * VAN DER WAALS = -30.6397 ELECTROSTATIC = -42.5988 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7637" Parameter: CONF_N -> "8002" Comparing "7637" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7638" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759654 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757703 ATOM PAIRS WERE FOUND FOR ATOM LIST 41702 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29362 from a total of 757703 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7638 -77.22614 3.98767 0.72426 INTE EXTERN> -27.02401 -50.20213 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2261" Parameter: A <- "-77.2261" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.024" Parameter: B <- "-27.024" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2021" Parameter: C <- "-50.2021" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7638 TOTAL ENERGY = -77.2261 RDTITL> * VAN DER WAALS = -27.024 ELECTROSTATIC = -50.2021 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7638" Parameter: CONF_N -> "8002" Comparing "7638" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7639" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757703 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760127 ATOM PAIRS WERE FOUND FOR ATOM LIST 41929 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29808 from a total of 760127 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7639 -79.18783 1.96169 0.67592 INTE EXTERN> -27.59751 -51.59032 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1878" Parameter: A <- "-79.1878" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5975" Parameter: B <- "-27.5975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5903" Parameter: C <- "-51.5903" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7639 TOTAL ENERGY = -79.1878 RDTITL> * VAN DER WAALS = -27.5975 ELECTROSTATIC = -51.5903 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7639" Parameter: CONF_N -> "8002" Comparing "7639" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7640" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760127 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761561 ATOM PAIRS WERE FOUND FOR ATOM LIST 41672 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29756 from a total of 761561 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7640 -75.57100 -3.61684 0.61931 INTE EXTERN> -30.86287 -44.70812 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.571" Parameter: A <- "-75.571" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8629" Parameter: B <- "-30.8629" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7081" Parameter: C <- "-44.7081" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7640 TOTAL ENERGY = -75.571 RDTITL> * VAN DER WAALS = -30.8629 ELECTROSTATIC = -44.7081 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7640" Parameter: CONF_N -> "8002" Comparing "7640" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7641" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761561 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759182 ATOM PAIRS WERE FOUND FOR ATOM LIST 41545 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29416 from a total of 759182 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7641 -76.22223 0.65124 0.61460 INTE EXTERN> -31.09721 -45.12502 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2222" Parameter: A <- "-76.2222" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.0972" Parameter: B <- "-31.0972" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.125" Parameter: C <- "-45.125" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7641 TOTAL ENERGY = -76.2222 RDTITL> * VAN DER WAALS = -31.0972 ELECTROSTATIC = -45.125 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7641" Parameter: CONF_N -> "8002" Comparing "7641" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7642" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759182 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762663 ATOM PAIRS WERE FOUND FOR ATOM LIST 41835 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30132 from a total of 762663 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7642 -77.70619 1.48396 0.88919 INTE EXTERN> -22.95785 -54.74834 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7062" Parameter: A <- "-77.7062" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.9579" Parameter: B <- "-22.9579" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.7483" Parameter: C <- "-54.7483" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7642 TOTAL ENERGY = -77.7062 RDTITL> * VAN DER WAALS = -22.9579 ELECTROSTATIC = -54.7483 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7642" Parameter: CONF_N -> "8002" Comparing "7642" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7643" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762663 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759122 ATOM PAIRS WERE FOUND FOR ATOM LIST 41692 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29474 from a total of 759122 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7643 -76.58971 -1.11648 0.68903 INTE EXTERN> -27.50951 -49.08020 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5897" Parameter: A <- "-76.5897" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5095" Parameter: B <- "-27.5095" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0802" Parameter: C <- "-49.0802" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7643 TOTAL ENERGY = -76.5897 RDTITL> * VAN DER WAALS = -27.5095 ELECTROSTATIC = -49.0802 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7643" Parameter: CONF_N -> "8002" Comparing "7643" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7644" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759122 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758537 ATOM PAIRS WERE FOUND FOR ATOM LIST 41676 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29631 from a total of 758537 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7644 -84.27482 7.68511 0.67898 INTE EXTERN> -30.19140 -54.08342 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.2748" Parameter: A <- "-84.2748" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1914" Parameter: B <- "-30.1914" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0834" Parameter: C <- "-54.0834" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7644 TOTAL ENERGY = -84.2748 RDTITL> * VAN DER WAALS = -30.1914 ELECTROSTATIC = -54.0834 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7644" Parameter: CONF_N -> "8002" Comparing "7644" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7645" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758537 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753659 ATOM PAIRS WERE FOUND FOR ATOM LIST 41344 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29870 from a total of 753659 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7645 -78.56276 -5.71206 0.63864 INTE EXTERN> -29.85614 -48.70662 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5628" Parameter: A <- "-78.5628" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8561" Parameter: B <- "-29.8561" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7066" Parameter: C <- "-48.7066" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7645 TOTAL ENERGY = -78.5628 RDTITL> * VAN DER WAALS = -29.8561 ELECTROSTATIC = -48.7066 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7645" Parameter: CONF_N -> "8002" Comparing "7645" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7646" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753659 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752809 ATOM PAIRS WERE FOUND FOR ATOM LIST 41364 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29809 from a total of 752809 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7646 -79.63971 1.07695 0.62024 INTE EXTERN> -30.52836 -49.11135 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6397" Parameter: A <- "-79.6397" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5284" Parameter: B <- "-30.5284" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1113" Parameter: C <- "-49.1113" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7646 TOTAL ENERGY = -79.6397 RDTITL> * VAN DER WAALS = -30.5284 ELECTROSTATIC = -49.1113 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7646" Parameter: CONF_N -> "8002" Comparing "7646" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7647" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752809 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755205 ATOM PAIRS WERE FOUND FOR ATOM LIST 41378 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29830 from a total of 755205 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7647 -78.48944 -1.15027 0.68011 INTE EXTERN> -27.17426 -51.31518 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4894" Parameter: A <- "-78.4894" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1743" Parameter: B <- "-27.1743" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3152" Parameter: C <- "-51.3152" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7647 TOTAL ENERGY = -78.4894 RDTITL> * VAN DER WAALS = -27.1743 ELECTROSTATIC = -51.3152 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7647" Parameter: CONF_N -> "8002" Comparing "7647" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7648" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755205 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748065 ATOM PAIRS WERE FOUND FOR ATOM LIST 41058 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28782 from a total of 748065 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7648 -78.78578 0.29634 0.61036 INTE EXTERN> -29.03278 -49.75300 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7858" Parameter: A <- "-78.7858" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0328" Parameter: B <- "-29.0328" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.753" Parameter: C <- "-49.753" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7648 TOTAL ENERGY = -78.7858 RDTITL> * VAN DER WAALS = -29.0328 ELECTROSTATIC = -49.753 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7648" Parameter: CONF_N -> "8002" Comparing "7648" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7649" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748065 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754853 ATOM PAIRS WERE FOUND FOR ATOM LIST 41461 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29236 from a total of 754853 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7649 -80.30169 1.51591 0.64354 INTE EXTERN> -28.63234 -51.66935 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3017" Parameter: A <- "-80.3017" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6323" Parameter: B <- "-28.6323" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6693" Parameter: C <- "-51.6693" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7649 TOTAL ENERGY = -80.3017 RDTITL> * VAN DER WAALS = -28.6323 ELECTROSTATIC = -51.6693 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7649" Parameter: CONF_N -> "8002" Comparing "7649" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7650" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754853 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752790 ATOM PAIRS WERE FOUND FOR ATOM LIST 41344 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29459 from a total of 752790 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7650 -68.14416 -12.15752 0.55718 INTE EXTERN> -29.72032 -38.42384 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1442" Parameter: A <- "-68.1442" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7203" Parameter: B <- "-29.7203" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.4238" Parameter: C <- "-38.4238" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7650 TOTAL ENERGY = -68.1442 RDTITL> * VAN DER WAALS = -29.7203 ELECTROSTATIC = -38.4238 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7650" Parameter: CONF_N -> "8002" Comparing "7650" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7651" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752790 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753016 ATOM PAIRS WERE FOUND FOR ATOM LIST 41292 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29762 from a total of 753016 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7651 -73.32305 5.17888 0.83070 INTE EXTERN> -24.54060 -48.78245 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.323" Parameter: A <- "-73.323" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5406" Parameter: B <- "-24.5406" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7824" Parameter: C <- "-48.7824" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7651 TOTAL ENERGY = -73.323 RDTITL> * VAN DER WAALS = -24.5406 ELECTROSTATIC = -48.7824 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7651" Parameter: CONF_N -> "8002" Comparing "7651" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7652" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753016 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752447 ATOM PAIRS WERE FOUND FOR ATOM LIST 41251 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29081 from a total of 752447 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7652 -80.34678 7.02374 0.60346 INTE EXTERN> -30.77501 -49.57177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3468" Parameter: A <- "-80.3468" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.775" Parameter: B <- "-30.775" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5718" Parameter: C <- "-49.5718" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7652 TOTAL ENERGY = -80.3468 RDTITL> * VAN DER WAALS = -30.775 ELECTROSTATIC = -49.5718 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7652" Parameter: CONF_N -> "8002" Comparing "7652" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7653" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752447 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758265 ATOM PAIRS WERE FOUND FOR ATOM LIST 41653 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30267 from a total of 758265 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7653 -75.09725 -5.24953 0.67588 INTE EXTERN> -27.94823 -47.14902 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0973" Parameter: A <- "-75.0973" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9482" Parameter: B <- "-27.9482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.149" Parameter: C <- "-47.149" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7653 TOTAL ENERGY = -75.0973 RDTITL> * VAN DER WAALS = -27.9482 ELECTROSTATIC = -47.149 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7653" Parameter: CONF_N -> "8002" Comparing "7653" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7654" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758265 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748387 ATOM PAIRS WERE FOUND FOR ATOM LIST 41008 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29226 from a total of 748387 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7654 -73.66772 -1.42953 0.69085 INTE EXTERN> -25.70124 -47.96648 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.6677" Parameter: A <- "-73.6677" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7012" Parameter: B <- "-25.7012" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9665" Parameter: C <- "-47.9665" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7654 TOTAL ENERGY = -73.6677 RDTITL> * VAN DER WAALS = -25.7012 ELECTROSTATIC = -47.9665 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7654" Parameter: CONF_N -> "8002" Comparing "7654" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7655" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748387 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749999 ATOM PAIRS WERE FOUND FOR ATOM LIST 41104 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29159 from a total of 749999 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7655 -73.93117 0.26345 0.65258 INTE EXTERN> -25.38273 -48.54844 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9312" Parameter: A <- "-73.9312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3827" Parameter: B <- "-25.3827" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5484" Parameter: C <- "-48.5484" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7655 TOTAL ENERGY = -73.9312 RDTITL> * VAN DER WAALS = -25.3827 ELECTROSTATIC = -48.5484 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7655" Parameter: CONF_N -> "8002" Comparing "7655" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7656" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749999 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748133 ATOM PAIRS WERE FOUND FOR ATOM LIST 41326 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29102 from a total of 748133 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7656 -75.26249 1.33133 0.60380 INTE EXTERN> -28.94169 -46.32080 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2625" Parameter: A <- "-75.2625" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9417" Parameter: B <- "-28.9417" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3208" Parameter: C <- "-46.3208" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7656 TOTAL ENERGY = -75.2625 RDTITL> * VAN DER WAALS = -28.9417 ELECTROSTATIC = -46.3208 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7656" Parameter: CONF_N -> "8002" Comparing "7656" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7657" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748133 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746853 ATOM PAIRS WERE FOUND FOR ATOM LIST 40921 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29764 from a total of 746853 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7657 -81.72053 6.45804 0.76781 INTE EXTERN> -25.96353 -55.75700 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.7205" Parameter: A <- "-81.7205" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9635" Parameter: B <- "-25.9635" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.757" Parameter: C <- "-55.757" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7657 TOTAL ENERGY = -81.7205 RDTITL> * VAN DER WAALS = -25.9635 ELECTROSTATIC = -55.757 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7657" Parameter: CONF_N -> "8002" Comparing "7657" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7658" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746853 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752822 ATOM PAIRS WERE FOUND FOR ATOM LIST 41293 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29485 from a total of 752822 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7658 -78.32855 -3.39199 0.61913 INTE EXTERN> -30.57918 -47.74937 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3285" Parameter: A <- "-78.3285" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5792" Parameter: B <- "-30.5792" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7494" Parameter: C <- "-47.7494" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7658 TOTAL ENERGY = -78.3285 RDTITL> * VAN DER WAALS = -30.5792 ELECTROSTATIC = -47.7494 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7658" Parameter: CONF_N -> "8002" Comparing "7658" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7659" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752822 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748829 ATOM PAIRS WERE FOUND FOR ATOM LIST 41066 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29478 from a total of 748829 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7659 -75.23775 -3.09080 0.59391 INTE EXTERN> -29.59297 -45.64478 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.2377" Parameter: A <- "-75.2377" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.593" Parameter: B <- "-29.593" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6448" Parameter: C <- "-45.6448" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7659 TOTAL ENERGY = -75.2377 RDTITL> * VAN DER WAALS = -29.593 ELECTROSTATIC = -45.6448 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7659" Parameter: CONF_N -> "8002" Comparing "7659" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7660" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748829 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748368 ATOM PAIRS WERE FOUND FOR ATOM LIST 41084 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29502 from a total of 748368 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7660 -73.88987 -1.34788 0.69893 INTE EXTERN> -24.01842 -49.87145 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8899" Parameter: A <- "-73.8899" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0184" Parameter: B <- "-24.0184" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8715" Parameter: C <- "-49.8715" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7660 TOTAL ENERGY = -73.8899 RDTITL> * VAN DER WAALS = -24.0184 ELECTROSTATIC = -49.8715 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7660" Parameter: CONF_N -> "8002" Comparing "7660" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7661" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748368 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 741130 ATOM PAIRS WERE FOUND FOR ATOM LIST 40723 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29349 from a total of 741130 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7661 -70.13272 -3.75715 0.59276 INTE EXTERN> -28.44436 -41.68837 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.1327" Parameter: A <- "-70.1327" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4444" Parameter: B <- "-28.4444" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.6884" Parameter: C <- "-41.6884" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7661 TOTAL ENERGY = -70.1327 RDTITL> * VAN DER WAALS = -28.4444 ELECTROSTATIC = -41.6884 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7661" Parameter: CONF_N -> "8002" Comparing "7661" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7662" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 741130 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747976 ATOM PAIRS WERE FOUND FOR ATOM LIST 41044 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29489 from a total of 747976 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7662 -73.77354 3.64082 0.74809 INTE EXTERN> -25.89090 -47.88264 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7735" Parameter: A <- "-73.7735" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8909" Parameter: B <- "-25.8909" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8826" Parameter: C <- "-47.8826" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7662 TOTAL ENERGY = -73.7735 RDTITL> * VAN DER WAALS = -25.8909 ELECTROSTATIC = -47.8826 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7662" Parameter: CONF_N -> "8002" Comparing "7662" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7663" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747976 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750473 ATOM PAIRS WERE FOUND FOR ATOM LIST 41408 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29667 from a total of 750473 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7663 -71.48078 -2.29277 0.70397 INTE EXTERN> -26.58661 -44.89416 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4808" Parameter: A <- "-71.4808" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5866" Parameter: B <- "-26.5866" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.8942" Parameter: C <- "-44.8942" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7663 TOTAL ENERGY = -71.4808 RDTITL> * VAN DER WAALS = -26.5866 ELECTROSTATIC = -44.8942 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7663" Parameter: CONF_N -> "8002" Comparing "7663" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7664" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750473 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753305 ATOM PAIRS WERE FOUND FOR ATOM LIST 41342 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29501 from a total of 753305 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7664 -78.60067 7.11989 0.69248 INTE EXTERN> -29.05545 -49.54521 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6007" Parameter: A <- "-78.6007" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0555" Parameter: B <- "-29.0555" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5452" Parameter: C <- "-49.5452" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7664 TOTAL ENERGY = -78.6007 RDTITL> * VAN DER WAALS = -29.0555 ELECTROSTATIC = -49.5452 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7664" Parameter: CONF_N -> "8002" Comparing "7664" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7665" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753305 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752704 ATOM PAIRS WERE FOUND FOR ATOM LIST 41277 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29643 from a total of 752704 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7665 -76.81062 -1.79005 0.61799 INTE EXTERN> -29.81890 -46.99172 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8106" Parameter: A <- "-76.8106" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8189" Parameter: B <- "-29.8189" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9917" Parameter: C <- "-46.9917" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7665 TOTAL ENERGY = -76.8106 RDTITL> * VAN DER WAALS = -29.8189 ELECTROSTATIC = -46.9917 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7665" Parameter: CONF_N -> "8002" Comparing "7665" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7666" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752704 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751022 ATOM PAIRS WERE FOUND FOR ATOM LIST 41108 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29479 from a total of 751022 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7666 -71.27277 -5.53785 0.66933 INTE EXTERN> -27.74821 -43.52456 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2728" Parameter: A <- "-71.2728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7482" Parameter: B <- "-27.7482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5246" Parameter: C <- "-43.5246" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7666 TOTAL ENERGY = -71.2728 RDTITL> * VAN DER WAALS = -27.7482 ELECTROSTATIC = -43.5246 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7666" Parameter: CONF_N -> "8002" Comparing "7666" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7667" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751022 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750523 ATOM PAIRS WERE FOUND FOR ATOM LIST 41210 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29405 from a total of 750523 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7667 -67.17430 -4.09846 0.62417 INTE EXTERN> -28.33056 -38.84375 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1743" Parameter: A <- "-67.1743" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3306" Parameter: B <- "-28.3306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8437" Parameter: C <- "-38.8437" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7667 TOTAL ENERGY = -67.1743 RDTITL> * VAN DER WAALS = -28.3306 ELECTROSTATIC = -38.8437 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7667" Parameter: CONF_N -> "8002" Comparing "7667" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7668" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750523 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 747188 ATOM PAIRS WERE FOUND FOR ATOM LIST 41024 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29134 from a total of 747188 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7668 -75.12366 7.94936 0.74403 INTE EXTERN> -25.78042 -49.34324 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1237" Parameter: A <- "-75.1237" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7804" Parameter: B <- "-25.7804" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3432" Parameter: C <- "-49.3432" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7668 TOTAL ENERGY = -75.1237 RDTITL> * VAN DER WAALS = -25.7804 ELECTROSTATIC = -49.3432 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7668" Parameter: CONF_N -> "8002" Comparing "7668" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7669" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 747188 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753530 ATOM PAIRS WERE FOUND FOR ATOM LIST 41433 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29506 from a total of 753530 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7669 -82.61146 7.48780 0.66937 INTE EXTERN> -30.73578 -51.87568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.6115" Parameter: A <- "-82.6115" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7358" Parameter: B <- "-30.7358" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8757" Parameter: C <- "-51.8757" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7669 TOTAL ENERGY = -82.6115 RDTITL> * VAN DER WAALS = -30.7358 ELECTROSTATIC = -51.8757 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7669" Parameter: CONF_N -> "8002" Comparing "7669" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7670" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753530 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753440 ATOM PAIRS WERE FOUND FOR ATOM LIST 41508 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29446 from a total of 753440 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7670 -72.68182 -9.92964 0.63043 INTE EXTERN> -29.14141 -43.54041 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6818" Parameter: A <- "-72.6818" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1414" Parameter: B <- "-29.1414" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5404" Parameter: C <- "-43.5404" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7670 TOTAL ENERGY = -72.6818 RDTITL> * VAN DER WAALS = -29.1414 ELECTROSTATIC = -43.5404 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7670" Parameter: CONF_N -> "8002" Comparing "7670" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7671" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753440 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750208 ATOM PAIRS WERE FOUND FOR ATOM LIST 41116 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29311 from a total of 750208 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7671 -74.41862 1.73679 0.55167 INTE EXTERN> -31.62872 -42.78990 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4186" Parameter: A <- "-74.4186" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6287" Parameter: B <- "-31.6287" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7899" Parameter: C <- "-42.7899" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7671 TOTAL ENERGY = -74.4186 RDTITL> * VAN DER WAALS = -31.6287 ELECTROSTATIC = -42.7899 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7671" Parameter: CONF_N -> "8002" Comparing "7671" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7672" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750208 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746856 ATOM PAIRS WERE FOUND FOR ATOM LIST 40933 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29605 from a total of 746856 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7672 -74.83773 0.41911 0.62999 INTE EXTERN> -29.36692 -45.47081 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8377" Parameter: A <- "-74.8377" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3669" Parameter: B <- "-29.3669" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4708" Parameter: C <- "-45.4708" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7672 TOTAL ENERGY = -74.8377 RDTITL> * VAN DER WAALS = -29.3669 ELECTROSTATIC = -45.4708 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7672" Parameter: CONF_N -> "8002" Comparing "7672" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7673" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746856 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746286 ATOM PAIRS WERE FOUND FOR ATOM LIST 41012 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28754 from a total of 746286 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7673 -80.11283 5.27510 0.80949 INTE EXTERN> -24.18746 -55.92537 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.1128" Parameter: A <- "-80.1128" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.1875" Parameter: B <- "-24.1875" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.9254" Parameter: C <- "-55.9254" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7673 TOTAL ENERGY = -80.1128 RDTITL> * VAN DER WAALS = -24.1875 ELECTROSTATIC = -55.9254 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7673" Parameter: CONF_N -> "8002" Comparing "7673" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7674" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746286 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748625 ATOM PAIRS WERE FOUND FOR ATOM LIST 41267 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29510 from a total of 748625 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7674 -81.96031 1.84748 0.70354 INTE EXTERN> -28.97839 -52.98191 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9603" Parameter: A <- "-81.9603" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9784" Parameter: B <- "-28.9784" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9819" Parameter: C <- "-52.9819" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7674 TOTAL ENERGY = -81.9603 RDTITL> * VAN DER WAALS = -28.9784 ELECTROSTATIC = -52.9819 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7674" Parameter: CONF_N -> "8002" Comparing "7674" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7675" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748625 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750345 ATOM PAIRS WERE FOUND FOR ATOM LIST 41153 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29621 from a total of 750345 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7675 -78.82145 -3.13886 0.72459 INTE EXTERN> -26.16597 -52.65547 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8214" Parameter: A <- "-78.8214" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.166" Parameter: B <- "-26.166" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6555" Parameter: C <- "-52.6555" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7675 TOTAL ENERGY = -78.8214 RDTITL> * VAN DER WAALS = -26.166 ELECTROSTATIC = -52.6555 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7675" Parameter: CONF_N -> "8002" Comparing "7675" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7676" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750345 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753200 ATOM PAIRS WERE FOUND FOR ATOM LIST 41243 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29185 from a total of 753200 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7676 -82.86087 4.03943 0.69112 INTE EXTERN> -30.99246 -51.86841 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.8609" Parameter: A <- "-82.8609" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.9925" Parameter: B <- "-30.9925" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8684" Parameter: C <- "-51.8684" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7676 TOTAL ENERGY = -82.8609 RDTITL> * VAN DER WAALS = -30.9925 ELECTROSTATIC = -51.8684 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7676" Parameter: CONF_N -> "8002" Comparing "7676" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7677" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753200 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 746611 ATOM PAIRS WERE FOUND FOR ATOM LIST 41145 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28624 from a total of 746611 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7677 -86.75185 3.89098 0.69947 INTE EXTERN> -28.01406 -58.73779 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-86.7518" Parameter: A <- "-86.7518" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0141" Parameter: B <- "-28.0141" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.7378" Parameter: C <- "-58.7378" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7677 TOTAL ENERGY = -86.7518 RDTITL> * VAN DER WAALS = -28.0141 ELECTROSTATIC = -58.7378 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7677" Parameter: CONF_N -> "8002" Comparing "7677" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7678" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 746611 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748325 ATOM PAIRS WERE FOUND FOR ATOM LIST 41152 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29042 from a total of 748325 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7678 -80.53910 -6.21275 0.68976 INTE EXTERN> -28.12734 -52.41175 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5391" Parameter: A <- "-80.5391" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1273" Parameter: B <- "-28.1273" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.4118" Parameter: C <- "-52.4118" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7678 TOTAL ENERGY = -80.5391 RDTITL> * VAN DER WAALS = -28.1273 ELECTROSTATIC = -52.4118 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7678" Parameter: CONF_N -> "8002" Comparing "7678" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7679" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748325 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751766 ATOM PAIRS WERE FOUND FOR ATOM LIST 41219 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29816 from a total of 751766 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7679 -79.14794 -1.39116 0.61632 INTE EXTERN> -27.80050 -51.34744 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1479" Parameter: A <- "-79.1479" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8005" Parameter: B <- "-27.8005" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3474" Parameter: C <- "-51.3474" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7679 TOTAL ENERGY = -79.1479 RDTITL> * VAN DER WAALS = -27.8005 ELECTROSTATIC = -51.3474 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7679" Parameter: CONF_N -> "8002" Comparing "7679" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7680" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751766 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749027 ATOM PAIRS WERE FOUND FOR ATOM LIST 41139 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29326 from a total of 749027 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7680 -79.09530 -0.05264 0.61585 INTE EXTERN> -29.93189 -49.16341 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0953" Parameter: A <- "-79.0953" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9319" Parameter: B <- "-29.9319" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1634" Parameter: C <- "-49.1634" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7680 TOTAL ENERGY = -79.0953 RDTITL> * VAN DER WAALS = -29.9319 ELECTROSTATIC = -49.1634 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7680" Parameter: CONF_N -> "8002" Comparing "7680" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7681" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749027 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760145 ATOM PAIRS WERE FOUND FOR ATOM LIST 41639 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29375 from a total of 760145 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7681 -73.23177 -5.86353 0.52911 INTE EXTERN> -31.67786 -41.55391 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2318" Parameter: A <- "-73.2318" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6779" Parameter: B <- "-31.6779" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.5539" Parameter: C <- "-41.5539" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7681 TOTAL ENERGY = -73.2318 RDTITL> * VAN DER WAALS = -31.6779 ELECTROSTATIC = -41.5539 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7681" Parameter: CONF_N -> "8002" Comparing "7681" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7682" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760145 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753347 ATOM PAIRS WERE FOUND FOR ATOM LIST 41230 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28970 from a total of 753347 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7682 -73.74021 0.50844 0.75054 INTE EXTERN> -25.31117 -48.42904 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7402" Parameter: A <- "-73.7402" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3112" Parameter: B <- "-25.3112" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.429" Parameter: C <- "-48.429" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7682 TOTAL ENERGY = -73.7402 RDTITL> * VAN DER WAALS = -25.3112 ELECTROSTATIC = -48.429 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7682" Parameter: CONF_N -> "8002" Comparing "7682" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7683" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753347 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754597 ATOM PAIRS WERE FOUND FOR ATOM LIST 41435 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29247 from a total of 754597 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7683 -76.50522 2.76501 0.71605 INTE EXTERN> -25.88029 -50.62493 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5052" Parameter: A <- "-76.5052" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8803" Parameter: B <- "-25.8803" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6249" Parameter: C <- "-50.6249" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7683 TOTAL ENERGY = -76.5052 RDTITL> * VAN DER WAALS = -25.8803 ELECTROSTATIC = -50.6249 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7683" Parameter: CONF_N -> "8002" Comparing "7683" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7684" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754597 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759897 ATOM PAIRS WERE FOUND FOR ATOM LIST 41613 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29392 from a total of 759897 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7684 -75.91165 -0.59357 0.71548 INTE EXTERN> -25.52129 -50.39036 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9117" Parameter: A <- "-75.9117" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5213" Parameter: B <- "-25.5213" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3904" Parameter: C <- "-50.3904" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7684 TOTAL ENERGY = -75.9117 RDTITL> * VAN DER WAALS = -25.5213 ELECTROSTATIC = -50.3904 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7684" Parameter: CONF_N -> "8002" Comparing "7684" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7685" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759897 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757719 ATOM PAIRS WERE FOUND FOR ATOM LIST 41543 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29898 from a total of 757719 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7685 -79.37413 3.46248 0.68467 INTE EXTERN> -29.17844 -50.19570 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.3741" Parameter: A <- "-79.3741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1784" Parameter: B <- "-29.1784" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1957" Parameter: C <- "-50.1957" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7685 TOTAL ENERGY = -79.3741 RDTITL> * VAN DER WAALS = -29.1784 ELECTROSTATIC = -50.1957 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7685" Parameter: CONF_N -> "8002" Comparing "7685" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7686" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757719 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750293 ATOM PAIRS WERE FOUND FOR ATOM LIST 41201 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29633 from a total of 750293 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7686 -79.55656 0.18243 0.66805 INTE EXTERN> -29.89745 -49.65912 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5566" Parameter: A <- "-79.5566" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8974" Parameter: B <- "-29.8974" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6591" Parameter: C <- "-49.6591" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7686 TOTAL ENERGY = -79.5566 RDTITL> * VAN DER WAALS = -29.8974 ELECTROSTATIC = -49.6591 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7686" Parameter: CONF_N -> "8002" Comparing "7686" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7687" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750293 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755196 ATOM PAIRS WERE FOUND FOR ATOM LIST 41439 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29351 from a total of 755196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7687 -81.89093 2.33436 0.67836 INTE EXTERN> -30.58832 -51.30261 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.8909" Parameter: A <- "-81.8909" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5883" Parameter: B <- "-30.5883" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3026" Parameter: C <- "-51.3026" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7687 TOTAL ENERGY = -81.8909 RDTITL> * VAN DER WAALS = -30.5883 ELECTROSTATIC = -51.3026 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7687" Parameter: CONF_N -> "8002" Comparing "7687" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7688" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755009 ATOM PAIRS WERE FOUND FOR ATOM LIST 41381 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29705 from a total of 755009 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7688 -76.17846 -5.71247 0.57669 INTE EXTERN> -30.23079 -45.94767 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1785" Parameter: A <- "-76.1785" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2308" Parameter: B <- "-30.2308" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9477" Parameter: C <- "-45.9477" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7688 TOTAL ENERGY = -76.1785 RDTITL> * VAN DER WAALS = -30.2308 ELECTROSTATIC = -45.9477 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7688" Parameter: CONF_N -> "8002" Comparing "7688" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7689" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755009 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753876 ATOM PAIRS WERE FOUND FOR ATOM LIST 41473 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29500 from a total of 753876 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7689 -75.18691 -0.99154 0.61853 INTE EXTERN> -30.83884 -44.34808 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1869" Parameter: A <- "-75.1869" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8388" Parameter: B <- "-30.8388" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3481" Parameter: C <- "-44.3481" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7689 TOTAL ENERGY = -75.1869 RDTITL> * VAN DER WAALS = -30.8388 ELECTROSTATIC = -44.3481 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7689" Parameter: CONF_N -> "8002" Comparing "7689" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7690" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753876 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759943 ATOM PAIRS WERE FOUND FOR ATOM LIST 41712 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30081 from a total of 759943 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7690 -76.90752 1.72061 0.69410 INTE EXTERN> -27.89150 -49.01602 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9075" Parameter: A <- "-76.9075" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8915" Parameter: B <- "-27.8915" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.016" Parameter: C <- "-49.016" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7690 TOTAL ENERGY = -76.9075 RDTITL> * VAN DER WAALS = -27.8915 ELECTROSTATIC = -49.016 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7690" Parameter: CONF_N -> "8002" Comparing "7690" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7691" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759943 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756462 ATOM PAIRS WERE FOUND FOR ATOM LIST 41582 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30301 from a total of 756462 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7691 -78.47864 1.57112 0.65480 INTE EXTERN> -28.59276 -49.88587 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4786" Parameter: A <- "-78.4786" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5928" Parameter: B <- "-28.5928" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8859" Parameter: C <- "-49.8859" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7691 TOTAL ENERGY = -78.4786 RDTITL> * VAN DER WAALS = -28.5928 ELECTROSTATIC = -49.8859 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7691" Parameter: CONF_N -> "8002" Comparing "7691" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7692" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756462 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751059 ATOM PAIRS WERE FOUND FOR ATOM LIST 41240 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29378 from a total of 751059 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7692 -74.76858 -3.71005 0.54141 INTE EXTERN> -30.23037 -44.53821 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7686" Parameter: A <- "-74.7686" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2304" Parameter: B <- "-30.2304" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5382" Parameter: C <- "-44.5382" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7692 TOTAL ENERGY = -74.7686 RDTITL> * VAN DER WAALS = -30.2304 ELECTROSTATIC = -44.5382 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7692" Parameter: CONF_N -> "8002" Comparing "7692" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7693" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751059 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751077 ATOM PAIRS WERE FOUND FOR ATOM LIST 41292 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29375 from a total of 751077 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7693 -76.80367 2.03509 0.66953 INTE EXTERN> -25.98258 -50.82110 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8037" Parameter: A <- "-76.8037" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9826" Parameter: B <- "-25.9826" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8211" Parameter: C <- "-50.8211" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7693 TOTAL ENERGY = -76.8037 RDTITL> * VAN DER WAALS = -25.9826 ELECTROSTATIC = -50.8211 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7693" Parameter: CONF_N -> "8002" Comparing "7693" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7694" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751077 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752783 ATOM PAIRS WERE FOUND FOR ATOM LIST 41195 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29819 from a total of 752783 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7694 -72.97789 -3.82578 0.53794 INTE EXTERN> -32.68870 -40.28919 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9779" Parameter: A <- "-72.9779" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6887" Parameter: B <- "-32.6887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.2892" Parameter: C <- "-40.2892" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7694 TOTAL ENERGY = -72.9779 RDTITL> * VAN DER WAALS = -32.6887 ELECTROSTATIC = -40.2892 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7694" Parameter: CONF_N -> "8002" Comparing "7694" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7695" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752783 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754797 ATOM PAIRS WERE FOUND FOR ATOM LIST 41451 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29795 from a total of 754797 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7695 -73.61202 0.63413 0.66456 INTE EXTERN> -28.59099 -45.02103 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.612" Parameter: A <- "-73.612" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.591" Parameter: B <- "-28.591" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.021" Parameter: C <- "-45.021" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7695 TOTAL ENERGY = -73.612 RDTITL> * VAN DER WAALS = -28.591 ELECTROSTATIC = -45.021 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7695" Parameter: CONF_N -> "8002" Comparing "7695" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7696" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754797 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758226 ATOM PAIRS WERE FOUND FOR ATOM LIST 41568 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29685 from a total of 758226 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7696 -78.15366 4.54164 0.64732 INTE EXTERN> -26.03380 -52.11986 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1537" Parameter: A <- "-78.1537" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0338" Parameter: B <- "-26.0338" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.1199" Parameter: C <- "-52.1199" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7696 TOTAL ENERGY = -78.1537 RDTITL> * VAN DER WAALS = -26.0338 ELECTROSTATIC = -52.1199 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7696" Parameter: CONF_N -> "8002" Comparing "7696" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7697" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758226 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757640 ATOM PAIRS WERE FOUND FOR ATOM LIST 41595 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29753 from a total of 757640 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7697 -76.43160 -1.72206 0.61055 INTE EXTERN> -29.64559 -46.78601 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4316" Parameter: A <- "-76.4316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6456" Parameter: B <- "-29.6456" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.786" Parameter: C <- "-46.786" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7697 TOTAL ENERGY = -76.4316 RDTITL> * VAN DER WAALS = -29.6456 ELECTROSTATIC = -46.786 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7697" Parameter: CONF_N -> "8002" Comparing "7697" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7698" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757640 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756708 ATOM PAIRS WERE FOUND FOR ATOM LIST 41429 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29408 from a total of 756708 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7698 -74.30091 -2.13069 0.71089 INTE EXTERN> -25.43505 -48.86586 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3009" Parameter: A <- "-74.3009" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.435" Parameter: B <- "-25.435" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8659" Parameter: C <- "-48.8659" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7698 TOTAL ENERGY = -74.3009 RDTITL> * VAN DER WAALS = -25.435 ELECTROSTATIC = -48.8659 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7698" Parameter: CONF_N -> "8002" Comparing "7698" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7699" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756708 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757527 ATOM PAIRS WERE FOUND FOR ATOM LIST 41592 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29062 from a total of 757527 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7699 -74.21557 -0.08534 0.72029 INTE EXTERN> -23.94325 -50.27232 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2156" Parameter: A <- "-74.2156" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9432" Parameter: B <- "-23.9432" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2723" Parameter: C <- "-50.2723" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7699 TOTAL ENERGY = -74.2156 RDTITL> * VAN DER WAALS = -23.9432 ELECTROSTATIC = -50.2723 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7699" Parameter: CONF_N -> "8002" Comparing "7699" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7700" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757527 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755368 ATOM PAIRS WERE FOUND FOR ATOM LIST 41488 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30124 from a total of 755368 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7700 -79.27303 5.05745 0.76008 INTE EXTERN> -24.36932 -54.90370 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.273" Parameter: A <- "-79.273" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3693" Parameter: B <- "-24.3693" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.9037" Parameter: C <- "-54.9037" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7700 TOTAL ENERGY = -79.273 RDTITL> * VAN DER WAALS = -24.3693 ELECTROSTATIC = -54.9037 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7700" Parameter: CONF_N -> "8002" Comparing "7700" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7701" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755368 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752970 ATOM PAIRS WERE FOUND FOR ATOM LIST 41247 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28994 from a total of 752970 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7701 -75.79740 -3.47562 0.73280 INTE EXTERN> -23.36399 -52.43341 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7974" Parameter: A <- "-75.7974" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.364" Parameter: B <- "-23.364" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.4334" Parameter: C <- "-52.4334" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7701 TOTAL ENERGY = -75.7974 RDTITL> * VAN DER WAALS = -23.364 ELECTROSTATIC = -52.4334 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7701" Parameter: CONF_N -> "8002" Comparing "7701" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7702" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752970 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751152 ATOM PAIRS WERE FOUND FOR ATOM LIST 41055 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29256 from a total of 751152 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7702 -73.24084 -2.55656 0.65294 INTE EXTERN> -29.36128 -43.87956 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2408" Parameter: A <- "-73.2408" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3613" Parameter: B <- "-29.3613" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8796" Parameter: C <- "-43.8796" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7702 TOTAL ENERGY = -73.2408 RDTITL> * VAN DER WAALS = -29.3613 ELECTROSTATIC = -43.8796 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7702" Parameter: CONF_N -> "8002" Comparing "7702" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7703" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751152 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756578 ATOM PAIRS WERE FOUND FOR ATOM LIST 41347 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29351 from a total of 756578 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7703 -79.03770 5.79686 0.60866 INTE EXTERN> -30.44148 -48.59622 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0377" Parameter: A <- "-79.0377" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4415" Parameter: B <- "-30.4415" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5962" Parameter: C <- "-48.5962" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7703 TOTAL ENERGY = -79.0377 RDTITL> * VAN DER WAALS = -30.4415 ELECTROSTATIC = -48.5962 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7703" Parameter: CONF_N -> "8002" Comparing "7703" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7704" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756578 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749900 ATOM PAIRS WERE FOUND FOR ATOM LIST 41165 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28666 from a total of 749900 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7704 -73.39835 -5.63935 0.72538 INTE EXTERN> -22.57295 -50.82540 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3984" Parameter: A <- "-73.3984" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.573" Parameter: B <- "-22.573" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8254" Parameter: C <- "-50.8254" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7704 TOTAL ENERGY = -73.3984 RDTITL> * VAN DER WAALS = -22.573 ELECTROSTATIC = -50.8254 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7704" Parameter: CONF_N -> "8002" Comparing "7704" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7705" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749900 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755162 ATOM PAIRS WERE FOUND FOR ATOM LIST 41358 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29410 from a total of 755162 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7705 -75.94810 2.54975 0.76179 INTE EXTERN> -25.82392 -50.12419 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9481" Parameter: A <- "-75.9481" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8239" Parameter: B <- "-25.8239" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1242" Parameter: C <- "-50.1242" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7705 TOTAL ENERGY = -75.9481 RDTITL> * VAN DER WAALS = -25.8239 ELECTROSTATIC = -50.1242 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7705" Parameter: CONF_N -> "8002" Comparing "7705" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7706" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755162 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756565 ATOM PAIRS WERE FOUND FOR ATOM LIST 41323 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29533 from a total of 756565 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7706 -78.44782 2.49972 0.64760 INTE EXTERN> -28.53816 -49.90966 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4478" Parameter: A <- "-78.4478" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5382" Parameter: B <- "-28.5382" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9097" Parameter: C <- "-49.9097" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7706 TOTAL ENERGY = -78.4478 RDTITL> * VAN DER WAALS = -28.5382 ELECTROSTATIC = -49.9097 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7706" Parameter: CONF_N -> "8002" Comparing "7706" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7707" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756565 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751656 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29019 from a total of 751656 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7707 -73.82567 -4.62215 0.68375 INTE EXTERN> -26.51275 -47.31291 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8257" Parameter: A <- "-73.8257" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5128" Parameter: B <- "-26.5128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3129" Parameter: C <- "-47.3129" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7707 TOTAL ENERGY = -73.8257 RDTITL> * VAN DER WAALS = -26.5128 ELECTROSTATIC = -47.3129 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7707" Parameter: CONF_N -> "8002" Comparing "7707" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7708" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751656 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759020 ATOM PAIRS WERE FOUND FOR ATOM LIST 41613 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29984 from a total of 759020 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7708 -74.44090 0.61523 0.67965 INTE EXTERN> -26.44911 -47.99179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4409" Parameter: A <- "-74.4409" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.4491" Parameter: B <- "-26.4491" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9918" Parameter: C <- "-47.9918" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7708 TOTAL ENERGY = -74.4409 RDTITL> * VAN DER WAALS = -26.4491 ELECTROSTATIC = -47.9918 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7708" Parameter: CONF_N -> "8002" Comparing "7708" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7709" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759020 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760692 ATOM PAIRS WERE FOUND FOR ATOM LIST 41919 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30006 from a total of 760692 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7709 -76.85288 2.41198 0.57518 INTE EXTERN> -29.66031 -47.19258 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8529" Parameter: A <- "-76.8529" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6603" Parameter: B <- "-29.6603" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1926" Parameter: C <- "-47.1926" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7709 TOTAL ENERGY = -76.8529 RDTITL> * VAN DER WAALS = -29.6603 ELECTROSTATIC = -47.1926 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7709" Parameter: CONF_N -> "8002" Comparing "7709" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7710" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760692 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756649 ATOM PAIRS WERE FOUND FOR ATOM LIST 41699 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29758 from a total of 756649 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7710 -73.30910 -3.54379 0.68395 INTE EXTERN> -27.33078 -45.97831 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3091" Parameter: A <- "-73.3091" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3308" Parameter: B <- "-27.3308" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9783" Parameter: C <- "-45.9783" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7710 TOTAL ENERGY = -73.3091 RDTITL> * VAN DER WAALS = -27.3308 ELECTROSTATIC = -45.9783 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7710" Parameter: CONF_N -> "8002" Comparing "7710" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7711" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756649 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753623 ATOM PAIRS WERE FOUND FOR ATOM LIST 41343 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30154 from a total of 753623 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7711 -78.83207 5.52297 0.63230 INTE EXTERN> -31.20220 -47.62987 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8321" Parameter: A <- "-78.8321" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2022" Parameter: B <- "-31.2022" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.6299" Parameter: C <- "-47.6299" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7711 TOTAL ENERGY = -78.8321 RDTITL> * VAN DER WAALS = -31.2022 ELECTROSTATIC = -47.6299 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7711" Parameter: CONF_N -> "8002" Comparing "7711" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7712" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753623 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755614 ATOM PAIRS WERE FOUND FOR ATOM LIST 41457 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29385 from a total of 755614 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7712 -75.69743 -3.13464 0.61460 INTE EXTERN> -31.78201 -43.91542 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.6974" Parameter: A <- "-75.6974" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.782" Parameter: B <- "-31.782" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9154" Parameter: C <- "-43.9154" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7712 TOTAL ENERGY = -75.6974 RDTITL> * VAN DER WAALS = -31.782 ELECTROSTATIC = -43.9154 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7712" Parameter: CONF_N -> "8002" Comparing "7712" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7713" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755614 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754627 ATOM PAIRS WERE FOUND FOR ATOM LIST 41421 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30251 from a total of 754627 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7713 -74.96522 -0.73221 0.66061 INTE EXTERN> -28.28543 -46.67980 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9652" Parameter: A <- "-74.9652" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2854" Parameter: B <- "-28.2854" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6798" Parameter: C <- "-46.6798" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7713 TOTAL ENERGY = -74.9652 RDTITL> * VAN DER WAALS = -28.2854 ELECTROSTATIC = -46.6798 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7713" Parameter: CONF_N -> "8002" Comparing "7713" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7714" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754627 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753907 ATOM PAIRS WERE FOUND FOR ATOM LIST 41298 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30325 from a total of 753907 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7714 -71.50861 -3.45662 0.58511 INTE EXTERN> -27.99849 -43.51012 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5086" Parameter: A <- "-71.5086" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9985" Parameter: B <- "-27.9985" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.5101" Parameter: C <- "-43.5101" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7714 TOTAL ENERGY = -71.5086 RDTITL> * VAN DER WAALS = -27.9985 ELECTROSTATIC = -43.5101 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7714" Parameter: CONF_N -> "8002" Comparing "7714" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7715" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753907 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758763 ATOM PAIRS WERE FOUND FOR ATOM LIST 41632 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30061 from a total of 758763 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7715 -79.82555 8.31694 0.64622 INTE EXTERN> -29.23038 -50.59517 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8255" Parameter: A <- "-79.8255" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2304" Parameter: B <- "-29.2304" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.5952" Parameter: C <- "-50.5952" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7715 TOTAL ENERGY = -79.8255 RDTITL> * VAN DER WAALS = -29.2304 ELECTROSTATIC = -50.5952 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7715" Parameter: CONF_N -> "8002" Comparing "7715" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7716" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758763 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760301 ATOM PAIRS WERE FOUND FOR ATOM LIST 41707 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30021 from a total of 760301 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7716 -74.75002 -5.07552 0.58632 INTE EXTERN> -29.17339 -45.57663 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.75" Parameter: A <- "-74.75" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1734" Parameter: B <- "-29.1734" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5766" Parameter: C <- "-45.5766" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7716 TOTAL ENERGY = -74.75 RDTITL> * VAN DER WAALS = -29.1734 ELECTROSTATIC = -45.5766 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7716" Parameter: CONF_N -> "8002" Comparing "7716" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7717" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760301 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755965 ATOM PAIRS WERE FOUND FOR ATOM LIST 41571 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30073 from a total of 755965 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7717 -78.12407 3.37404 0.59804 INTE EXTERN> -29.95153 -48.17253 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1241" Parameter: A <- "-78.1241" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9515" Parameter: B <- "-29.9515" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1725" Parameter: C <- "-48.1725" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7717 TOTAL ENERGY = -78.1241 RDTITL> * VAN DER WAALS = -29.9515 ELECTROSTATIC = -48.1725 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7717" Parameter: CONF_N -> "8002" Comparing "7717" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7718" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755965 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759226 ATOM PAIRS WERE FOUND FOR ATOM LIST 41748 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30590 from a total of 759226 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7718 -76.92266 -1.20141 0.61061 INTE EXTERN> -31.52468 -45.39798 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9227" Parameter: A <- "-76.9227" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5247" Parameter: B <- "-31.5247" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.398" Parameter: C <- "-45.398" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7718 TOTAL ENERGY = -76.9227 RDTITL> * VAN DER WAALS = -31.5247 ELECTROSTATIC = -45.398 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7718" Parameter: CONF_N -> "8002" Comparing "7718" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7719" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759226 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752778 ATOM PAIRS WERE FOUND FOR ATOM LIST 41298 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29272 from a total of 752778 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7719 -76.15476 -0.76790 0.63438 INTE EXTERN> -27.51610 -48.63866 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.1548" Parameter: A <- "-76.1548" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5161" Parameter: B <- "-27.5161" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6387" Parameter: C <- "-48.6387" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7719 TOTAL ENERGY = -76.1548 RDTITL> * VAN DER WAALS = -27.5161 ELECTROSTATIC = -48.6387 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7719" Parameter: CONF_N -> "8002" Comparing "7719" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7720" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752778 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751387 ATOM PAIRS WERE FOUND FOR ATOM LIST 41321 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29949 from a total of 751387 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7720 -74.81780 -1.33696 0.56639 INTE EXTERN> -32.52022 -42.29757 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.8178" Parameter: A <- "-74.8178" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5202" Parameter: B <- "-32.5202" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.2976" Parameter: C <- "-42.2976" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7720 TOTAL ENERGY = -74.8178 RDTITL> * VAN DER WAALS = -32.5202 ELECTROSTATIC = -42.2976 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7720" Parameter: CONF_N -> "8002" Comparing "7720" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7721" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751387 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754174 ATOM PAIRS WERE FOUND FOR ATOM LIST 41338 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29722 from a total of 754174 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7721 -81.55759 6.73979 0.59892 INTE EXTERN> -31.97837 -49.57922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5576" Parameter: A <- "-81.5576" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9784" Parameter: B <- "-31.9784" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5792" Parameter: C <- "-49.5792" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7721 TOTAL ENERGY = -81.5576 RDTITL> * VAN DER WAALS = -31.9784 ELECTROSTATIC = -49.5792 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7721" Parameter: CONF_N -> "8002" Comparing "7721" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7722" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754174 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760735 ATOM PAIRS WERE FOUND FOR ATOM LIST 41854 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30352 from a total of 760735 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7722 -74.92384 -6.63375 0.67695 INTE EXTERN> -24.95558 -49.96826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.9238" Parameter: A <- "-74.9238" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9556" Parameter: B <- "-24.9556" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9683" Parameter: C <- "-49.9683" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7722 TOTAL ENERGY = -74.9238 RDTITL> * VAN DER WAALS = -24.9556 ELECTROSTATIC = -49.9683 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7722" Parameter: CONF_N -> "8002" Comparing "7722" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7723" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760735 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754906 ATOM PAIRS WERE FOUND FOR ATOM LIST 41424 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29781 from a total of 754906 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7723 -73.03149 -1.89235 0.59723 INTE EXTERN> -27.39621 -45.63528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0315" Parameter: A <- "-73.0315" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3962" Parameter: B <- "-27.3962" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6353" Parameter: C <- "-45.6353" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7723 TOTAL ENERGY = -73.0315 RDTITL> * VAN DER WAALS = -27.3962 ELECTROSTATIC = -45.6353 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7723" Parameter: CONF_N -> "8002" Comparing "7723" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7724" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754906 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760134 ATOM PAIRS WERE FOUND FOR ATOM LIST 41608 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29703 from a total of 760134 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7724 -71.04989 -1.98160 0.56688 INTE EXTERN> -28.91253 -42.13736 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0499" Parameter: A <- "-71.0499" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9125" Parameter: B <- "-28.9125" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1374" Parameter: C <- "-42.1374" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7724 TOTAL ENERGY = -71.0499 RDTITL> * VAN DER WAALS = -28.9125 ELECTROSTATIC = -42.1374 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7724" Parameter: CONF_N -> "8002" Comparing "7724" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7725" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760134 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762143 ATOM PAIRS WERE FOUND FOR ATOM LIST 41831 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29946 from a total of 762143 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7725 -73.81824 2.76836 0.76192 INTE EXTERN> -24.42907 -49.38918 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8182" Parameter: A <- "-73.8182" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.4291" Parameter: B <- "-24.4291" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3892" Parameter: C <- "-49.3892" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7725 TOTAL ENERGY = -73.8182 RDTITL> * VAN DER WAALS = -24.4291 ELECTROSTATIC = -49.3892 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7725" Parameter: CONF_N -> "8002" Comparing "7725" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7726" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762143 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762828 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29298 from a total of 762828 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7726 -70.27529 -3.54295 0.69033 INTE EXTERN> -24.62844 -45.64685 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2753" Parameter: A <- "-70.2753" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6284" Parameter: B <- "-24.6284" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6469" Parameter: C <- "-45.6469" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7726 TOTAL ENERGY = -70.2753 RDTITL> * VAN DER WAALS = -24.6284 ELECTROSTATIC = -45.6469 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7726" Parameter: CONF_N -> "8002" Comparing "7726" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7727" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762828 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756333 ATOM PAIRS WERE FOUND FOR ATOM LIST 41533 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29665 from a total of 756333 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7727 -77.39800 7.12271 0.70625 INTE EXTERN> -23.51069 -53.88731 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.398" Parameter: A <- "-77.398" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.5107" Parameter: B <- "-23.5107" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8873" Parameter: C <- "-53.8873" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7727 TOTAL ENERGY = -77.398 RDTITL> * VAN DER WAALS = -23.5107 ELECTROSTATIC = -53.8873 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7727" Parameter: CONF_N -> "8002" Comparing "7727" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7728" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756333 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759266 ATOM PAIRS WERE FOUND FOR ATOM LIST 41612 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30311 from a total of 759266 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7728 -73.31507 -4.08293 0.58826 INTE EXTERN> -27.85765 -45.45743 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3151" Parameter: A <- "-73.3151" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8576" Parameter: B <- "-27.8576" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4574" Parameter: C <- "-45.4574" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7728 TOTAL ENERGY = -73.3151 RDTITL> * VAN DER WAALS = -27.8576 ELECTROSTATIC = -45.4574 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7728" Parameter: CONF_N -> "8002" Comparing "7728" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7729" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759266 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754479 ATOM PAIRS WERE FOUND FOR ATOM LIST 41472 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29225 from a total of 754479 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7729 -68.99699 -4.31809 0.63963 INTE EXTERN> -25.39116 -43.60582 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.997" Parameter: A <- "-68.997" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3912" Parameter: B <- "-25.3912" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6058" Parameter: C <- "-43.6058" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7729 TOTAL ENERGY = -68.997 RDTITL> * VAN DER WAALS = -25.3912 ELECTROSTATIC = -43.6058 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7729" Parameter: CONF_N -> "8002" Comparing "7729" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7730" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754479 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757164 ATOM PAIRS WERE FOUND FOR ATOM LIST 41467 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29957 from a total of 757164 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7730 -66.18270 -2.81429 0.67632 INTE EXTERN> -25.17167 -41.01103 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.1827" Parameter: A <- "-66.1827" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1717" Parameter: B <- "-25.1717" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.011" Parameter: C <- "-41.011" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7730 TOTAL ENERGY = -66.1827 RDTITL> * VAN DER WAALS = -25.1717 ELECTROSTATIC = -41.011 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7730" Parameter: CONF_N -> "8002" Comparing "7730" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7731" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757164 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758001 ATOM PAIRS WERE FOUND FOR ATOM LIST 41507 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29785 from a total of 758001 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7731 -66.65600 0.47330 0.58514 INTE EXTERN> -26.95112 -39.70487 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.656" Parameter: A <- "-66.656" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9511" Parameter: B <- "-26.9511" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.7049" Parameter: C <- "-39.7049" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7731 TOTAL ENERGY = -66.656 RDTITL> * VAN DER WAALS = -26.9511 ELECTROSTATIC = -39.7049 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7731" Parameter: CONF_N -> "8002" Comparing "7731" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7732" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758001 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758407 ATOM PAIRS WERE FOUND FOR ATOM LIST 41436 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29178 from a total of 758407 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7732 -72.99789 6.34190 0.55813 INTE EXTERN> -28.45789 -44.54000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9979" Parameter: A <- "-72.9979" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4579" Parameter: B <- "-28.4579" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.54" Parameter: C <- "-44.54" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7732 TOTAL ENERGY = -72.9979 RDTITL> * VAN DER WAALS = -28.4579 ELECTROSTATIC = -44.54 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7732" Parameter: CONF_N -> "8002" Comparing "7732" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7733" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758407 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762347 ATOM PAIRS WERE FOUND FOR ATOM LIST 41629 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30132 from a total of 762347 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7733 -76.01003 3.01214 0.54130 INTE EXTERN> -33.45575 -42.55428 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.01" Parameter: A <- "-76.01" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.4557" Parameter: B <- "-33.4557" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.5543" Parameter: C <- "-42.5543" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7733 TOTAL ENERGY = -76.01 RDTITL> * VAN DER WAALS = -33.4557 ELECTROSTATIC = -42.5543 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7733" Parameter: CONF_N -> "8002" Comparing "7733" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7734" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762347 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757373 ATOM PAIRS WERE FOUND FOR ATOM LIST 41626 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29531 from a total of 757373 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7734 -70.06922 -5.94081 0.75311 INTE EXTERN> -20.59119 -49.47803 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.0692" Parameter: A <- "-70.0692" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.5912" Parameter: B <- "-20.5912" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.478" Parameter: C <- "-49.478" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7734 TOTAL ENERGY = -70.0692 RDTITL> * VAN DER WAALS = -20.5912 ELECTROSTATIC = -49.478 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7734" Parameter: CONF_N -> "8002" Comparing "7734" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7735" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757373 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760095 ATOM PAIRS WERE FOUND FOR ATOM LIST 41821 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29638 from a total of 760095 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7735 -73.88672 3.81749 0.74651 INTE EXTERN> -24.36847 -49.51824 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8867" Parameter: A <- "-73.8867" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3685" Parameter: B <- "-24.3685" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5182" Parameter: C <- "-49.5182" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7735 TOTAL ENERGY = -73.8867 RDTITL> * VAN DER WAALS = -24.3685 ELECTROSTATIC = -49.5182 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7735" Parameter: CONF_N -> "8002" Comparing "7735" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7736" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760095 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755522 ATOM PAIRS WERE FOUND FOR ATOM LIST 41536 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29357 from a total of 755522 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7736 -69.01960 -4.86712 0.66317 INTE EXTERN> -26.01021 -43.00939 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.0196" Parameter: A <- "-69.0196" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0102" Parameter: B <- "-26.0102" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0094" Parameter: C <- "-43.0094" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7736 TOTAL ENERGY = -69.0196 RDTITL> * VAN DER WAALS = -26.0102 ELECTROSTATIC = -43.0094 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7736" Parameter: CONF_N -> "8002" Comparing "7736" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7737" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755522 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758043 ATOM PAIRS WERE FOUND FOR ATOM LIST 41573 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29674 from a total of 758043 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7737 -73.74742 4.72782 0.62008 INTE EXTERN> -27.69263 -46.05478 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7474" Parameter: A <- "-73.7474" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6926" Parameter: B <- "-27.6926" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.0548" Parameter: C <- "-46.0548" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7737 TOTAL ENERGY = -73.7474 RDTITL> * VAN DER WAALS = -27.6926 ELECTROSTATIC = -46.0548 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7737" Parameter: CONF_N -> "8002" Comparing "7737" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7738" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758043 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761795 ATOM PAIRS WERE FOUND FOR ATOM LIST 41768 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29491 from a total of 761795 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7738 -72.56133 -1.18608 0.51838 INTE EXTERN> -32.22846 -40.33288 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5613" Parameter: A <- "-72.5613" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.2285" Parameter: B <- "-32.2285" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.3329" Parameter: C <- "-40.3329" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7738 TOTAL ENERGY = -72.5613 RDTITL> * VAN DER WAALS = -32.2285 ELECTROSTATIC = -40.3329 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7738" Parameter: CONF_N -> "8002" Comparing "7738" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7739" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761795 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753151 ATOM PAIRS WERE FOUND FOR ATOM LIST 41306 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29060 from a total of 753151 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7739 -69.12626 -3.43507 0.55079 INTE EXTERN> -31.80326 -37.32300 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.1263" Parameter: A <- "-69.1263" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.8033" Parameter: B <- "-31.8033" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.323" Parameter: C <- "-37.323" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7739 TOTAL ENERGY = -69.1263 RDTITL> * VAN DER WAALS = -31.8033 ELECTROSTATIC = -37.323 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7739" Parameter: CONF_N -> "8002" Comparing "7739" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7740" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753151 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757458 ATOM PAIRS WERE FOUND FOR ATOM LIST 41667 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29852 from a total of 757458 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7740 -65.67888 -3.44738 0.51691 INTE EXTERN> -30.23671 -35.44217 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.6789" Parameter: A <- "-65.6789" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2367" Parameter: B <- "-30.2367" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.4422" Parameter: C <- "-35.4422" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7740 TOTAL ENERGY = -65.6789 RDTITL> * VAN DER WAALS = -30.2367 ELECTROSTATIC = -35.4422 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7740" Parameter: CONF_N -> "8002" Comparing "7740" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7741" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757458 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754964 ATOM PAIRS WERE FOUND FOR ATOM LIST 41378 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29414 from a total of 754964 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7741 -71.40078 5.72190 0.78007 INTE EXTERN> -24.23791 -47.16287 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4008" Parameter: A <- "-71.4008" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.2379" Parameter: B <- "-24.2379" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.1629" Parameter: C <- "-47.1629" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7741 TOTAL ENERGY = -71.4008 RDTITL> * VAN DER WAALS = -24.2379 ELECTROSTATIC = -47.1629 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7741" Parameter: CONF_N -> "8002" Comparing "7741" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7742" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754964 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760177 ATOM PAIRS WERE FOUND FOR ATOM LIST 41727 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29880 from a total of 760177 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7742 -69.38195 -2.01883 0.73576 INTE EXTERN> -23.45466 -45.92729 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.382" Parameter: A <- "-69.382" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.4547" Parameter: B <- "-23.4547" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9273" Parameter: C <- "-45.9273" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7742 TOTAL ENERGY = -69.382 RDTITL> * VAN DER WAALS = -23.4547 ELECTROSTATIC = -45.9273 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7742" Parameter: CONF_N -> "8002" Comparing "7742" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7743" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760177 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756312 ATOM PAIRS WERE FOUND FOR ATOM LIST 41393 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29536 from a total of 756312 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7743 -78.87311 9.49116 0.71419 INTE EXTERN> -25.39518 -53.47792 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8731" Parameter: A <- "-78.8731" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.3952" Parameter: B <- "-25.3952" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4779" Parameter: C <- "-53.4779" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7743 TOTAL ENERGY = -78.8731 RDTITL> * VAN DER WAALS = -25.3952 ELECTROSTATIC = -53.4779 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7743" Parameter: CONF_N -> "8002" Comparing "7743" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7744" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756312 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750914 ATOM PAIRS WERE FOUND FOR ATOM LIST 41364 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29514 from a total of 750914 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7744 -68.28612 -10.58699 0.68584 INTE EXTERN> -27.42399 -40.86213 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.2861" Parameter: A <- "-68.2861" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.424" Parameter: B <- "-27.424" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.8621" Parameter: C <- "-40.8621" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7744 TOTAL ENERGY = -68.2861 RDTITL> * VAN DER WAALS = -27.424 ELECTROSTATIC = -40.8621 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7744" Parameter: CONF_N -> "8002" Comparing "7744" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7745" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750914 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756455 ATOM PAIRS WERE FOUND FOR ATOM LIST 41660 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29006 from a total of 756455 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7745 -73.73556 5.44944 0.64169 INTE EXTERN> -27.02189 -46.71367 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.7356" Parameter: A <- "-73.7356" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0219" Parameter: B <- "-27.0219" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7137" Parameter: C <- "-46.7137" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7745 TOTAL ENERGY = -73.7356 RDTITL> * VAN DER WAALS = -27.0219 ELECTROSTATIC = -46.7137 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7745" Parameter: CONF_N -> "8002" Comparing "7745" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7746" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756455 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756600 ATOM PAIRS WERE FOUND FOR ATOM LIST 41499 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29503 from a total of 756600 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7746 -70.34848 -3.38708 0.61995 INTE EXTERN> -30.37221 -39.97627 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.3485" Parameter: A <- "-70.3485" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3722" Parameter: B <- "-30.3722" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.9763" Parameter: C <- "-39.9763" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7746 TOTAL ENERGY = -70.3485 RDTITL> * VAN DER WAALS = -30.3722 ELECTROSTATIC = -39.9763 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7746" Parameter: CONF_N -> "8002" Comparing "7746" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7747" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756600 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757457 ATOM PAIRS WERE FOUND FOR ATOM LIST 41572 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29765 from a total of 757457 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7747 -73.80541 3.45693 0.61502 INTE EXTERN> -30.44221 -43.36320 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8054" Parameter: A <- "-73.8054" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4422" Parameter: B <- "-30.4422" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.3632" Parameter: C <- "-43.3632" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7747 TOTAL ENERGY = -73.8054 RDTITL> * VAN DER WAALS = -30.4422 ELECTROSTATIC = -43.3632 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7747" Parameter: CONF_N -> "8002" Comparing "7747" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7748" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757457 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757413 ATOM PAIRS WERE FOUND FOR ATOM LIST 41588 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30176 from a total of 757413 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7748 -76.88822 3.08281 0.65509 INTE EXTERN> -28.52598 -48.36224 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8882" Parameter: A <- "-76.8882" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.526" Parameter: B <- "-28.526" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.3622" Parameter: C <- "-48.3622" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7748 TOTAL ENERGY = -76.8882 RDTITL> * VAN DER WAALS = -28.526 ELECTROSTATIC = -48.3622 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7748" Parameter: CONF_N -> "8002" Comparing "7748" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7749" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757413 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759475 ATOM PAIRS WERE FOUND FOR ATOM LIST 41518 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30182 from a total of 759475 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7749 -78.81198 1.92375 0.69672 INTE EXTERN> -29.21765 -49.59433 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.812" Parameter: A <- "-78.812" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2176" Parameter: B <- "-29.2176" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5943" Parameter: C <- "-49.5943" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7749 TOTAL ENERGY = -78.812 RDTITL> * VAN DER WAALS = -29.2176 ELECTROSTATIC = -49.5943 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7749" Parameter: CONF_N -> "8002" Comparing "7749" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7750" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759475 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759021 ATOM PAIRS WERE FOUND FOR ATOM LIST 41653 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30034 from a total of 759021 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7750 -74.51815 -4.29382 0.64023 INTE EXTERN> -28.27949 -46.23866 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5182" Parameter: A <- "-74.5182" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2795" Parameter: B <- "-28.2795" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2387" Parameter: C <- "-46.2387" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7750 TOTAL ENERGY = -74.5182 RDTITL> * VAN DER WAALS = -28.2795 ELECTROSTATIC = -46.2387 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7750" Parameter: CONF_N -> "8002" Comparing "7750" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7751" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759021 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751891 ATOM PAIRS WERE FOUND FOR ATOM LIST 41298 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29443 from a total of 751891 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7751 -71.57400 -2.94415 0.66412 INTE EXTERN> -27.76436 -43.80964 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.574" Parameter: A <- "-71.574" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7644" Parameter: B <- "-27.7644" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8096" Parameter: C <- "-43.8096" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7751 TOTAL ENERGY = -71.574 RDTITL> * VAN DER WAALS = -27.7644 ELECTROSTATIC = -43.8096 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7751" Parameter: CONF_N -> "8002" Comparing "7751" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7752" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751891 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760155 ATOM PAIRS WERE FOUND FOR ATOM LIST 41647 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29748 from a total of 760155 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7752 -75.64105 4.06704 0.54758 INTE EXTERN> -31.91740 -43.72365 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.641" Parameter: A <- "-75.641" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.9174" Parameter: B <- "-31.9174" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7237" Parameter: C <- "-43.7237" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7752 TOTAL ENERGY = -75.641 RDTITL> * VAN DER WAALS = -31.9174 ELECTROSTATIC = -43.7237 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7752" Parameter: CONF_N -> "8002" Comparing "7752" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7753" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760155 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755196 ATOM PAIRS WERE FOUND FOR ATOM LIST 41331 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29691 from a total of 755196 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7753 -78.59210 2.95105 0.58105 INTE EXTERN> -29.03666 -49.55544 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5921" Parameter: A <- "-78.5921" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0367" Parameter: B <- "-29.0367" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5554" Parameter: C <- "-49.5554" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7753 TOTAL ENERGY = -78.5921 RDTITL> * VAN DER WAALS = -29.0367 ELECTROSTATIC = -49.5554 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7753" Parameter: CONF_N -> "8002" Comparing "7753" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7754" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755196 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41403 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29808 from a total of 753526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7754 -71.06279 -7.52931 0.60404 INTE EXTERN> -27.23659 -43.82620 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0628" Parameter: A <- "-71.0628" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2366" Parameter: B <- "-27.2366" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8262" Parameter: C <- "-43.8262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7754 TOTAL ENERGY = -71.0628 RDTITL> * VAN DER WAALS = -27.2366 ELECTROSTATIC = -43.8262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7754" Parameter: CONF_N -> "8002" Comparing "7754" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7755" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756426 ATOM PAIRS WERE FOUND FOR ATOM LIST 41396 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29372 from a total of 756426 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7755 -65.46420 -5.59860 0.71011 INTE EXTERN> -22.61149 -42.85270 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.4642" Parameter: A <- "-65.4642" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.6115" Parameter: B <- "-22.6115" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8527" Parameter: C <- "-42.8527" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7755 TOTAL ENERGY = -65.4642 RDTITL> * VAN DER WAALS = -22.6115 ELECTROSTATIC = -42.8527 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7755" Parameter: CONF_N -> "8002" Comparing "7755" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7756" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756426 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753367 ATOM PAIRS WERE FOUND FOR ATOM LIST 41308 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29042 from a total of 753367 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7756 -72.67874 7.21454 0.63092 INTE EXTERN> -25.92546 -46.75328 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.6787" Parameter: A <- "-72.6787" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9255" Parameter: B <- "-25.9255" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7533" Parameter: C <- "-46.7533" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7756 TOTAL ENERGY = -72.6787 RDTITL> * VAN DER WAALS = -25.9255 ELECTROSTATIC = -46.7533 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7756" Parameter: CONF_N -> "8002" Comparing "7756" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7757" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753367 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752688 ATOM PAIRS WERE FOUND FOR ATOM LIST 41471 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29516 from a total of 752688 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7757 -69.66870 -3.01003 0.68270 INTE EXTERN> -24.97809 -44.69062 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6687" Parameter: A <- "-69.6687" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9781" Parameter: B <- "-24.9781" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6906" Parameter: C <- "-44.6906" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7757 TOTAL ENERGY = -69.6687 RDTITL> * VAN DER WAALS = -24.9781 ELECTROSTATIC = -44.6906 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7757" Parameter: CONF_N -> "8002" Comparing "7757" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7758" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752688 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755970 ATOM PAIRS WERE FOUND FOR ATOM LIST 41480 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30200 from a total of 755970 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7758 -75.45381 5.78510 0.72738 INTE EXTERN> -27.85993 -47.59388 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4538" Parameter: A <- "-75.4538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8599" Parameter: B <- "-27.8599" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.5939" Parameter: C <- "-47.5939" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7758 TOTAL ENERGY = -75.4538 RDTITL> * VAN DER WAALS = -27.8599 ELECTROSTATIC = -47.5939 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7758" Parameter: CONF_N -> "8002" Comparing "7758" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7759" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755970 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751919 ATOM PAIRS WERE FOUND FOR ATOM LIST 41363 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29549 from a total of 751919 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7759 -75.45110 -0.00271 0.58741 INTE EXTERN> -29.82256 -45.62854 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4511" Parameter: A <- "-75.4511" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8226" Parameter: B <- "-29.8226" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6285" Parameter: C <- "-45.6285" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7759 TOTAL ENERGY = -75.4511 RDTITL> * VAN DER WAALS = -29.8226 ELECTROSTATIC = -45.6285 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7759" Parameter: CONF_N -> "8002" Comparing "7759" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7760" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751919 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755726 ATOM PAIRS WERE FOUND FOR ATOM LIST 41581 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29845 from a total of 755726 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7760 -80.04497 4.59387 0.71824 INTE EXTERN> -26.22476 -53.82021 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.045" Parameter: A <- "-80.045" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2248" Parameter: B <- "-26.2248" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.8202" Parameter: C <- "-53.8202" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7760 TOTAL ENERGY = -80.045 RDTITL> * VAN DER WAALS = -26.2248 ELECTROSTATIC = -53.8202 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7760" Parameter: CONF_N -> "8002" Comparing "7760" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7761" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755726 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750765 ATOM PAIRS WERE FOUND FOR ATOM LIST 41382 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29309 from a total of 750765 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7761 -75.86760 -4.17736 0.64368 INTE EXTERN> -27.75267 -48.11493 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8676" Parameter: A <- "-75.8676" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7527" Parameter: B <- "-27.7527" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.1149" Parameter: C <- "-48.1149" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7761 TOTAL ENERGY = -75.8676 RDTITL> * VAN DER WAALS = -27.7527 ELECTROSTATIC = -48.1149 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7761" Parameter: CONF_N -> "8002" Comparing "7761" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7762" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750765 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754655 ATOM PAIRS WERE FOUND FOR ATOM LIST 41350 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29487 from a total of 754655 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7762 -66.92626 -8.94134 0.49246 INTE EXTERN> -29.17516 -37.75110 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9263" Parameter: A <- "-66.9263" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1752" Parameter: B <- "-29.1752" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.7511" Parameter: C <- "-37.7511" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7762 TOTAL ENERGY = -66.9263 RDTITL> * VAN DER WAALS = -29.1752 ELECTROSTATIC = -37.7511 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7762" Parameter: CONF_N -> "8002" Comparing "7762" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7763" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754655 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761887 ATOM PAIRS WERE FOUND FOR ATOM LIST 41822 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29801 from a total of 761887 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7763 -76.22843 9.30216 0.68205 INTE EXTERN> -27.03727 -49.19116 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2284" Parameter: A <- "-76.2284" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0373" Parameter: B <- "-27.0373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1912" Parameter: C <- "-49.1912" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7763 TOTAL ENERGY = -76.2284 RDTITL> * VAN DER WAALS = -27.0373 ELECTROSTATIC = -49.1912 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7763" Parameter: CONF_N -> "8002" Comparing "7763" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7764" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761887 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752085 ATOM PAIRS WERE FOUND FOR ATOM LIST 41355 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28927 from a total of 752085 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7764 -71.11166 -5.11676 0.59608 INTE EXTERN> -27.28630 -43.82536 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1117" Parameter: A <- "-71.1117" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2863" Parameter: B <- "-27.2863" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.8254" Parameter: C <- "-43.8254" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7764 TOTAL ENERGY = -71.1117 RDTITL> * VAN DER WAALS = -27.2863 ELECTROSTATIC = -43.8254 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7764" Parameter: CONF_N -> "8002" Comparing "7764" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7765" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752085 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752343 ATOM PAIRS WERE FOUND FOR ATOM LIST 41254 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29048 from a total of 752343 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7765 -82.95878 11.84711 0.63775 INTE EXTERN> -29.29459 -53.66419 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.9588" Parameter: A <- "-82.9588" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2946" Parameter: B <- "-29.2946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6642" Parameter: C <- "-53.6642" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7765 TOTAL ENERGY = -82.9588 RDTITL> * VAN DER WAALS = -29.2946 ELECTROSTATIC = -53.6642 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7765" Parameter: CONF_N -> "8002" Comparing "7765" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7766" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752343 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750930 ATOM PAIRS WERE FOUND FOR ATOM LIST 41393 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29413 from a total of 750930 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7766 -78.09000 -4.86878 0.75309 INTE EXTERN> -26.02068 -52.06931 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.09" Parameter: A <- "-78.09" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0207" Parameter: B <- "-26.0207" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0693" Parameter: C <- "-52.0693" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7766 TOTAL ENERGY = -78.09 RDTITL> * VAN DER WAALS = -26.0207 ELECTROSTATIC = -52.0693 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7766" Parameter: CONF_N -> "8002" Comparing "7766" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7767" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750930 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750820 ATOM PAIRS WERE FOUND FOR ATOM LIST 41373 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29449 from a total of 750820 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7767 -76.07629 -2.01370 0.64599 INTE EXTERN> -29.47712 -46.59918 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0763" Parameter: A <- "-76.0763" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4771" Parameter: B <- "-29.4771" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.5992" Parameter: C <- "-46.5992" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7767 TOTAL ENERGY = -76.0763 RDTITL> * VAN DER WAALS = -29.4771 ELECTROSTATIC = -46.5992 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7767" Parameter: CONF_N -> "8002" Comparing "7767" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7768" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750820 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753305 ATOM PAIRS WERE FOUND FOR ATOM LIST 41242 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29190 from a total of 753305 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7768 -75.14116 -0.93514 0.57442 INTE EXTERN> -30.69371 -44.44744 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1412" Parameter: A <- "-75.1412" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6937" Parameter: B <- "-30.6937" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4474" Parameter: C <- "-44.4474" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7768 TOTAL ENERGY = -75.1412 RDTITL> * VAN DER WAALS = -30.6937 ELECTROSTATIC = -44.4474 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7768" Parameter: CONF_N -> "8002" Comparing "7768" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7769" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753305 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757010 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29183 from a total of 757010 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7769 -72.02256 -3.11859 0.69616 INTE EXTERN> -23.36220 -48.66036 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0226" Parameter: A <- "-72.0226" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.3622" Parameter: B <- "-23.3622" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6604" Parameter: C <- "-48.6604" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7769 TOTAL ENERGY = -72.0226 RDTITL> * VAN DER WAALS = -23.3622 ELECTROSTATIC = -48.6604 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7769" Parameter: CONF_N -> "8002" Comparing "7769" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7770" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757010 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757334 ATOM PAIRS WERE FOUND FOR ATOM LIST 41556 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29532 from a total of 757334 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7770 -73.26233 1.23976 0.66520 INTE EXTERN> -27.29563 -45.96670 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2623" Parameter: A <- "-73.2623" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2956" Parameter: B <- "-27.2956" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.9667" Parameter: C <- "-45.9667" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7770 TOTAL ENERGY = -73.2623 RDTITL> * VAN DER WAALS = -27.2956 ELECTROSTATIC = -45.9667 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7770" Parameter: CONF_N -> "8002" Comparing "7770" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7771" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757334 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754484 ATOM PAIRS WERE FOUND FOR ATOM LIST 41476 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29407 from a total of 754484 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7771 -79.24009 5.97776 0.67262 INTE EXTERN> -28.05561 -51.18448 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.2401" Parameter: A <- "-79.2401" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0556" Parameter: B <- "-28.0556" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.1845" Parameter: C <- "-51.1845" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7771 TOTAL ENERGY = -79.2401 RDTITL> * VAN DER WAALS = -28.0556 ELECTROSTATIC = -51.1845 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7771" Parameter: CONF_N -> "8002" Comparing "7771" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7772" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754484 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763257 ATOM PAIRS WERE FOUND FOR ATOM LIST 41600 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29523 from a total of 763257 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7772 -77.16138 -2.07871 0.65122 INTE EXTERN> -28.51984 -48.64154 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1614" Parameter: A <- "-77.1614" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5198" Parameter: B <- "-28.5198" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6415" Parameter: C <- "-48.6415" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7772 TOTAL ENERGY = -77.1614 RDTITL> * VAN DER WAALS = -28.5198 ELECTROSTATIC = -48.6415 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7772" Parameter: CONF_N -> "8002" Comparing "7772" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7773" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763257 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756329 ATOM PAIRS WERE FOUND FOR ATOM LIST 41650 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29337 from a total of 756329 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7773 -67.06944 -10.09194 0.57483 INTE EXTERN> -27.63133 -39.43811 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.0694" Parameter: A <- "-67.0694" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6313" Parameter: B <- "-27.6313" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.4381" Parameter: C <- "-39.4381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7773 TOTAL ENERGY = -67.0694 RDTITL> * VAN DER WAALS = -27.6313 ELECTROSTATIC = -39.4381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7773" Parameter: CONF_N -> "8002" Comparing "7773" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7774" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756329 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751646 ATOM PAIRS WERE FOUND FOR ATOM LIST 41167 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29039 from a total of 751646 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7774 -69.65682 2.58738 0.61148 INTE EXTERN> -28.48588 -41.17094 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.6568" Parameter: A <- "-69.6568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.4859" Parameter: B <- "-28.4859" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1709" Parameter: C <- "-41.1709" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7774 TOTAL ENERGY = -69.6568 RDTITL> * VAN DER WAALS = -28.4859 ELECTROSTATIC = -41.1709 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7774" Parameter: CONF_N -> "8002" Comparing "7774" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7775" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751646 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754676 ATOM PAIRS WERE FOUND FOR ATOM LIST 41289 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29467 from a total of 754676 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7775 -72.48606 2.82925 0.59294 INTE EXTERN> -29.32945 -43.15661 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4861" Parameter: A <- "-72.4861" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3294" Parameter: B <- "-29.3294" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1566" Parameter: C <- "-43.1566" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7775 TOTAL ENERGY = -72.4861 RDTITL> * VAN DER WAALS = -29.3294 ELECTROSTATIC = -43.1566 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7775" Parameter: CONF_N -> "8002" Comparing "7775" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7776" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754676 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755847 ATOM PAIRS WERE FOUND FOR ATOM LIST 41507 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28863 from a total of 755847 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7776 -72.87361 0.38755 0.56171 INTE EXTERN> -28.23588 -44.63774 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.8736" Parameter: A <- "-72.8736" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2359" Parameter: B <- "-28.2359" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6377" Parameter: C <- "-44.6377" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7776 TOTAL ENERGY = -72.8736 RDTITL> * VAN DER WAALS = -28.2359 ELECTROSTATIC = -44.6377 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7776" Parameter: CONF_N -> "8002" Comparing "7776" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7777" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755847 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756257 ATOM PAIRS WERE FOUND FOR ATOM LIST 41564 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28900 from a total of 756257 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7777 -71.83050 -1.04311 0.68230 INTE EXTERN> -29.43567 -42.39483 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8305" Parameter: A <- "-71.8305" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4357" Parameter: B <- "-29.4357" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.3948" Parameter: C <- "-42.3948" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7777 TOTAL ENERGY = -71.8305 RDTITL> * VAN DER WAALS = -29.4357 ELECTROSTATIC = -42.3948 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7777" Parameter: CONF_N -> "8002" Comparing "7777" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7778" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756257 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760933 ATOM PAIRS WERE FOUND FOR ATOM LIST 41820 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29888 from a total of 760933 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7778 -76.23337 4.40287 0.59993 INTE EXTERN> -32.15469 -44.07869 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2334" Parameter: A <- "-76.2334" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.1547" Parameter: B <- "-32.1547" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0787" Parameter: C <- "-44.0787" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7778 TOTAL ENERGY = -76.2334 RDTITL> * VAN DER WAALS = -32.1547 ELECTROSTATIC = -44.0787 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7778" Parameter: CONF_N -> "8002" Comparing "7778" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7779" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760933 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757515 ATOM PAIRS WERE FOUND FOR ATOM LIST 41555 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29543 from a total of 757515 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7779 -76.99094 0.75756 0.67926 INTE EXTERN> -27.89314 -49.09780 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9909" Parameter: A <- "-76.9909" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8931" Parameter: B <- "-27.8931" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0978" Parameter: C <- "-49.0978" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7779 TOTAL ENERGY = -76.9909 RDTITL> * VAN DER WAALS = -27.8931 ELECTROSTATIC = -49.0978 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7779" Parameter: CONF_N -> "8002" Comparing "7779" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7780" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757515 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754535 ATOM PAIRS WERE FOUND FOR ATOM LIST 41399 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29558 from a total of 754535 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7780 -73.12568 -3.86526 0.83361 INTE EXTERN> -22.40510 -50.72057 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.1257" Parameter: A <- "-73.1257" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.4051" Parameter: B <- "-22.4051" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7206" Parameter: C <- "-50.7206" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7780 TOTAL ENERGY = -73.1257 RDTITL> * VAN DER WAALS = -22.4051 ELECTROSTATIC = -50.7206 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7780" Parameter: CONF_N -> "8002" Comparing "7780" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7781" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754535 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760839 ATOM PAIRS WERE FOUND FOR ATOM LIST 41586 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29307 from a total of 760839 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7781 -79.57383 6.44815 0.78440 INTE EXTERN> -25.58874 -53.98509 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.5738" Parameter: A <- "-79.5738" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5887" Parameter: B <- "-25.5887" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.9851" Parameter: C <- "-53.9851" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7781 TOTAL ENERGY = -79.5738 RDTITL> * VAN DER WAALS = -25.5887 ELECTROSTATIC = -53.9851 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7781" Parameter: CONF_N -> "8002" Comparing "7781" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7782" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760839 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755799 ATOM PAIRS WERE FOUND FOR ATOM LIST 41599 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29196 from a total of 755799 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7782 -82.03006 2.45623 0.62490 INTE EXTERN> -33.51533 -48.51472 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.0301" Parameter: A <- "-82.0301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.5153" Parameter: B <- "-33.5153" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.5147" Parameter: C <- "-48.5147" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7782 TOTAL ENERGY = -82.0301 RDTITL> * VAN DER WAALS = -33.5153 ELECTROSTATIC = -48.5147 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7782" Parameter: CONF_N -> "8002" Comparing "7782" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7783" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755799 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754725 ATOM PAIRS WERE FOUND FOR ATOM LIST 41487 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29354 from a total of 754725 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7783 -79.01489 -3.01516 0.70730 INTE EXTERN> -29.40161 -49.61329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0149" Parameter: A <- "-79.0149" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.4016" Parameter: B <- "-29.4016" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.6133" Parameter: C <- "-49.6133" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7783 TOTAL ENERGY = -79.0149 RDTITL> * VAN DER WAALS = -29.4016 ELECTROSTATIC = -49.6133 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7783" Parameter: CONF_N -> "8002" Comparing "7783" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7784" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754725 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758654 ATOM PAIRS WERE FOUND FOR ATOM LIST 41865 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29664 from a total of 758654 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7784 -80.72628 1.71139 0.67915 INTE EXTERN> -29.86459 -50.86169 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7263" Parameter: A <- "-80.7263" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.8646" Parameter: B <- "-29.8646" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8617" Parameter: C <- "-50.8617" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7784 TOTAL ENERGY = -80.7263 RDTITL> * VAN DER WAALS = -29.8646 ELECTROSTATIC = -50.8617 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7784" Parameter: CONF_N -> "8002" Comparing "7784" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7785" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758654 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757169 ATOM PAIRS WERE FOUND FOR ATOM LIST 41398 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29283 from a total of 757169 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7785 -82.76060 2.03432 0.62418 INTE EXTERN> -31.42607 -51.33453 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.7606" Parameter: A <- "-82.7606" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4261" Parameter: B <- "-31.4261" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3345" Parameter: C <- "-51.3345" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7785 TOTAL ENERGY = -82.7606 RDTITL> * VAN DER WAALS = -31.4261 ELECTROSTATIC = -51.3345 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7785" Parameter: CONF_N -> "8002" Comparing "7785" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7786" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757169 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757405 ATOM PAIRS WERE FOUND FOR ATOM LIST 41425 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29471 from a total of 757405 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7786 -78.49784 -4.26276 0.87415 INTE EXTERN> -22.71074 -55.78710 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4978" Parameter: A <- "-78.4978" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.7107" Parameter: B <- "-22.7107" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.7871" Parameter: C <- "-55.7871" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7786 TOTAL ENERGY = -78.4978 RDTITL> * VAN DER WAALS = -22.7107 ELECTROSTATIC = -55.7871 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7786" Parameter: CONF_N -> "8002" Comparing "7786" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7787" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757405 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755102 ATOM PAIRS WERE FOUND FOR ATOM LIST 41278 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28950 from a total of 755102 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7787 -78.19087 -0.30697 0.72573 INTE EXTERN> -26.84973 -51.34114 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.1909" Parameter: A <- "-78.1909" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8497" Parameter: B <- "-26.8497" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3411" Parameter: C <- "-51.3411" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7787 TOTAL ENERGY = -78.1909 RDTITL> * VAN DER WAALS = -26.8497 ELECTROSTATIC = -51.3411 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7787" Parameter: CONF_N -> "8002" Comparing "7787" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7788" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755102 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754119 ATOM PAIRS WERE FOUND FOR ATOM LIST 41242 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29589 from a total of 754119 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7788 -78.97490 0.78403 0.64727 INTE EXTERN> -30.27015 -48.70475 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9749" Parameter: A <- "-78.9749" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.2702" Parameter: B <- "-30.2702" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7047" Parameter: C <- "-48.7047" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7788 TOTAL ENERGY = -78.9749 RDTITL> * VAN DER WAALS = -30.2702 ELECTROSTATIC = -48.7047 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7788" Parameter: CONF_N -> "8002" Comparing "7788" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7789" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754119 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759574 ATOM PAIRS WERE FOUND FOR ATOM LIST 41710 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29306 from a total of 759574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7789 -73.25914 -5.71576 0.63656 INTE EXTERN> -27.88499 -45.37415 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2591" Parameter: A <- "-73.2591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.885" Parameter: B <- "-27.885" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3742" Parameter: C <- "-45.3742" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7789 TOTAL ENERGY = -73.2591 RDTITL> * VAN DER WAALS = -27.885 ELECTROSTATIC = -45.3742 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7789" Parameter: CONF_N -> "8002" Comparing "7789" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7790" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758567 ATOM PAIRS WERE FOUND FOR ATOM LIST 41634 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29352 from a total of 758567 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7790 -77.56548 4.30634 0.78476 INTE EXTERN> -23.81767 -53.74781 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5655" Parameter: A <- "-77.5655" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.8177" Parameter: B <- "-23.8177" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.7478" Parameter: C <- "-53.7478" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7790 TOTAL ENERGY = -77.5655 RDTITL> * VAN DER WAALS = -23.8177 ELECTROSTATIC = -53.7478 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7790" Parameter: CONF_N -> "8002" Comparing "7790" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7791" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758567 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758789 ATOM PAIRS WERE FOUND FOR ATOM LIST 41581 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29575 from a total of 758789 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7791 -67.70389 -9.86159 0.62681 INTE EXTERN> -27.26887 -40.43502 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.7039" Parameter: A <- "-67.7039" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2689" Parameter: B <- "-27.2689" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.435" Parameter: C <- "-40.435" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7791 TOTAL ENERGY = -67.7039 RDTITL> * VAN DER WAALS = -27.2689 ELECTROSTATIC = -40.435 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7791" Parameter: CONF_N -> "8002" Comparing "7791" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7792" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758789 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758244 ATOM PAIRS WERE FOUND FOR ATOM LIST 41683 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29897 from a total of 758244 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7792 -75.49976 7.79587 0.81486 INTE EXTERN> -23.66724 -51.83253 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.4998" Parameter: A <- "-75.4998" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6672" Parameter: B <- "-23.6672" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8325" Parameter: C <- "-51.8325" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7792 TOTAL ENERGY = -75.4998 RDTITL> * VAN DER WAALS = -23.6672 ELECTROSTATIC = -51.8325 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7792" Parameter: CONF_N -> "8002" Comparing "7792" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7793" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758244 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757272 ATOM PAIRS WERE FOUND FOR ATOM LIST 41563 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29907 from a total of 757272 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7793 -77.34906 1.84930 0.63910 INTE EXTERN> -29.32350 -48.02557 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3491" Parameter: A <- "-77.3491" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3235" Parameter: B <- "-29.3235" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.0256" Parameter: C <- "-48.0256" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7793 TOTAL ENERGY = -77.3491 RDTITL> * VAN DER WAALS = -29.3235 ELECTROSTATIC = -48.0256 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7793" Parameter: CONF_N -> "8002" Comparing "7793" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7794" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757272 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757685 ATOM PAIRS WERE FOUND FOR ATOM LIST 41647 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29587 from a total of 757685 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7794 -84.16449 6.81543 0.62206 INTE EXTERN> -32.35007 -51.81442 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.1645" Parameter: A <- "-84.1645" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.3501" Parameter: B <- "-32.3501" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.8144" Parameter: C <- "-51.8144" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7794 TOTAL ENERGY = -84.1645 RDTITL> * VAN DER WAALS = -32.3501 ELECTROSTATIC = -51.8144 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7794" Parameter: CONF_N -> "8002" Comparing "7794" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7795" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757685 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759673 ATOM PAIRS WERE FOUND FOR ATOM LIST 41487 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30061 from a total of 759673 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7795 -83.15568 -1.00881 0.62616 INTE EXTERN> -33.33112 -49.82457 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.1557" Parameter: A <- "-83.1557" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3311" Parameter: B <- "-33.3311" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.8246" Parameter: C <- "-49.8246" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7795 TOTAL ENERGY = -83.1557 RDTITL> * VAN DER WAALS = -33.3311 ELECTROSTATIC = -49.8246 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7795" Parameter: CONF_N -> "8002" Comparing "7795" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7796" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759673 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753639 ATOM PAIRS WERE FOUND FOR ATOM LIST 41365 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29731 from a total of 753639 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7796 -80.23400 -2.92168 0.69025 INTE EXTERN> -28.98268 -51.25132 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.234" Parameter: A <- "-80.234" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9827" Parameter: B <- "-28.9827" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.2513" Parameter: C <- "-51.2513" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7796 TOTAL ENERGY = -80.234 RDTITL> * VAN DER WAALS = -28.9827 ELECTROSTATIC = -51.2513 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7796" Parameter: CONF_N -> "8002" Comparing "7796" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7797" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753639 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759621 ATOM PAIRS WERE FOUND FOR ATOM LIST 41698 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29830 from a total of 759621 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7797 -80.69147 0.45747 0.64148 INTE EXTERN> -29.94970 -50.74177 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6915" Parameter: A <- "-80.6915" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.9497" Parameter: B <- "-29.9497" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7418" Parameter: C <- "-50.7418" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7797 TOTAL ENERGY = -80.6915 RDTITL> * VAN DER WAALS = -29.9497 ELECTROSTATIC = -50.7418 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7797" Parameter: CONF_N -> "8002" Comparing "7797" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7798" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759621 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756990 ATOM PAIRS WERE FOUND FOR ATOM LIST 41370 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29907 from a total of 756990 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7798 -78.40241 -2.28905 0.62073 INTE EXTERN> -31.56109 -46.84132 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4024" Parameter: A <- "-78.4024" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.5611" Parameter: B <- "-31.5611" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8413" Parameter: C <- "-46.8413" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7798 TOTAL ENERGY = -78.4024 RDTITL> * VAN DER WAALS = -31.5611 ELECTROSTATIC = -46.8413 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7798" Parameter: CONF_N -> "8002" Comparing "7798" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7799" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756990 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759674 ATOM PAIRS WERE FOUND FOR ATOM LIST 41587 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29473 from a total of 759674 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7799 -76.61623 -1.78618 0.66201 INTE EXTERN> -29.26359 -47.35264 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6162" Parameter: A <- "-76.6162" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2636" Parameter: B <- "-29.2636" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3526" Parameter: C <- "-47.3526" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7799 TOTAL ENERGY = -76.6162 RDTITL> * VAN DER WAALS = -29.2636 ELECTROSTATIC = -47.3526 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7799" Parameter: CONF_N -> "8002" Comparing "7799" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7800" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759674 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759454 ATOM PAIRS WERE FOUND FOR ATOM LIST 41584 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30117 from a total of 759454 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7800 -85.50006 8.88382 0.71416 INTE EXTERN> -29.79541 -55.70464 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-85.5001" Parameter: A <- "-85.5001" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7954" Parameter: B <- "-29.7954" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.7046" Parameter: C <- "-55.7046" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7800 TOTAL ENERGY = -85.5001 RDTITL> * VAN DER WAALS = -29.7954 ELECTROSTATIC = -55.7046 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7800" Parameter: CONF_N -> "8002" Comparing "7800" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7801" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759454 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758365 ATOM PAIRS WERE FOUND FOR ATOM LIST 41616 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30175 from a total of 758365 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7801 -84.02650 -1.47355 0.62165 INTE EXTERN> -32.06558 -51.96093 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.0265" Parameter: A <- "-84.0265" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.0656" Parameter: B <- "-32.0656" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.9609" Parameter: C <- "-51.9609" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7801 TOTAL ENERGY = -84.0265 RDTITL> * VAN DER WAALS = -32.0656 ELECTROSTATIC = -51.9609 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7801" Parameter: CONF_N -> "8002" Comparing "7801" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7802" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758365 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754260 ATOM PAIRS WERE FOUND FOR ATOM LIST 41333 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29595 from a total of 754260 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7802 -70.98066 -13.04584 0.70670 INTE EXTERN> -25.49776 -45.48291 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9807" Parameter: A <- "-70.9807" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4978" Parameter: B <- "-25.4978" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4829" Parameter: C <- "-45.4829" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7802 TOTAL ENERGY = -70.9807 RDTITL> * VAN DER WAALS = -25.4978 ELECTROSTATIC = -45.4829 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7802" Parameter: CONF_N -> "8002" Comparing "7802" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7803" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754260 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755577 ATOM PAIRS WERE FOUND FOR ATOM LIST 41298 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29624 from a total of 755577 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7803 -76.08793 5.10727 0.53930 INTE EXTERN> -30.83919 -45.24874 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0879" Parameter: A <- "-76.0879" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8392" Parameter: B <- "-30.8392" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2487" Parameter: C <- "-45.2487" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7803 TOTAL ENERGY = -76.0879 RDTITL> * VAN DER WAALS = -30.8392 ELECTROSTATIC = -45.2487 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7803" Parameter: CONF_N -> "8002" Comparing "7803" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7804" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755577 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757537 ATOM PAIRS WERE FOUND FOR ATOM LIST 41387 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29854 from a total of 757537 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7804 -80.79744 4.70951 0.76086 INTE EXTERN> -26.17932 -54.61812 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.7974" Parameter: A <- "-80.7974" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1793" Parameter: B <- "-26.1793" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.6181" Parameter: C <- "-54.6181" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7804 TOTAL ENERGY = -80.7974 RDTITL> * VAN DER WAALS = -26.1793 ELECTROSTATIC = -54.6181 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7804" Parameter: CONF_N -> "8002" Comparing "7804" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7805" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757537 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756294 ATOM PAIRS WERE FOUND FOR ATOM LIST 41433 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29713 from a total of 756294 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7805 -81.61381 0.81637 0.78335 INTE EXTERN> -26.32976 -55.28405 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.6138" Parameter: A <- "-81.6138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.3298" Parameter: B <- "-26.3298" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.2841" Parameter: C <- "-55.2841" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7805 TOTAL ENERGY = -81.6138 RDTITL> * VAN DER WAALS = -26.3298 ELECTROSTATIC = -55.2841 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7805" Parameter: CONF_N -> "8002" Comparing "7805" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7806" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756294 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750825 ATOM PAIRS WERE FOUND FOR ATOM LIST 41233 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29423 from a total of 750825 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7806 -79.70596 -1.90785 0.77404 INTE EXTERN> -27.39878 -52.30718 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.706" Parameter: A <- "-79.706" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3988" Parameter: B <- "-27.3988" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3072" Parameter: C <- "-52.3072" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7806 TOTAL ENERGY = -79.706 RDTITL> * VAN DER WAALS = -27.3988 ELECTROSTATIC = -52.3072 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7806" Parameter: CONF_N -> "8002" Comparing "7806" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7807" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750825 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752864 ATOM PAIRS WERE FOUND FOR ATOM LIST 41179 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29188 from a total of 752864 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7807 -82.42950 2.72354 0.68372 INTE EXTERN> -28.37682 -54.05268 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.4295" Parameter: A <- "-82.4295" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3768" Parameter: B <- "-28.3768" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.0527" Parameter: C <- "-54.0527" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7807 TOTAL ENERGY = -82.4295 RDTITL> * VAN DER WAALS = -28.3768 ELECTROSTATIC = -54.0527 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7807" Parameter: CONF_N -> "8002" Comparing "7807" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7808" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752864 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755222 ATOM PAIRS WERE FOUND FOR ATOM LIST 41405 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29169 from a total of 755222 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7808 -79.16018 -3.26932 0.70637 INTE EXTERN> -30.36737 -48.79281 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1602" Parameter: A <- "-79.1602" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3674" Parameter: B <- "-30.3674" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.7928" Parameter: C <- "-48.7928" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7808 TOTAL ENERGY = -79.1602 RDTITL> * VAN DER WAALS = -30.3674 ELECTROSTATIC = -48.7928 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7808" Parameter: CONF_N -> "8002" Comparing "7808" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7809" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755222 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765538 ATOM PAIRS WERE FOUND FOR ATOM LIST 41866 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29174 from a total of 765538 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7809 -79.00339 -0.15679 0.73478 INTE EXTERN> -28.83774 -50.16565 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0034" Parameter: A <- "-79.0034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8377" Parameter: B <- "-28.8377" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1657" Parameter: C <- "-50.1657" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7809 TOTAL ENERGY = -79.0034 RDTITL> * VAN DER WAALS = -28.8377 ELECTROSTATIC = -50.1657 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7809" Parameter: CONF_N -> "8002" Comparing "7809" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7810" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765538 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 764759 ATOM PAIRS WERE FOUND FOR ATOM LIST 41855 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29824 from a total of 764759 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7810 -80.99652 1.99313 0.77466 INTE EXTERN> -26.14818 -54.84835 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9965" Parameter: A <- "-80.9965" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1482" Parameter: B <- "-26.1482" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.8483" Parameter: C <- "-54.8483" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7810 TOTAL ENERGY = -80.9965 RDTITL> * VAN DER WAALS = -26.1482 ELECTROSTATIC = -54.8483 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7810" Parameter: CONF_N -> "8002" Comparing "7810" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7811" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 764759 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765830 ATOM PAIRS WERE FOUND FOR ATOM LIST 41909 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30161 from a total of 765830 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7811 -75.94147 -5.05506 0.77364 INTE EXTERN> -25.04694 -50.89453 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9415" Parameter: A <- "-75.9415" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0469" Parameter: B <- "-25.0469" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.8945" Parameter: C <- "-50.8945" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7811 TOTAL ENERGY = -75.9415 RDTITL> * VAN DER WAALS = -25.0469 ELECTROSTATIC = -50.8945 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7811" Parameter: CONF_N -> "8002" Comparing "7811" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7812" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765830 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757497 ATOM PAIRS WERE FOUND FOR ATOM LIST 41502 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29410 from a total of 757497 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7812 -87.20478 11.26332 0.74093 INTE EXTERN> -28.53060 -58.67418 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-87.2048" Parameter: A <- "-87.2048" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5306" Parameter: B <- "-28.5306" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-58.6742" Parameter: C <- "-58.6742" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7812 TOTAL ENERGY = -87.2048 RDTITL> * VAN DER WAALS = -28.5306 ELECTROSTATIC = -58.6742 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7812" Parameter: CONF_N -> "8002" Comparing "7812" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7813" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757497 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754888 ATOM PAIRS WERE FOUND FOR ATOM LIST 41514 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30208 from a total of 754888 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7813 -84.82093 -2.38385 0.69470 INTE EXTERN> -28.72963 -56.09130 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.8209" Parameter: A <- "-84.8209" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7296" Parameter: B <- "-28.7296" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.0913" Parameter: C <- "-56.0913" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7813 TOTAL ENERGY = -84.8209 RDTITL> * VAN DER WAALS = -28.7296 ELECTROSTATIC = -56.0913 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7813" Parameter: CONF_N -> "8002" Comparing "7813" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7814" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754888 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753130 ATOM PAIRS WERE FOUND FOR ATOM LIST 41171 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29358 from a total of 753130 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7814 -83.17098 -1.64995 0.84035 INTE EXTERN> -27.53492 -55.63606 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.171" Parameter: A <- "-83.171" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5349" Parameter: B <- "-27.5349" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.6361" Parameter: C <- "-55.6361" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7814 TOTAL ENERGY = -83.171 RDTITL> * VAN DER WAALS = -27.5349 ELECTROSTATIC = -55.6361 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7814" Parameter: CONF_N -> "8002" Comparing "7814" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7815" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753130 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751495 ATOM PAIRS WERE FOUND FOR ATOM LIST 41207 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29478 from a total of 751495 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7815 -79.68431 -3.48667 0.76469 INTE EXTERN> -28.75328 -50.93103 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.6843" Parameter: A <- "-79.6843" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7533" Parameter: B <- "-28.7533" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.931" Parameter: C <- "-50.931" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7815 TOTAL ENERGY = -79.6843 RDTITL> * VAN DER WAALS = -28.7533 ELECTROSTATIC = -50.931 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7815" Parameter: CONF_N -> "8002" Comparing "7815" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7816" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751495 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761733 ATOM PAIRS WERE FOUND FOR ATOM LIST 41500 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29743 from a total of 761733 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7816 -78.96584 -0.71846 0.65419 INTE EXTERN> -29.58108 -49.38476 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9658" Parameter: A <- "-78.9658" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.5811" Parameter: B <- "-29.5811" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3848" Parameter: C <- "-49.3848" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7816 TOTAL ENERGY = -78.9658 RDTITL> * VAN DER WAALS = -29.5811 ELECTROSTATIC = -49.3848 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7816" Parameter: CONF_N -> "8002" Comparing "7816" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7817" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761733 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755254 ATOM PAIRS WERE FOUND FOR ATOM LIST 41421 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29539 from a total of 755254 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7817 -84.35639 5.39055 0.65059 INTE EXTERN> -31.67100 -52.68539 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.3564" Parameter: A <- "-84.3564" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.671" Parameter: B <- "-31.671" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6854" Parameter: C <- "-52.6854" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7817 TOTAL ENERGY = -84.3564 RDTITL> * VAN DER WAALS = -31.671 ELECTROSTATIC = -52.6854 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7817" Parameter: CONF_N -> "8002" Comparing "7817" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7818" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755254 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760525 ATOM PAIRS WERE FOUND FOR ATOM LIST 41499 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29806 from a total of 760525 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7818 -80.88058 -3.47581 0.65665 INTE EXTERN> -30.44278 -50.43780 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.8806" Parameter: A <- "-80.8806" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4428" Parameter: B <- "-30.4428" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4378" Parameter: C <- "-50.4378" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7818 TOTAL ENERGY = -80.8806 RDTITL> * VAN DER WAALS = -30.4428 ELECTROSTATIC = -50.4378 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7818" Parameter: CONF_N -> "8002" Comparing "7818" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7819" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760525 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757944 ATOM PAIRS WERE FOUND FOR ATOM LIST 41667 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29584 from a total of 757944 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7819 -84.61840 3.73781 0.61559 INTE EXTERN> -31.92101 -52.69739 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.6184" Parameter: A <- "-84.6184" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.921" Parameter: B <- "-31.921" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6974" Parameter: C <- "-52.6974" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7819 TOTAL ENERGY = -84.6184 RDTITL> * VAN DER WAALS = -31.921 ELECTROSTATIC = -52.6974 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7819" Parameter: CONF_N -> "8002" Comparing "7819" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7820" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757944 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754191 ATOM PAIRS WERE FOUND FOR ATOM LIST 41351 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29146 from a total of 754191 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7820 -84.93462 0.31623 0.68069 INTE EXTERN> -32.57693 -52.35769 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.9346" Parameter: A <- "-84.9346" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.5769" Parameter: B <- "-32.5769" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3577" Parameter: C <- "-52.3577" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7820 TOTAL ENERGY = -84.9346 RDTITL> * VAN DER WAALS = -32.5769 ELECTROSTATIC = -52.3577 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7820" Parameter: CONF_N -> "8002" Comparing "7820" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7821" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754191 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758538 ATOM PAIRS WERE FOUND FOR ATOM LIST 41521 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29597 from a total of 758538 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7821 -78.91755 -6.01707 0.61702 INTE EXTERN> -31.12584 -47.79172 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.9176" Parameter: A <- "-78.9176" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1258" Parameter: B <- "-31.1258" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7917" Parameter: C <- "-47.7917" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7821 TOTAL ENERGY = -78.9176 RDTITL> * VAN DER WAALS = -31.1258 ELECTROSTATIC = -47.7917 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7821" Parameter: CONF_N -> "8002" Comparing "7821" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7822" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758538 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760152 ATOM PAIRS WERE FOUND FOR ATOM LIST 41685 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29797 from a total of 760152 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7822 -77.93738 -0.98017 0.68049 INTE EXTERN> -30.07993 -47.85745 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.9374" Parameter: A <- "-77.9374" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0799" Parameter: B <- "-30.0799" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8574" Parameter: C <- "-47.8574" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7822 TOTAL ENERGY = -77.9374 RDTITL> * VAN DER WAALS = -30.0799 ELECTROSTATIC = -47.8574 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7822" Parameter: CONF_N -> "8002" Comparing "7822" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7823" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760152 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756004 ATOM PAIRS WERE FOUND FOR ATOM LIST 41350 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29623 from a total of 756004 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7823 -79.17455 1.23717 0.68156 INTE EXTERN> -31.20858 -47.96597 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1746" Parameter: A <- "-79.1746" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2086" Parameter: B <- "-31.2086" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.966" Parameter: C <- "-47.966" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7823 TOTAL ENERGY = -79.1746 RDTITL> * VAN DER WAALS = -31.2086 ELECTROSTATIC = -47.966 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7823" Parameter: CONF_N -> "8002" Comparing "7823" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7824" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756004 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758496 ATOM PAIRS WERE FOUND FOR ATOM LIST 41754 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29954 from a total of 758496 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7824 -76.29970 -2.87485 0.76525 INTE EXTERN> -24.89750 -51.40221 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2997" Parameter: A <- "-76.2997" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.8975" Parameter: B <- "-24.8975" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4022" Parameter: C <- "-51.4022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7824 TOTAL ENERGY = -76.2997 RDTITL> * VAN DER WAALS = -24.8975 ELECTROSTATIC = -51.4022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7824" Parameter: CONF_N -> "8002" Comparing "7824" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7825" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758496 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763601 ATOM PAIRS WERE FOUND FOR ATOM LIST 41949 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30190 from a total of 763601 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7825 -83.16610 6.86640 0.67421 INTE EXTERN> -31.69201 -51.47409 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.1661" Parameter: A <- "-83.1661" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.692" Parameter: B <- "-31.692" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.4741" Parameter: C <- "-51.4741" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7825 TOTAL ENERGY = -83.1661 RDTITL> * VAN DER WAALS = -31.692 ELECTROSTATIC = -51.4741 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7825" Parameter: CONF_N -> "8002" Comparing "7825" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7826" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763601 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756855 ATOM PAIRS WERE FOUND FOR ATOM LIST 41355 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30013 from a total of 756855 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7826 -78.29904 -4.86706 0.68601 INTE EXTERN> -28.94661 -49.35243 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.299" Parameter: A <- "-78.299" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9466" Parameter: B <- "-28.9466" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.3524" Parameter: C <- "-49.3524" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7826 TOTAL ENERGY = -78.299 RDTITL> * VAN DER WAALS = -28.9466 ELECTROSTATIC = -49.3524 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7826" Parameter: CONF_N -> "8002" Comparing "7826" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7827" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756855 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757379 ATOM PAIRS WERE FOUND FOR ATOM LIST 41645 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29962 from a total of 757379 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7827 -71.38478 -6.91425 0.88886 INTE EXTERN> -22.05082 -49.33397 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3848" Parameter: A <- "-71.3848" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.0508" Parameter: B <- "-22.0508" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.334" Parameter: C <- "-49.334" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7827 TOTAL ENERGY = -71.3848 RDTITL> * VAN DER WAALS = -22.0508 ELECTROSTATIC = -49.334 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7827" Parameter: CONF_N -> "8002" Comparing "7827" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7828" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757379 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754216 ATOM PAIRS WERE FOUND FOR ATOM LIST 41382 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30064 from a total of 754216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7828 -77.57991 6.19513 0.70460 INTE EXTERN> -26.28892 -51.29099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5799" Parameter: A <- "-77.5799" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2889" Parameter: B <- "-26.2889" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.291" Parameter: C <- "-51.291" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7828 TOTAL ENERGY = -77.5799 RDTITL> * VAN DER WAALS = -26.2889 ELECTROSTATIC = -51.291 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7828" Parameter: CONF_N -> "8002" Comparing "7828" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7829" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760924 ATOM PAIRS WERE FOUND FOR ATOM LIST 41585 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29939 from a total of 760924 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7829 -77.06025 -0.51966 0.77380 INTE EXTERN> -24.99834 -52.06192 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0603" Parameter: A <- "-77.0603" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9983" Parameter: B <- "-24.9983" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.0619" Parameter: C <- "-52.0619" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7829 TOTAL ENERGY = -77.0603 RDTITL> * VAN DER WAALS = -24.9983 ELECTROSTATIC = -52.0619 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7829" Parameter: CONF_N -> "8002" Comparing "7829" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7830" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760924 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765568 ATOM PAIRS WERE FOUND FOR ATOM LIST 41876 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30281 from a total of 765568 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7830 -82.47701 5.41675 0.74443 INTE EXTERN> -26.95750 -55.51951 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.477" Parameter: A <- "-82.477" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9575" Parameter: B <- "-26.9575" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.5195" Parameter: C <- "-55.5195" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7830 TOTAL ENERGY = -82.477 RDTITL> * VAN DER WAALS = -26.9575 ELECTROSTATIC = -55.5195 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7830" Parameter: CONF_N -> "8002" Comparing "7830" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7831" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765568 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 765184 ATOM PAIRS WERE FOUND FOR ATOM LIST 41881 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30330 from a total of 765184 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7831 -81.39563 -1.08138 0.64084 INTE EXTERN> -31.02204 -50.37359 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.3956" Parameter: A <- "-81.3956" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.022" Parameter: B <- "-31.022" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.3736" Parameter: C <- "-50.3736" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7831 TOTAL ENERGY = -81.3956 RDTITL> * VAN DER WAALS = -31.022 ELECTROSTATIC = -50.3736 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7831" Parameter: CONF_N -> "8002" Comparing "7831" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7832" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 765184 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760219 ATOM PAIRS WERE FOUND FOR ATOM LIST 41847 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30507 from a total of 760219 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7832 -77.57195 -3.82368 0.77630 INTE EXTERN> -23.91208 -53.65987 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.572" Parameter: A <- "-77.572" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9121" Parameter: B <- "-23.9121" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.6599" Parameter: C <- "-53.6599" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7832 TOTAL ENERGY = -77.572 RDTITL> * VAN DER WAALS = -23.9121 ELECTROSTATIC = -53.6599 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7832" Parameter: CONF_N -> "8002" Comparing "7832" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7833" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760219 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759905 ATOM PAIRS WERE FOUND FOR ATOM LIST 41550 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29709 from a total of 759905 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7833 -77.16011 -0.41184 0.73232 INTE EXTERN> -27.68611 -49.47399 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1601" Parameter: A <- "-77.1601" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6861" Parameter: B <- "-27.6861" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.474" Parameter: C <- "-49.474" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7833 TOTAL ENERGY = -77.1601 RDTITL> * VAN DER WAALS = -27.6861 ELECTROSTATIC = -49.474 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7833" Parameter: CONF_N -> "8002" Comparing "7833" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7834" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759905 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759995 ATOM PAIRS WERE FOUND FOR ATOM LIST 41958 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29332 from a total of 759995 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7834 -68.70661 -8.45350 0.95983 INTE EXTERN> -20.78695 -47.91966 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7066" Parameter: A <- "-68.7066" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.787" Parameter: B <- "-20.787" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.9197" Parameter: C <- "-47.9197" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7834 TOTAL ENERGY = -68.7066 RDTITL> * VAN DER WAALS = -20.787 ELECTROSTATIC = -47.9197 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7834" Parameter: CONF_N -> "8002" Comparing "7834" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7835" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759995 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763317 ATOM PAIRS WERE FOUND FOR ATOM LIST 41718 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29932 from a total of 763317 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7835 -77.59388 8.88727 0.71009 INTE EXTERN> -28.80087 -48.79301 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5939" Parameter: A <- "-77.5939" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8009" Parameter: B <- "-28.8009" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.793" Parameter: C <- "-48.793" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7835 TOTAL ENERGY = -77.5939 RDTITL> * VAN DER WAALS = -28.8009 ELECTROSTATIC = -48.793 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7835" Parameter: CONF_N -> "8002" Comparing "7835" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7836" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763317 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763289 ATOM PAIRS WERE FOUND FOR ATOM LIST 41785 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29765 from a total of 763289 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7836 -79.79958 2.20570 0.67851 INTE EXTERN> -28.13739 -51.66219 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7996" Parameter: A <- "-79.7996" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1374" Parameter: B <- "-28.1374" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.6622" Parameter: C <- "-51.6622" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7836 TOTAL ENERGY = -79.7996 RDTITL> * VAN DER WAALS = -28.1374 ELECTROSTATIC = -51.6622 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7836" Parameter: CONF_N -> "8002" Comparing "7836" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7837" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763289 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759404 ATOM PAIRS WERE FOUND FOR ATOM LIST 41735 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30121 from a total of 759404 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7837 -76.05522 -3.74436 0.76982 INTE EXTERN> -25.01928 -51.03594 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.0552" Parameter: A <- "-76.0552" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0193" Parameter: B <- "-25.0193" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0359" Parameter: C <- "-51.0359" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7837 TOTAL ENERGY = -76.0552 RDTITL> * VAN DER WAALS = -25.0193 ELECTROSTATIC = -51.0359 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7837" Parameter: CONF_N -> "8002" Comparing "7837" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7838" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759404 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759396 ATOM PAIRS WERE FOUND FOR ATOM LIST 41782 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29925 from a total of 759396 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7838 -70.72120 -5.33402 0.68983 INTE EXTERN> -25.46772 -45.25348 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7212" Parameter: A <- "-70.7212" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4677" Parameter: B <- "-25.4677" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.2535" Parameter: C <- "-45.2535" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7838 TOTAL ENERGY = -70.7212 RDTITL> * VAN DER WAALS = -25.4677 ELECTROSTATIC = -45.2535 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7838" Parameter: CONF_N -> "8002" Comparing "7838" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7839" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759396 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757400 ATOM PAIRS WERE FOUND FOR ATOM LIST 41577 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30067 from a total of 757400 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7839 -73.21948 2.49827 0.65035 INTE EXTERN> -28.23890 -44.98058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2195" Parameter: A <- "-73.2195" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2389" Parameter: B <- "-28.2389" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.9806" Parameter: C <- "-44.9806" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7839 TOTAL ENERGY = -73.2195 RDTITL> * VAN DER WAALS = -28.2389 ELECTROSTATIC = -44.9806 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7839" Parameter: CONF_N -> "8002" Comparing "7839" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7840" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757400 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753528 ATOM PAIRS WERE FOUND FOR ATOM LIST 41210 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29990 from a total of 753528 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7840 -74.34568 1.12620 0.59332 INTE EXTERN> -30.69450 -43.65118 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3457" Parameter: A <- "-74.3457" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6945" Parameter: B <- "-30.6945" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6512" Parameter: C <- "-43.6512" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7840 TOTAL ENERGY = -74.3457 RDTITL> * VAN DER WAALS = -30.6945 ELECTROSTATIC = -43.6512 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7840" Parameter: CONF_N -> "8002" Comparing "7840" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7841" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753528 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757485 ATOM PAIRS WERE FOUND FOR ATOM LIST 41700 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29947 from a total of 757485 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7841 -74.33436 -0.01132 0.67132 INTE EXTERN> -24.78551 -49.54885 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3344" Parameter: A <- "-74.3344" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.7855" Parameter: B <- "-24.7855" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5489" Parameter: C <- "-49.5489" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7841 TOTAL ENERGY = -74.3344 RDTITL> * VAN DER WAALS = -24.7855 ELECTROSTATIC = -49.5489 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7841" Parameter: CONF_N -> "8002" Comparing "7841" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7842" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757485 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753814 ATOM PAIRS WERE FOUND FOR ATOM LIST 41340 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29716 from a total of 753814 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7842 -80.93871 6.60435 0.76122 INTE EXTERN> -27.53811 -53.40059 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9387" Parameter: A <- "-80.9387" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5381" Parameter: B <- "-27.5381" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4006" Parameter: C <- "-53.4006" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7842 TOTAL ENERGY = -80.9387 RDTITL> * VAN DER WAALS = -27.5381 ELECTROSTATIC = -53.4006 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7842" Parameter: CONF_N -> "8002" Comparing "7842" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7843" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753814 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757141 ATOM PAIRS WERE FOUND FOR ATOM LIST 41467 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29561 from a total of 757141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7843 -71.84518 -9.09353 0.60895 INTE EXTERN> -29.06080 -42.78438 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8452" Parameter: A <- "-71.8452" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.0608" Parameter: B <- "-29.0608" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7844" Parameter: C <- "-42.7844" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7843 TOTAL ENERGY = -71.8452 RDTITL> * VAN DER WAALS = -29.0608 ELECTROSTATIC = -42.7844 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7843" Parameter: CONF_N -> "8002" Comparing "7843" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7844" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760102 ATOM PAIRS WERE FOUND FOR ATOM LIST 41840 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29863 from a total of 760102 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7844 -80.40347 8.55829 0.66967 INTE EXTERN> -26.96243 -53.44104 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4035" Parameter: A <- "-80.4035" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9624" Parameter: B <- "-26.9624" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.441" Parameter: C <- "-53.441" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7844 TOTAL ENERGY = -80.4035 RDTITL> * VAN DER WAALS = -26.9624 ELECTROSTATIC = -53.441 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7844" Parameter: CONF_N -> "8002" Comparing "7844" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7845" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760102 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756071 ATOM PAIRS WERE FOUND FOR ATOM LIST 41460 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29145 from a total of 756071 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7845 -75.00599 -5.39748 0.59951 INTE EXTERN> -28.67632 -46.32967 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.006" Parameter: A <- "-75.006" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6763" Parameter: B <- "-28.6763" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3297" Parameter: C <- "-46.3297" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7845 TOTAL ENERGY = -75.006 RDTITL> * VAN DER WAALS = -28.6763 ELECTROSTATIC = -46.3297 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7845" Parameter: CONF_N -> "8002" Comparing "7845" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7846" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756071 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762141 ATOM PAIRS WERE FOUND FOR ATOM LIST 41889 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29902 from a total of 762141 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7846 -78.75912 3.75313 0.76869 INTE EXTERN> -21.73158 -57.02754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7591" Parameter: A <- "-78.7591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.7316" Parameter: B <- "-21.7316" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.0275" Parameter: C <- "-57.0275" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7846 TOTAL ENERGY = -78.7591 RDTITL> * VAN DER WAALS = -21.7316 ELECTROSTATIC = -57.0275 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7846" Parameter: CONF_N -> "8002" Comparing "7846" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7847" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762141 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761527 ATOM PAIRS WERE FOUND FOR ATOM LIST 41751 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29764 from a total of 761527 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7847 -73.30263 -5.45650 0.64441 INTE EXTERN> -27.25864 -46.04398 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3026" Parameter: A <- "-73.3026" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2586" Parameter: B <- "-27.2586" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.044" Parameter: C <- "-46.044" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7847 TOTAL ENERGY = -73.3026 RDTITL> * VAN DER WAALS = -27.2586 ELECTROSTATIC = -46.044 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7847" Parameter: CONF_N -> "8002" Comparing "7847" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7848" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761527 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754004 ATOM PAIRS WERE FOUND FOR ATOM LIST 41209 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28817 from a total of 754004 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7848 -70.51169 -2.79093 0.70942 INTE EXTERN> -23.76625 -46.74545 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5117" Parameter: A <- "-70.5117" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7662" Parameter: B <- "-23.7662" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.7454" Parameter: C <- "-46.7454" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7848 TOTAL ENERGY = -70.5117 RDTITL> * VAN DER WAALS = -23.7662 ELECTROSTATIC = -46.7454 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7848" Parameter: CONF_N -> "8002" Comparing "7848" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7849" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754004 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752079 ATOM PAIRS WERE FOUND FOR ATOM LIST 41250 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28939 from a total of 752079 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7849 -72.47511 1.96342 0.68151 INTE EXTERN> -25.02924 -47.44587 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.4751" Parameter: A <- "-72.4751" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0292" Parameter: B <- "-25.0292" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4459" Parameter: C <- "-47.4459" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7849 TOTAL ENERGY = -72.4751 RDTITL> * VAN DER WAALS = -25.0292 ELECTROSTATIC = -47.4459 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7849" Parameter: CONF_N -> "8002" Comparing "7849" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7850" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752079 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754813 ATOM PAIRS WERE FOUND FOR ATOM LIST 41299 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29496 from a total of 754813 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7850 -75.17140 2.69629 0.68533 INTE EXTERN> -27.79690 -47.37451 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1714" Parameter: A <- "-75.1714" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7969" Parameter: B <- "-27.7969" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.3745" Parameter: C <- "-47.3745" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7850 TOTAL ENERGY = -75.1714 RDTITL> * VAN DER WAALS = -27.7969 ELECTROSTATIC = -47.3745 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7850" Parameter: CONF_N -> "8002" Comparing "7850" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7851" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754813 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755132 ATOM PAIRS WERE FOUND FOR ATOM LIST 41251 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29627 from a total of 755132 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7851 -69.74187 -5.42954 0.60214 INTE EXTERN> -29.31099 -40.43088 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.7419" Parameter: A <- "-69.7419" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.311" Parameter: B <- "-29.311" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4309" Parameter: C <- "-40.4309" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7851 TOTAL ENERGY = -69.7419 RDTITL> * VAN DER WAALS = -29.311 ELECTROSTATIC = -40.4309 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7851" Parameter: CONF_N -> "8002" Comparing "7851" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7852" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755132 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749974 ATOM PAIRS WERE FOUND FOR ATOM LIST 41101 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28723 from a total of 749974 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7852 -66.08088 -3.66099 0.66589 INTE EXTERN> -23.11091 -42.96997 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0809" Parameter: A <- "-66.0809" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.1109" Parameter: B <- "-23.1109" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.97" Parameter: C <- "-42.97" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7852 TOTAL ENERGY = -66.0809 RDTITL> * VAN DER WAALS = -23.1109 ELECTROSTATIC = -42.97 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7852" Parameter: CONF_N -> "8002" Comparing "7852" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7853" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749974 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754305 ATOM PAIRS WERE FOUND FOR ATOM LIST 41314 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29139 from a total of 754305 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7853 -65.06608 -1.01480 0.58521 INTE EXTERN> -28.36668 -36.69939 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.0661" Parameter: A <- "-65.0661" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3667" Parameter: B <- "-28.3667" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.6994" Parameter: C <- "-36.6994" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7853 TOTAL ENERGY = -65.0661 RDTITL> * VAN DER WAALS = -28.3667 ELECTROSTATIC = -36.6994 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7853" Parameter: CONF_N -> "8002" Comparing "7853" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7854" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754305 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753184 ATOM PAIRS WERE FOUND FOR ATOM LIST 41445 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28868 from a total of 753184 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7854 -75.82926 10.76318 0.65686 INTE EXTERN> -28.82157 -47.00769 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.8293" Parameter: A <- "-75.8293" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8216" Parameter: B <- "-28.8216" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.0077" Parameter: C <- "-47.0077" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7854 TOTAL ENERGY = -75.8293 RDTITL> * VAN DER WAALS = -28.8216 ELECTROSTATIC = -47.0077 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7854" Parameter: CONF_N -> "8002" Comparing "7854" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7855" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753184 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753845 ATOM PAIRS WERE FOUND FOR ATOM LIST 41293 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28726 from a total of 753845 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7855 -67.41704 -8.41222 0.68295 INTE EXTERN> -23.66261 -43.75443 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.417" Parameter: A <- "-67.417" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.6626" Parameter: B <- "-23.6626" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.7544" Parameter: C <- "-43.7544" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7855 TOTAL ENERGY = -67.417 RDTITL> * VAN DER WAALS = -23.6626 ELECTROSTATIC = -43.7544 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7855" Parameter: CONF_N -> "8002" Comparing "7855" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7856" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753845 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756795 ATOM PAIRS WERE FOUND FOR ATOM LIST 41413 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29672 from a total of 756795 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7856 -68.73350 1.31646 0.71209 INTE EXTERN> -25.64389 -43.08961 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.7335" Parameter: A <- "-68.7335" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.6439" Parameter: B <- "-25.6439" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.0896" Parameter: C <- "-43.0896" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7856 TOTAL ENERGY = -68.7335 RDTITL> * VAN DER WAALS = -25.6439 ELECTROSTATIC = -43.0896 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7856" Parameter: CONF_N -> "8002" Comparing "7856" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7857" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756795 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752347 ATOM PAIRS WERE FOUND FOR ATOM LIST 41135 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29708 from a total of 752347 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7857 -70.52547 1.79197 0.67686 INTE EXTERN> -26.59461 -43.93087 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.5255" Parameter: A <- "-70.5255" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5946" Parameter: B <- "-26.5946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9309" Parameter: C <- "-43.9309" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7857 TOTAL ENERGY = -70.5255 RDTITL> * VAN DER WAALS = -26.5946 ELECTROSTATIC = -43.9309 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7857" Parameter: CONF_N -> "8002" Comparing "7857" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7858" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752347 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748043 ATOM PAIRS WERE FOUND FOR ATOM LIST 40949 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28953 from a total of 748043 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7858 -70.28632 -0.23915 0.62921 INTE EXTERN> -27.84270 -42.44361 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.2863" Parameter: A <- "-70.2863" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8427" Parameter: B <- "-27.8427" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4436" Parameter: C <- "-42.4436" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7858 TOTAL ENERGY = -70.2863 RDTITL> * VAN DER WAALS = -27.8427 ELECTROSTATIC = -42.4436 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7858" Parameter: CONF_N -> "8002" Comparing "7858" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7859" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748043 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759672 ATOM PAIRS WERE FOUND FOR ATOM LIST 41426 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29322 from a total of 759672 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7859 -75.02999 4.74367 0.70095 INTE EXTERN> -27.27938 -47.75061 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.03" Parameter: A <- "-75.03" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.2794" Parameter: B <- "-27.2794" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.7506" Parameter: C <- "-47.7506" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7859 TOTAL ENERGY = -75.03 RDTITL> * VAN DER WAALS = -27.2794 ELECTROSTATIC = -47.7506 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7859" Parameter: CONF_N -> "8002" Comparing "7859" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7860" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759672 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754353 ATOM PAIRS WERE FOUND FOR ATOM LIST 41321 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28860 from a total of 754353 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7860 -71.28429 -3.74570 0.60970 INTE EXTERN> -30.80041 -40.48388 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2843" Parameter: A <- "-71.2843" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8004" Parameter: B <- "-30.8004" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4839" Parameter: C <- "-40.4839" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7860 TOTAL ENERGY = -71.2843 RDTITL> * VAN DER WAALS = -30.8004 ELECTROSTATIC = -40.4839 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7860" Parameter: CONF_N -> "8002" Comparing "7860" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7861" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754353 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756082 ATOM PAIRS WERE FOUND FOR ATOM LIST 41208 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29544 from a total of 756082 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7861 -65.19584 -6.08844 0.56815 INTE EXTERN> -33.35047 -31.84538 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.1958" Parameter: A <- "-65.1958" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-33.3505" Parameter: B <- "-33.3505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.8454" Parameter: C <- "-31.8454" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7861 TOTAL ENERGY = -65.1958 RDTITL> * VAN DER WAALS = -33.3505 ELECTROSTATIC = -31.8454 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7861" Parameter: CONF_N -> "8002" Comparing "7861" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7862" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756082 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759671 ATOM PAIRS WERE FOUND FOR ATOM LIST 41661 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29348 from a total of 759671 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7862 -71.81140 6.61556 0.65152 INTE EXTERN> -28.36263 -43.44877 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8114" Parameter: A <- "-71.8114" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3626" Parameter: B <- "-28.3626" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.4488" Parameter: C <- "-43.4488" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7862 TOTAL ENERGY = -71.8114 RDTITL> * VAN DER WAALS = -28.3626 ELECTROSTATIC = -43.4488 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7862" Parameter: CONF_N -> "8002" Comparing "7862" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7863" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759671 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753018 ATOM PAIRS WERE FOUND FOR ATOM LIST 41220 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29238 from a total of 753018 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7863 -64.34468 -7.46672 0.54765 INTE EXTERN> -29.40801 -34.93667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.3447" Parameter: A <- "-64.3447" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.408" Parameter: B <- "-29.408" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.9367" Parameter: C <- "-34.9367" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7863 TOTAL ENERGY = -64.3447 RDTITL> * VAN DER WAALS = -29.408 ELECTROSTATIC = -34.9367 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7863" Parameter: CONF_N -> "8002" Comparing "7863" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7864" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753018 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757375 ATOM PAIRS WERE FOUND FOR ATOM LIST 41609 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29710 from a total of 757375 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7864 -68.84869 4.50401 0.61785 INTE EXTERN> -28.39329 -40.45540 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8487" Parameter: A <- "-68.8487" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3933" Parameter: B <- "-28.3933" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4554" Parameter: C <- "-40.4554" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7864 TOTAL ENERGY = -68.8487 RDTITL> * VAN DER WAALS = -28.3933 ELECTROSTATIC = -40.4554 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7864" Parameter: CONF_N -> "8002" Comparing "7864" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7865" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757375 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756514 ATOM PAIRS WERE FOUND FOR ATOM LIST 41214 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30048 from a total of 756514 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7865 -70.46914 1.62045 0.72792 INTE EXTERN> -25.42853 -45.04061 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.4691" Parameter: A <- "-70.4691" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4285" Parameter: B <- "-25.4285" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.0406" Parameter: C <- "-45.0406" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7865 TOTAL ENERGY = -70.4691 RDTITL> * VAN DER WAALS = -25.4285 ELECTROSTATIC = -45.0406 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7865" Parameter: CONF_N -> "8002" Comparing "7865" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7866" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756514 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761216 ATOM PAIRS WERE FOUND FOR ATOM LIST 41808 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29769 from a total of 761216 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7866 -72.96778 2.49864 0.71589 INTE EXTERN> -27.61131 -45.35647 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9678" Parameter: A <- "-72.9678" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6113" Parameter: B <- "-27.6113" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3565" Parameter: C <- "-45.3565" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7866 TOTAL ENERGY = -72.9678 RDTITL> * VAN DER WAALS = -27.6113 ELECTROSTATIC = -45.3565 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7866" Parameter: CONF_N -> "8002" Comparing "7866" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7867" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761216 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757680 ATOM PAIRS WERE FOUND FOR ATOM LIST 41606 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29910 from a total of 757680 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7867 -77.37481 4.40703 0.67028 INTE EXTERN> -27.78424 -49.59058 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.3748" Parameter: A <- "-77.3748" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7842" Parameter: B <- "-27.7842" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5906" Parameter: C <- "-49.5906" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7867 TOTAL ENERGY = -77.3748 RDTITL> * VAN DER WAALS = -27.7842 ELECTROSTATIC = -49.5906 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7867" Parameter: CONF_N -> "8002" Comparing "7867" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7868" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757680 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753733 ATOM PAIRS WERE FOUND FOR ATOM LIST 41446 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29693 from a total of 753733 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7868 -71.30990 -6.06491 0.71423 INTE EXTERN> -28.39077 -42.91913 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3099" Parameter: A <- "-71.3099" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3908" Parameter: B <- "-28.3908" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9191" Parameter: C <- "-42.9191" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7868 TOTAL ENERGY = -71.3099 RDTITL> * VAN DER WAALS = -28.3908 ELECTROSTATIC = -42.9191 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7868" Parameter: CONF_N -> "8002" Comparing "7868" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7869" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753733 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755131 ATOM PAIRS WERE FOUND FOR ATOM LIST 41410 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30136 from a total of 755131 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7869 -80.27354 8.96364 0.67069 INTE EXTERN> -27.72258 -52.55096 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2735" Parameter: A <- "-80.2735" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7226" Parameter: B <- "-27.7226" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.551" Parameter: C <- "-52.551" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7869 TOTAL ENERGY = -80.2735 RDTITL> * VAN DER WAALS = -27.7226 ELECTROSTATIC = -52.551 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7869" Parameter: CONF_N -> "8002" Comparing "7869" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7870" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755131 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759625 ATOM PAIRS WERE FOUND FOR ATOM LIST 41771 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30609 from a total of 759625 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7870 -76.72805 -3.54549 0.68993 INTE EXTERN> -30.58507 -46.14298 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.728" Parameter: A <- "-76.728" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5851" Parameter: B <- "-30.5851" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.143" Parameter: C <- "-46.143" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7870 TOTAL ENERGY = -76.728 RDTITL> * VAN DER WAALS = -30.5851 ELECTROSTATIC = -46.143 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7870" Parameter: CONF_N -> "8002" Comparing "7870" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7871" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759625 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754107 ATOM PAIRS WERE FOUND FOR ATOM LIST 41367 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29885 from a total of 754107 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7871 -63.16740 -13.56064 0.57241 INTE EXTERN> -31.41849 -31.74892 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.1674" Parameter: A <- "-63.1674" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.4185" Parameter: B <- "-31.4185" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-31.7489" Parameter: C <- "-31.7489" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7871 TOTAL ENERGY = -63.1674 RDTITL> * VAN DER WAALS = -31.4185 ELECTROSTATIC = -31.7489 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7871" Parameter: CONF_N -> "8002" Comparing "7871" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7872" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754107 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758031 ATOM PAIRS WERE FOUND FOR ATOM LIST 41499 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30005 from a total of 758031 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7872 -72.00490 8.83749 0.69323 INTE EXTERN> -26.48703 -45.51786 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.0049" Parameter: A <- "-72.0049" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.487" Parameter: B <- "-26.487" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5179" Parameter: C <- "-45.5179" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7872 TOTAL ENERGY = -72.0049 RDTITL> * VAN DER WAALS = -26.487 ELECTROSTATIC = -45.5179 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7872" Parameter: CONF_N -> "8002" Comparing "7872" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7873" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758031 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762574 ATOM PAIRS WERE FOUND FOR ATOM LIST 41668 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29839 from a total of 762574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7873 -72.99539 0.99049 0.62909 INTE EXTERN> -26.78864 -46.20675 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.9954" Parameter: A <- "-72.9954" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.7886" Parameter: B <- "-26.7886" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.2067" Parameter: C <- "-46.2067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7873 TOTAL ENERGY = -72.9954 RDTITL> * VAN DER WAALS = -26.7886 ELECTROSTATIC = -46.2067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7873" Parameter: CONF_N -> "8002" Comparing "7873" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7874" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762249 ATOM PAIRS WERE FOUND FOR ATOM LIST 41752 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30256 from a total of 762249 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7874 -64.88876 -8.10663 0.63993 INTE EXTERN> -29.36587 -35.52289 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.8888" Parameter: A <- "-64.8888" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3659" Parameter: B <- "-29.3659" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.5229" Parameter: C <- "-35.5229" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7874 TOTAL ENERGY = -64.8888 RDTITL> * VAN DER WAALS = -29.3659 ELECTROSTATIC = -35.5229 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7874" Parameter: CONF_N -> "8002" Comparing "7874" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7875" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762249 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759648 ATOM PAIRS WERE FOUND FOR ATOM LIST 41821 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29926 from a total of 759648 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7875 -66.41379 1.52503 0.71001 INTE EXTERN> -28.82887 -37.58492 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.4138" Parameter: A <- "-66.4138" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8289" Parameter: B <- "-28.8289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.5849" Parameter: C <- "-37.5849" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7875 TOTAL ENERGY = -66.4138 RDTITL> * VAN DER WAALS = -28.8289 ELECTROSTATIC = -37.5849 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7875" Parameter: CONF_N -> "8002" Comparing "7875" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7876" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759648 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762841 ATOM PAIRS WERE FOUND FOR ATOM LIST 41684 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30481 from a total of 762841 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7876 -66.99107 0.57728 0.70859 INTE EXTERN> -25.89858 -41.09249 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9911" Parameter: A <- "-66.9911" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8986" Parameter: B <- "-25.8986" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.0925" Parameter: C <- "-41.0925" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7876 TOTAL ENERGY = -66.9911 RDTITL> * VAN DER WAALS = -25.8986 ELECTROSTATIC = -41.0925 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7876" Parameter: CONF_N -> "8002" Comparing "7876" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7877" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762841 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763391 ATOM PAIRS WERE FOUND FOR ATOM LIST 41864 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29546 from a total of 763391 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7877 -73.29805 6.30699 0.74336 INTE EXTERN> -25.04532 -48.25274 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2981" Parameter: A <- "-73.2981" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0453" Parameter: B <- "-25.0453" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.2527" Parameter: C <- "-48.2527" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7877 TOTAL ENERGY = -73.2981 RDTITL> * VAN DER WAALS = -25.0453 ELECTROSTATIC = -48.2527 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7877" Parameter: CONF_N -> "8002" Comparing "7877" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7878" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763391 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759594 ATOM PAIRS WERE FOUND FOR ATOM LIST 41782 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30113 from a total of 759594 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7878 -77.18591 3.88785 0.61691 INTE EXTERN> -28.53825 -48.64766 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1859" Parameter: A <- "-77.1859" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.5382" Parameter: B <- "-28.5382" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6477" Parameter: C <- "-48.6477" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7878 TOTAL ENERGY = -77.1859 RDTITL> * VAN DER WAALS = -28.5382 ELECTROSTATIC = -48.6477 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7878" Parameter: CONF_N -> "8002" Comparing "7878" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7879" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759594 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755338 ATOM PAIRS WERE FOUND FOR ATOM LIST 41592 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30717 from a total of 755338 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7879 -76.69087 -0.49503 0.88308 INTE EXTERN> -20.42886 -56.26202 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6909" Parameter: A <- "-76.6909" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-20.4289" Parameter: B <- "-20.4289" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.262" Parameter: C <- "-56.262" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7879 TOTAL ENERGY = -76.6909 RDTITL> * VAN DER WAALS = -20.4289 ELECTROSTATIC = -56.262 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7879" Parameter: CONF_N -> "8002" Comparing "7879" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7880" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755338 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760125 ATOM PAIRS WERE FOUND FOR ATOM LIST 41726 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30032 from a total of 760125 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7880 -82.68768 5.99680 0.65910 INTE EXTERN> -28.90027 -53.78740 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.6877" Parameter: A <- "-82.6877" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9003" Parameter: B <- "-28.9003" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.7874" Parameter: C <- "-53.7874" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7880 TOTAL ENERGY = -82.6877 RDTITL> * VAN DER WAALS = -28.9003 ELECTROSTATIC = -53.7874 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7880" Parameter: CONF_N -> "8002" Comparing "7880" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7881" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760125 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761080 ATOM PAIRS WERE FOUND FOR ATOM LIST 41899 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30473 from a total of 761080 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7881 -80.40413 -2.28354 0.75401 INTE EXTERN> -27.57734 -52.82679 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.4041" Parameter: A <- "-80.4041" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5773" Parameter: B <- "-27.5773" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8268" Parameter: C <- "-52.8268" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7881 TOTAL ENERGY = -80.4041 RDTITL> * VAN DER WAALS = -27.5773 ELECTROSTATIC = -52.8268 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7881" Parameter: CONF_N -> "8002" Comparing "7881" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7882" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761080 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753143 ATOM PAIRS WERE FOUND FOR ATOM LIST 41174 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29967 from a total of 753143 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7882 -84.40271 3.99858 0.64349 INTE EXTERN> -29.69683 -54.70588 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.4027" Parameter: A <- "-84.4027" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6968" Parameter: B <- "-29.6968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.7059" Parameter: C <- "-54.7059" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7882 TOTAL ENERGY = -84.4027 RDTITL> * VAN DER WAALS = -29.6968 ELECTROSTATIC = -54.7059 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7882" Parameter: CONF_N -> "8002" Comparing "7882" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7883" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753143 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758210 ATOM PAIRS WERE FOUND FOR ATOM LIST 41476 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30546 from a total of 758210 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7883 -74.10979 -10.29292 0.65567 INTE EXTERN> -24.36184 -49.74795 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.1098" Parameter: A <- "-74.1098" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.3618" Parameter: B <- "-24.3618" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7479" Parameter: C <- "-49.7479" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7883 TOTAL ENERGY = -74.1098 RDTITL> * VAN DER WAALS = -24.3618 ELECTROSTATIC = -49.7479 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7883" Parameter: CONF_N -> "8002" Comparing "7883" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7884" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758210 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759703 ATOM PAIRS WERE FOUND FOR ATOM LIST 41705 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29909 from a total of 759703 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7884 -83.46451 9.35472 0.68029 INTE EXTERN> -30.01520 -53.44932 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.4645" Parameter: A <- "-83.4645" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0152" Parameter: B <- "-30.0152" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.4493" Parameter: C <- "-53.4493" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7884 TOTAL ENERGY = -83.4645 RDTITL> * VAN DER WAALS = -30.0152 ELECTROSTATIC = -53.4493 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7884" Parameter: CONF_N -> "8002" Comparing "7884" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7885" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759703 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753113 ATOM PAIRS WERE FOUND FOR ATOM LIST 41363 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29474 from a total of 753113 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7885 -79.83003 -3.63449 0.74523 INTE EXTERN> -22.34037 -57.48966 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.83" Parameter: A <- "-79.83" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.3404" Parameter: B <- "-22.3404" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-57.4897" Parameter: C <- "-57.4897" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7885 TOTAL ENERGY = -79.83 RDTITL> * VAN DER WAALS = -22.3404 ELECTROSTATIC = -57.4897 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7885" Parameter: CONF_N -> "8002" Comparing "7885" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7886" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753113 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750510 ATOM PAIRS WERE FOUND FOR ATOM LIST 41169 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29880 from a total of 750510 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7886 -83.03593 3.20590 0.63906 INTE EXTERN> -30.42004 -52.61589 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.0359" Parameter: A <- "-83.0359" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.42" Parameter: B <- "-30.42" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.6159" Parameter: C <- "-52.6159" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7886 TOTAL ENERGY = -83.0359 RDTITL> * VAN DER WAALS = -30.42 ELECTROSTATIC = -52.6159 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7886" Parameter: CONF_N -> "8002" Comparing "7886" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7887" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750510 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755242 ATOM PAIRS WERE FOUND FOR ATOM LIST 41299 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30138 from a total of 755242 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7887 -77.55074 -5.48519 0.70555 INTE EXTERN> -25.76041 -51.79034 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5507" Parameter: A <- "-77.5507" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7604" Parameter: B <- "-25.7604" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7903" Parameter: C <- "-51.7903" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7887 TOTAL ENERGY = -77.5507 RDTITL> * VAN DER WAALS = -25.7604 ELECTROSTATIC = -51.7903 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7887" Parameter: CONF_N -> "8002" Comparing "7887" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7888" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755242 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756074 ATOM PAIRS WERE FOUND FOR ATOM LIST 41642 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30173 from a total of 756074 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7888 -78.85945 1.30870 0.60564 INTE EXTERN> -32.60842 -46.25103 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8594" Parameter: A <- "-78.8594" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6084" Parameter: B <- "-32.6084" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.251" Parameter: C <- "-46.251" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7888 TOTAL ENERGY = -78.8594 RDTITL> * VAN DER WAALS = -32.6084 ELECTROSTATIC = -46.251 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7888" Parameter: CONF_N -> "8002" Comparing "7888" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7889" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756074 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755008 ATOM PAIRS WERE FOUND FOR ATOM LIST 41188 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30232 from a total of 755008 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7889 -79.72337 0.86392 0.67960 INTE EXTERN> -26.91264 -52.81073 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7234" Parameter: A <- "-79.7234" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9126" Parameter: B <- "-26.9126" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.8107" Parameter: C <- "-52.8107" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7889 TOTAL ENERGY = -79.7234 RDTITL> * VAN DER WAALS = -26.9126 ELECTROSTATIC = -52.8107 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7889" Parameter: CONF_N -> "8002" Comparing "7889" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7890" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755008 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763523 ATOM PAIRS WERE FOUND FOR ATOM LIST 41778 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30445 from a total of 763523 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7890 -74.65962 -5.06375 0.58580 INTE EXTERN> -31.76195 -42.89768 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.6596" Parameter: A <- "-74.6596" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7619" Parameter: B <- "-31.7619" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8977" Parameter: C <- "-42.8977" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7890 TOTAL ENERGY = -74.6596 RDTITL> * VAN DER WAALS = -31.7619 ELECTROSTATIC = -42.8977 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7890" Parameter: CONF_N -> "8002" Comparing "7890" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7891" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763523 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757407 ATOM PAIRS WERE FOUND FOR ATOM LIST 41452 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30127 from a total of 757407 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7891 -75.08733 0.42771 0.74113 INTE EXTERN> -25.82762 -49.25971 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0873" Parameter: A <- "-75.0873" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8276" Parameter: B <- "-25.8276" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.2597" Parameter: C <- "-49.2597" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7891 TOTAL ENERGY = -75.0873 RDTITL> * VAN DER WAALS = -25.8276 ELECTROSTATIC = -49.2597 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7891" Parameter: CONF_N -> "8002" Comparing "7891" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7892" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757407 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756067 ATOM PAIRS WERE FOUND FOR ATOM LIST 41505 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29968 from a total of 756067 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7892 -76.35164 1.26431 0.71445 INTE EXTERN> -26.27433 -50.07730 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3516" Parameter: A <- "-76.3516" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2743" Parameter: B <- "-26.2743" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.0773" Parameter: C <- "-50.0773" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7892 TOTAL ENERGY = -76.3516 RDTITL> * VAN DER WAALS = -26.2743 ELECTROSTATIC = -50.0773 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7892" Parameter: CONF_N -> "8002" Comparing "7892" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7893" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756067 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41546 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30154 from a total of 758110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7893 -73.25066 -3.10098 0.68542 INTE EXTERN> -25.56967 -47.68099 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2507" Parameter: A <- "-73.2507" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5697" Parameter: B <- "-25.5697" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.681" Parameter: C <- "-47.681" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7893 TOTAL ENERGY = -73.2507 RDTITL> * VAN DER WAALS = -25.5697 ELECTROSTATIC = -47.681 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7893" Parameter: CONF_N -> "8002" Comparing "7893" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7894" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755110 ATOM PAIRS WERE FOUND FOR ATOM LIST 41263 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29965 from a total of 755110 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7894 -71.56875 -1.68191 0.65105 INTE EXTERN> -29.39463 -42.17411 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5687" Parameter: A <- "-71.5687" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3946" Parameter: B <- "-29.3946" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.1741" Parameter: C <- "-42.1741" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7894 TOTAL ENERGY = -71.5687 RDTITL> * VAN DER WAALS = -29.3946 ELECTROSTATIC = -42.1741 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7894" Parameter: CONF_N -> "8002" Comparing "7894" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7895" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755110 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756201 ATOM PAIRS WERE FOUND FOR ATOM LIST 41455 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30014 from a total of 756201 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7895 -66.95031 -4.61844 0.78634 INTE EXTERN> -23.08730 -43.86301 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.9503" Parameter: A <- "-66.9503" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.0873" Parameter: B <- "-23.0873" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.863" Parameter: C <- "-43.863" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7895 TOTAL ENERGY = -66.9503 RDTITL> * VAN DER WAALS = -23.0873 ELECTROSTATIC = -43.863 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7895" Parameter: CONF_N -> "8002" Comparing "7895" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7896" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756201 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754509 ATOM PAIRS WERE FOUND FOR ATOM LIST 41517 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29835 from a total of 754509 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7896 -66.86124 -0.08907 0.64973 INTE EXTERN> -28.96272 -37.89852 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8612" Parameter: A <- "-66.8612" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9627" Parameter: B <- "-28.9627" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-37.8985" Parameter: C <- "-37.8985" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7896 TOTAL ENERGY = -66.8612 RDTITL> * VAN DER WAALS = -28.9627 ELECTROSTATIC = -37.8985 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7896" Parameter: CONF_N -> "8002" Comparing "7896" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7897" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754509 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750283 ATOM PAIRS WERE FOUND FOR ATOM LIST 41184 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29343 from a total of 750283 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7897 -71.40820 4.54696 0.57937 INTE EXTERN> -30.02648 -41.38172 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.4082" Parameter: A <- "-71.4082" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.0265" Parameter: B <- "-30.0265" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.3817" Parameter: C <- "-41.3817" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7897 TOTAL ENERGY = -71.4082 RDTITL> * VAN DER WAALS = -30.0265 ELECTROSTATIC = -41.3817 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7897" Parameter: CONF_N -> "8002" Comparing "7897" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7898" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750283 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758526 ATOM PAIRS WERE FOUND FOR ATOM LIST 41672 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29964 from a total of 758526 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7898 -64.41668 -6.99152 0.67148 INTE EXTERN> -23.98635 -40.43034 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-64.4167" Parameter: A <- "-64.4167" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.9863" Parameter: B <- "-23.9863" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.4303" Parameter: C <- "-40.4303" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7898 TOTAL ENERGY = -64.4167 RDTITL> * VAN DER WAALS = -23.9863 ELECTROSTATIC = -40.4303 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7898" Parameter: CONF_N -> "8002" Comparing "7898" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7899" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758526 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752868 ATOM PAIRS WERE FOUND FOR ATOM LIST 41173 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29316 from a total of 752868 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7899 -78.30271 13.88603 0.65109 INTE EXTERN> -29.66393 -48.63878 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3027" Parameter: A <- "-78.3027" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6639" Parameter: B <- "-29.6639" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.6388" Parameter: C <- "-48.6388" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7899 TOTAL ENERGY = -78.3027 RDTITL> * VAN DER WAALS = -29.6639 ELECTROSTATIC = -48.6388 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7899" Parameter: CONF_N -> "8002" Comparing "7899" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7900" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752868 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755303 ATOM PAIRS WERE FOUND FOR ATOM LIST 41388 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29549 from a total of 755303 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7900 -69.42863 -8.87408 0.74599 INTE EXTERN> -24.07100 -45.35763 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-69.4286" Parameter: A <- "-69.4286" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.071" Parameter: B <- "-24.071" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3576" Parameter: C <- "-45.3576" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7900 TOTAL ENERGY = -69.4286 RDTITL> * VAN DER WAALS = -24.071 ELECTROSTATIC = -45.3576 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7900" Parameter: CONF_N -> "8002" Comparing "7900" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7901" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755303 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760381 ATOM PAIRS WERE FOUND FOR ATOM LIST 41616 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29948 from a total of 760381 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7901 -71.62998 2.20135 0.69800 INTE EXTERN> -27.30186 -44.32812 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.63" Parameter: A <- "-71.63" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3019" Parameter: B <- "-27.3019" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.3281" Parameter: C <- "-44.3281" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7901 TOTAL ENERGY = -71.63 RDTITL> * VAN DER WAALS = -27.3019 ELECTROSTATIC = -44.3281 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7901" Parameter: CONF_N -> "8002" Comparing "7901" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7902" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760381 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759726 ATOM PAIRS WERE FOUND FOR ATOM LIST 41539 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29740 from a total of 759726 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7902 -72.29887 0.66889 0.60104 INTE EXTERN> -31.14738 -41.15149 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2989" Parameter: A <- "-72.2989" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1474" Parameter: B <- "-31.1474" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1515" Parameter: C <- "-41.1515" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7902 TOTAL ENERGY = -72.2989 RDTITL> * VAN DER WAALS = -31.1474 ELECTROSTATIC = -41.1515 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7902" Parameter: CONF_N -> "8002" Comparing "7902" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7903" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759726 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760558 ATOM PAIRS WERE FOUND FOR ATOM LIST 41678 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29649 from a total of 760558 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7903 -70.97228 -1.32659 0.58179 INTE EXTERN> -31.70821 -39.26407 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.9723" Parameter: A <- "-70.9723" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7082" Parameter: B <- "-31.7082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.2641" Parameter: C <- "-39.2641" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7903 TOTAL ENERGY = -70.9723 RDTITL> * VAN DER WAALS = -31.7082 ELECTROSTATIC = -39.2641 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7903" Parameter: CONF_N -> "8002" Comparing "7903" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7904" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760558 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759574 ATOM PAIRS WERE FOUND FOR ATOM LIST 41718 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29746 from a total of 759574 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7904 -74.26211 3.28983 0.69285 INTE EXTERN> -28.63732 -45.62479 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.2621" Parameter: A <- "-74.2621" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6373" Parameter: B <- "-28.6373" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.6248" Parameter: C <- "-45.6248" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7904 TOTAL ENERGY = -74.2621 RDTITL> * VAN DER WAALS = -28.6373 ELECTROSTATIC = -45.6248 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7904" Parameter: CONF_N -> "8002" Comparing "7904" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7905" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759574 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757991 ATOM PAIRS WERE FOUND FOR ATOM LIST 41554 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29869 from a total of 757991 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7905 -60.62552 -13.63659 0.75396 INTE EXTERN> -26.11333 -34.51219 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-60.6255" Parameter: A <- "-60.6255" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1133" Parameter: B <- "-26.1133" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-34.5122" Parameter: C <- "-34.5122" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7905 TOTAL ENERGY = -60.6255 RDTITL> * VAN DER WAALS = -26.1133 ELECTROSTATIC = -34.5122 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7905" Parameter: CONF_N -> "8002" Comparing "7905" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7906" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757991 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748636 ATOM PAIRS WERE FOUND FOR ATOM LIST 41081 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28890 from a total of 748636 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7906 -63.64921 3.02369 0.62404 INTE EXTERN> -27.59964 -36.04957 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-63.6492" Parameter: A <- "-63.6492" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5996" Parameter: B <- "-27.5996" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-36.0496" Parameter: C <- "-36.0496" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7906 TOTAL ENERGY = -63.6492 RDTITL> * VAN DER WAALS = -27.5996 ELECTROSTATIC = -36.0496 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7906" Parameter: CONF_N -> "8002" Comparing "7906" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7907" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748636 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751088 ATOM PAIRS WERE FOUND FOR ATOM LIST 41177 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29639 from a total of 751088 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7907 -73.93415 10.28494 0.72371 INTE EXTERN> -24.94776 -48.98639 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.9341" Parameter: A <- "-73.9341" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.9478" Parameter: B <- "-24.9478" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9864" Parameter: C <- "-48.9864" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7907 TOTAL ENERGY = -73.9341 RDTITL> * VAN DER WAALS = -24.9478 ELECTROSTATIC = -48.9864 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7907" Parameter: CONF_N -> "8002" Comparing "7907" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7908" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751088 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753318 ATOM PAIRS WERE FOUND FOR ATOM LIST 41244 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 753318 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7908 -68.80343 -5.13072 0.70770 INTE EXTERN> -27.03186 -41.77157 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.8034" Parameter: A <- "-68.8034" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0319" Parameter: B <- "-27.0319" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.7716" Parameter: C <- "-41.7716" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7908 TOTAL ENERGY = -68.8034 RDTITL> * VAN DER WAALS = -27.0319 ELECTROSTATIC = -41.7716 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7908" Parameter: CONF_N -> "8002" Comparing "7908" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7909" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753318 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757675 ATOM PAIRS WERE FOUND FOR ATOM LIST 41549 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29546 from a total of 757675 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7909 -68.37075 -0.43267 0.73410 INTE EXTERN> -25.51427 -42.85648 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.3708" Parameter: A <- "-68.3708" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5143" Parameter: B <- "-25.5143" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8565" Parameter: C <- "-42.8565" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7909 TOTAL ENERGY = -68.3708 RDTITL> * VAN DER WAALS = -25.5143 ELECTROSTATIC = -42.8565 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7909" Parameter: CONF_N -> "8002" Comparing "7909" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7910" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757675 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757505 ATOM PAIRS WERE FOUND FOR ATOM LIST 41562 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29789 from a total of 757505 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7910 -67.23475 -1.13600 0.71779 INTE EXTERN> -23.53564 -43.69911 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.2348" Parameter: A <- "-67.2348" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.5356" Parameter: B <- "-23.5356" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.6991" Parameter: C <- "-43.6991" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7910 TOTAL ENERGY = -67.2348 RDTITL> * VAN DER WAALS = -23.5356 ELECTROSTATIC = -43.6991 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7910" Parameter: CONF_N -> "8002" Comparing "7910" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7911" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757505 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754964 ATOM PAIRS WERE FOUND FOR ATOM LIST 41390 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29537 from a total of 754964 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7911 -65.70139 -1.53336 0.59857 INTE EXTERN> -30.41362 -35.28777 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-65.7014" Parameter: A <- "-65.7014" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.4136" Parameter: B <- "-30.4136" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-35.2878" Parameter: C <- "-35.2878" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7911 TOTAL ENERGY = -65.7014 RDTITL> * VAN DER WAALS = -30.4136 ELECTROSTATIC = -35.2878 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7911" Parameter: CONF_N -> "8002" Comparing "7911" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7912" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754964 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752124 ATOM PAIRS WERE FOUND FOR ATOM LIST 41420 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29799 from a total of 752124 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7912 -71.08308 5.38170 0.63675 INTE EXTERN> -29.64086 -41.44223 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0831" Parameter: A <- "-71.0831" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6409" Parameter: B <- "-29.6409" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.4422" Parameter: C <- "-41.4422" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7912 TOTAL ENERGY = -71.0831 RDTITL> * VAN DER WAALS = -29.6409 ELECTROSTATIC = -41.4422 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7912" Parameter: CONF_N -> "8002" Comparing "7912" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7913" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752124 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757394 ATOM PAIRS WERE FOUND FOR ATOM LIST 41474 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30459 from a total of 757394 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7913 -66.80572 -4.27736 0.66235 INTE EXTERN> -27.98961 -38.81611 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.8057" Parameter: A <- "-66.8057" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.9896" Parameter: B <- "-27.9896" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-38.8161" Parameter: C <- "-38.8161" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7913 TOTAL ENERGY = -66.8057 RDTITL> * VAN DER WAALS = -27.9896 ELECTROSTATIC = -38.8161 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7913" Parameter: CONF_N -> "8002" Comparing "7913" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7914" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757394 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753584 ATOM PAIRS WERE FOUND FOR ATOM LIST 41362 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29476 from a total of 753584 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7914 -72.54487 5.73915 0.61938 INTE EXTERN> -30.11385 -42.43102 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5449" Parameter: A <- "-72.5449" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1138" Parameter: B <- "-30.1138" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.431" Parameter: C <- "-42.431" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7914 TOTAL ENERGY = -72.5449 RDTITL> * VAN DER WAALS = -30.1138 ELECTROSTATIC = -42.431 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7914" Parameter: CONF_N -> "8002" Comparing "7914" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7915" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753584 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748057 ATOM PAIRS WERE FOUND FOR ATOM LIST 40960 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29898 from a total of 748057 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7915 -79.07979 6.53492 0.91675 INTE EXTERN> -18.82367 -60.25613 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.0798" Parameter: A <- "-79.0798" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-18.8237" Parameter: B <- "-18.8237" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-60.2561" Parameter: C <- "-60.2561" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7915 TOTAL ENERGY = -79.0798 RDTITL> * VAN DER WAALS = -18.8237 ELECTROSTATIC = -60.2561 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7915" Parameter: CONF_N -> "8002" Comparing "7915" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7916" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748057 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755093 ATOM PAIRS WERE FOUND FOR ATOM LIST 41444 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29576 from a total of 755093 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7916 -76.91236 -2.16744 0.70142 INTE EXTERN> -26.17441 -50.73795 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.9124" Parameter: A <- "-76.9124" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.1744" Parameter: B <- "-26.1744" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.7379" Parameter: C <- "-50.7379" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7916 TOTAL ENERGY = -76.9124 RDTITL> * VAN DER WAALS = -26.1744 ELECTROSTATIC = -50.7379 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7916" Parameter: CONF_N -> "8002" Comparing "7916" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7917" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755093 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755179 ATOM PAIRS WERE FOUND FOR ATOM LIST 41565 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29909 from a total of 755179 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7917 -68.16235 -8.75000 0.77013 INTE EXTERN> -23.75523 -44.40713 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.1624" Parameter: A <- "-68.1624" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.7552" Parameter: B <- "-23.7552" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.4071" Parameter: C <- "-44.4071" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7917 TOTAL ENERGY = -68.1624 RDTITL> * VAN DER WAALS = -23.7552 ELECTROSTATIC = -44.4071 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7917" Parameter: CONF_N -> "8002" Comparing "7917" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7918" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755179 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748359 ATOM PAIRS WERE FOUND FOR ATOM LIST 40929 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29562 from a total of 748359 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7918 -78.41593 10.25357 0.65930 INTE EXTERN> -29.60450 -48.81143 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4159" Parameter: A <- "-78.4159" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6045" Parameter: B <- "-29.6045" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.8114" Parameter: C <- "-48.8114" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7918 TOTAL ENERGY = -78.4159 RDTITL> * VAN DER WAALS = -29.6045 ELECTROSTATIC = -48.8114 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7918" Parameter: CONF_N -> "8002" Comparing "7918" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7919" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748359 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757475 ATOM PAIRS WERE FOUND FOR ATOM LIST 41567 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29745 from a total of 757475 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7919 -73.87972 -4.53621 0.60969 INTE EXTERN> -29.32965 -44.55007 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8797" Parameter: A <- "-73.8797" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3297" Parameter: B <- "-29.3297" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5501" Parameter: C <- "-44.5501" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7919 TOTAL ENERGY = -73.8797 RDTITL> * VAN DER WAALS = -29.3297 ELECTROSTATIC = -44.5501 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7919" Parameter: CONF_N -> "8002" Comparing "7919" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7920" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757475 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754763 ATOM PAIRS WERE FOUND FOR ATOM LIST 41426 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30553 from a total of 754763 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7920 -66.00362 -7.87610 0.84656 INTE EXTERN> -19.07312 -46.93050 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-66.0036" Parameter: A <- "-66.0036" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-19.0731" Parameter: B <- "-19.0731" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.9305" Parameter: C <- "-46.9305" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7920 TOTAL ENERGY = -66.0036 RDTITL> * VAN DER WAALS = -19.0731 ELECTROSTATIC = -46.9305 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7920" Parameter: CONF_N -> "8002" Comparing "7920" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7921" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754763 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757109 ATOM PAIRS WERE FOUND FOR ATOM LIST 41418 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29866 from a total of 757109 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7921 -76.69335 10.68973 0.66590 INTE EXTERN> -28.85810 -47.83525 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.6933" Parameter: A <- "-76.6933" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.8581" Parameter: B <- "-28.8581" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8352" Parameter: C <- "-47.8352" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7921 TOTAL ENERGY = -76.6933 RDTITL> * VAN DER WAALS = -28.8581 ELECTROSTATIC = -47.8352 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7921" Parameter: CONF_N -> "8002" Comparing "7921" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7922" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757109 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755050 ATOM PAIRS WERE FOUND FOR ATOM LIST 41447 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29673 from a total of 755050 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7922 -78.31553 1.62218 0.72412 INTE EXTERN> -24.08818 -54.22735 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.3155" Parameter: A <- "-78.3155" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.0882" Parameter: B <- "-24.0882" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.2273" Parameter: C <- "-54.2273" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7922 TOTAL ENERGY = -78.3155 RDTITL> * VAN DER WAALS = -24.0882 ELECTROSTATIC = -54.2273 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7922" Parameter: CONF_N -> "8002" Comparing "7922" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7923" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755050 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756690 ATOM PAIRS WERE FOUND FOR ATOM LIST 41575 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29838 from a total of 756690 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7923 -78.81892 0.50338 0.72457 INTE EXTERN> -26.89289 -51.92602 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8189" Parameter: A <- "-78.8189" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8929" Parameter: B <- "-26.8929" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.926" Parameter: C <- "-51.926" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7923 TOTAL ENERGY = -78.8189 RDTITL> * VAN DER WAALS = -26.8929 ELECTROSTATIC = -51.926 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7923" Parameter: CONF_N -> "8002" Comparing "7923" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7924" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756690 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756393 ATOM PAIRS WERE FOUND FOR ATOM LIST 41334 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29829 from a total of 756393 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7924 -84.82927 6.01036 0.76036 INTE EXTERN> -28.20280 -56.62648 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.8293" Parameter: A <- "-84.8293" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2028" Parameter: B <- "-28.2028" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-56.6265" Parameter: C <- "-56.6265" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7924 TOTAL ENERGY = -84.8293 RDTITL> * VAN DER WAALS = -28.2028 ELECTROSTATIC = -56.6265 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7924" Parameter: CONF_N -> "8002" Comparing "7924" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7925" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756393 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755236 ATOM PAIRS WERE FOUND FOR ATOM LIST 41483 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29664 from a total of 755236 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7925 -74.70577 -10.12351 0.60406 INTE EXTERN> -31.75959 -42.94617 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7058" Parameter: A <- "-74.7058" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7596" Parameter: B <- "-31.7596" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9462" Parameter: C <- "-42.9462" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7925 TOTAL ENERGY = -74.7058 RDTITL> * VAN DER WAALS = -31.7596 ELECTROSTATIC = -42.9462 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7925" Parameter: CONF_N -> "8002" Comparing "7925" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7926" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755236 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754132 ATOM PAIRS WERE FOUND FOR ATOM LIST 41389 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29210 from a total of 754132 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7926 -83.13467 8.42890 0.66914 INTE EXTERN> -30.58909 -52.54558 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-83.1347" Parameter: A <- "-83.1347" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.5891" Parameter: B <- "-30.5891" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5456" Parameter: C <- "-52.5456" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7926 TOTAL ENERGY = -83.1347 RDTITL> * VAN DER WAALS = -30.5891 ELECTROSTATIC = -52.5456 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7926" Parameter: CONF_N -> "8002" Comparing "7926" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7927" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754132 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758953 ATOM PAIRS WERE FOUND FOR ATOM LIST 41716 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29927 from a total of 758953 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7927 -80.84220 -2.29247 0.73302 INTE EXTERN> -25.03221 -55.80998 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.8422" Parameter: A <- "-80.8422" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.0322" Parameter: B <- "-25.0322" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.81" Parameter: C <- "-55.81" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7927 TOTAL ENERGY = -80.8422 RDTITL> * VAN DER WAALS = -25.0322 ELECTROSTATIC = -55.81 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7927" Parameter: CONF_N -> "8002" Comparing "7927" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7928" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758953 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753355 ATOM PAIRS WERE FOUND FOR ATOM LIST 41344 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29884 from a total of 753355 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7928 -71.20105 -9.64115 0.66208 INTE EXTERN> -26.40400 -44.79705 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2011" Parameter: A <- "-71.2011" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.404" Parameter: B <- "-26.404" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.7971" Parameter: C <- "-44.7971" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7928 TOTAL ENERGY = -71.2011 RDTITL> * VAN DER WAALS = -26.404 ELECTROSTATIC = -44.7971 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7928" Parameter: CONF_N -> "8002" Comparing "7928" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7929" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753355 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752920 ATOM PAIRS WERE FOUND FOR ATOM LIST 41145 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29988 from a total of 752920 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7929 -70.73684 -0.46421 0.68316 INTE EXTERN> -25.23680 -45.50004 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.7368" Parameter: A <- "-70.7368" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2368" Parameter: B <- "-25.2368" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.5" Parameter: C <- "-45.5" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7929 TOTAL ENERGY = -70.7368 RDTITL> * VAN DER WAALS = -25.2368 ELECTROSTATIC = -45.5 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7929" Parameter: CONF_N -> "8002" Comparing "7929" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7930" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752920 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754986 ATOM PAIRS WERE FOUND FOR ATOM LIST 41265 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30474 from a total of 754986 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7930 -78.44232 7.70548 0.76050 INTE EXTERN> -22.92240 -55.51991 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.4423" Parameter: A <- "-78.4423" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-22.9224" Parameter: B <- "-22.9224" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.5199" Parameter: C <- "-55.5199" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7930 TOTAL ENERGY = -78.4423 RDTITL> * VAN DER WAALS = -22.9224 ELECTROSTATIC = -55.5199 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7930" Parameter: CONF_N -> "8002" Comparing "7930" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7931" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754986 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758541 ATOM PAIRS WERE FOUND FOR ATOM LIST 41738 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30594 from a total of 758541 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7931 -73.30834 -5.13397 0.74202 INTE EXTERN> -25.81717 -47.49117 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.3083" Parameter: A <- "-73.3083" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.8172" Parameter: B <- "-25.8172" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.4912" Parameter: C <- "-47.4912" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7931 TOTAL ENERGY = -73.3083 RDTITL> * VAN DER WAALS = -25.8172 ELECTROSTATIC = -47.4912 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7931" Parameter: CONF_N -> "8002" Comparing "7931" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7932" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758541 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761737 ATOM PAIRS WERE FOUND FOR ATOM LIST 41702 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30584 from a total of 761737 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7932 -75.05677 1.74843 0.66858 INTE EXTERN> -29.19635 -45.86043 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.0568" Parameter: A <- "-75.0568" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1963" Parameter: B <- "-29.1963" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.8604" Parameter: C <- "-45.8604" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7932 TOTAL ENERGY = -75.0568 RDTITL> * VAN DER WAALS = -29.1963 ELECTROSTATIC = -45.8604 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7932" Parameter: CONF_N -> "8002" Comparing "7932" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7933" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761737 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753348 ATOM PAIRS WERE FOUND FOR ATOM LIST 41477 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30001 from a total of 753348 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7933 -75.93443 0.87766 0.69762 INTE EXTERN> -28.08509 -47.84934 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9344" Parameter: A <- "-75.9344" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.0851" Parameter: B <- "-28.0851" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8493" Parameter: C <- "-47.8493" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7933 TOTAL ENERGY = -75.9344 RDTITL> * VAN DER WAALS = -28.0851 ELECTROSTATIC = -47.8493 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7933" Parameter: CONF_N -> "8002" Comparing "7933" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7934" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753348 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756021 ATOM PAIRS WERE FOUND FOR ATOM LIST 41499 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30260 from a total of 756021 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7934 -78.83406 2.89963 0.69846 INTE EXTERN> -29.75257 -49.08149 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.8341" Parameter: A <- "-78.8341" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7526" Parameter: B <- "-29.7526" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.0815" Parameter: C <- "-49.0815" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7934 TOTAL ENERGY = -78.8341 RDTITL> * VAN DER WAALS = -29.7526 ELECTROSTATIC = -49.0815 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7934" Parameter: CONF_N -> "8002" Comparing "7934" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7935" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756021 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749759 ATOM PAIRS WERE FOUND FOR ATOM LIST 41116 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29694 from a total of 749759 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7935 -71.09918 -7.73488 0.60203 INTE EXTERN> -31.22673 -39.87245 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.0992" Parameter: A <- "-71.0992" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2267" Parameter: B <- "-31.2267" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8725" Parameter: C <- "-39.8725" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7935 TOTAL ENERGY = -71.0992 RDTITL> * VAN DER WAALS = -31.2267 ELECTROSTATIC = -39.8725 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7935" Parameter: CONF_N -> "8002" Comparing "7935" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7936" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749759 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750116 ATOM PAIRS WERE FOUND FOR ATOM LIST 41065 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29766 from a total of 750116 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7936 -72.53225 1.43307 0.74786 INTE EXTERN> -25.24244 -47.28981 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.5323" Parameter: A <- "-72.5323" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.2424" Parameter: B <- "-25.2424" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.2898" Parameter: C <- "-47.2898" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7936 TOTAL ENERGY = -72.5323 RDTITL> * VAN DER WAALS = -25.2424 ELECTROSTATIC = -47.2898 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7936" Parameter: CONF_N -> "8002" Comparing "7936" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7937" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750116 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753329 ATOM PAIRS WERE FOUND FOR ATOM LIST 41359 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29627 from a total of 753329 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7937 -80.65225 8.12000 0.70296 INTE EXTERN> -26.02862 -54.62363 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.6523" Parameter: A <- "-80.6523" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0286" Parameter: B <- "-26.0286" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.6236" Parameter: C <- "-54.6236" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7937 TOTAL ENERGY = -80.6523 RDTITL> * VAN DER WAALS = -26.0286 ELECTROSTATIC = -54.6236 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7937" Parameter: CONF_N -> "8002" Comparing "7937" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7938" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753329 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752266 ATOM PAIRS WERE FOUND FOR ATOM LIST 41423 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29798 from a total of 752266 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7938 -75.73773 -4.91452 0.70017 INTE EXTERN> -29.12315 -46.61459 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.7377" Parameter: A <- "-75.7377" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1231" Parameter: B <- "-29.1231" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.6146" Parameter: C <- "-46.6146" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7938 TOTAL ENERGY = -75.7377 RDTITL> * VAN DER WAALS = -29.1231 ELECTROSTATIC = -46.6146 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7938" Parameter: CONF_N -> "8002" Comparing "7938" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7939" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752266 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754575 ATOM PAIRS WERE FOUND FOR ATOM LIST 41531 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29514 from a total of 754575 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7939 -72.54698 -3.19075 0.88214 INTE EXTERN> -23.60799 -48.93899 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.547" Parameter: A <- "-72.547" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.608" Parameter: B <- "-23.608" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.939" Parameter: C <- "-48.939" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7939 TOTAL ENERGY = -72.547 RDTITL> * VAN DER WAALS = -23.608 ELECTROSTATIC = -48.939 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7939" Parameter: CONF_N -> "8002" Comparing "7939" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7940" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754575 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750942 ATOM PAIRS WERE FOUND FOR ATOM LIST 41310 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29733 from a total of 750942 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7940 -75.91325 3.36627 0.66425 INTE EXTERN> -29.11109 -46.80216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.9132" Parameter: A <- "-75.9132" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.1111" Parameter: B <- "-29.1111" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.8022" Parameter: C <- "-46.8022" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7940 TOTAL ENERGY = -75.9132 RDTITL> * VAN DER WAALS = -29.1111 ELECTROSTATIC = -46.8022 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7940" Parameter: CONF_N -> "8002" Comparing "7940" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7941" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750942 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751834 ATOM PAIRS WERE FOUND FOR ATOM LIST 41232 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30425 from a total of 751834 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7941 -80.80440 4.89115 0.68795 INTE EXTERN> -30.19640 -50.60800 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.8044" Parameter: A <- "-80.8044" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1964" Parameter: B <- "-30.1964" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.608" Parameter: C <- "-50.608" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7941 TOTAL ENERGY = -80.8044 RDTITL> * VAN DER WAALS = -30.1964 ELECTROSTATIC = -50.608 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7941" Parameter: CONF_N -> "8002" Comparing "7941" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7942" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751834 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749379 ATOM PAIRS WERE FOUND FOR ATOM LIST 41204 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29998 from a total of 749379 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7942 -79.96169 -0.84270 0.74720 INTE EXTERN> -27.39679 -52.56491 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9617" Parameter: A <- "-79.9617" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3968" Parameter: B <- "-27.3968" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.5649" Parameter: C <- "-52.5649" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7942 TOTAL ENERGY = -79.9617 RDTITL> * VAN DER WAALS = -27.3968 ELECTROSTATIC = -52.5649 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7942" Parameter: CONF_N -> "8002" Comparing "7942" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7943" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749379 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749659 ATOM PAIRS WERE FOUND FOR ATOM LIST 41185 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29709 from a total of 749659 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7943 -77.17328 -2.78842 0.65974 INTE EXTERN> -30.78676 -46.38651 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.1733" Parameter: A <- "-77.1733" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7868" Parameter: B <- "-30.7868" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.3865" Parameter: C <- "-46.3865" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7943 TOTAL ENERGY = -77.1733 RDTITL> * VAN DER WAALS = -30.7868 ELECTROSTATIC = -46.3865 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7943" Parameter: CONF_N -> "8002" Comparing "7943" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7944" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749659 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753428 ATOM PAIRS WERE FOUND FOR ATOM LIST 41436 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29839 from a total of 753428 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7944 -71.57091 -5.60237 0.72534 INTE EXTERN> -25.50389 -46.06702 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.5709" Parameter: A <- "-71.5709" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5039" Parameter: B <- "-25.5039" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.067" Parameter: C <- "-46.067" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7944 TOTAL ENERGY = -71.5709 RDTITL> * VAN DER WAALS = -25.5039 ELECTROSTATIC = -46.067 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7944" Parameter: CONF_N -> "8002" Comparing "7944" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7945" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753428 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756181 ATOM PAIRS WERE FOUND FOR ATOM LIST 41579 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30032 from a total of 756181 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7945 -71.37315 -0.19776 0.69975 INTE EXTERN> -25.58524 -45.78792 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.3732" Parameter: A <- "-71.3732" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5852" Parameter: B <- "-25.5852" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.7879" Parameter: C <- "-45.7879" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7945 TOTAL ENERGY = -71.3732 RDTITL> * VAN DER WAALS = -25.5852 ELECTROSTATIC = -45.7879 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7945" Parameter: CONF_N -> "8002" Comparing "7945" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7946" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756181 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750936 ATOM PAIRS WERE FOUND FOR ATOM LIST 41297 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29296 from a total of 750936 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7946 -70.62392 -0.74923 0.70664 INTE EXTERN> -25.15752 -45.46640 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.6239" Parameter: A <- "-70.6239" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.1575" Parameter: B <- "-25.1575" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.4664" Parameter: C <- "-45.4664" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7946 TOTAL ENERGY = -70.6239 RDTITL> * VAN DER WAALS = -25.1575 ELECTROSTATIC = -45.4664 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7946" Parameter: CONF_N -> "8002" Comparing "7946" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7947" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750936 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753002 ATOM PAIRS WERE FOUND FOR ATOM LIST 41262 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29711 from a total of 753002 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7947 -88.12914 17.50522 0.68246 INTE EXTERN> -28.19344 -59.93570 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-88.1291" Parameter: A <- "-88.1291" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1934" Parameter: B <- "-28.1934" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-59.9357" Parameter: C <- "-59.9357" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7947 TOTAL ENERGY = -88.1291 RDTITL> * VAN DER WAALS = -28.1934 ELECTROSTATIC = -59.9357 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7947" Parameter: CONF_N -> "8002" Comparing "7947" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7948" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753002 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751048 ATOM PAIRS WERE FOUND FOR ATOM LIST 41478 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29627 from a total of 751048 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7948 -75.40495 -12.72419 0.66705 INTE EXTERN> -25.26602 -50.13894 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.405" Parameter: A <- "-75.405" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.266" Parameter: B <- "-25.266" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.1389" Parameter: C <- "-50.1389" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7948 TOTAL ENERGY = -75.405 RDTITL> * VAN DER WAALS = -25.266 ELECTROSTATIC = -50.1389 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7948" Parameter: CONF_N -> "8002" Comparing "7948" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7949" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751048 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753516 ATOM PAIRS WERE FOUND FOR ATOM LIST 41273 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29874 from a total of 753516 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7949 -80.30775 4.90280 0.71458 INTE EXTERN> -25.59013 -54.71762 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.3078" Parameter: A <- "-80.3078" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.5901" Parameter: B <- "-25.5901" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.7176" Parameter: C <- "-54.7176" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7949 TOTAL ENERGY = -80.3078 RDTITL> * VAN DER WAALS = -25.5901 ELECTROSTATIC = -54.7176 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7949" Parameter: CONF_N -> "8002" Comparing "7949" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7950" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753516 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750356 ATOM PAIRS WERE FOUND FOR ATOM LIST 40949 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29660 from a total of 750356 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7950 -72.20769 -8.10006 0.61460 INTE EXTERN> -28.28464 -43.92305 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.2077" Parameter: A <- "-72.2077" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2846" Parameter: B <- "-28.2846" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.9231" Parameter: C <- "-43.9231" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7950 TOTAL ENERGY = -72.2077 RDTITL> * VAN DER WAALS = -28.2846 ELECTROSTATIC = -43.9231 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7950" Parameter: CONF_N -> "8002" Comparing "7950" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7951" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750356 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750368 ATOM PAIRS WERE FOUND FOR ATOM LIST 41197 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29702 from a total of 750368 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7951 -77.00121 4.79352 0.67756 INTE EXTERN> -27.85898 -49.14223 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.0012" Parameter: A <- "-77.0012" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.859" Parameter: B <- "-27.859" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1422" Parameter: C <- "-49.1422" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7951 TOTAL ENERGY = -77.0012 RDTITL> * VAN DER WAALS = -27.859 ELECTROSTATIC = -49.1422 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7951" Parameter: CONF_N -> "8002" Comparing "7951" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7952" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750368 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748732 ATOM PAIRS WERE FOUND FOR ATOM LIST 41104 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29650 from a total of 748732 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7952 -73.82581 -3.17540 0.65109 INTE EXTERN> -29.69018 -44.13562 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8258" Parameter: A <- "-73.8258" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.6902" Parameter: B <- "-29.6902" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.1356" Parameter: C <- "-44.1356" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7952 TOTAL ENERGY = -73.8258 RDTITL> * VAN DER WAALS = -29.6902 ELECTROSTATIC = -44.1356 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7952" Parameter: CONF_N -> "8002" Comparing "7952" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7953" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748732 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758098 ATOM PAIRS WERE FOUND FOR ATOM LIST 41609 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29889 from a total of 758098 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7953 -77.45912 3.63331 0.65089 INTE EXTERN> -27.70994 -49.74918 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.4591" Parameter: A <- "-77.4591" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.7099" Parameter: B <- "-27.7099" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7492" Parameter: C <- "-49.7492" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7953 TOTAL ENERGY = -77.4591 RDTITL> * VAN DER WAALS = -27.7099 ELECTROSTATIC = -49.7492 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7953" Parameter: CONF_N -> "8002" Comparing "7953" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7954" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758098 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755900 ATOM PAIRS WERE FOUND FOR ATOM LIST 41389 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30250 from a total of 755900 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7954 -79.86590 2.40678 0.69540 INTE EXTERN> -26.77298 -53.09293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.8659" Parameter: A <- "-79.8659" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.773" Parameter: B <- "-26.773" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.0929" Parameter: C <- "-53.0929" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7954 TOTAL ENERGY = -79.8659 RDTITL> * VAN DER WAALS = -26.773 ELECTROSTATIC = -53.0929 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7954" Parameter: CONF_N -> "8002" Comparing "7954" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7955" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755900 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754407 ATOM PAIRS WERE FOUND FOR ATOM LIST 41283 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29957 from a total of 754407 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7955 -77.52317 -2.34273 0.69886 INTE EXTERN> -27.60686 -49.91631 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.5232" Parameter: A <- "-77.5232" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.6069" Parameter: B <- "-27.6069" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.9163" Parameter: C <- "-49.9163" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7955 TOTAL ENERGY = -77.5232 RDTITL> * VAN DER WAALS = -27.6069 ELECTROSTATIC = -49.9163 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7955" Parameter: CONF_N -> "8002" Comparing "7955" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7956" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754407 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752938 ATOM PAIRS WERE FOUND FOR ATOM LIST 41484 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30013 from a total of 752938 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7956 -74.33313 -3.19004 0.72115 INTE EXTERN> -24.78702 -49.54611 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.3331" Parameter: A <- "-74.3331" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.787" Parameter: B <- "-24.787" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.5461" Parameter: C <- "-49.5461" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7956 TOTAL ENERGY = -74.3331 RDTITL> * VAN DER WAALS = -24.787 ELECTROSTATIC = -49.5461 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7956" Parameter: CONF_N -> "8002" Comparing "7956" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7957" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752938 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755891 ATOM PAIRS WERE FOUND FOR ATOM LIST 41438 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30007 from a total of 755891 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7957 -73.27525 -1.05788 0.75532 INTE EXTERN> -25.41607 -47.85918 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2752" Parameter: A <- "-73.2752" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.4161" Parameter: B <- "-25.4161" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.8592" Parameter: C <- "-47.8592" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7957 TOTAL ENERGY = -73.2752 RDTITL> * VAN DER WAALS = -25.4161 ELECTROSTATIC = -47.8592 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7957" Parameter: CONF_N -> "8002" Comparing "7957" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7958" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755891 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756666 ATOM PAIRS WERE FOUND FOR ATOM LIST 41652 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29769 from a total of 756666 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7958 -73.03117 -0.24408 0.55684 INTE EXTERN> -30.31478 -42.71639 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0312" Parameter: A <- "-73.0312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.3148" Parameter: B <- "-30.3148" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.7164" Parameter: C <- "-42.7164" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7958 TOTAL ENERGY = -73.0312 RDTITL> * VAN DER WAALS = -30.3148 ELECTROSTATIC = -42.7164 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7958" Parameter: CONF_N -> "8002" Comparing "7958" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7959" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756666 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757579 ATOM PAIRS WERE FOUND FOR ATOM LIST 41754 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30149 from a total of 757579 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7959 -82.41551 9.38434 0.83113 INTE EXTERN> -19.32749 -63.08802 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-82.4155" Parameter: A <- "-82.4155" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-19.3275" Parameter: B <- "-19.3275" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-63.088" Parameter: C <- "-63.088" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7959 TOTAL ENERGY = -82.4155 RDTITL> * VAN DER WAALS = -19.3275 ELECTROSTATIC = -63.088 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7959" Parameter: CONF_N -> "8002" Comparing "7959" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7960" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757579 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756422 ATOM PAIRS WERE FOUND FOR ATOM LIST 41549 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29333 from a total of 756422 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7960 -81.58029 -0.83522 0.61668 INTE EXTERN> -30.18058 -51.39970 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.5803" Parameter: A <- "-81.5803" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1806" Parameter: B <- "-30.1806" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.3997" Parameter: C <- "-51.3997" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7960 TOTAL ENERGY = -81.5803 RDTITL> * VAN DER WAALS = -30.1806 ELECTROSTATIC = -51.3997 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7960" Parameter: CONF_N -> "8002" Comparing "7960" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7961" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756422 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755358 ATOM PAIRS WERE FOUND FOR ATOM LIST 41458 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29896 from a total of 755358 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7961 -74.74220 -6.83809 0.61688 INTE EXTERN> -30.11951 -44.62270 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7422" Parameter: A <- "-74.7422" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.1195" Parameter: B <- "-30.1195" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6227" Parameter: C <- "-44.6227" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7961 TOTAL ENERGY = -74.7422 RDTITL> * VAN DER WAALS = -30.1195 ELECTROSTATIC = -44.6227 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7961" Parameter: CONF_N -> "8002" Comparing "7961" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7962" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755358 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757100 ATOM PAIRS WERE FOUND FOR ATOM LIST 41650 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29605 from a total of 757100 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7962 -77.75486 3.01266 0.58882 INTE EXTERN> -30.61282 -47.14204 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.7549" Parameter: A <- "-77.7549" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.6128" Parameter: B <- "-30.6128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.142" Parameter: C <- "-47.142" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7962 TOTAL ENERGY = -77.7549 RDTITL> * VAN DER WAALS = -30.6128 ELECTROSTATIC = -47.142 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7962" Parameter: CONF_N -> "8002" Comparing "7962" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7963" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757100 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751607 ATOM PAIRS WERE FOUND FOR ATOM LIST 41229 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28947 from a total of 751607 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7963 -71.10646 -6.64840 0.67011 INTE EXTERN> -27.07795 -44.02851 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.1065" Parameter: A <- "-71.1065" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.0779" Parameter: B <- "-27.0779" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.0285" Parameter: C <- "-44.0285" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7963 TOTAL ENERGY = -71.1065 RDTITL> * VAN DER WAALS = -27.0779 ELECTROSTATIC = -44.0285 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7963" Parameter: CONF_N -> "8002" Comparing "7963" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7964" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751607 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 750286 ATOM PAIRS WERE FOUND FOR ATOM LIST 41066 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28401 from a total of 750286 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7964 -77.82578 6.71932 0.67541 INTE EXTERN> -28.91794 -48.90784 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.8258" Parameter: A <- "-77.8258" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.9179" Parameter: B <- "-28.9179" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-48.9078" Parameter: C <- "-48.9078" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7964 TOTAL ENERGY = -77.8258 RDTITL> * VAN DER WAALS = -28.9179 ELECTROSTATIC = -48.9078 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7964" Parameter: CONF_N -> "8002" Comparing "7964" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7965" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 750286 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751751 ATOM PAIRS WERE FOUND FOR ATOM LIST 41169 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29220 from a total of 751751 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7965 -72.74334 -5.08244 0.52998 INTE EXTERN> -31.77255 -40.97079 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-72.7433" Parameter: A <- "-72.7433" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.7726" Parameter: B <- "-31.7726" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-40.9708" Parameter: C <- "-40.9708" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7965 TOTAL ENERGY = -72.7433 RDTITL> * VAN DER WAALS = -31.7726 ELECTROSTATIC = -40.9708 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7965" Parameter: CONF_N -> "8002" Comparing "7965" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7966" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751751 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752402 ATOM PAIRS WERE FOUND FOR ATOM LIST 41420 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29491 from a total of 752402 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7966 -74.44908 1.70574 0.55072 INTE EXTERN> -31.61276 -42.83632 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.4491" Parameter: A <- "-74.4491" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.6128" Parameter: B <- "-31.6128" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8363" Parameter: C <- "-42.8363" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7966 TOTAL ENERGY = -74.4491 RDTITL> * VAN DER WAALS = -31.6128 ELECTROSTATIC = -42.8363 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7966" Parameter: CONF_N -> "8002" Comparing "7966" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7967" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752402 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752685 ATOM PAIRS WERE FOUND FOR ATOM LIST 41203 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28626 from a total of 752685 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7967 -67.19192 -7.25716 0.61341 INTE EXTERN> -26.01649 -41.17543 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.1919" Parameter: A <- "-67.1919" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0165" Parameter: B <- "-26.0165" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-41.1754" Parameter: C <- "-41.1754" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7967 TOTAL ENERGY = -67.1919 RDTITL> * VAN DER WAALS = -26.0165 ELECTROSTATIC = -41.1754 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7967" Parameter: CONF_N -> "8002" Comparing "7967" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7968" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752685 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745159 ATOM PAIRS WERE FOUND FOR ATOM LIST 40915 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28530 from a total of 745159 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7968 -74.70443 7.51250 0.57082 INTE EXTERN> -28.50499 -46.19944 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.7044" Parameter: A <- "-74.7044" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.505" Parameter: B <- "-28.505" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.1994" Parameter: C <- "-46.1994" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7968 TOTAL ENERGY = -74.7044 RDTITL> * VAN DER WAALS = -28.505 ELECTROSTATIC = -46.1994 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7968" Parameter: CONF_N -> "8002" Comparing "7968" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7969" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745159 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751519 ATOM PAIRS WERE FOUND FOR ATOM LIST 41081 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28842 from a total of 751519 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7969 -76.76338 2.05895 0.69585 INTE EXTERN> -27.58083 -49.18255 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.7634" Parameter: A <- "-76.7634" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.5808" Parameter: B <- "-27.5808" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.1825" Parameter: C <- "-49.1825" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7969 TOTAL ENERGY = -76.7634 RDTITL> * VAN DER WAALS = -27.5808 ELECTROSTATIC = -49.1825 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7969" Parameter: CONF_N -> "8002" Comparing "7969" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7970" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751519 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 749337 ATOM PAIRS WERE FOUND FOR ATOM LIST 41246 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29540 from a total of 749337 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7970 -73.86071 -2.90267 0.62715 INTE EXTERN> -29.24045 -44.62025 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.8607" Parameter: A <- "-73.8607" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.2405" Parameter: B <- "-29.2405" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.6203" Parameter: C <- "-44.6203" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7970 TOTAL ENERGY = -73.8607 RDTITL> * VAN DER WAALS = -29.2405 ELECTROSTATIC = -44.6203 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7970" Parameter: CONF_N -> "8002" Comparing "7970" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7971" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 749337 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 745998 ATOM PAIRS WERE FOUND FOR ATOM LIST 40986 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28783 from a total of 745998 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7971 -81.62999 7.76929 0.71988 INTE EXTERN> -27.14131 -54.48869 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.63" Parameter: A <- "-81.63" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.1413" Parameter: B <- "-27.1413" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.4887" Parameter: C <- "-54.4887" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7971 TOTAL ENERGY = -81.63 RDTITL> * VAN DER WAALS = -27.1413 ELECTROSTATIC = -54.4887 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7971" Parameter: CONF_N -> "8002" Comparing "7971" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7972" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 745998 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755815 ATOM PAIRS WERE FOUND FOR ATOM LIST 41589 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29004 from a total of 755815 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7972 -79.13555 -2.49444 0.67745 INTE EXTERN> -27.37037 -51.76518 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.1356" Parameter: A <- "-79.1356" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.3704" Parameter: B <- "-27.3704" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7652" Parameter: C <- "-51.7652" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7972 TOTAL ENERGY = -79.1356 RDTITL> * VAN DER WAALS = -27.3704 ELECTROSTATIC = -51.7652 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7972" Parameter: CONF_N -> "8002" Comparing "7972" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7973" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755815 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 756644 ATOM PAIRS WERE FOUND FOR ATOM LIST 41512 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29875 from a total of 756644 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7973 -73.29081 -5.84474 0.60748 INTE EXTERN> -31.25229 -42.03852 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2908" Parameter: A <- "-73.2908" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.2523" Parameter: B <- "-31.2523" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.0385" Parameter: C <- "-42.0385" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7973 TOTAL ENERGY = -73.2908 RDTITL> * VAN DER WAALS = -31.2523 ELECTROSTATIC = -42.0385 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7973" Parameter: CONF_N -> "8002" Comparing "7973" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7974" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 756644 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759929 ATOM PAIRS WERE FOUND FOR ATOM LIST 41642 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29836 from a total of 759929 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7974 -78.68436 5.39355 0.70003 INTE EXTERN> -28.25348 -50.43088 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6844" Parameter: A <- "-78.6844" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.2535" Parameter: B <- "-28.2535" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.4309" Parameter: C <- "-50.4309" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7974 TOTAL ENERGY = -78.6844 RDTITL> * VAN DER WAALS = -28.2535 ELECTROSTATIC = -50.4309 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7974" Parameter: CONF_N -> "8002" Comparing "7974" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7975" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759929 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755108 ATOM PAIRS WERE FOUND FOR ATOM LIST 41603 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29338 from a total of 755108 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7975 -76.21445 -2.46992 0.62902 INTE EXTERN> -29.77635 -46.43810 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.2144" Parameter: A <- "-76.2144" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.7764" Parameter: B <- "-29.7764" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4381" Parameter: C <- "-46.4381" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7975 TOTAL ENERGY = -76.2144 RDTITL> * VAN DER WAALS = -29.7764 ELECTROSTATIC = -46.4381 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7975" Parameter: CONF_N -> "8002" Comparing "7975" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7976" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755108 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 748273 ATOM PAIRS WERE FOUND FOR ATOM LIST 41346 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29726 from a total of 748273 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7976 -80.53121 4.31676 0.82366 INTE EXTERN> -26.09125 -54.43996 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.5312" Parameter: A <- "-80.5312" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.0913" Parameter: B <- "-26.0913" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.44" Parameter: C <- "-54.44" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7976 TOTAL ENERGY = -80.5312 RDTITL> * VAN DER WAALS = -26.0913 ELECTROSTATIC = -54.44 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7976" Parameter: CONF_N -> "8002" Comparing "7976" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7977" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 748273 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752912 ATOM PAIRS WERE FOUND FOR ATOM LIST 41270 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29836 from a total of 752912 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7977 -78.63591 -1.89530 0.77691 INTE EXTERN> -23.27067 -55.36524 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.6359" Parameter: A <- "-78.6359" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.2707" Parameter: B <- "-23.2707" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.3652" Parameter: C <- "-55.3652" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7977 TOTAL ENERGY = -78.6359 RDTITL> * VAN DER WAALS = -23.2707 ELECTROSTATIC = -55.3652 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7977" Parameter: CONF_N -> "8002" Comparing "7977" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7978" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 752912 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755442 ATOM PAIRS WERE FOUND FOR ATOM LIST 41463 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29705 from a total of 755442 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7978 -80.93014 2.29423 0.67632 INTE EXTERN> -26.62528 -54.30486 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.9301" Parameter: A <- "-80.9301" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.6253" Parameter: B <- "-26.6253" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-54.3049" Parameter: C <- "-54.3049" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7978 TOTAL ENERGY = -80.9301 RDTITL> * VAN DER WAALS = -26.6253 ELECTROSTATIC = -54.3049 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7978" Parameter: CONF_N -> "8002" Comparing "7978" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7979" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755442 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 757933 ATOM PAIRS WERE FOUND FOR ATOM LIST 41648 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29836 from a total of 757933 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7979 -78.77409 -2.15605 0.70897 INTE EXTERN> -26.99974 -51.77435 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.7741" Parameter: A <- "-78.7741" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9997" Parameter: B <- "-26.9997" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.7744" Parameter: C <- "-51.7744" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7979 TOTAL ENERGY = -78.7741 RDTITL> * VAN DER WAALS = -26.9997 ELECTROSTATIC = -51.7744 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7979" Parameter: CONF_N -> "8002" Comparing "7979" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7980" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 757933 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759550 ATOM PAIRS WERE FOUND FOR ATOM LIST 41547 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29166 from a total of 759550 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7980 -70.85382 -7.92027 0.67506 INTE EXTERN> -25.50903 -45.34479 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-70.8538" Parameter: A <- "-70.8538" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.509" Parameter: B <- "-25.509" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-45.3448" Parameter: C <- "-45.3448" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7980 TOTAL ENERGY = -70.8538 RDTITL> * VAN DER WAALS = -25.509 ELECTROSTATIC = -45.3448 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7980" Parameter: CONF_N -> "8002" Comparing "7980" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7981" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759550 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753102 ATOM PAIRS WERE FOUND FOR ATOM LIST 41377 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29311 from a total of 753102 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7981 -79.72682 8.87300 0.67937 INTE EXTERN> -28.65421 -51.07261 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.7268" Parameter: A <- "-79.7268" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.6542" Parameter: B <- "-28.6542" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.0726" Parameter: C <- "-51.0726" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7981 TOTAL ENERGY = -79.7268 RDTITL> * VAN DER WAALS = -28.6542 ELECTROSTATIC = -51.0726 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7981" Parameter: CONF_N -> "8002" Comparing "7981" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7982" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753102 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754517 ATOM PAIRS WERE FOUND FOR ATOM LIST 41409 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29704 from a total of 754517 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7982 -78.58011 -1.14671 0.72063 INTE EXTERN> -26.98567 -51.59444 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-78.5801" Parameter: A <- "-78.5801" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.9857" Parameter: B <- "-26.9857" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-51.5944" Parameter: C <- "-51.5944" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7982 TOTAL ENERGY = -78.5801 RDTITL> * VAN DER WAALS = -26.9857 ELECTROSTATIC = -51.5944 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7982" Parameter: CONF_N -> "8002" Comparing "7982" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7983" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754517 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758312 ATOM PAIRS WERE FOUND FOR ATOM LIST 41684 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30182 from a total of 758312 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7983 -76.34653 -2.23358 0.77763 INTE EXTERN> -23.41400 -52.93253 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.3465" Parameter: A <- "-76.3465" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-23.414" Parameter: B <- "-23.414" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.9325" Parameter: C <- "-52.9325" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7983 TOTAL ENERGY = -76.3465 RDTITL> * VAN DER WAALS = -23.414 ELECTROSTATIC = -52.9325 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7983" Parameter: CONF_N -> "8002" Comparing "7983" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7984" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758312 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760098 ATOM PAIRS WERE FOUND FOR ATOM LIST 41674 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30348 from a total of 760098 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7984 -80.23452 3.88798 0.68488 INTE EXTERN> -27.89566 -52.33886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-80.2345" Parameter: A <- "-80.2345" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-27.8957" Parameter: B <- "-27.8957" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-52.3389" Parameter: C <- "-52.3389" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7984 TOTAL ENERGY = -80.2345 RDTITL> * VAN DER WAALS = -27.8957 ELECTROSTATIC = -52.3389 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7984" Parameter: CONF_N -> "8002" Comparing "7984" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7985" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760098 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758876 ATOM PAIRS WERE FOUND FOR ATOM LIST 41640 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29533 from a total of 758876 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7985 -74.39303 -5.84148 0.76512 INTE EXTERN> -24.59661 -49.79642 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.393" Parameter: A <- "-74.393" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.5966" Parameter: B <- "-24.5966" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-49.7964" Parameter: C <- "-49.7964" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7985 TOTAL ENERGY = -74.393 RDTITL> * VAN DER WAALS = -24.5966 ELECTROSTATIC = -49.7964 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7985" Parameter: CONF_N -> "8002" Comparing "7985" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7986" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758876 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 763119 ATOM PAIRS WERE FOUND FOR ATOM LIST 42039 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29751 from a total of 763119 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7986 -79.91883 5.52580 0.70879 INTE EXTERN> -24.67014 -55.24868 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-79.9188" Parameter: A <- "-79.9188" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-24.6701" Parameter: B <- "-24.6701" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-55.2487" Parameter: C <- "-55.2487" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7986 TOTAL ENERGY = -79.9188 RDTITL> * VAN DER WAALS = -24.6701 ELECTROSTATIC = -55.2487 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7986" Parameter: CONF_N -> "8002" Comparing "7986" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7987" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 763119 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 762740 ATOM PAIRS WERE FOUND FOR ATOM LIST 41871 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29602 from a total of 762740 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7987 -81.98885 2.07002 0.76586 INTE EXTERN> -21.80120 -60.18765 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-81.9889" Parameter: A <- "-81.9889" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-21.8012" Parameter: B <- "-21.8012" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-60.1877" Parameter: C <- "-60.1877" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7987 TOTAL ENERGY = -81.9889 RDTITL> * VAN DER WAALS = -21.8012 ELECTROSTATIC = -60.1877 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7987" Parameter: CONF_N -> "8002" Comparing "7987" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7988" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 762740 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 751286 ATOM PAIRS WERE FOUND FOR ATOM LIST 41230 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29293 from a total of 751286 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7988 -84.31602 2.32717 0.58688 INTE EXTERN> -31.10449 -53.21153 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-84.316" Parameter: A <- "-84.316" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-31.1045" Parameter: B <- "-31.1045" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-53.2115" Parameter: C <- "-53.2115" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7988 TOTAL ENERGY = -84.316 RDTITL> * VAN DER WAALS = -31.1045 ELECTROSTATIC = -53.2115 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7988" Parameter: CONF_N -> "8002" Comparing "7988" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7989" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 751286 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754858 ATOM PAIRS WERE FOUND FOR ATOM LIST 41413 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30067 from a total of 754858 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7989 -71.26740 -13.04862 0.66734 INTE EXTERN> -28.33517 -42.93223 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2674" Parameter: A <- "-71.2674" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.3352" Parameter: B <- "-28.3352" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.9322" Parameter: C <- "-42.9322" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7989 TOTAL ENERGY = -71.2674 RDTITL> * VAN DER WAALS = -28.3352 ELECTROSTATIC = -42.9322 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7989" Parameter: CONF_N -> "8002" Comparing "7989" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7990" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754858 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 761356 ATOM PAIRS WERE FOUND FOR ATOM LIST 41680 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 30061 from a total of 761356 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7990 -76.47765 5.21025 0.67978 INTE EXTERN> -26.26573 -50.21192 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.4777" Parameter: A <- "-76.4777" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.2657" Parameter: B <- "-26.2657" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.2119" Parameter: C <- "-50.2119" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7990 TOTAL ENERGY = -76.4777 RDTITL> * VAN DER WAALS = -26.2657 ELECTROSTATIC = -50.2119 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7990" Parameter: CONF_N -> "8002" Comparing "7990" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7991" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 761356 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755169 ATOM PAIRS WERE FOUND FOR ATOM LIST 41536 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29096 from a total of 755169 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7991 -71.28306 -5.19459 0.58979 INTE EXTERN> -28.17772 -43.10534 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.2831" Parameter: A <- "-71.2831" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1777" Parameter: B <- "-28.1777" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-43.1053" Parameter: C <- "-43.1053" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7991 TOTAL ENERGY = -71.2831 RDTITL> * VAN DER WAALS = -28.1777 ELECTROSTATIC = -43.1053 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7991" Parameter: CONF_N -> "8002" Comparing "7991" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7992" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755169 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760022 ATOM PAIRS WERE FOUND FOR ATOM LIST 41652 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29765 from a total of 760022 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7992 -73.29750 2.01445 0.63194 INTE EXTERN> -26.83113 -46.46637 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.2975" Parameter: A <- "-73.2975" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.8311" Parameter: B <- "-26.8311" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-46.4664" Parameter: C <- "-46.4664" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7992 TOTAL ENERGY = -73.2975 RDTITL> * VAN DER WAALS = -26.8311 ELECTROSTATIC = -46.4664 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7992" Parameter: CONF_N -> "8002" Comparing "7992" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7993" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760022 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753838 ATOM PAIRS WERE FOUND FOR ATOM LIST 41562 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28733 from a total of 753838 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7993 -74.55308 1.25557 0.50423 INTE EXTERN> -32.40712 -42.14596 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-74.5531" Parameter: A <- "-74.5531" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.4071" Parameter: B <- "-32.4071" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.146" Parameter: C <- "-42.146" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7993 TOTAL ENERGY = -74.5531 RDTITL> * VAN DER WAALS = -32.4071 ELECTROSTATIC = -42.146 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7993" Parameter: CONF_N -> "8002" Comparing "7993" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7994" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753838 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 760224 ATOM PAIRS WERE FOUND FOR ATOM LIST 41598 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29326 from a total of 760224 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7994 -73.51859 -1.03449 0.51271 INTE EXTERN> -30.70373 -42.81486 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.5186" Parameter: A <- "-73.5186" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.7037" Parameter: B <- "-30.7037" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.8149" Parameter: C <- "-42.8149" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7994 TOTAL ENERGY = -73.5186 RDTITL> * VAN DER WAALS = -30.7037 ELECTROSTATIC = -42.8149 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7994" Parameter: CONF_N -> "8002" Comparing "7994" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7995" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 760224 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 753175 ATOM PAIRS WERE FOUND FOR ATOM LIST 41359 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29406 from a total of 753175 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7995 -76.53227 3.01368 0.65507 INTE EXTERN> -25.90817 -50.62410 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.5323" Parameter: A <- "-76.5323" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.9082" Parameter: B <- "-25.9082" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.6241" Parameter: C <- "-50.6241" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7995 TOTAL ENERGY = -76.5323 RDTITL> * VAN DER WAALS = -25.9082 ELECTROSTATIC = -50.6241 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7995" Parameter: CONF_N -> "8002" Comparing "7995" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7996" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 753175 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759906 ATOM PAIRS WERE FOUND FOR ATOM LIST 41638 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29019 from a total of 759906 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7996 -73.04874 -3.48353 0.61788 INTE EXTERN> -25.74374 -47.30500 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-73.0487" Parameter: A <- "-73.0487" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-25.7437" Parameter: B <- "-25.7437" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-47.305" Parameter: C <- "-47.305" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7996 TOTAL ENERGY = -73.0487 RDTITL> * VAN DER WAALS = -25.7437 ELECTROSTATIC = -47.305 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7996" Parameter: CONF_N -> "8002" Comparing "7996" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7997" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759906 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758372 ATOM PAIRS WERE FOUND FOR ATOM LIST 41599 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28651 from a total of 758372 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7997 -71.85110 -1.19763 0.53837 INTE EXTERN> -29.37258 -42.47853 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-71.8511" Parameter: A <- "-71.8511" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-29.3726" Parameter: B <- "-29.3726" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-42.4785" Parameter: C <- "-42.4785" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7997 TOTAL ENERGY = -71.8511 RDTITL> * VAN DER WAALS = -29.3726 ELECTROSTATIC = -42.4785 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7997" Parameter: CONF_N -> "8002" Comparing "7997" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7998" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758372 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 759619 ATOM PAIRS WERE FOUND FOR ATOM LIST 41513 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29471 from a total of 759619 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7998 -76.84128 4.99018 0.67672 INTE EXTERN> -26.55225 -50.28903 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-76.8413" Parameter: A <- "-76.8413" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-26.5523" Parameter: B <- "-26.5523" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-50.289" Parameter: C <- "-50.289" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7998 TOTAL ENERGY = -76.8413 RDTITL> * VAN DER WAALS = -26.5523 ELECTROSTATIC = -50.289 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7998" Parameter: CONF_N -> "8002" Comparing "7998" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "7999" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 759619 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 754478 ATOM PAIRS WERE FOUND FOR ATOM LIST 41366 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29166 from a total of 754478 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 7999 -77.21414 0.37286 0.54309 INTE EXTERN> -32.65991 -44.55423 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-77.2141" Parameter: A <- "-77.2141" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-32.6599" Parameter: B <- "-32.6599" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.5542" Parameter: C <- "-44.5542" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 7999 TOTAL ENERGY = -77.2141 RDTITL> * VAN DER WAALS = -32.6599 ELECTROSTATIC = -44.5542 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "7999" Parameter: CONF_N -> "8002" Comparing "7999" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "8000" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 754478 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 755838 ATOM PAIRS WERE FOUND FOR ATOM LIST 41596 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28671 from a total of 755838 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 8000 -68.64662 -8.56751 0.54241 INTE EXTERN> -28.77589 -39.87073 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-68.6466" Parameter: A <- "-68.6466" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.7759" Parameter: B <- "-28.7759" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.8707" Parameter: C <- "-39.8707" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 8000 TOTAL ENERGY = -68.6466 RDTITL> * VAN DER WAALS = -28.7759 ELECTROSTATIC = -39.8707 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "8000" Parameter: CONF_N -> "8002" Comparing "8000" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "8001" CHARMM> CHARMM> traj read CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 755838 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 758481 ATOM PAIRS WERE FOUND FOR ATOM LIST 41686 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 28628 from a total of 758481 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 8001 -67.49292 -1.15371 0.58529 INTE EXTERN> -28.16684 -39.32608 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-67.4929" Parameter: A <- "-67.4929" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-28.1668" Parameter: B <- "-28.1668" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-39.3261" Parameter: C <- "-39.3261" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 8001 TOTAL ENERGY = -67.4929 RDTITL> * VAN DER WAALS = -28.1668 ELECTROSTATIC = -39.3261 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "8001" Parameter: CONF_N -> "8002" Comparing "8001" and "8002". IF test evaluated as true. Performing command CHARMM> incr i by 1 Parameter: I <- "8002" CHARMM> CHARMM> traj read ***** WARNING ***** ONLY 8001 OF THE 20005 REQUESTED STEPS WERE IN THE INPUT FILE(S) 8002 CORD RECORDS READ FROM 1 UNITS STARTING WITH UNIT 21 RUNNING FROM STEP 0 TO 8001 SKIPPING 1 STEPS BETWEEN RECORDS Time step was 1.000000 AKMA time units. CHARMM> CHARMM> !NBONds ELEC ATOM SHIF CDIE VATOM VSHI VDIS CUTNb 8.500000 - CHARMM> !TOFnb 7.500000 CTONnbr 6.500000 WMIN 0.9 EPS 1.0 - CHARMM> !E14F 0.4 NBXM 5 CHARMM> CHARMM> NBONDS cutnb 13.5 ctonnb 8.5 ctofnb 12.5 - CHARMM> vswitch shift cdie eps 1 !- NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 13.500 CTEXNB =999.000 CTONNB = 8.500 CTOFNB = 12.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 758481 atom pairs and 14588 atom exclusions. There are 0 group pairs and 2383 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 1036934 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 752400 ATOM PAIRS WERE FOUND FOR ATOM LIST 41337 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> CHARMM> SKIPe ALL EXCLude ELECtrostatic VDW SKIPE> The following energy terms will be computed : VDW ELEC CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !puts the good keyword to select the 2 parts of the system! CHARMM> !the order of the selection isn't important ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> inte sele @fp end sele @sp end Parameter: FP -> "(SEGID L)" Parameter: SP -> "(SEGID Z)" SELRPN> 2639 atoms have been selected out of 2683 SELRPN> 44 atoms have been selected out of 2683 INTER: Normal Atom Nonbondselected 29485 from a total of 752400 INTE ENR: Eval# ENERgy Delta-E GRMS INTE EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- INTE> 8002 -75.10494 7.61202 0.54039 INTE EXTERN> -30.83160 -44.27334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! this is also the total int. energy, for consistency check CHARMM> set a = ?ENER RDCMND substituted energy or value "?ENER" to "-75.1049" Parameter: A <- "-75.1049" CHARMM> set b = ?VDW RDCMND substituted energy or value "?VDW" to "-30.8316" Parameter: B <- "-30.8316" CHARMM> set c = ?ELEC RDCMND substituted energy or value "?ELEC" to "-44.2733" Parameter: C <- "-44.2733" CHARMM> CHARMM> ! Compare the 2 values of total energy, just to check CHARMM> write title unit 12 RDTITL> * CONFORMATIONAL NUMBER = 8002 TOTAL ENERGY = -75.1049 RDTITL> * VAN DER WAALS = -30.8316 ELECTROSTATIC = -44.2733 RDTITL> * CHARMM> CHARMM> IF @i LT @{conf_n} GOTO loop1 Parameter: I -> "8002" Parameter: CONF_N -> "8002" Comparing "8002" and "8002". IF test evaluated as false. Skipping command CHARMM> CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> stop !pfew VCLOSE: Closing unit 21 with status "KEEP" $$$$$$ New timer profile $$$$$ Electrostatic & VDW 10.57 Other: 0.00 Nonbond force 10.57 Other: 0.00 Energy time 10.57 Other: 0.00 Total time 191.00 Other: 180.43 NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 50218 STACK CURRENTLY IN USE IS 0 NO WARNINGS WERE ISSUED HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 27648 MAXIMUM SPACE USED IS 2329930 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10211812 NEXT: 10239461 PRINHP> ADDRESS: 10239461 LENGTH: 540 NEXT: 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 3.18 MINUTES CPU TIME: 0.02 SECONDS